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  • Biochemistry and Biotechnology  (16.218)
  • Engineering General  (9.884)
  • Bone
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  • 1
    Digitale Medien
    Digitale Medien
    Springer
    Skeletal radiology 29 (2000), S. 548-552 
    ISSN: 1432-2161
    Schlagwort(e): Key words Melorheostosis ; Dysplasia ; Bone ; Lower extremity ; Radiographs ; Specimen radiographs
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract  Melorheostosis is an unusual mesenchymal dysplasia, which commonly presents on radiographs as longitudinal bars of hyperostosis in osseous structures. We present a case of melorheostosis in the lower extremity of a 20-year-old woman for which detailed radiologic– pathologic correlation was achieved due to amputation of the involved limb.
    Materialart: Digitale Medien
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  • 2
    Digitale Medien
    Digitale Medien
    Springer
    Pediatric nephrology 14 (2000), S. 629-635 
    ISSN: 1432-198X
    Schlagwort(e): Key words Histomorphometry ; In situ hybridization histochemistry ; Molecular morphometry ; Immunohistochemistry ; Bone
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract  Quantitative histomorphometric assessment of bone biopsies represents a powerful and informative method for the study of metabolic bone diseases. It is the gold standard against which the noninvasive ”diagnostic” markers of bone metabolism as well as newly available therapeutic modalities are tested. With the rapid progress in technology of molecular biology, identification of systemic and local biomolecules known to regulate bone metabolism can now be achieved. The study of localization, levels of expression, and synthesis of these factors in bone and its microenvironment is possible through applications of in situ hybridization histochemistry (ISHH) and immunohistochemistry (IHC). Application of ISHH allows study of specific mRNA expression. IHC determines the presence and distribution of target protein in cells. These two methodologies provide the link between the cellular processes of mRNA transcription and translation to the working protein. Combining the established bone histomorphometric techniques with ISHH and IHC elevates the study of bone to new heights, i.e., cellular and molecular mechanistic issues can now be studied.
    Materialart: Digitale Medien
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  • 3
    Digitale Medien
    Digitale Medien
    Springer
    Pediatric nephrology 14 (2000), S. 669-672 
    ISSN: 1432-198X
    Schlagwort(e): Key words Renal disease ; Bone ; Muscle ; Renal osteopathy
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract  Bone structure and muscular strength of 30 children with renal disease were investigated by peripheral computed tomography and grip strength. Sixteen children suffered from nephrotic syndrome (NS) and had previously been treated with corticosteroids. Fourteen children suffered from chronic renal failure (CRF) ranging from mild renal failure to end-stage renal disease. Six children had received kidney transplants and corticosteroids for immunosuppression. There was a significant decrease in grip strength of children with NS (SD –0.91± 1.5; P=0.042) and children with CRF (SD –1.38±1.4; P〈0.001) compared with normal children. Furthermore, there was a significant correlation between cortical area and grip strength in all children with renal disease (r=0.92; P〈0.0001). Trabecular bone mineral density did not correlate well with grip strength. These findings resemble results found in healthy children. Trabecular bone mineral density was significantly elevated in children with CRF compared with normal children (SD 1.14±1.4; P=0.008).Grip strength as a marker of muscle mass and cortical area as a marker of bone strength correlate well in children with renal disease, similar to the correlation in healthy children. Grip strength is significantly lower in children with NS and CRF compared with normal children. These data suggest that muscular impairment could be involved in renal osteopathy.
    Materialart: Digitale Medien
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  • 4
    Digitale Medien
    Digitale Medien
    Springer
    Der Chirurg 71 (2000), S. 1001-1008 
    ISSN: 1433-0385
    Schlagwort(e): Schlüsselwörter: Tissue Engineering ; Mesenchymale Stammzellen ; Knochen ; Knorpel. ; Keywords: Tissue engineering ; Mesenchymal stem cells ; Bone ; Cartilage.
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Beschreibung / Inhaltsverzeichnis: Abstract. Tissue engineering offers the possibility to fabricate living substitutes for tissues and organs by combining histogenic cells and biocompatible carrier materials. Pluripotent mesenchymal stem cells are isolated and subcultured ex vivo and then their histogenic differentiation is induced by external factors. The fabrication of bone and cartilage constructs, their combinations and gene therapeutic approaches are demonstrated. Advantages and disadvantages of these methods are described by in vitro and in vitro testing. The proof of histotypical function after implantation in vivo is essential. The use of autologous cells and tissue engineering methods offers the possibility to overcome the disadvantages of classical tissue reconstruction – donor site morbidity of autologous grafts, immunogenicity of allogenic grafts and loosening of alloplastic implants. Furthermore, tissue engineering widens the spectrum of surgical indications in bone and cartilage reconstruction.
    Notizen: Zusammenfassung. Tissue engineering ermöglicht die Herstellung lebender Konstrukte zum Gewebeersatz durch die Kombination histogener Zellen und biokompatiblen Trägermaterialien. Pluripotente mesenchymale Stammzellen können isoliert, ex vivo vermehrt und ihre gewebetypische Differenzierung durch Faktoren induziert werden. Es wird die Herstellung von Knochen- und Knorpelkonstrukten, deren Kombination sowie gentherapeutische Ansätze dargestellt. Vor- und Nachteile der Methoden werden durch in vitro und in vivo Testung beschrieben. Essentiell ist der Nachweis der gewebetypischen Funktion der Konstrukte nach Implantation in den Defekt. Die Verwendung autogener Zellen und Methoden des Tissue engineerings bietet die Möglichkeit die Probleme des klassischen Gewebeersatzes – Morbidität der autogenen Spenderstelle, Immunogenität des allogenen Transplantats und Lockerung von alloplastischen Implantaten – zu überwinden und erweitert das Indikationsspektrum in der rekonstruktiven Chirurgie.
    Materialart: Digitale Medien
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  • 5
    Digitale Medien
    Digitale Medien
    Springer
    European radiology 10 (2000), S. 1832-1835 
    ISSN: 1432-1084
    Schlagwort(e): Key words: Platyspondyly ; MRI ; Progressive pseudorheumatoid dysplasia ; Bone ; Osteochondrodysplasia
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract. A rare case of progressive pseudorheumatoid dysplasia (PPD) in a 9-year-old girl is presented. Clinically, chronic painless swollen joints, accompanied by progressive motion restriction and progressive walking difficulties, were found. Radiologically, there was enlargement of the epimetaphyseal portions of the large joints, metacarpal heads, and phalanges, and generalized platyspondyly with irregular delineation of the endplates of the vertebral bodies. The radioclinical features at the peripheral joints were originally misdiagnosed as juvenile rheumatoid arthritis (JRA), and the structural spinal abnormalities were neglected and interpreted as Scheuermann's disease. However, the absence of active inflammatory parameters argues against JRA, whereas the low age of onset of the irregularities at the vertebral endplates is an argument against the diagnosis of Scheuermann's disease. The combination of the dysplastic abnormalities of the spine, with platyspondyly and Scheuermann-like lesions at an unusually low age of onset, and radiological features mimicking JRA of the peripheral joints, is the clue to the diagnosis of this rare autosomal-recessive disease. This case is the first to document the MRI features of PPD of the spine.
    Materialart: Digitale Medien
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  • 6
    Digitale Medien
    Digitale Medien
    Springer
    Journal of bone and mineral metabolism 18 (2000), S. 305-316 
    ISSN: 1435-5604
    Schlagwort(e): Key words Utah paradigm ; Bone ; Joint ; Ligament ; Biomechanics ; Osteoporosis
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract In a 1960 paradigm of skeletal physiology, effector cells (chondroblasts, fibroblasts, osteoblasts, osteoclasts, etc.) regulated by nonmechanical agents wholly determined the architecture, strength, and health of bones, joints, fascia, ligaments, and tendons. Biomechanical and tissue-level phenomena had no roles in that paradigm. Subsequent studies and evidence slowly revealed skeletal tissue-level mechanisms and their functions, including biomechanical ones, as well as "game rules" that seem to govern them. That slow discovery process found that effector cells are only parts of tissue-level mechanisms, as kidney cells are only parts of nephrons and wheels are only parts of cars. Normally all those things help to determine skeletal architecture, strength, and health, and adding them to the 1960 paradigm led to the still-evolving Utah paradigm of skeletal physiology that concerns, in part, how load-bearing skeletal organs adapt to the voluntary mechanical loads on them. That caused controversies this article does not try to resolve; instead, it describes some issues they concern. In that regard, controversy can depend on how one assesses the relevance of facts to a problem more than on their accuracy. If a paradigm added new facts to a former one and the new one's advocates viewed all those facts as relevant, but the former's advocates questioned the relevance of some of the new facts, their views about a problem could differ even though each view depended on accurate facts. Readers would make their own judgments about the bearing of those ideas on this article's content.
    Materialart: Digitale Medien
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  • 7
    ISSN: 1433-0385
    Schlagwort(e): Schlüsselwörter: Gentherapie ; Knochen ; Fraktur ; Wachstumsfaktoren. ; Keywords: Gene therapy ; Bone ; Fracture ; Growth factors.
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Beschreibung / Inhaltsverzeichnis: Abstract. Gene therapy in orthopedic surgery is a new technic based on the idea of biological tissue healing. External gene segments are transferred to cells that overexpress growth factors locally to achieve this effect. The influence of growth factors on fracture healing is very well documented in the literature. Experimental data demonstrate that defect healing in bone can be accelerated by the application of different cytokines in vivo. Gene transfer is a promising, new technic of in situ tissue engineering that will enter clinics within the next decade.
    Notizen: Zusammenfassung. Gentherapie in der Orthopädischen Chirurgie ist eine neue Technik, die auf der Idee basiert, die biologische Gewebeheilung zu unterstützen. Um dies zu erreichen, werden externe Gensegmente auf Zellen transferiert, die in Folge vermehrt Wachstumsfaktoren im Bereich der Fraktur produzieren. Die Wirkung von Wachstumsfaktoren auf die Frakturheilung ist gut dokumentiert. Die bislang durchgeführten tierexperimentellen Studien demonstrieren eine gute Beeinflussbarkeit der knöchernen Defektheilung. Der Gentransfer kann als eine neue erfolgversprechende Technik des in situ Tissue Engineering angesehen werden, mit deren klinischer Anwendung in der nächsten Dekade gerechnet werden darf.
    Materialart: Digitale Medien
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  • 8
    Digitale Medien
    Digitale Medien
    Springer
    Annals of biomedical engineering 28 (2000), S. 1200-1209 
    ISSN: 1573-9686
    Schlagwort(e): Bone ; Bone fluid ; Mixing ; Lacunar-canalicular porosity ; Metabolism ; Mass transport ; Poroelasticity
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin , Technik allgemein
    Notizen: Abstract A mathematical model is developed to explain the fundamental conundrum as to how during cyclic mechanical loading there can be net solute (e.g., nutrient, tracer) transport in bone via the lacunar-canalicular porosity when there is no net fluid movement in the canaliculi over a loading cycle. Our hypothesis is that the fluid space in an osteocytic lacuna facilitates a nearly instantaneous mixing process of bone fluid that creates a difference in tracer concentration between the inward and outward canalicular flow and thus ensures net tracer transport to the osteocytes during cyclic loading, as has been shown experimentally. The sequential spread of the tracer from the osteonal canal to the lacunae is investigated for an osteon experiencing sinusoidal loading. The fluid pressure in the canaliculi is calculated using poroelasticity theory and the mixing process in the lacunae is then simulated computationally. The tracer concentration in lacunae extending radially from the osteonal canal to the cement line is calculated as a function of the loading frequency, loading magnitude, and number of loading cycles as well as the permeability of the lacunar-canalicular porosity. Our results show that net tracer transport to the lacunae does occur for cyclic loading. Tracer transport is found to increase with higher loading magnitude and higher permeability and to decrease with increasing loading frequency. This work will be helpful in designing experimental studies of tracer movement and bone fluid flow, which will enhance our understanding of bone metabolism as well as bone adaptation. © 2000 Biomedical Engineering Society. PAC00: 8716Uv, 8719Rr, 8716Ac
    Materialart: Digitale Medien
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  • 9
    Digitale Medien
    Digitale Medien
    Springer
    Supportive care in cancer 8 (2000), S. 398-404 
    ISSN: 1433-7339
    Schlagwort(e): Key words Bisphosphonate ; Hypercalcemia ; Breast cancer ; Bone ; Osteoclast
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract  Bisphosphonates are now the standard treatment for tumor-induced hypercalcemia (TIH), and pamidronate can normalize serum Ca in at least 90% of the patients treated for the first time. However, there are few data on the treatment of TIH when it recurs, and published results are contradictory. We studied 29 patients with solid tumors, 14 of whom had breast cancer and all of whom were naive to bisphosphonate therapy. They were retreated with pamidronate (median dose 1 mg/kg for both courses) for recurrence of TIH after a median interval of 78 (range 7–297) days. Fourteen of them, 7 of whom had breast cancer, were treated a third time 28 (range 5–79) days after the second course (median dose of pamidronate 1.5 mg/kg). Baseline Ca levels were not significantly different before each course, but the nadirs after each treatment progressively increased, 9.3±0.2 mg/dl, 10.5±0.3 mg/dl, and 12.3±0.4 mg/dl after the 1st, 2nd and 3rd administrations, respectively (P〈0.05). The percentage of treatment failures also progressively increased: 10%, 31% and 85% (P〈0.05). This decreased hypocalcemic effect was essentially observed in patients without bone metastases or with tumors other than breast cancer. Thus, in patients without bone metastases, Ca levels did not decrease at all after the 3rd course, whereas the responses were not significantly different between the three courses in patients with bone metastases. Baseline urinary hydroxyproline, a marker of bone resorption, increased progressively from course to course, especially in patients with bone metastases or breast cancer, but this was not the case for parameters of bone formation. There was also a progressive increase in PTHrP levels accompanied by an increase in the number of patients with enhanced kidney reabsorption of Ca and a decrease in the threshold for Pi excretion, which was significant in patients without bone metastases. In conclusion, pamidronate was progressively less efficient when hypercalcemia recurred. This was observed mainly in patients with hypercalcemia of humoral origin. Tumor progression is accompanied by an enhanced release of osteolytic factors, notably PTHrP, that increase bone resorption and enhance kidney calcium reabsorption, especially in patients without bone metastases. When both phenomena occur, the response to bisphosphonates becomes minimal and the usefulness of therapy questionable.
    Materialart: Digitale Medien
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  • 10
    Digitale Medien
    Digitale Medien
    Springer
    Virchows Archiv 436 (2000), S. 74-81 
    ISSN: 1432-2307
    Schlagwort(e): Key words Ochronosis ; Bone ; Cartilage ; Arthropathy ; Alkaptonuria
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract  An ochronotic femoral head has been studied morphologically under the light and the electron microscope. Its articular cartilage showed the alterations already reported in the literature, mainly consisting of erosions of the surface, pigment accumulation in chondrocytes and intercellular matrix, chondrocyte degeneration, the formation of pigmented, calcified and uncalcified microshards, and the presence of granulation tissue with macrophagic cells. The changes in bone were less severe than those in cartilage. Pigment was present in the calcified matrix. This did not seem to disturb the organization of the bone tissue, although it was diffusely osteoporotic, perhaps because of limb disuse. The preservation of calcified matrix might depend on the fact that its collagen fibrils are encrusted by mineral substance, which avoids the dangerous effects that the deposition of ochronotic pigment induces in the fibrils of soft connective tissues. On the other hand, the newly formed osteoid matrix remains uncalcified for too short a time to be modified by the pigment. Diffuse or granular pigmentation was found in a few osteocytes, while several of them were condensed or reduced to cellular fragments. Bone resorption often occurred near these osteocytes. However, this did not seem to alter the degree of bone remodelling, possibly because of the relatively low numbers of degenerated or dead osteocytes. Pigment was also contained in the cytoplasmic vacuoles of otherwise active osteoclasts, whereas it was not found in osteoblasts. On the whole, ochronosis in bone seems to induce the same changes as in other connective tissues. However, their severity appears to be limited by calcification, which prevents modifications in collagen fibrils, and by bone remodelling, which to some extent eliminates the oldest, pigment-richest parts of the tissue.
    Materialart: Digitale Medien
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  • 11
    Digitale Medien
    Digitale Medien
    Springer
    Journal of orthopaedics and traumatology 1 (2000), S. 11-16 
    ISSN: 1590-9999
    Schlagwort(e): Key words Hydroxyapatite ; Bone ; Interface ; Electron microscopy
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract We performed a back-scattered electron microscopy analysis of the interface between newly formed bone and hydroxyapatite coating, in an experimental rabbit model. Twenty cylinders made of Ti6A14V and coated with hydroxyapatite at different crystallinity were implanted in the distal femural canal and retrieved at 4, 8, 26 an 34 weeks. Crystallinity of the coating varied from 90% to 60% and thickness varied between 50 and 100 μm. Osteocytes were detectable a few micrometers in proximity of the coating. They produced new bone which was so tightly apposed to the coating that high magnification BSEM did not resolve any discontinuity at the interface. This was not observed in uncoated implants. Degradation of the hydroxyapatite coating is not a simple hydrolytic process because newly formed bone is remodelled in areas were a tight apposition with hydroxyapatite is present. The coatint itself is likely to be attacked by the resorptive action of multinucleated giant cells and osteoclasts. In conclusion, response to coated samples is morphologically characterized by tight apposition with bone. The substitution of areas of the coating by newly formed bone is possible.
    Materialart: Digitale Medien
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  • 12
    ISSN: 1615-3146
    Schlagwort(e): Key words Alkaline phosphatase ; Bone ; Lectin precipitation ; Fracture ; Osteoblast activity
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract Serum activity of bone specific alkaline phosphatase, a product of differentiated osteoblasts, is thought to mirror fracture healing. The precise time course after various conditions involving bone healing is, however, poorly described. The aim of our study was to evaluate sequential changes of bone alkaline phosphatase over a period of 20 weeks in traumatized patients with and without bone injuries. The bone isoenzyme of alkaline phosphatase was determined in frozen serum samples using a new automated procedure based on the wheat germ lectin precipitation method. Patients were stratified into different groups: 1. ST – soft tissue injury without bone participation; 2. DF – diaphysial fracture of tibia or femur; 3. MT – patients suffering from multiple traumas; 4. PF – proximal femur fracture, treated with dynamic hip screw; and 5. EP – femur neck fracture, treated with cemented endoprosthesis. Similar values were obtained in all measured groups on the day of admission (ST 35.83±6.15 U/l; PF 27.37±4.43 U/l; EP 31.09±7.42 U/l). In the following measurements, enzyme activity decreased significantly in all groups to reach a nadir within the first week, ranging between 41 and 82% of the activity immediatly postoperative. Thereafter, a substantial increase occurred in all groups investigated. In the ST group, this increase led to an activity level that was comparable to the first posttraumatic value (39.06±7.81 U/l). In contrast, average values in all other groups revealed a further increase, which was significantly elevated compared to measurements taken the first day after trauma (DF 74.36±10.84 U/l; MT 177.87±30.0 U/l; PF 93.39±22.08 U/l; EP 51,52±7.33 U/l). Additionally, the time to reach the peak in enzyme activity differed between groups. In the MT group, it was observed as early as 3 weeks after injury, in the DF group the peak was reached as late as 6 weeks after trauma. The results of the study indicate that bone alkaline phophatase activity undergoes a specific pattern of changes after trauma. It may be assumed that the initial decrease is part of a general stress response to trauma and operation. The subsequent increase seems to depend from the magnitude of bone repair and the type of fracture healing, e.g. diaphysial fracture healing takes longer time than cancellous bone healing. These results seem to be a useful basis in order to establish a laboratory monitoring of fracture healing in subsequent studies.
    Materialart: Digitale Medien
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  • 13
    Digitale Medien
    Digitale Medien
    Springer
    Der Nervenarzt 71 (2000), S. 9-18 
    ISSN: 1433-0407
    Schlagwort(e): Schlüsselwörter PET ; SPECT ; Neurotransmitter ; Interaktionen ; Psychopharmakologie ; Key words PET ; SPECT ; Neurotransmitter ; Interactions ; Psychopharmacology
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Beschreibung / Inhaltsverzeichnis: Summary Functional brain imaging with positron emission tomography (PET) and single photon emission computerized tomography (SPECT) enables the in vivo study of specific neurochemical processes in the context of normal regulatory mechanisms and pathophysiological alterations of the brain. By combining these methods with pharmacological challenge-paradigms, the study of functional interactions of different neurotransmitter systems is possible. This review will present data from animal and healthy volunteer studies as well as first data from investigations in different patient populations with regard to this research direction. Especially, interactions of different neurotransmitter systems with the dopaminergic and the cholinergic system will be discussed. The database acquired so far confirms existing models of neuronal feedback -circuits, and the first clinical results are consistent with the hypothesis of an increased dopaminergic responsivity in schizophrenic patients. These results open up new perspectives for a further evaluation of treatment response predictors from drug -challenge studies and for the development of new drug treatments for neuropsychiatric disorders.
    Notizen: Zusammenfassung Positronenemissionstomographie (PET) und Single Photonenemissionscomputertomographie (SPECT) ermöglichen als funktionelle bildgebende Verfahren die In-vivo-Untersuchung von spezifischen neurochemischen Prozessen im Zusammenhang mit physiologischen Regulationsvorgängen und pathophysiologischen Veränderungen des Gehirns. Durch die Kombination mit pharmakologischen Challenge-Paradigmen kann auf dieser methodischen Grundlage auch den funktionellen Interaktionen zwischen Neurotransmittersystemen nachgegangen werden. In dem vorliegenden Übersichtsartikel werden unter dieser Fragestellung durchgeführte tierexperimentelle Studien, Untersuchungen bei gesunden Probanden sowie klinische Ergebnisse dargestellt. Insbesondere der vielfältige Einfluss auf das dopaminerge und das cholinerge System wird dabei näher betrachtet. Die gewonnenen Daten bestätigen existierende Modelle von neuronalen Feedback-Regelkreisen. Erste klinische Resultate sind konsistent mit Hypothesen einer verstärkten dopaminergen Response bei schizophrenen Patienten. Die bisherigen Ergebnisse eröffnen eine Perspektive für die Entwicklung neuer Strategien zur Therapie neuropsychiatrischer Erkrankungen und bereiten zugleich den Boden für weitere Untersuchungen zur prädiktiven Bedeutung einer Challenge-Antwort bezüglich eines nachfolgenden Therapieerfolgs.
    Materialart: Digitale Medien
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  • 14
    Digitale Medien
    Digitale Medien
    Springer
    Materials research innovations 3 (2000), S. 313-323 
    ISSN: 1433-075X
    Schlagwort(e): Keywords Glass ; Cell cycle ; Genes ; Bone ; Bioactive materials ; Osteogenesis ; Prostheses ; Omplants ; Ageing ; Osteoblasts
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Maschinenbau
    Notizen: Abstract  Many of the present generation biomaterials are still based upon the early concept that implantable materials should be bioinert and therefore designed to evoke minimal tissue response, if none. However, a growing body of clinical data demonstrates that the long survivability of these materials is hampered by high rates of failure, which is primarily attributed to interfacial instability. It has therefore become understood that this approach is not optimal. Modern approaches implicate the use of biomaterials that can actively interact with tissues and induce their intrinsic repair and regenerative potential. This involves control over the cell cycle, the molecular framework that controls cell proliferation and differentiation. Class A bioactive glass-ceramic materials were the first materials shown to endorse these properties and, depending upon the rate of resorption and release of ions, can create chemical gradients with specific biological actions over cells and tissues. Optimising this bioactive regenerative capacity of Bioactive glass-ceramics offers great hope for producing biomaterials that can stimulate growth, repair, and regeneration of any human tissue.
    Materialart: Digitale Medien
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  • 15
    Digitale Medien
    Digitale Medien
    Springer
    European journal of plastic surgery 23 (2000), S. 301-304 
    ISSN: 1435-0130
    Schlagwort(e): Key words Titanium ; Implants ; Bone ; TOF–SIMS
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract  In order to study commercially pure (CP) titanium bone interaction and integration mechanism, titanium implant bone interface formed for 1, 3 and 6 months was examined and analyzed by advanced TOF–SIMS analysis. The results obtained show: 1) Titanium and bone tissue integrated closely; 2) The action between CP titanium and bone tissue is a reactive process; both physical and chemical integration occur at the titanium–bone interface; 3) Titanium diffuses into the bone tissue, though the diffusion density is limited; 4) The diffusion area of titanium into bone tissue noted during the follow-up period is up to 100 μm. In this paper the titanium bone integration mechanism was studied, both at molecular and anatomic level.
    Materialart: Digitale Medien
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  • 16
    Digitale Medien
    Digitale Medien
    Springer
    European journal of plastic surgery 23 (2000), S. 423-428 
    ISSN: 1435-0130
    Schlagwort(e): Key words Absorbable ; Bone ; Membrane ; Osteogenesis ; Polyglycolide ; Tissue engineering
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract  This study is part of a series of studies evaluating self-reinforced polyglycolide (SR-PGA) membranes. The aim of this study was to evaluate the effect of SR-PGA membrane on osteogenesis in order to assess its use in tissue engineering and bone regeneration. SR-PGA membranes (15×20 mm) were implanted over the femoral diaphyseal bone of 27 Wistar rats (over the periosteum). Each membrane was stabilized using a Dexon suture cerclage. Rats were followed-up for 1, 2, 3, 6, 8, 15 and 30 weeks. Histology and microradiography were used to evaluate bone formation. The membranes were excised and tested for their tensile strength properties, the results of which are published in a separate report. Bone formation periosteally was seen in 21/27 cases (77.8%, confidence interval 57.7–91.4). It occurred in all cases at 1, 2 and 3 weeks. At 6 weeks, it was seen in three out of four cases but at 8 weeks, only in one out of three cases. Bone formation seen as thickened cortex was detected at 15 weeks in all of the three cases and at 30 weeks in three out of six cases. Hence, bone formation was seen in most of the cases when SR-PGA membranes were applied around rats’ femora. They can be recommended for use in bone tissue engineering and regeneration.
    Materialart: Digitale Medien
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  • 17
    Digitale Medien
    Digitale Medien
    Springer
    Skeletal radiology 28 (1999), S. 90-95 
    ISSN: 1432-2161
    Schlagwort(e): Key words DXA ; Bone ; Cadaver ; Biomechanics ; Metastases ; Fracture
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract  Objective. To determine whether the load-bearing capacity of human proximal femora with metastatic defects can be predicted from the bone mineral content. Design. The bone mineral content (BMC) of the total proximal femur was measured by dual-energy X-ray absorptiometry (DXA). The femurs were loaded so as to simulate stair ascent or external rotation. Patients. Simulated lytic defects were created using specialized cutting tools in the intertrochanteric region of 32 human cadaveric femora. Bone density measurements were made before and after creating defects. Results. A linear relation could be used to predict failure load from BMC or bone mineral density. The slope of the linear relation was greater for loads representing external rotation than for loads representing stair ascent. The linear relations suggest that the BMC measurements account for both the density of the host bone and the amount of bone removed by the defect. Conclusions. The data suggest that between 70% and 80% of the variation in failure load of human femora with lytic metastatic defects can be predicted from the BMC and that relations between BMC and failure load are sensitive to the type of loading. Combined with information on the loads associated with the activities of daily living, these data may be used to help identify patients in whom prophylactic stabilization might prevent a pathologic fracture.
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  • 18
    ISSN: 1432-5233
    Schlagwort(e): Key words Non-enzymatic glycosylation ; Advanced glycation endproducts ; Receptor for advanced glycation endproducts ; Diabetes mellitus ; Osteoblasts ; Bone ; Osteopenia
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract Advanced glycation endproducts have been implicated in the development of diabetic complications. In addition, these products could also mediate certain bone alterations such as diabetic osteopenia. Several receptors specific for advanced glycation endproduct-modified proteins have been characterized in different cell types, contributing to the recognition and degradation of senescent proteins. In the present report, we investigated the possible presence of advanced glycation endproduct-binding proteins on osteoblast-like cells. Both UMR106 and MC3T3E1 cell lines express specific advanced glycation endproduct-binding sites, with an affinity constant between 0.4 and 1.7 · 106 M−1, depending on the stage of osteoblastic differentiation; and with a receptor capacity of 1.5–2.0 · 107 sites/cell. Osteoblast-like cells were also found to participate both in the uptake and degradation of advanced glycation endproduct-modified bovine serum albumin at 37°C. Radiolabelled ligand blotting studies confirmed the presence of several membrane binding proteins, with apparent molecular masses of 50, 45–40, 30, 25 and 18 kDa; the major bands corresponded to 30 and 25 kDa proteins. This study provides evidence of the presence of advanced glycation endproduct-specific binding sites, and for their regulation with the stage of differentiation, in two osteoblast-like cells in culture.
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  • 19
    Digitale Medien
    Digitale Medien
    Springer
    Der Nervenarzt 70 (1999), S. 1-10 
    ISSN: 1433-0407
    Schlagwort(e): Schlüsselwörter Tic-Störung ; Zwangsstörung ; Kinder ; Jugendliche ; Neurobiologie ; Psycho- pharmakologie ; Verhaltenstherapie ; Key words Tic-disorder ; Obsessive-compulsive disorder ; Children ; Adolescents ; Neurobiology ; Psychopharmacology ; Behavior therapy
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Beschreibung / Inhaltsverzeichnis: Summary In children and adolescents motor/vocal tics and obsessive-compulsive behavior are known to be closely related. Thereby, a continuum of symptoms ranging from single tics to a mixed picture of tics/rituals/obsessive-compulsive traits to clinically relevant obsessions and compulsions could be described. As neurobiological substrates dysfunctions in corresponding cortico-striato-thalamo-cortical circuits (sensorimotor circuit in tic symptomatology, orbitofrontal circuit in obsessive-compulsive behavior) were postulated. For both disturbances behavioral therapy can be used to improve control mechanisms to counterregulate tics and obsessive-compulsive behavior, respectively, and psychopharmacological agents can be administerd to compensate dysbalances in neurotransmitter systems. In case of a mixed symptomatologic picture it is necessary to include interventions for both pols of the symptom-continuum in the therapeutic programme to achieve extensive improvement as a basis for a further positive development of the patient.
    Notizen: Zusammenfassung Motorische/vokale Tics und zwanghafte Verhaltensweisen kommen bei Kindern und Jugendlichen häufig gemeinsam vor; dabei kann ein Symptomkontinuum von solitär auftretenden Tics über ein Mischbild von Tics und Ritualen/zwanghaften Gedanken und/oder Handlungen bis hin zu eindeutigen Zwangsphänomenen beschrieben werden. Neurobiologisch können diesem Symptomkontinuum unterschiedlich ausgebreitete Dysfunktionen entsprechender kortiko-striato-pallido-thalamo-kortikaler Regulationssysteme zugrunde liegen. Therapeutisch lassen sich bei beiden Verhaltensauffälligkeiten mittels verhaltenstherapeutischer Techniken Steuerungs- und Kontrollmöglichkeiten zur Gegenregulation der Auffälligkeiten verbessern sowie durch Einsatz von Psychopharmaka Dysbalancen von Neurotransmittersystemen ausgleichen. Bei einem Mischbild von Tics und Zwängen sind therapeutische Interventionen für beide Zielbereiche erforderlich. Nur so können umfassende Verbesserungen erreicht und günstige Entwicklungsbedingungen für die betroffenen Kinder und Jugendlichen eröffnet werden.
    Materialart: Digitale Medien
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  • 20
    Digitale Medien
    Digitale Medien
    Springer
    European journal of orthopaedic surgery & traumatology 9 (1999), S. 251-254 
    ISSN: 1432-1068
    Schlagwort(e): Bone ; Scintigraphy ; symptomatic ; Knee ; Arthroplasty ; Os ; Scintigraphie ; Genou ; Arthroplastie ; Symptomatique
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Beschreibung / Inhaltsverzeichnis: Résumé Objectif: Evaluation de la scintigraphie osseuse dans l'arthroplastie totale de genou douloureux. Lieu: Hôpital universitaire, Maastricht et Hôpital Maasland, Sittard. Projet: Investigation clinique retrospective. Méthode: Les dossiers cliniques de 27 patients ayant subi une scintigraphie de l'os, ont été étudiés afin d'analyser les plaintes et la façon de décider le diagnostic. Ces patients avaient des symptômes persistants après l'arthroplastie totale du genou. En plus ont été étudiées les radiographies conventionelles et les scanographies isotopes, sans connaître les dossiers cliniques. Sur la base de ces données nous avons évalué les cas dans lesquels la scanographie isotope du genou a contribué de façon décisive au traitement future. Résultats: La scanographie isotope ne contribue pas à la planification du traitement, si l'examen physique ou les radiographies conventionelles n'ont pas apporté de diagnostic clinique. Il s'agissait ici de 37 % des patients de cette série. Dans les cas où le diagnostic clinique était fait, la scanographie isotope a influencé la décision de diagnostic de 65 % des patients. Cependant, pour les autres patients avec diagnostic clinique (35 %), ce ne fut pas le cas. Conclusion : La répresentation radionucléide est de valeur limitée dans le diagnostic d'une arthroplastie symptomatique totale du genou. Elle peut supporter ou rejeter un diagnostic clinique mais entraînera rarement un changement de traitement, dans l'absence de constatations anormales pendant les examens physiques ou radiologiques.
    Notizen: Summary Objective: Determination of the value of bone scanning in symptomatic total knee arthroplasties. Setting Academic Hospital Maastricht and Maasland Hospital Sittard. Design: Retrospective clinical investigation. Method: The clinical reports of 27 patients, who underwent a bone scintigraphic study, were investigated for complaints and analysis of diagnostic decision making. These patients had persistent symptoms after total knee arthroplasty. In addition, conventional radiographs and the isotope scans were studied without knowledge of the clinical records. Based on these data we evaluated in which cases isotope scanning of the knee had contributed decisively to the further treatment. Results: Isotope scanning did not contribute to the treatment planning if physical examination or conventional radiographs had not led to a clinical diagnosis. This comprised 37% of the patients in our series. If a clinical diagnosis was present, isotope scanning did influence decision making in 65% of the patients. However in the remaining patients with a clinical diagnosis (35%) this was not the case. Conclusion: Radionuclide imaging is of limited value in the diagnostic process of symptomatic total knee arthroplasty. It may support or reject a clinical diagnosis, but in the absence of abnormal findings at physical examinations or radiologic studies, it seldom will induce a change in treatment
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  • 21
    Digitale Medien
    Digitale Medien
    Springer
    European journal of orthopaedic surgery & traumatology 9 (1999), S. 161-165 
    ISSN: 1432-1068
    Schlagwort(e): Bone ; Bone substitutes
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Summary Biocompatible calcium phosphate ceramics has been used for several years in orthopeadic surgery. We have been using two new synthetic biphasic calcium phosphate ceramics (BCP) since September 1996 for bone defect filling in any orthopaedic or trauma operation where autograft use was not possible or even wanted. The first, Eurocer 400® has 300 to 500 micron wide macropores with a totally interconnected porosity. This salt seed like product can be used in bone defect filling, when solidity is not a major concern. The second, Eurocer 200® has not totally interconnected 200 micron large pores. Its main characteristic is a mechanical resistance up to 30 Mpa. We use it in any case of weight-bearing surgery. Different sizes and presentation forms are available and will be chosen according to the recipient site shape. We report one hundred and fifty cases with a six to thirty month follow-up. In one third of the patients hip revision surgery was addressed. Another third concerned recent trauma or sequelae cases,.whereas the last third involved cold orthopaedic procedures. General principles are the need of a living and non-infected site after thorough debridement if necessary. Osteocompatibility of calcium phosphate ceramic is confirmed by our results. We report no mechanical failure. In all cases X-rays show a progressive integration, with new bone formation. Our substitutes have been histologically studied in nine cases, four to fifteen months after implantation. New bone formation around and in the substitute is impressive. Indeed, their good mechanical properties without loss of biological quality is the most relevant feature of these BCPs, leading to a wider indication field; therefore we have now abandoned the use of any bony auto, allo or xenograft.
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  • 22
    Digitale Medien
    Digitale Medien
    Springer
    Psychopharmacology 146 (1999), S. 339-347 
    ISSN: 1432-2072
    Schlagwort(e): Key words Hyperbolic discounting ; Impulsivity ; Self-control ; Reward bundling ; Psychopharmacology
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract  Animal studies of impulsivity have typically used one of three models: a delay of reward procedure, a differential reinforcement for low rate responding (DRL) procedure, or an autoshaping procedure. In each of these paradigms, we argue, measurement of impulsivity is implicitly or explicitly equated with the effect delay has on the value of reward. The steepness by which delay diminishes value (the temporal discount function) is treated as an index of impulsivity. In order to provide a better analog of human impulsivity, this model needs to be expanded to include the converse of impulsivity – self-control. Through mechanisms such as committing to long range interests before the onset of temptation, or through bundling individual choices into classes of choices that are made at once, human decision-making can often look far less myopic than single trial experiments predict. For people, impulsive behavior may be more often the result of the breakdown of self-control mechanisms than of steep discount functions. Existing animal models of self-control are discussed, and future directions are suggested for psychopharmacological research.
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  • 23
    Digitale Medien
    Digitale Medien
    Springer
    Diseases of the colon & rectum 42 (1999), S. 1225-1227 
    ISSN: 1530-0358
    Schlagwort(e): Colon cancer ; Adenocarcinoma ; Intramuscular metastasis ; Bone ; Heterotopic ossification ; Soft tissue tumor
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract PURPOSE: This report presents a patient who developed severe buttock pain because of an ossified intramuscular metastasis from a sigmoid colon cancer. METHODS: This is a case report and review of the literature for intramuscular metastasis from colon cancer. RESULTS: Computed tomography and magnetic resonance imaging showed a soft-tissue mass with heavy calcification. Histologically, mature compact bone was observed with adenocarcinoma cells dispersed among the bony trabeculae. CONCLUSION: When an intramuscular mass is seen, even if it contains extensive calcification, metastasis from colon cancer should be included in differential diagnosis.
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  • 24
    Digitale Medien
    Digitale Medien
    Springer
    International journal of legal medicine 112 (1999), S. 195-197 
    ISSN: 1437-1596
    Schlagwort(e): Key words Trauma ; Calcification ; Bone ; Embolism ; Autopsy
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin , Rechtswissenschaft
    Notizen: Abstract Embolism of bone marrow to the lungs is a quite frequent finding after trauma but transport and deposition of solid bone is rarely seen, which may simply be because pulmonary calcifications are not recognized as bone fragments. We report on three patients with embolism of bone spicules to small lung arteries of about 0.5 mm in diameter which were plentiful in two of the patients on postmortem examination. However, the true nature of the emboli was only recognizable after decalcification of lung tissues. It appears that trauma occurring in a septic bone lesion has the greatest chance to provoke bone embolism. The bone spicules do not usually occlude vessel lumina and thus do not severely disturb the blood circulation in the lungs. The bone fragments become covered by endothelium and can remain recognizable for months or even years.
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  • 25
    Digitale Medien
    Digitale Medien
    Springer
    Mund-, Kiefer- und Gesichtschirurgie 3 (1999), S. 140-145 
    ISSN: 1434-3940
    Schlagwort(e): Schlüsselwörter Konfokale Laser-Scanning-Mikroskopie ; Dunkelfeldmikroskopie ; Bisbenzimidmarkierung ; Knochen ; Strahlenfolgen ; Radiogener Osteozytentod ; Key words Confocal laser scanning microscopy ; Microscopy ; Bisbenzimide labelling ; Bone ; Radiation effects ; Osteocytes ; Osteoradionecrosis
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Beschreibung / Inhaltsverzeichnis: Early radiation effects on human bone may lead to osteoradionecrosis (ORN). Direct bone cellular lesions [28] as well as fibrous degeneration of blood vessels [21] are considered to be pathologically relevant. Only few data on initial subclinical radiation effects are available. Patients were grouped according to the dose of radiation and clinical findings. Group 1: sound human bone of lower jaw, mostly collected during orthodontic surgery (n = 10 patients); group 2: specimens of lower jaw from patients with ORN (n = 12 patients); group 3: specimens of lower jaw from patients with head and neck cancer who were preoperatively treated with 36 Gy radiation; group 4: specimens of lower jaw from patients with head and neck cancer (n = 9) who were treated with 60–70 Gy radiation. Specimens were studied by confocal laser scanning microscopy (CLSM), by conventional light microscopy (DL) and by flourescence darkfield microscopy (DFM) after bisbenzimide staining (H 33258) of the viable cellular nuclei. For the correlating study of identical areas in CLSM and DL the specimens were prepared according to the sawing and grinding technique [8]. All the radiated bony specimens, regardless of the dose of radiation, showed areas of extensive or total loss of vitality of the osteocytes. This finding was also evident after 36 Gy and a short interval between radiation and sample collection (group 3). Additionally, in CLSM micromorphologic lesions of the lamellate structure were seen. With these results we can confirm the loss of vitality of the osteocytes as an initial radiation effect as described earlier [10, 23, 28]. In addition to these findings, alteration of the lamellate microstructure was found in the early phase after radiation. The functional and mechanical significance of these findings should be the subject of further studies.
    Notizen: Für die infizierte Osteoradionekrose (IORN) des Kiefers werden unterschiedliche pathogenetische Mechanismen initialer Strahlenfolgen im Knochen diskutiert: Wichtige Parameter sind dabei die direkte Zellschädigung der Osteozyten [28] und die Gefäßfibrosierung [21]. Bislang liegen wenige Kenntnisse zum Ausmaß der initialen, subklinischen Veränderungen vor. 4 Probengruppen wurden anhand verschiedener Patientenkollektive definiert: Gruppe 1: gesunde Unterkieferproben meist von orthodontischen Operationen (n = 10 Patienten); Gruppe 2: Unterkieferproben mit manifester IORN (n = 12 Patienten); Grruppe 3: Unterkieferproben nach 36 Gy präoperativer Radio(chemo)therapie (n = 9 Patienten); Gruppe 4: Unterkieferproben nach 60–70 Gy Bestrahlung ohne Hinweise auf IORN (n = 9 Patienten). Alle Proben wurden histotomographisch mit konfokaler Laser-Scanning-Mikroskopie (CLSM), durchlichtmikroskopisch (DL) und dunkelfeldmikroskopisch (DFM) nach Fluoreszenzmarkierung des intakten Zellkerns (Bisbenzimid H 33258) untersucht. Korrelierende Histologien identischer Probenareale erfolgten an Trenndünnschliffen [8]. Als Ergebnisse wurden gefunden: 1. Alle unterschiedlich bestrahlte Knochenproben zeigten Areale mit weitgehendem bis vollständigem Verlust vitaler Osteozyten. Diese Strahlenfolge trat auch schon nach 36 Gy und kurzem Intervall bis zur Operation (Gruppe 3) auf. 2. Im CLSM zeigten sich zusätzlich mikromorphologische Veränderungen der lamellären Struktur, die zwischen den Probengruppen progredient waren. Hieraus können folgende Schlußfolgerungen gezogen werden: 1. Der vorbeschriebene Vitalitätsverlust der Osteozyten [10, 23, 28] konnte als sehr frühe, initiale, radiogene Läsion bestätigt werden. 2. Zusätzlich zeigten sich Veränderungen der lamellären Mikroarchitektur des Knochens als frühe und im Gruppenvergleich progrediente Strahlenläsion. Die mikromechanisch funktionelle Bedeutung dieser Veränderung muß in weiterführenden Untersuchungen eruiert werden.
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  • 26
    Digitale Medien
    Digitale Medien
    Springer
    Annals of biomedical engineering 27 (1999), S. 508-516 
    ISSN: 1573-9686
    Schlagwort(e): Angiogenesis ; Artery ; Bone ; Creeping substitution ; Leukocytes ; Osteocytes ; Reperfusion injury ; Trauma
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin , Technik allgemein
    Notizen: Abstract An in vivo model has been developed for chronic observation of the effects of ischemia on cortical bone remodeling and perfused vascularity. Diaphragm occluders were implanted around the right common iliac artery of four rabbits and inflated to produce 10 h of ischemia to the limb. Microcirculation was monitored with intravital microscopy of injected fluorescent microspheres and FITC-Dextran 70 through a bone window, the tibial bone chamber implant (BCI). Bone resorption and apposition in the BCI were indicated with mineralization dyes. Between 2 and 12 h following release of the occluder, secondary ischemia/no-reflow and other evidence of reperfusion injury were observed. Vessel damage was suggested by abnormally high leakage of FITC-D70 from the few vessels perfused during secondary ischemia. In the weeks following occluder release perfused vasculature increased beyond pre-occlusion levels. Net bone resorption reached a maximum when vascularity passed normal levels. In order to further validate the arterial occlusion model for osteonecrosis, techniques for (1) confirming bone death and (2) detecting increased leukocyte adherence to endothelial cells were added. The dead cell stain Ethidium homodimer-1 was used to tag dead osteocytes immediately after occlusion and produced a measure designated “osteonecrosis index.” To detect leukocytes adhering to vessel walls, carboxyfluorescein diacetate, succinimidyl ester was injected at occluder release. An increase in the number of adherent leukocytes was detected. © 1999 Biomedical Engineering Society. PAC99: 8764Rr, 8717-d, 8719Tt
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  • 27
    ISSN: 1433-7347
    Schlagwort(e): Key words Anterior cruciate ; ligament reconstruction ; Bone ; tunnel enlargement ; Hamstring ; tendons ; Magnetic resonance ; imaging ; Radiographic evaluation
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin , Sportwissenschaft
    Notizen: Abstract The aim of this study was to describe the contrast-enhanced magnetic resonance imaging (MRI) appearance of bone tunnel enlargement detected on radiography after anterior cruciate ligament (ACL) reconstruction with semitendinosus and gracilis tendon endobutton (STG-endobutton) fixation technique. Fourteen patients with a STG-endobutton ACL reconstruction were examined 3 months (n = 1), 1 year (n = 1) and 2 years (n = 12) postoperatively. An age- and sex-matched group with a bone–patellar tendon–bone (BTB) autograft ACL reconstruction with similar follow-up was taken as control. Data on clinical examination, laxity and isokinetic muscle torque measurements, anteroposterior and lateral view radiography were obtained, and knee scores (Lysholm and Tegner) were collected. Contrast-enhanced MRI was performed in the STG-endobutton group with a 1.5-T imager. There were no statistical differences between the groups with respect to clinical findings, stability tests, or knee scores. In the STG-endobutton group the average femoral and tibial bone tunnel diameter detected on anteroposterior view radiography had increased at 2-year follow-up by 33% and 23%, respectively. On MRI the ligamentous graft itself was not enhanced by the contrast medium whereas periligamentous tissue within and around the STG graft bundles showed mild contrast enhancement. In conclusion, the MRI results suggest that enhancing periligamentous tissue accumulated in and around the STG graft associated with the tunnel expansion. In spite of the significant bone tunnel enlargement observed on the follow-up radiography the STG-endobutton knees were stable and the patients satisfied.
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  • 28
    Digitale Medien
    Digitale Medien
    Springer
    European journal of trauma 25 (1999), S. 230-236 
    ISSN: 1615-3146
    Schlagwort(e): Aneurysmatische Knochenzyste ; Knochentumor ; Hand ; Aneurysmal bone cyst ; Bone ; Hand
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Beschreibung / Inhaltsverzeichnis: Abstract The aneurysmal bone cyst localizised at the longfingers of the hand is an extremely rare clinical entity, particularly considering the age and the distinct aggressiveness in our case. In this specific case of a 53-year-old male the differentialdiagnosis as well as problems of the aneurysmal bone cyst with affection of the phalangeal bone will be discussed. Furthermore the various possibilities of therapy will be focussed on. At first the patient was treated with curettage followed by bone grafting. Already 5 months later a local recurrence appeared. The proximal phalangeal bone and the metacarpophalangeal joint V were almost distroyed. Aiming at preservation of a high funcionality of the hand we amputated the 5th finger in the metacarpophalangeal joint.
    Notizen: Zusammenfassung Die aneurysmatische Knochenzyste mit Lokalisation an der Hand, insbesondere an den Phalangen, ist ein extrem seltenes Krankheitsbild. Auch das Alter des Patienten und die ausgeprägte Aggressivität unseres Falles sind bemerkenswert. Anhand der Krankengeschichte eines 53jährigen Mannes mit Befall der Grundphalanx des fünften Fingers der rechten Hand werden die Problemstellung bzw. Differentialdiagnose verdeutlicht und die verschiedenen Therapiemöglichkeiten besprochen. In unserem Fall wurde zunächst eine Kürettage mit anschließender Spongiosaaufftüllung durchgeführt. Bereits nach fünf Monaten kam es zu einem aggressiven Rezidiv mit Zerstörung der gesamten Grundphalanx und des Grundgelenks, so daß wir uns schließlich unter Berücksichtigung der bestmöglichen Funktion der Hand für eine Amputation des Kleinfingers entschieden haben.
    Materialart: Digitale Medien
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  • 29
    Digitale Medien
    Digitale Medien
    Springer
    Reproduktionsmedizin 15 (1999), S. 405-409 
    ISSN: 1434-808X
    Schlagwort(e): Schlüsselwörter Estrogenrezeptoren ; Knochen ; Arteriosklerose ; Endometrium ; Zentralnervensystem ; Key words Estrogen receptors ; Bone ; Arteriosclerosis ; Endometrium ; Central nervous system
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Beschreibung / Inhaltsverzeichnis: Summary Almost each cell in the body is estrogen-receptive. The strength of estrogen influence on organs or organ systems, however, may vary. Thus, estrogen withdrawal may have more or less severe pathophysiological consequences. Recently, the existence of two estrogen receptors has been established (estrogen receptor α and β = ERα and ERβ and several splice variants of these two basic receptor types have been desribed). This, together with our increasing knowledge about tissue-specific enhancer and repressor genes now allows a better understanding of the organ-specific effects of estrogens. In view of gynecological endocrinology, hormone replacement therapy with estrogens is beneficial for most organs in the body (bone, cardiovascular system, CNS). However, pure estrogen therapy may have deleterious effects in the endometrium of the uterus because it may initiate the development of uterine cancer. In the uterus of most species studied so far, no ERβ but only the classical ERα gene has been described. Hence, drug companies have now intensively begun to search for ERβ-specific estrogens. The first, relatively specific, non-steroidal product that addresses primarily the ERβ is the drug raloxifen, which has been recently introduced clinically. However, also some natural phyto-estrogens appear to be ERβ-specific.
    Notizen: Zusammenfassung Fast jede Körperzelle ist estrogenrezeptiv. Es gibt allerdings Organe und Organsysteme, die besonders unter dem Einfluß von Estrogenen stehen und die sich bei Estrogenmangel krankhaft verändern können. Die vielfältigen Wirkungen von Estrogenen konnten nicht vollständig verstanden werden, solange die Existenz von nur einem Estrogenrezeptor quasi ein Dogma war. Erst die Klonierung eines zweiten (Estrogenrezeptor β = ERβ) sowie das bessere Verständnis von gewebespezifischen Enhancer- und Repressor-Genen konnten die vielfältigen und z. T. organspezifischen Wirkungen der Estrogene aufklären. Aus der Sicht der gynäkologischen Endokrinologie ist die Hormonersatztherapie mit Estrogenen für fast alle Organe des Körpers (Knochen, Herz-Kreislauf-System, Zentralnervensystem) segensreich. Eine nicht gestagenbegleitete Estrogentherapie kann allerdings verheerende Folgen am Endometrium mit Entwicklung eines Corpus-Karzinoms haben. Da der Uterus praktisch kein ERβ sondern nur den klassischen ERα exprimiert, hat eine intensive Suche nach ERβ-spezifischen Estrogenen begonnen. Ein erstes, halbwegs spezifisches nicht-steroidales Produkt scheint das kürzlich in die Klinik eingeführte Raloxifen zu sein, aber auch einige Phytoestrogene scheinen ERβ-spezifisch zu wirken.
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  • 30
    Digitale Medien
    Digitale Medien
    Springer
    Skeletal radiology 27 (1998), S. 98-102 
    ISSN: 1432-2161
    Schlagwort(e): Key words Hemangiopericytoma ; Brain ; Bone ; Metastasis
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract  Two cases of osseous hemangiopericytoma are presented that were initially diagnosed as primary in origin, but later reclassified as metastases, after a history of resection for an intracranial tumor was discovered. An intracranial source should be excluded before an isolated osseous tumor is determined to be a primary hemangiopericytoma.
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  • 31
    Digitale Medien
    Digitale Medien
    Springer
    Skeletal radiology 27 (1998), S. 346-349 
    ISSN: 1432-2161
    Schlagwort(e): Key words Neurofibromatosis ; Malignant peripheral nerve sheath tumor ; Bone
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract  Malignant peripheral nerve sheath tumors (MPNSTs) are uncommon sarcomas that almost always arise in soft tissue. They can develop in pre-existing neurofibromas or schwannomas, de novo from peripheral nerves, or following radiation therapy. Primary intraosseous MPNST is rare and has been reported most frequently in the mandible. Of the reported cases involving the long bones, none has been associated with neurofibromatosis type 1 (NF-1). We report a case of MPNST arising in the femur in a patient with NF-1.
    Materialart: Digitale Medien
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  • 32
    ISSN: 1432-198X
    Schlagwort(e): Key words: Neonatal Bartter syndrome ; Bone ; Cal- cium ; Heparin
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract. The neonatal Bartter syndrome (NBS) is associated with a complex disorder of mineral metabolism in children, including hypercalciuria, nephrocalcinosis, and diminished bone mineral density. Although cyclooxygenase inhibition usually brings about improvement in these findings, there is a variable component which is resistant to such therapy in many children. The factor mediating this disorder has not been identified. Blood and urine from 12 children with NBS were examined. When compared with samples from normal children and adults, all (NBS) sera reduced bone calcium uptake in a bone disc bioassay. This effect persisted in the presence of parathyroid hormone (PTH) antibody and PTH receptor blockade, indicating that neither PTH nor PTH related peptide was responsible. It was eliminated by indomethacin, suggesting that prostanoid generation was essential. Protamine was also inhibitory, as was the addition of ecteola, an anion binder. Activity could be recovered from ecteola by elution with hypertonic buffer. Urine samples from children with NBS had the same calcitropic effect. The agent was removed by ecteola and recovered by hypertonic elution. Activity was eliminated by protamine and by heparinase, but not by trypsin digestion. Size exclusion centrifugation showed that the activity was associated with a material between 10 and 30 kilodaltons. Finally, urine ecteola eluates from NBS patients raised serum concentrations of calcium after intraperitoneal injection in rats. These data suggest that children with NBS have a calcitropic substance in their serum and urine which is not found in normal individuals. The substance is heparin like, and mediates its effects through prostanoid production. These studies provide additional evidence against a direct renal cause of the urinary calcium disturbance characteristic of the disorder.
    Materialart: Digitale Medien
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  • 33
    ISSN: 1423-0127
    Schlagwort(e): Muscular dystrophy ; Central nuclei ; Avian muscle ; Inflammation ; Dwarfism ; Lymphocyte ; Mechanochemical transducer ; Bone ; Steroid ; Fiber splitting
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Biologie , Medizin
    Notizen: Abstract Muscular dystrophy has long been believed to be characterized by degeneration and abortive regeneration of muscle fibers (the muscle degeneration theory), but unfortunately its pathogenesis is still unclear and an effective treatment has yet to be developed. As a challenge to the theory, we have proposed an alternative muscle-defective-growth theory and a further bone muscle growth imbalance hypothesis supposing possible defects in bone-growth-dependent muscle growth based on our findings in hereditary dystrophic dy mice (C57BL/6Jdy/dy). This review presents some new insights into the pathogenesis of the disease along with our hypothesis, focusing on the physiological meaning of centronucleation, one of the major pathological changes commonly observed in dystrophic muscles of man and experimental animals.
    Materialart: Digitale Medien
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  • 34
    Digitale Medien
    Digitale Medien
    Springer
    European spine journal 7 (1998), S. 257-259 
    ISSN: 1432-0932
    Schlagwort(e): Key words Angiomatosis ; Bone ; Osteolysis ; Cervical spine
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract The case of a 21/2-year-old boy with diffuse cystic angiomatosis of bone is presented. No evidence of visceral involvement was recorded. The clinical, radiographic and histologic findings during the course of the disease process are discussed. At the age of 15 years the patient died of neurologic alterations developed due to massive osteolysis and collapse of the cervical spine, and severe dyspnoea, secondary to persistent bilateral pleural effusions.
    Materialart: Digitale Medien
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  • 35
    Digitale Medien
    Digitale Medien
    Springer
    Experimental biology online 3 (1998), S. 1-15 
    ISSN: 1430-3418
    Schlagwort(e): Bone ; Cell behaviour ; Chondrocyte ; Endothelia ; Epitenon
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Biologie
    Notizen: Abstract The motile behaviour, growth and reactions of osteoblasts, chondrocytes, epitenal cells and endothelia to culture on extended concave surfaces inside tubes is reported. Time-lapse video observations show that these cells can be successfully grown in quartz tubes for up to 21days. The cells would attach to the concave surfaces even when the radius of curvature was as low as 25 μm. The cells attached to the walls were not oriented. As culturing progressed the chondrocytes, osteoblasts and epitenon cells tended to detach from the walls of the tubes, forming long cords of cells attached to the walls at a few points only. Endothelial cells did not detach. These cords showed extensive lamellipodial activity at their points of attachment to the tube wall. The cells in these cords do not show contact inhibition of movement.
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  • 36
    Digitale Medien
    Digitale Medien
    Springer
    Transplant international 11 (1998), S. S487 
    ISSN: 1432-2277
    Schlagwort(e): Key words Knee joint ; Vascularized graft ; Bone ; Transplantation
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Notizen: Abstract Four transplantations of an allogeneic vascularized human knee joint were performed at the Trauma Center Murnau between April 1996 and July 1997. The indication for the procedure was the total loss of the knee joint including the extensor apparatus due to severe trauma. These were the first transplants of this type. Management of patients started with closure of soft-tissue defects. After successful completion, stabilization was achieved with femoral and tibial nails plus a temporary arthroplasty. AB0 compatibility and a negative cross-match were the main criteria for selecting patients for transplantation. Interlocking compression nails were used for osteosynthesis. Vascular anastomoses between graft and recipient vessels were established by the end-to-side technique. Immunosuppression was started as a quadruple induction therapy for 3 days, then reduced to a two-drug maintenance therapy with cyclosporine and azathioprine. Six months posttransplantation the osteotomies were bridged by callus and the patients became completely mobile. Radiographic and histological examinations revealed vital graft tissue.
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  • 37
    Digitale Medien
    Digitale Medien
    Springer
    Mund-, Kiefer- und Gesichtschirurgie 2 (1998), S. 141-145 
    ISSN: 1434-3940
    Schlagwort(e): Schlüsselwörter Konfokale Laser-Scanning-Mikroskopie ; Knochen ; Histotomographie ; Key words Confocal laser scanning microscopy ; Bone ; Histotomography
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Beschreibung / Inhaltsverzeichnis: Objectives: Fixation (formalin), decalcification (sections) or mechanical treatment (grinding) all bear the risk of artifacts occurring during hard-tissue histology. Because studies on the etiology of pathological changes mostly focus on subclinical lesions, artifacts can simulate early changes or even be superimposed on existing changes. The objective of this study was to determine how artifacts can be reduced. Material and methods: In confocal laser scanning microscopy (CLSM) a focused laser beam scans the surface of the specimens and penetrates into the tissue. The intensity of the remitted light is recorded. The confocal effect is due to an extremely small aperture (pinhole), excluding light from out-of-focus planes of the sample. By stepwise movement of the object table, a tomographic series of tomographic images is obtained. Sound cortical bone samples of the lower jaw (n = 20) were studied by light microscopy and by CLSM, visualizing identical areas of a ground sectioned sample after H & E staining. Additionally, embedded and fresh blocks of tissue of the same bone sample were studied histotomographically in the CLSM. Results: (1) Light microscopic micromorphology of cortical bone can be visualized adequately in the CLSM; (2) many structures that can be visualized by light microscopy only after special staining (e.g., osteozyte processes) can be visualized by the CLSM using sample blocks without pretreatment. Conclusion: (1) Nondestructive subsurface histotomography by CLSM totally excludes mechanical artifacts; (2) physicochemical artifacts can be handled more easily because fresh samples can be studied; (3) pseudo-three-dimensional imaging allows histological interpretation of the tissue that is equivalent to macroscopic tomographic techniques (CT, MRT).
    Notizen: Durch Fixierung (Formalin), Entkalkung (Schnitte) oder mechanische Bearbeitung (Schliffe) besteht bei der Hartgewebshistologie das Risiko physikalisch-chemischer oder mechanischer Artefakte. Da Studien zur Ätiopathogenese pathologischer Veränderungen meist auf subklinische Läsionen zielen, besteht die Gefahr, daß Artefakte frühe Veränderungen vortäuschen oder vorhandene überdecken. Es wird der Frage einer artefaktminimierten Histologie nachgegangen. Bei der konfokalen Laser-Scanning-Mikroskopie (CLSM) rastert ein monochromatischer Laserstrahl über die Probenoberfläche und dringt in das Gewebe ein. Die Intensität der remittierten Strahlung wird in einem Detektor gemessen. Durch eine konfokale Blende (pinhole) erreicht nur Laserlicht aus einer extrem dünnen In-Fokus-Ebene den Detektor, so daß schrittweises Bewegen des Objekttischs eine tomographische Serie von Einzelbildern visualisiert. Gesunde kortikale Knochenproben des Unterkiefers (n = 20) wurden durchlichtmikroskopisch und im CLSM untersucht: Dabei wurden identische Probenareale an Dünnschliffen nach HE-Färbung visualisiert. Außerdem wurden eingebettete und frische Gewebeblöcke derselben Knochenproben im CLSM histotomographiert. Als Ergebnisse wurden gefunden: 1. Lichtmikroskopische Mikromorphologie kortikalen Knochens ist im CLSM valide visualisierbar. 2. Viele lichtmikroskopisch erst nach Spezialfärbungen darstellbare Strukturen (z.B. Osteozytenfortsätze) können im CLSM an Probenblöcken ohne Vorbereitung mikroskopiert werden. Hieraus können folgende Schlußfolgerungen gezogen werden: 1. Die zerstörungsfreie Histotomographie des CLSM unter der Probenoberfläche vermeidet mechanische Artefakte völlig. 2. Physikalisch-chemische Artefakte werden kontrollierbar, da auch frische Proben mikroskopiert werden können. 3. Die pseudo-dreidimensionale Darstellung erlaubt eine histologische Gewebeinterpretation, die makroskopischen Schichtbildverfahren (CT, MRT) vergleichbar ist.
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  • 38
    Digitale Medien
    Digitale Medien
    Springer
    Mund-, Kiefer- und Gesichtschirurgie 2 (1998), S. S37 
    ISSN: 1434-3940
    Schlagwort(e): Schlüsselwörter Kalzium ; Phosphat ; Hydroxylapatit ; Zement ; Knochenersatz ; Augmentation ; Key words Calcium ; Phosphate ; Hydroxyapatite ; Cement ; Bone ; Augmentation
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin
    Beschreibung / Inhaltsverzeichnis: Summary A new stoechiometric mixture of 27% dicalcium-phosphate (DCPA) and 73% tetra-calcium-phosphate (TTCP) can be prepared with water intraoperatively to a paste that subsequently sets to a structurally stabile implant composed of hydroxyapatite (HA). Primary setting time is about 20 min; pH during setting ranges from 6.5 to 8.5. There is no relevant curing heat or expansion or contraction. Compressive strength is about 50 MPa, tensile strength about 8 MPa. Over a period of about 4 h in physiological milieu, the cement converts to hydroxyapatite. This product is no longer redissolvable in normal body fluid. This cement can be used for non-load-bearing applications especially in craniofacial bone surgery. Cranial defects due to tumour or trauma as well as deficits in the facial skeleton may be reconstructed using this new biomaterial. In nine of ten patients we used the hydroxyapatite cement successfully for reconstructions in the craniofacial area. Fluid control of the operation field and implant site is extremely important and sometimes difficult to achieve. Further applications could be all non-load-bearing augmentations such as filling of blocked paranasal sinuses, of dentoalveolar cysts and defects following dental apectomy or fixation of implanted hearing-aid electrodes. The perspectives for the hydroxyapatite cement include its application as a carrier for osteogenic protein preparations, especially because of its isothermic reaction and intrinsic osteoconductive characteristics.
    Notizen: Zusammenfassung Ein neuer Kalziumphosphatzement besteht aus 73% Tetrakalziumphosphat und 27% Kalziumhydrogenphosphat. Er bindet bei Körpertemperaturen nach Zugabe von Wasser innerhalb von 20 min ab. Innerhalb von 4 h wird der Zement zu Hydroxylapatitkristallen umgesetzt und damit wasserunlöslich. Der Abbindeprozeß verläuft nahezu isotherm im pH-Bereich von 6,5–8,5 ohne Schrumpfung. Die Druckfestigkeit liegt im ausgehärteten Zustand oberhalb von 50 MPa, die Zugfestigkeit bei mehr als 8 Mpa. Der Zement ist für alle nicht lasttragenden Knochenaugmentationen und Knochenersatzanwendungen insbesondere am Gesichtsschädel geeignet. Bei 9 von 10 Patienten benutzten wir den Zement erfolgreich für Rekonstruktionen im kraniofazialen Bereich. Beim klinischen Einsatz muß besonders auf sorgfältige Trockenlegung des Operations- und Implantationsfelds geachtet werden. Weitere Anwendungsmöglichkeiten sind das Auffüllen von ausgeräumten und verblockten Schädelhöhlen, die Fixation von implantierten Hörelektroden in der Hals-Nasen-Ohren-Heilkunde sowie das Auffüllen von Zysten und Wurzelspitzenresektionsdefekten in der dentoalveolären Chirurgie. Besondere Perspektiven bietet der Hydroxylapatitzement wegen seiner isothermen Abbindereaktion und seiner intrinsischen osteokonduktiven Eigenschaften als Trägermaterial für osteogene Proteinkomplexe.
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  • 39
    ISSN: 1434-5196
    Schlagwort(e): Key words Identification ; Forensic osteology ; DNA typing ; PCR ; Brain ; Bone ; Schlüsselwörter Identifikation ; Forensische ; Osteologie ; DNA-Typisierung ; PCR ; Gehirn ; Knochen
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Medizin , Rechtswissenschaft
    Beschreibung / Inhaltsverzeichnis: Zusammenfassung Ein weitgehend skelettierter Kleinkind-Schädel konnte mittels forensisch-anthropologischer Befunderhebung klassifiziert und mittels erfolgreicher DNA-PCR-Typisierung am Hirnbrei, nicht jedoch am Schädelknochen identifiziert werden. Die vorgestellte Kasuistik belegt eindrücklich, daß eine sorgfältige forensisch-anthropologische Befunderhebung eine wesentliche Grundlage für die molekularbiologische Identifizierung an Skeletteilen bildet und daß auch an fortgeschritten fäulnisverändertem Gehirn bei feuchtem Lagerungsmilieu eine DNA-PCR-Typisierung erfolgreich sein kann.
    Notizen: Abstract The skull of a small child, which was largely devoid of soft tissue, was classified according to forensic/anthropological findings and could be identified on the basis of DNA typing by PCR using residual brain tissue, but not bone. This case illustrates the fact that careful forensic/anthropological investigation is an important basis for molecular biological identification from skeletal remains and that DNA typing by PCR may even be possible on brain tissue that has been exposed to damp conditions and is an advanced state of decomposition.
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  • 40
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 321-336 
    ISSN: 0887-3585
    Schlagwort(e): surface characterization ; DOCK ; structure-based molecular design ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The characterization of receptor binding sites is an important aspect of molecular docking, molecular recognition, and the structure-based design process. This characterization can take several forms: the receptor surface itself can be delineated or described, the space adjacent to the surface can be chemically mapped, or a negative image of the protein binding region can be generated. In this report, we describe a new method of constructing a negative image through generation of a set of spheres. These spheres lie along the receptor surface, and their centers represent possible ligand atom positions. By the method in which they are constructed, these spheres carry a limited amount of energetic and chemical information in addition to their primary geometric information. We test the accuracy of the image by comparing sphere positions to the positions of bound ligand atoms and propose a figure of merit for such tests. Then, we use the spheres to orient ligands in enzyme active sites and show how they can be used to generate low scoring configurations more efficiently than other approaches that search orientation space. In addition, two novel applications of these spheres are described: they are used to help identify structural differences among families of enzymes and to suggest points for ligand modification in analog design. Proteins 30:321-336, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 41
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 352-356 
    ISSN: 0887-3585
    Schlagwort(e): myoglobin ; nitric oxide ; ligand binding ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The structure of the ferrous nitric oxide form of native sperm whale myoglobin has been determined by X-ray crystallography to 1.7 Å resolution. The nitric oxide ligand is bent with respect to the heme plane: the Fe-N-O angle is 112°. This angle is smaller than those observed in model compounds and in lupin leghemoglobin. The exact angle appears to be influenced by the strength of the proximal bond and hydrogen bonding interactions between the distal histidine and the bound ligand. Specifically, the Nε atom of histidine64 is located 2.8 Å away from the nitrogen atom of the bound ligand, implying electrostatic stabilization of the FeNO complex. This interpretation is supported by mutagenesis studies. When histidine64 is replaced with apolar amino acids, the rate of nitric oxide dissociation from myoglobin increases tenfold. Proteins 30:352-356, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
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  • 42
    ISSN: 0887-3585
    Schlagwort(e): protein modeling ; crystal structure ; conformation change ; prediction ; mechanism ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The occurrence of large domain motions associated with the mechanism of action of many proteins is well established. We present a general method of predicting domain closure applicable to proteins containing domains separated by an apparent hinge. The method attempts to allow for natural directional bias within the closing protein by repeatedly applying a weak pulling force over a short distance between pairs of atoms chosen at random in the two domains in question. Appropriate parameters governing the pulling function were determined empirically. The method was applied to the bi-lobal protein PGK and a closed-form activated ternary complex generated for Bacillus stearothermophilus PGK. This model was compared with the recently determined crystal structure of closed-form Trypanosoma brucei PGK. The model predicts the correct hinge regions, although the magnitude of movement at one hinge point was overestimated, and provides a reasonable representation of the closed-form ternary complex. Proteins 30:372-380, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 43
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 388-400 
    ISSN: 0887-3585
    Schlagwort(e): molecular dynamics ; free energy perturbation ; thermodynamics integration ; spherical solvent boundary potential ; cell multipole method ; Nosé-Hoover equation ; component analysis ; chymotrypsin inhibitor 2 ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We developed a software package for improved free energy calculation, in which spherical solvent boundary potential, cell multipole method, and Nosé-Hoover equation are employed. The performance of the developed software package is demonstrated in the case of valine to alanine mutation of the 57th residue in chymotrypsin inhibitor 2. By using this package, we obtained results quantitatively comparable to experimental results. By the free energy component analysis, it is shown that leucine 51, arginine 65, arginine 67, and phenylalanine 69 residues contribute significantly to the total free energy shift, ΔΔG. Among them, contribution from the hydrophilic arginine 67 residue, which is in close contact with the mutation site, is the largest. Structure around the mutation site is largely changed by the mutation. The structure change is caused mainly by two effects, hydrophobic interaction and short-range interaction along the sequence. Effects of Nosé-Hoover algorithm and Kirkwood reaction field are also discussed. Proteins 30:388-400, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 44
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 435-441 
    ISSN: 0887-3585
    Schlagwort(e): cytochrome c ; thermal unfolding ; proteolysis ; proteinase K ; thermolysin ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Recent hydrogen exchange experiments on native cytochrome c implicate a sequential unfolding pathway in contrast to a simple two-state process. We have studied the heat-induced unfolding of this protein by using spectroscopic measurements to detect changes in conformation and proteolytic enzyme digestion to identify regions of the protein that are labile. Several spectroscopic profiles were monitored: CD at 222 nm, a measurement of secondary structure change in the protein, the absorbance at 280 nm, involving the local environment of Trp 59, and absorbance at 420 nm, the Soret band of the heme. The apparent Tm values for these probes differ, consistent with an unfolding pathway containing intermediates. The limited digestion by proteinase K is consistent with population of an intermediate state in unfolding. We find a single strong region of cleavage at low temperature with retention of structure in each fragment. Proteins 30:435-441, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 45
    ISSN: 0887-3585
    Schlagwort(e): venom toxin ; protein-membrane interaction ; X-ray diffraction ; spectroscopy ; quaternary structural change ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Bothropstoxin I (BthTX-I) from the venom of Bothrops jararacussuis a myotoxic phospholipase A2 (PLA2) homologue which, although catalytically inactive due to an Asp49→Lys substitution, disrupts the integrity of lipid membranes by a Ca2+-independent mechanism. The crystal structures of two dimeric forms of BthTX-I which diffract X-rays to resolutions of 3.1 and 2.1 Å have been determined. The monomers in both structures are related by an almost perfect twofold axis of rotation and the dimer interfaces are defined by contacts between the N-terminal α-helical regions and the tips of the β-wings of partner monomers. Significant differences in the relative orientation of the monomers in the two crystal forms results in “open” and “closed” dimer conformations. Spectroscopic investigations of BthTX-I in solution have correlated these conformational differences with changes in the intrinsic fluorescence emission of the single tryptophan residues located at the dimer interface. The possible relevance of this structural transition in the Ca2+-independent membrane damaging activity is discussed. Proteins 30:442-454, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 46
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 10-20 
    ISSN: 0887-3585
    Schlagwort(e): protein design ; lattice model ; protein stability ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A structure-based, sequence-design procedure is proposed in which one considers a set of decoy structures that compete significantly with the target structure in being low energy conformations. The decoy structures are chosen to have strong overlaps in contacts with the putative native state. The procedure allows the design of sequences with large and small stability gaps in a random-bond heteropolymer model in both two and three dimensions by an appropriate assignment of the contact energies to both the native and nonnative contacts. The design procedure is also successfully applied to the two-dimensional HP model. Proteins 31:10-20, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 47
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 535-549 
    ISSN: 0887-3585
    Schlagwort(e): docking ; protein-DNA ; prediction ; structure ; base recognition ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The docking of repressor proteins to DNA starting from the unbound protein and model-built DNA coordinates is modeled computationally. The approach was evaluated on eight repressor/DNA complexes that employed different modes for protein/ DNA recognition. The global search is based on a protein-protein docking algorithm that evaluates shape and electrostatic complementarity, which was modified to consider the importance of electrostatic features in DNA-protein recognition. Complexes were then ranked by an empirical score for the observed amino acid /nucleotide pairings (i.e., protein-DNA pair potentials) derived from a database of 20 protein/DNA complexes. A good prediction had at least 65% of the correct contacts modeled. This approach was able to identify a good solution at rank four or better for three out of the eight complexes. Predicted complexes were filtered by a distance constraint based on experimental data defining the DNA footprint. This improved coverage to four out of eight complexes having a good model at rank four or better. The additional use of amino acid mutagenesis and phylogenetic data defining residues on the repressor resulted in between 2 and 27 models that would have to be examined to find a good solution for seven of the eight test systems. This study shows that starting with unbound coordinates one can predict three-dimensional models for protein/DNA complexes that do not involve gross conformational changes on association. Proteins 33:535-549, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 48
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 139-149 
    ISSN: 0887-3585
    Schlagwort(e): protein structure ; statistical potentials ; protein structure database ; assessing protein models ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A long standing goal in protein structure studies is the development of reliable energy functions that can be used both to verify protein models derived from experimental constraints as well as for theoretical protein folding and inverse folding computer experiments. In that respect, knowledge-based statistical pair potentials have attracted considerable interests recently mainly because they include the essential features of protein structures as well as solvent effects at a low computing cost. However, the basis on which statistical potentials are derived have been questioned. In this paper, we investigate statistical pair potentials derived from protein three-dimensional structures, addressing in particular questions related to the form of these potentials, as well as to the content of the database from which they are derived. We have shown that statistical pair potentials depend on the size of the proteins included in the database, and that this dependence can be reduced by considering only pairs of residue close in space (i.e., with a cutoff of 8 Å). We have shown also that statistical potentials carry a memory of the quality of the database in terms of the amount and diversity of secondary structure it contains. We find, for example, that potentials derived from a database containing α-proteins will only perform best on α-proteins in fold recognition computer experiments. We believe that this is an overall weakness of these potentials, which must be kept in mind when constructing a database. Proteins 31:139-149, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 7 Ill.
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  • 49
    ISSN: 0887-3585
    Schlagwort(e): antibody ; antitumor ; single chain Fv ; variable domains ; X-ray crystallography ; protein structure ; protein stability ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A recombinant Fv construct of the B1 monoclonal antibody that recognizes the LewisY-related carbohydrate epitope on human carcinoma cells has been prepared. The Fv is composed of the polypeptide chains of the VH and VL domains expressed independently and isolated as inclusion bodies. The Fv is prepared by combining and refolding equimolar amounts of guanidine chloride solubilized inclusion bodies. The Fv is stabilized by an engineered interchain disulfide bridge between residues VL100 and VH44. This construct has a similar binding affinity as that of the single-chain construct (Benhar and Pastan, Clin. Cancer Res. 1:1023-1029, 1995). The B1 disulfide-stabilized Fv (B1dsFv) crystallizes in space group P6122 with the unit cell parameters a = b = 80.1 Å, and c = 138.1 Å. The crystal structure of the B1dsFv has been determined at 2.1-Å resolution using the molecular replacement technique. The final structure has a crystallographic R-value of 0.187 with a root mean square deviation in bond distance of 0.014 Å and in bond angle of 2.74°. Comparisons of the B1dsFv structure with known structures of Fv regions of other immunoglobulin fragments shows closely related secondary and tertiary structures. The antigen combining site of B1dsFv is a deep depression 10-Å wide and 17-Å long with the walls of the depression composed of residues, many of which are tyrosines, from complementarity determining regions L1, L3, H1, H2, and H3. Model building studies indicate that the LewisY tetrasaccharide, Fuc-Gal-Nag-Fuc, can be accommodated in the antigen combining site in a manner consistent with the epitope predicted in earlier biochemical studies (Pastan, Lovelace, Gallo, Rutherford, Magnani, and Willingham, Cancer Res. 51:3781-3787, 1991). Thus, the engineered disulfide bridge appears to cause little, if any, distortion in the Fv structure, making it an effective substitute for the B1 Fab. Proteins 31:128-138, 1998. Published 1998 Wiley-Liss, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
    Zusätzliches Material: 10 Ill.
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  • 50
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 150-159 
    ISSN: 0887-3585
    Schlagwort(e): photosynthetic reaction center ; bacteriorhodopsin ; cytochrome C oxidase ; zipper ; packing ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Membrane-embedded protein domains frequently exist as α-helical bundles, as exemplified by photosynthetic reaction centers, bacteriorhodopsin, and cytochrome C oxidase. The sidechain packing between their transmembrane helices was investigated by a nearest-neighbor analysis which identified sets of interfacial residues for each analyzed helix-helix interface. For the left-handed helix-helix pairs, the interfacial residues almost exclusively occupy positions a, d, e, or g within a heptad motif (abcdefg) which is repeated two to three times for each interacting helical surface. The connectivity between the interfacial residues of adjacent helices conforms to the knobs-into-holes type of sidechain packing known from soluble coiled coils. These results demonstrate on a quantitative basis that the geometry of sidechain packing is similar for left-handed helix-helix pairs embedded in membranes and coiled coils of soluble proteins. The transmembrane helix-helix interfaces studied are somewhat less compact and regular as compared to soluble coiled coils and tolerate all hydrophobic amino acid types to similar degrees. The results are discussed with respect to previous experimental findings which demonstrate that specific interactions between transmembrane helices are important for membrane protein folding and/or oligomerization. Proteins 31:150-159, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 51
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 2-33 
    ISSN: 0887-3585
    Schlagwort(e): chevron plot ; energy landscape ; folding funnel ; kinetic trap ; lattice models ; non-Arrhenius behavior ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We use two simple models and the energy landscape perspective to study protein folding kinetics. A major challenge has been to use the landscape perspective to interpret experimental data, which requires ensemble averaging over the microscopic trajectories usually observed in such models. Here, because of the simplicity of the model, this can be achieved. The kinetics of protein folding falls into two classes: multiple-exponential and two-state (single-exponential) kinetics. Experiments show that two-state relaxation times have “chevron plot” dependences on denaturant and non-Arrhenius dependences on temperature. We find that HP and HP+ models can account for these behaviors. The HP model often gives bumpy landscapes with many kinetic traps and multiple-exponental behavior, whereas the HP+ model gives more smooth funnels and two-state behavior. Multiple-exponential kinetics often involves fast collapse into kinetic traps and slower barrier climbing out of the traps. Two-state kinetics often involves entropic barriers where conformational searching limits the folding speed. Transition states and activation barriers need not define a single conformation; they can involve a broad ensemble of the conformations searched on the way to the native state. We find that unfolding is not always a direct reversal of the folding process. Proteins 30:2-33, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 35 Ill.
    Materialart: Digitale Medien
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  • 52
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 49-60 
    ISSN: 0887-3585
    Schlagwort(e): kohonen network ; mitochondrial processing peptidase (MPP) ; mitochondrial intermediate peptidase (MIP) ; neural network ; protein import ; sequence motif ; mitochondrial targeting ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Cleavage sites in nuclear-encoded mitochondrial protein targeting peptides (mTPs) from mammals, yeast, and plants have been analysed for characteristic physicochemical features using statistical methods, perceptrons, multilayer neural networks, and self-organizing feature maps. Three different sequence motifs were found, revealing loosely defined arginine motifs with Arg in positions -10, -3, and -2. A self-organizing feature map was able to cluster these three types of endopeptidase target sites but did not identify any species-specific characteristics in mTPs. Neural networks were used to define local sequence features around precursor cleavage sites. Proteins 30:49-60, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 53
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 109-112 
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
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  • 54
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 136-143 
    ISSN: 0887-3585
    Schlagwort(e): protein design ; protein structure ; circular dichroism ; trifluoroethanol ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Inspired by the Paracelsus Challenge of Rose and Creamer (Proteins 19:1-3, 1994), we have designed a protein sequence that is 50% identical to an all-helical protein but is intended to fold into a largely β-sheet structure. Rather than attempt a de novo design, our strategy was to construct a hybrid sequence based on a helical “parent” protein (434 Cro) and a “target” protein with the desired fold (the B1 domain of protein G). The hybrid sequence (Crotein-G) is 50% identical to 434 Cro but is also 62% identical to the B1 domain of protein G. We also created a variant of Crotein-G (ZCrotein-G) that contains a potential His3Cys1 zinc binding site. At low protein concentrations and in the presence of 20% 2,2,2-trifluoroethanol (TFE) (v/v), the circular dichroism spectra of the designed proteins are distinct from that of 434 Cro and similar to that of the B1 domain of protein G. However, the proteins fail to denature in a cooperative manner. Furthermore, aggregation occurs at moderate protein concentrations or in the absence of TFE. Addition of zinc to ZCrotein-G does not promote structure formation. In summary, 434 Cro has been altered to something that may resemble the B1 domain of protein G, but the protein does not adopt a native structure. Proteins 30:136-143, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 55
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 168-176 
    ISSN: 0887-3585
    Schlagwort(e): denaturation kinetics ; irreversible conformational changes ; metastable states ; folding temperature ; lattice model ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Denaturation of model proteinlike molecules at the liquid-solid interface is simulated over a wide temperature range by employing the lattice Monte Carlo technique. Initially, the molecule containing 27 monomers of two types (A and B) is assumed to be adsorbed in the native folded state (a 3 × 3 × 3 cube) so that one of its sides is in contact with the surface. The details of the denaturation kinetics are found to be slightly dependent on the choice of the side, but the main qualitative conclusions hold for all the sides. In particular, the kinetics obey approximately the conventional first-order law at T 〉 Tc (Tc is the collapse temperature for solution). With decreasing temperature, below Tc but above Tf (Tf is the folding temperature for solution), deviations appear from the first-order kinetics. For the most interesting temperatures, that is, below Tf, the denaturation kinetics are shown to be qualitatively different from the conventional ones. In particular, the denaturation process occurs via several intermediate steps due to trapping in metastable states. Mathematically, this means that (i) the transition to the denatured state of a given molecule is nonexponential, and (ii) the denaturation process cannot be described by a single rate constant kr. One should rather introduce a distribution of values of this rate constant (different values of kr correspond to the transitions to the altered state via different metastable states). Proteins 30:168-176, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 56
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 177-182 
    ISSN: 0887-3585
    Schlagwort(e): adsorption ; irreversible conformational changes ; denaturation rate constant ; kinetic control ; diffusion control ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Adsorption of proteins occurs via diffusion toward the interface, actual adsorption, and subsequent irreversible conformational changes resulting in denaturation of the native protein structure. The conventional kinetic models describing these steps are based on the assumption that the denaturation transitions obey the first-order law with a single value of the denaturation rate constant kr. Meanwhile, recent Monte Carlo simulations indicate that, in general, the denaturation process cannot be described by a single rate constant kr. One should rather introduce a distribution of this rate constant (physically, different values of kr correspond to the transitions to the altered state via different metastable states). We have calculated the kinetics of irreversible adsorption of proteins with and without distribution of the denaturation rate constant kr in the limits when protein diffusion in the solution is, respectively, rapid or slow. In both cases, the adsorption kinetics with distribution of kr are found to be close to those with a single-valued rate constant kr provided that the average value of kr in the former case is equal to kr for the latter case. This conclusion holds even for wide distributions of kr. The consequences of this finding for the fitting of global experimental kinetics on the basis of phenomenological equations are briefly discussed. Proteins 30:177-182, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 3 Ill.
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  • 57
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 228-231 
    ISSN: 0887-3585
    Schlagwort(e): protein folding ; local vs. non-local interactions ; secondary structure prediction ; fragment matching algorithms ; PDB ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: One of the most important questions in the protein folding problem is whether secondary structures are formed entirely by local interactions. One way to answer this question is to compare identical subsequences of proteins to see if they have identical structures. Such an exercise would also reveal a lower limit on the number of amino acids needed to form unique secondary structures. In this context, we have searched the April 1996 release of the Protein Data Bank for sequentially identical subsequences of proteins and compared their structures. We find that identical octamers can have different conformations. In addition, there are several examples of identical heptamers with different conformations, and the number of identical hexamers with different conformations has increased since the previous PDB releases. These observations imply that secondary structure can be formed entirely by non-local interactions and that an identical match of up to eight amino acids may not imply structural similarity. In addition to the larger context of the protein folding problem, these observations have implications for protein structure prediction methods. Proteins 30:228-231, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 1 Ill.
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  • 58
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 249-263 
    ISSN: 0887-3585
    Schlagwort(e): antibody-antigen complex ; snake toxin ; protein docking ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The antibody Mα2-3 neutralizes the functional, acetylcholine receptor binding activity of its antigen, neurotoxin α, and exhibits several other properties in common with the receptor itself. We present here the results of calculations examining the three-dimensional structure of the toxin α:Mα2-3 complex. The antigen structure, determined by nuclear magnetic resonance spectroscopy,1 was docked to models of the variable fragment of the antibody combining site2 by using a method based on surface complementarity and maximization of buried surface area3,4 while taking into account the possibility of conformational change on complexation. Extensive experimental information on the location of the functional epitope was incorporated into the analysis and used to screen candidate geometries of the complex resulting from the modeling. Eight plausible structures that are in accord with the experimental data were derived. Common structural features of the models are discussed, and residues of the antibody-combining site that are expected to play important roles in complexation are identified. In particular, three epitope residues that, according to mutagenesis experiments, make particularly strong contributions to the binding, interact excentrically and do not make contact with the central loops of the combining site, L3 and H3. Proteins 30:249-263, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 59
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 287-294 
    ISSN: 0887-3585
    Schlagwort(e): protein structure prediction ; side chain contact prediction ; lattice protein models ; CREB-binding protein ; KIX domain ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Using a recently developed protein folding algorithm, a prediction of the tertiary structure of the KIX domain of the CREB binding protein is described. The method incorporates predicted secondary and tertiary restraints derived from multiple sequence alignments in a reduced protein model whose conformational space is explored by Monte Carlo dynamics. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that was modified for the presence of predicted U-turns, i.e., regions where the chain reverses global direction. Tertiary restraints are obtained via a two-step process: First, seed side-chain contacts are identified from a correlated mutation analysis, and then, a threading-based algorithm expands the number of these seed contacts. Blind predictions indicate that the KIX domain is a putative three-helix bundle, although the chirality of the bundle could not be uniquely determined. The expected root-mean-square deviation for the correct chirality of the KIX domain is between 5.0 and 6.2 Å. This is to be compared with the estimate of 12.9 Å that would be expected by a random prediction, using the model of F. Cohen and M. Sternberg (J. Mol. Biol. 138:321-333, 1980). Proteins 30:287-294, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 60
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 74-89 
    ISSN: 0887-3585
    Schlagwort(e): mass spectrometry ; matrix-assisted laser desorption/ionization ; electrospray ; database searching ; gel electrophoresis ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The entire genomic DNA sequences of a number of prokaryotic and eukaryotic species are now available and many more, including the human genome, will be completed in the near future. The state-of-life of a cell at any given time, however, is defined by its protein composition, i.e., its proteome. Gel electrophoresis, mass spectrometry, and bioinformatics will be important tools for protein and proteome analysis in the post-genome era. Protein identification from electrophoretic gels by mass spectrometric peptide mapping or peptide sequencing combined with sequence database searching is established and has been applied to numerous biological systems. We describe current strategies and selected applications in molecular and cell biology. The next challenges are detailed structure/function analyses, which include studying the molecular composition of multiprotein complexes and characterization of secondary modifications of proteins. The advantages and limitations of a number of mass spectrometry-based strategies designed for microcharacterization of low amounts of protein from electrophoretic gels are discussed and illustrated by examples. Proteins Suppl. 2:74-89, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 61
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 381-387 
    ISSN: 0887-3585
    Schlagwort(e): serum amyloid A ; fluorescence ; circular dichroism ; acute phase ; denaturation ; nuclease ; amyloidosis ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We developed a recombinant DNA system to overexpress a fusion protein between the small, minimally soluble acute phase serum protein, serum amyloid A (SAA), and the bacterial enzyme staphylococcal nuclease (SN). This fusion protein is very soluble and is immunoreactive to polyclonal anti-SAA antibodies. Tryptophan fluorescence shows smooth denaturation curves for the fusion protein in guanidinium HCl or potassium thiocyanate. Fluorescence also indicates that only a single tryptophan residue (of the four present) is accessible to iodide quenching and, presumably, is exposed on the surface of the fusion protein. Circular dichroism (CD) shows a significant signal indicating α-helix, which can be attributed to the SAA portion of the molecule; these are the first CD spectral data available for SAA. pH titration shows persistence of helix domains for the fusion protein at pH 3.0, in contrast to the denaturation of SN under the same conditions. (The entire fusion protein shows a random coil pattern below pH 3.0.) By exploiting the structural and solubility properties of SN, this fusion protein has provided the first structural data about SAA - the precursor of the amyloid deposits in secondary amyloidosis. This fusion protein should be useful for further physical and physiologic studies of SAA. Proteins 30:381-387, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
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  • 62
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 1-1 
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 63
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 383-390 
    ISSN: 0887-3585
    Schlagwort(e): time-resolved small-angle X-ray scattering ; allosterism ; domain closure ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Time-resolved small-angle X-ray scattering (TR-SAXS) was used to monitor the structural changes that occur upon the binding of the natural substrates to a mutant version of the allosteric enzyme aspartate transcarbamoylase from Escherichia coli, in which the creation of a critical link stabilizing the R state of the enzyme is hindered. Previously, SAXS experiments at equilibrium showed that the structures of the unligated mutant enzyme and the mutant enzyme saturated with a bisubstrate analog are indistinguishable from the T and R state structures, respectively, of the wild-type enzyme (Tauc et al., Protein Sci. 3:1998-2004, 1994). However, as opposed to the wild-type enzyme, the combination of one substrate, carbamoyl phosphate, and succinate, an analog of aspartate, did not convert the mutant enzyme into the R state. By using TR-SAXS we have been able to study the transient steady-state during catalysis using the natural substrates rather than the nonreactive substrate analogs. The steady-state in the presence of saturating amount of substrates is a mixture of 60% T and 40% R structures, which is further converted entirely to R in the additional presence of ATP. These results provide a structural explanation for the reduced cooperativity observed with the mutant enzyme as well as for the stimulation by ATP at saturating concentrations of substrates. They also illustrate the crucial role played by domain motions and quaternary-structure changes for both the homotropic and heterotropic aspects of allostery. Proteins 31:383-390, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 64
    ISSN: 0887-3585
    Schlagwort(e): complement control protein ; protein modeling ; blood coagulation ; C4b-binding protein ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: C4b-binding protein (C4BP) contributes to the regulation of the classical pathway of the complement system and plays an important role in blood coagulation. The main human C4BP isoform is composed of one β-chain and seven α-chains essentially built from three and eight complement control protein (CCP) modules, respectively, followed by a nonrepeat carboxy-terminal region involved in polymerization of the chains. C4BP is known to interact with heparin, C4b, complement factor I, serum amyloid P component, streptococcal Arp and Sir proteins, and factor VIII/VIIIa via its α-chains and with protein S through its β-chain. The principal aim of the present study was to localize regions of C4BP involved in the interaction with C4b, Arp, and heparin. For this purpose, a computer model of the 8 CCP modules of C4BP α-chain was constructed, taking into account data from previous electron microscopy (EM) studies. This structure was investigated in the context of known and/or new experimental data. Analysis of the α-chain model, together with monoclonal antibody studies and heparin binding experiments, suggests that a patch of positively charged residues, at the interface between the first and second CCP modules, plays an important role in the interaction between C4BP and C4b/Arp/Sir/heparin. Putative binding sites, secondary-structure prediction for the central core, and an overall reevaluation of the size of the C4BP molecule are also presented. An understanding of these intermolecular interactions should contribute to the rational design of potential therapeutic agents aiming at interfering specifically some of these protein-protein interactions. Proteins 31:391-405, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 9 Ill.
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  • 65
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 406-416 
    ISSN: 0887-3585
    Schlagwort(e): electrostatics ; Brownian dynamics ; triose phosphate isomerase ; diffusion-control ; similarity index ; rate enhancement ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Triose phosphate isomerase (TIM) is a diffusion-controlled enzyme whose rate is limited by the diffusional encounter of the negatively charged substrate glyceraldehyde 3-phosphate (GAP) with the homodimeric enzyme's active sites. Translational and orientational steering of GAP toward the active sites by the electrostatic field of chicken muscle TIM has been observed in previous Brownian dynamics (BD) simulations. Here we report simulations of the association of GAP with TIMs from four species with net charges at pH 7 varying from -12e to +12e. Computed second-order rate constants are in good agreement with experimental data. The BD simulations and computation of average Boltzmann factors of substrate-protein interaction energies show that the protein electrostatic potential enhances the rates for all the enzymes. There is much less variation in the computed rates than might be expected on the basis of the net charges. Comparison of the electrostatic potentials by means of similarity indices shows that this is due to conservation of the local electrostatic potentials around the active sites which are the primary determinants of electrostatic steering of the substrate. Proteins 31:406-416, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 3 Ill.
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  • 66
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 434-444 
    ISSN: 0887-3585
    Schlagwort(e): hinge ; structural change ; xylose ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Recent crystallographic studies have revealed a range of structural changes in the three-dimensional structure of endo-1,4-xylanase (XYNII) from Trichoderma reesei. The observed conformational changes can be described as snapshots of an open-close movement of the active site of XYNII. These structures were further analyzed in this study. In addition, a total of four 1 ns molecular dynamics (MD) simulations were performed representing different states of the enzyme. A comparison of the global and local changes found in the X-ray structures and the MD runs suggested that the simulations reproduced a similar kind of active site opening and closing as predicted by the crystal structures. The open-close movement was characterized by the use of distance difference matrixes and the Hingefind program (Wriggers and Schulten, Proteins 29:1-14, 1997) to be a ‘hinge-bending’ motion involving two large rigidly-moving regions and an extended hinge. This conformational feature is probably inherent to this molecular architecture and probably plays a role in the function of XYNII. Proteins 31:434-444, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
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  • 67
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 417-433 
    ISSN: 0887-3585
    Schlagwort(e): molecular dynamics ; sex-determining region Y (SRY) protein ; high mobility group (HMG) box ; DNA-binding proteins ; DNA bending ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Molecular dynamics simulations have been conducted to study the interaction of human sex-determining region Y (hSRY) protein with DNA. For this purpose, simulations of the hSRY high mobility group (HMG) domain (hSRY-HMG) with and without its DNA target site, a DNA octamer, and the DNA octamer alone have been carried out, employing the NMR solution structure of hSRY-HMG-DNA complex as a starting model. Analyses of the simulation results demonstrated that the interaction between hSRY and DNA was hydrophobic, just a few hydrogen bonds and only one water molecule as hydrogen-bonding bridge were observed at the protein-DNA interface. These two hydrophobic cores in the hSRY-HMG domain were the physical basis of hSRY-HMG-DNA specific interaction. They not only maintained the stability of the complex, but also primarily caused the DNA deformation. The salt bridges formed between the positive-charged residues of hSRY and phosphate groups of DNA made the phosphate electroneutral, which was advantageous for the deformation of DNA and the formation of a stable complex. We predicted the structure of hSRY-HMG domain in the free state and found that both hSRY and DNA changed their conformations to achieve greater complementarity of geometries and properties during the binding process; that is, the protein increased the angle between its long and short arms to accommodate the DNA, and the DNA became bent severely to adapt to the protein, although the conformational change of DNA was more severe than that of the hSRY-HMG domain. The sequence specificity and the role of residue Met9 are also discussed. Proteins 31:417-433, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 12 Ill.
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  • 68
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 453-459 
    ISSN: 0887-3585
    Schlagwort(e): quantum mechanical calculations ; substrate-enzyme interactions ; mutants ; functional role of amino acids ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The enzyme herpes simplex virus type 1 thymidine kinase (HSV1 TK) salvages thymidine into the DNA metabolism of the virus. In the active site, the thymine ring of the nucleoside binds in a pocket, formed by two residues, Tyr-172 and Met-128, in a sandwich-type orientation. To investigate the nature of the thymine-enzyme pocket interactions, we have carried out density functional theory calculations with gradient-corrected exchange-correlation functionals of models of the thymine-HSV1 TK adduct. Our calculations indicate that the role of Met-128 in the substrate fixation is purely steric and hydrophobic, while the substrate-Tyr-172 interaction is essentially electrostatic in nature. These findings are completely consistent with the available catalytic properties of mutants on the 128 position. Proteins 31:453-459, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 69
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 445-452 
    ISSN: 0887-3585
    Schlagwort(e): chorismate mutase ; activity ; allosteric ; electrostatics ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The predicted active site of chorismate mutase of baker's yeast Saccharomyces cerevisiae has been studied by continuum electrostatics, molecular surface/volume calculations, and molecular modeling. Our study shows that despite being subject to an allosteric transition, the enzyme's active-site pocket neither decreased in volume nor deformed significantly in shape between the active R state and the inactive T state. We find that the polar atmosphere in the pocket is responsible for the enzyme's affinity. A single amino acid, Glu23, can adequately account for the atmospheric variation. This residue swings into the active-site pocket from the R state to the T state. In the R state, Glu23 on helix H2 doubly pairs with Arg204 and Lys208 of H11, which is packed against H2. In the T state, a slide occurs between H11 and H2 such that Glu23 can no longer interact with Lys208 and competes with Asp24 for interacting with Arg204. Consequently, Glu23 is found in the T state to couple with Arg157, an active-site residue critical to substrate binding. The tandem sliding of H11 in both monomers profoundly changes the interactions in the dimer interface. The loop between H11 and H12 demonstrates the largest conformational change. Hence, we establish a connection between the allosteric transition and the activity of the enzyme. The conformational change in the transition is suggested to propagate into the active-site pocket via a series of polar interactions that result in polarity reversal in the active-site pocket, which regulates the enzyme's activity. Proteins 31:445-452, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 70
    ISSN: 0887-3585
    Schlagwort(e): X-ray structure ; L-chain apoferritin ; metal binding sites ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We refined the structure of the tetragonal form of recombinant horse L-chain apoferritin to 2.0 Å and we compared it with that of the cubic form previously refined to the same resolution. The major differences between the two structures concern the cadmium ions bound to the residues E130 at the threefold axes of the molecule. Taking advantage of the significant anomalous signal (f′′ = 3.6 e-) of cadmium at 1.375 Å, the wavelength used here, we performed anomalous Fourier difference maps with the refined model phases. These maps reveal the positions of anomalous scatterers at different locations in the structure. Among these, some are found near residues that were known previously to bind metal ions, C48, E57, C126, D127, E130, and H132. But new cadmium binding sites are evidenced near residues E53, E56, E57, E60, and H114, which were suggested to be involved in the iron loading process. The quality of the anomalous Fourier difference map increases significantly with noncrystallographic symmetry map averaging. Such maps reveal density peaks that fit the positions of Met and Cys sulfur atoms, which are weak anomalous scatterers (f′′ = 0.44 e-). Proteins 31:477-485, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 7 Ill.
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  • 71
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 1-2 
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 72
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 39-48 
    ISSN: 0887-3585
    Schlagwort(e): antibody ; antigen ; electrostatics ; binding ; finite difference ; Poisson-Boltzmann ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The change in free energy of binding of hen egg white lysozyme (HEL) to the antibody HyHel-10 arising from ten point mutations in HEL (D101K, D101G, K96M, K97D, K97G, K97G, R21E, R21K, W62Y, and W63Y) was calculated using a combination of the finite difference Poisson-Boltzmann method for the electrostatic contribution, a solvent accessible surface area term for the non-polar contribution, and rotamer counting for the sidechain entropy contribution. Comparison of experimental and calculated results indicate that because of pKa shifts in some of the mutated residues, primarily those involving Aspartate or Glutamate, proton uptake or release occurs in binding. When this effect was incorporated into the binding free energy calculations, the agreement with experiment improved significantly, and resulted in a mean error of about 1.9 kcal/mole. Thus these calculations predict that there should be a significant pH dependence to the change in binding caused by these mutations. The other major contributions to binding energy changes comes from solvation and charge charge interactions, which tend to oppose each other. Smaller contributions come from nonpolar interactions and sidechain entropy changes. The structures of the HyHel-10-HEL complexes with mutant HEL were obtained by modeling, and the effect of the modeled structure on the calculations was also examined. “Knowledge based” modeling and automatic generation of models using molecular mechanics produced comparable results. Proteins 33:39-48, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 2 Ill.
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  • 73
    ISSN: 0887-3585
    Schlagwort(e): lactoferrin ; proteinase K ; complex, hydrolysis ; structure ; inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Lactoferrin is an iron binding glycoprotein with a molecular weight of 80 kDa. The molecule is divided into two lobes representing the N-terminal and C-terminal halves of the polypeptide chain, each containing an iron binding site. The serine proteinases such as trypsin, chymotrypsin, and pepsin hydrolyze lactoferrin into two unequal halves while proteinase K divides this protein into two equal halves. In the first step of hydrolysis by proteinase K, the C- and N-lobes, each having a molecular weight of approximately 40 kDa, are generated. In the next step, the lobes are further hydrolyzed into small molecular weight peptides. The proteinase K isolated from the hydrolyzed product does not show enzymatic activity suggesting that the enzyme is inhibited. Furthermore, the hydrolysis experiments on N-lobe and C-lobe showed that the inhibitory fragment came from the C-lobe. The purified lactoferrin fragment was found to be a decapeptide with an amino acid sequence of H2N-Val-Ala-Gln-Gly-Ala-Ala-Gly-Leu-Ala-COOH. The complex formed between proteinase K and lactoferrin fragment was crystallized by microdialysis. The crystals belonged to the monoclinic space group P21with cell dimensions a = 44.4 Å, b = 38.6 Å, c = 79.2 Å, β = 105.8o and Z = 2. The crystal structure has been determined at 2.4 Å resolution. It has been refined to an R factor of 0.163 for 9044 reflections. The Lf-fragment forms several intermolecular interactions with proteinase K. The Ser-224 Oγ and His-57 Nε2 move away to a distance of 3.68 Å in the complex. In the crystal structure, Gln-3I (I indicates inhibitor i.e., lactoferrin fragment) is involved in a direct intermolecular interaction with a symmetry related proteinase K molecule through a strong hydrogen bond with Asp-254. The mode of intermolecular interactions in the complex conformational features of the enzyme and placement of the fragment with respect to the enzyme resemble with the molecular complex of proteinase K with its natural inhibitor PKI3 from wheat. Proteins 33:30-38, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
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  • 74
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 88-96 
    ISSN: 0887-3585
    Schlagwort(e): fold classification ; substructures ; Dali ; protein families ; structural similarity ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The rapid growth in the number of experimentally determined three-dimensional protein structures has sharpened the need for comprehensive and up-to-date surveys of known structures. Classic work on protein structure classification has made it clear that a structural survey is best carried out at the level of domains, i.e., substructures that recur in evolution as functional units in different protein contexts. We present a method for automated domain identification from protein structure atomic coordinates based on quantitative measures of compactness and, as the new element, recurrence. Compactness criteria are used to recursively divide a protein into a series of successively smaller and smaller substructures. Recurrence criteria are used to select an optimal size level of these substructures, so that many of the chosen substructures are common to different proteins at a high level of statistical significance. The joint application of these criteria automatically yields consistent domain definitions between remote homologs, a result difficult to achieve using compactness criteria alone. The method is applied to a representative set of 1,137 sequence-unique protein families covering 6,500 known structures. Clustering of the resulting set of domains (substructures) yields 594 distinct fold classes (types of substructures). The Dali Domain Dictionary (http://www.embl-ebi.ac.uk/dali) not only provides a global structural classification, but also a comprehensive description of families of protein sequences grouped around representative proteins of known structure. The classification will be continuously updated and can serve as a basis for improving our understanding of protein evolution and function and for evolving optimal strategies to complete the map of all natural protein structures. Proteins 33:88-96, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 7 Ill.
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  • 75
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 97-106 
    ISSN: 0887-3585
    Schlagwort(e): antigenic peptides ; class I MHC molecules ; HLA-A2 complexes ; hydrogen bonds ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The crystal structures of class I major histocompatibility complex (MHC) molecules complexed with antigenic peptides revealed a network of hydrogen bonds between the charged amino- and carboxyl-termini of the peptides and conserved MHC residues at both ends of the peptide binding site. These interactions were shown to contribute substantially to the stability of class I MHC/peptide complexes by thermal denaturation studies using synthetic peptides in which either the amino- or carboxyl-terminal group is substituted by a methyl group. Here we report crystal structures of HLA-A*0201 complexed with these terminally modified synthetic peptides showing that they adopt the same bound conformation as antigenic peptides. A number of variations in peptide conformation were observed for the terminally modified peptides, including in one case, a large conformational difference in four central peptide residues that is apparently caused by the lattice contact. This is reminiscent of the way binding a T-cell receptor changed the conformation of central residues of an MHC-bound peptide. The structures determined identify which conserved hydrogen bonds are eliminated in terminally substituted peptides and suggest an increased energetic importance of the interactions at the peptide termini for MHC-peptide stability. Proteins 33:97-106, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
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  • 76
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 26-42 
    ISSN: 0887-3585
    Schlagwort(e): intermolecular restraints ; solid-state NMR ; symmetric multimer ; branch and bound ; amyloid ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The determination of structures of multimers presents interesting new challenges. The structure(s) of the individual monomers must be found and the transformations to produce the packing interfaces must be described. A substantial difficulty results from ambiguities in assigning intermolecular distance measurements (from nuclear magnetic resonance, for example) to particular intermolecular interfaces in the structure. Here we present a rapid and efficient method to solve the packing and the assignment problems simultaneously given rigid monomer structures and (potentially ambiguous) intermolecular distance measurements. A promising application of this algorithm is to couple it with a monomer searching protocol such that each monomer structure consistent with intramolecular constraints can be subsequently input to the current algorithm to check whether it is consistent with (potentially ambiguous) intermolecular constraints. The algorithm AmbiPack uses a hierarchical division of the search space and the branch-and-bound algorithm to eliminate infeasible regions of the space. Local search methods are then focused on the remaining space. The algorithm generally runs faster as more constraints are included because more regions of the search space can be eliminated. This is not the case for other methods, for which additional constraints increase the complexity of the search space. The algorithm presented is guaranteed to find all solutions to a predetermined resolution. This resolution can be chosen arbitrarily to produce outputs at various level of detail. Illustrative applications are presented for the P22 tailspike protein (a trimer) and portions of β-amyloid (an ordered aggregate). Proteins 32:26-42, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 17 Ill.
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  • 77
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 204-217 
    ISSN: 0887-3585
    Schlagwort(e): rotamer libraries ; energy minimization ; self consistent mean-field theory ; torsion space ; modeling ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The ab initio folding problem can be divided into two sequential tasks of approximately equal computational complexity: the generation of native-like backbone folds and the positioning of side chains upon these backbones. The prediction of side-chain conformation in this context is challenging, because at best only the near-native global fold of the protein is known. To test the effect of displacements in the protein backbones on side-chain prediction for folds generated ab initio, sets of near-native backbones (≤ 4 Å Cα RMS error) for four small proteins were generated by two methods. The steric environment surrounding each residue was probed by placing the side chains in the native conformation on each of these decoys, followed by torsion-space optimization to remove steric clashes on a rigid backbone. We observe that on average 40% of the χ1 angles were displaced by 40° or more, effectively setting the limits in accuracy for side-chain modeling under these conditions. Three different algorithms were subsequently used for prediction of side-chain conformation. The average prediction accuracy for the three methods was remarkably similar: 49% to 51% of the χ1 angles were predicted correctly overall (33% to 36% of the χ1+2 angles). Interestingly, when the inter-side-chain interactions were disregarded, the mean accuracy increased. A consensus approach is described, in which side-chain conformations are defined based on the most frequently predicted χ angles for a given method upon each set of near-native backbones. We find that consensus modeling, which de facto includes backbone flexibility, improves side-chain prediction: χ1 accuracy improved to 51-54% (36-42% of χ1+2). Implications of a consensus method for ab initio protein structure prediction are discussed. Proteins 33:204-217, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
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  • 78
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 119-134 
    ISSN: 0887-3585
    Schlagwort(e): molecular modeling ; proton transfer ; enzyme catalysis ; mutations ; molecular mechanics ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: In this paper, the carbonic anhydrase II (CA II) enzyme active site is modeled using ab initio calculations and molecular dynamics simulations to examine a number of important issues for the enzyme function. It is found that the Zn2+ ion is dominantly tetrahedrally coordinated, which agrees with X-ray crystallographic studies. However, a transient five-fold coordination with an extra water molecule is also found. Studies of His64 conformations upon a change in the protonation states of the Zn-bound water and the His64 residue also confirm the results of an X-ray study which suggest that the His64 conformation is quite flexible. However, the degree of water solvation is found to affect this behavior. Water bridge formation between the Zn-bound water and the His64 residue was found to involve a free energy barrier of 2-3 kcal/mol and an average lifetime of several picoseconds, which supports the concept of a proton transfer mechanism through such a bridge. Mutations of various residues around the active site provide further insight into the corresponding experimental results and, in fact, suggest an important role for the solvent water molecules in the CA II catalytic mechanism. Proteins 33:119-134, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 79
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 358-366 
    ISSN: 0887-3585
    Schlagwort(e): homologous proteins ; superfamilies ; sequence conservation ; protein structure ; protein evolution ; sequence-structure relationships ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: In order to study structural aspects of sequence conservation in families of homologous proteins, we have analyzed structurally aligned sequences of 585 proteins grouped into 128 homologous families. The conservation of a residue in a family is defined as the average residue similarity in a given position of aligned sequences. The residue similarities were expressed in the form of log-odd substitution tables that take into account the environments of amino acids in three-dimensional structures. The protein core is defined as those residues that have less then 7% solvent accessibility. The density of a protein core is described in terms of atom packing, which is investigated as a criterion for residue substitution and conservation. Although there is no significant correlation between sequence conservation and average atom packing around nonpolar residues such as leucine, valine and isoleucine, a significant correlation is observed for polar residues in the protein core. This may be explained by the hydrogen bonds in which polar residues are involved; the better their protection from water access the more stable should be the structure in that position. Proteins 33:358-366, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 80
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 320-328 
    ISSN: 0887-3585
    Schlagwort(e): structural similarity ; optimal superposition ; common substructure ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: In analysis, comparison and classification of conformations of proteins, a common computational task involves extractions of similar substructures. Structural comparisons are usually based on either of two measures of similarity: the root-mean-square (r.m.s.) deviation upon optimal superposition, or the maximal element of the difference distance matrix. The analysis presented here clarifies the relationships between different measures of structural similarity, and can provide a basis for developing algorithms and software to extract all maximal common well-fitting substructures from proteins.Given atomic coordinates of two proteins, many methods have been described for extracting some substantial (if not provably maximal) common substructure with low r.m.s. deviation. This is a relatively easy task compared with the problem addressed here, i.e., that of finding all common substructures with r.m.s. deviation less than a prespecified threshold. The combinatorial problems associated with similar subset extraction are more tractable if expressed in terms of the maximal element of the difference distance matrix than in terms of the r.m.s. deviation. However, it has been difficult to correlate these alternative measures of structural similarity. The purpose of this article is to make this connection.We first introduce a third measure of structural similarity: the maximum distance between corresponding pairs of points after superposition to minimize this value. This corresponds to fitting in the Chebyshev norm. Properties of Chebyshev superposition are derived.We describe relationships between the r.m.s. and minimax (Chebyshev) deviations upon optimal superposition, and between the Chebyshev deviation and the maximal element of the difference distance matrix. Combining these produces a relationship between the r.m.s. deviation upon optimal superposition and the maximal element of the difference distance matrix. Based on these results, we can apply algorithms and software for finding subsets of the difference distance matrix for which all elements are less than a specified bound, either to select only subsets for which the r.m.s.deviation is less than or equal to a specified threshold, or to select subsets that include all subsets for which the r.m.s. deviation is less than or equal to a threshold. Proteins 33:320-328, 1998. © 1998 Wiley-Liss, Inc.
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  • 81
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 367-382 
    ISSN: 0887-3585
    Schlagwort(e): ligand-protein docking ; molecular recognition ; tabu search ; empirical scoring function ; binding affinity prediction ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: This article describes the implementation of a new docking approach. The method uses a Tabu search methodology to dock flexibly ligand molecules into rigid receptor structures. It uses an empirical objective function with a small number of physically based terms derived from fitting experimental binding affinities for crystallographic complexes. This means that docking energies produced by the searching algorithm provide direct estimates of the binding affinities of the ligands. The method has been tested on 50 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. All water molecules are removed from the structures and ligand molecules are minimized in vacuo before docking. The lowest energy geometry produced by the docking protocol is within 1.5 Å root-mean square of the experimental binding mode for 86% of the complexes. The lowest energies produced by the docking are in fair agreement with the known free energies of binding for the ligands. Proteins 33:367-382, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 10 Ill.
    Materialart: Digitale Medien
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  • 82
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 408-416 
    ISSN: 0887-3585
    Schlagwort(e): protein folding ; potential energy curve ; two state model ; semi-empirical calculation ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We have calculated the free energy of a spherical model of a protein or part of a protein generated in the way of protein folding. Two spherical models are examined; one is a homogeneous model consisting of only one residue type - hydrophobic. The other is a heterogeneous model consisting of two residue types - strong hydrophobic and weak hydrophobic. Both models show a folding transition state, and the latter model reproduces the trend of the experimental folded-unfolded energy change. The heterogeneous model suggests that in the folding process of a protein of more than 70 residues, a specific region of the protein folds first to form a stable region, then the other residues follow the folding process. The energy landscape of folding of a small protein is approximately a funnel model, whereas a flatter energy landscape is suggested for larger proteins of more than 55-70 residues. Proteins 33:408-416, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 83
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 383-395 
    ISSN: 0887-3585
    Schlagwort(e): glycosidases ; protein structure prediction ; correlated mutations ; sequence space ; phylogenic relationships ; threading ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A structural model is presented for family 32 of the glycosyl-hydrolase enzymes based on the beta-propeller fold. The model is derived from the common prediction of two different threading methods, TOPITS and THREADER. In addition, we used a correlated mutation analysis and prediction of active-site residues to corroborate the proposed model. Physical techniques (circular dichroism and differential scanning calorimetry) confirmed two aspects of the prediction, the proposed all-beta fold and the multi-domain structure. The most reliable three-dimensional model was obtained using the structure of neuraminidase (1nscA) as template. The analysis of the position of the active site residues in this model is compatible with the catalytic mechanism proposed by Reddy and Maley (J. Biol. Chem. 271:13953-13958, 1996), which includes three conserved residues, Asp, Glu, and Cys. Based on this analysis, we propose the participation of one more conserved residue (Asp 162) in the catalytic mechanism. The model will facilitate further studies of the physical and biochemical characteristics of family 32 of the glycosyl-hydrolases. Proteins 33:383-395, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 11 Ill.
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  • 84
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 396-407 
    ISSN: 0887-3585
    Schlagwort(e): AMBER ; epidermal growth factor ; transforming growth factor-alpha ; conformation ; receptor binding ; domain movement ; weakly polar interaction ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: AMBER v. 4.1 force field in 1.5 ns NPT molecular dynamics simulations of murine epidermal growth factor (mEGF), human epidermal growth factor (hEGF), and human transforming growth factor-α (hTGF-α) structures with explicit TIP3P solvation were used to investigate differences in backbone stability, changes in secondary structure, interdomain flexibility, and weakly polar interactions. Backbone root mean square deviations of sections of each peptide show that the most stable regions in mEGF and hEGF are the A-, B-, and C-loops, whereas the most stable regions in hTGF-α are the A- and B-loops. The secondary structure in the B-loops of mEGF and hEGF differ significantly from the nuclear magnetic resonance (NMR) structures of mEGF and hEGF. The position and type of turns in the B-loop of mEGF and hEGF increase the interstrand distance of the antiparallel β-sheets thereby disrupting their structure. The interdomain flexibility of simulated hTGF-α structure is greater than in either mEGF or hEGF. The φ, ψ dihedrals of hTGF-α occupy two distinct populations of phase space corresponding to either a C7eq or an α-helical conformation. This change in dihedral angle is stabilized by Phe15 with Arg42 and Phe17 with Arg42 N-π weakly polar interactions that are present only in hTGF-α but not in mEGF or hEGF. Proteins 33:396-407, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 85
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 417-429 
    ISSN: 0887-3585
    Schlagwort(e): protein energy surface ; crambin ; lysozyme ; ATCase ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The identification of dynamical domains in proteins and the description of the low-frequency domain motions are one of the important applications of numerical simulation techniques. The application of these techniques to large proteins requires a substantial computational effort and therefore cannot be performed routinely, if at all. This article shows how physically motivated approximations permit the calculation of low-frequency normal modes in a few minutes on standard desktop computers. The technique is based on the observation that the low-frequency modes, which describe domain motions, are independent of force field details and can be obtained with simplified mechanical models. These models also provide a useful measure for rigidity in proteins, allowing the identification of quasi-rigid domains. The methods are validated by application to three well-studied proteins, crambin, lysozyme, and ATCase. In addition to being useful techniques for studying domain motions, the success of the approximations provides new insight into the relevance of normal mode calculations and the nature of the potential energy surface of proteins. Proteins 33:417-429, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 86
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 457-459 
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Recently, James Bowie addressed the question of how to normalize correctly the distribution of observed helix-helix packing angles in proteins (Bowie, Nature Struct. Biol. 4:915-917, 1997). A hitherto unrealized yet significant bias toward crossed packing angles was revealed. However, the derived random reference distribution of packing angles requires that helices have to be assumed as infinite in length. Here, we complement Bowie's analysis by consideration of the more realistic case where helices are of finite length. As a result, the statistical bias toward near perpendicular packings appears to be even stronger. Proteins 33:457-459, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
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  • 87
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 444-454 
    ISSN: 0887-3585
    Schlagwort(e): hGSTT1-1 ; homology modeling ; menaphthyl sulfate ; dichloromethane ; dehalogenase ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A manual threading approach is used to model the human glutathione transferase T1-1 based on the coordinates of the related Theta class enzyme T2-2. The low level of sequence identity (about 20%), found in the C-terminal extension in conjunction with a relative deletion of about five residues makes this a challenging modeling problem. The C-terminal extension contributes to the active site of the molecule and is thus of particular interest for understanding the molecular mechanism of the enzyme. Manual docking of known substrates and non-substrates has implicated potential candidates for the T1-1 catalytic residues involved in the dehalogenation and epoxide-ring opening activities. These include the conserved Theta class residues Arg 107, Trp 115, and the conserved GSTT1 subclass residue His 176. Also, the residue at position 234 is implicated in the modulation of T1-1 activity with different substrates between species. Proteins 33:444-454, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 88
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 430-443 
    ISSN: 0887-3585
    Schlagwort(e): pyrimidine biosynthesis ; protein crystallography ; allostery ; long-range interactions ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Tyr 165 in the catalytic subunit of Escherichia coli aspartate transcarbamoylase (ATCase, EC 2.1.3.2) forms an intersubunit hydrogen bond in the T state with Glu 239 in the 240s loop of a second catalytic subunit, which is broken in the T to R transition. Substitution of Tyr 165 by Phe lowers substrate affinity by approximately an order of magnitude and alters the pH profile for enzyme function. We have determined the crystal structure of Y165F at 2.4 Å resolution by molecular replacement, using a wild-type T state structure as the probe, and refined it to an R value of 25.2%. The Y165F mutation induces a global conformational change that is in the opposite direction to the T to R transition and therefore results in an extreme T state. The two catalytic trimers move closer by ∼0.14 Å and rotate by ∼0.2°, in the opposite direction to the T→R rotation; the two domains of each catalytic chain rotate by ∼2.1°, also in the opposite direction to the T→R transition; and the 240s loop adopts a new conformation. Residues 229 to 236 shift by ∼2.4 Å so that the active site is more open. Residues 237 to 244 rotate by ∼24.1°, altering interactions within the 240s loop and at the C1-C4 and C1-R4 interfaces. Arg 167, a key residue in domain closure and interactions with L-Asp, swings out from the active site to interact with Tyr 197. This crystal structure is consistent with the functional properties of Y165F, expands our knowledge of the conformational repertoire of ATCase, and indicates that the canonical T state does not represent an extreme. Proteins 33:430-443, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 89
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 475-495 
    ISSN: 0887-3585
    Schlagwort(e): docking ; landscape ; dynamics ; dielectric ; affinity ; binding ; methotrexate ; thermolysin ; dihydrofolate reductase ; HIV protease ; generalized Born ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A novel dynamical protocol for finding the low-energy conformations of a protein-ligand complex is described. The energy functions examined consist of an empirical force field with four different dielectric screening models; the generalized Born/surface area model also is examined. Application of the method to three complexes of known crystal structure provides insights into the energy functions used for selecting low-energy docked conformations and into the structure of the binding-energy surface. Evidence is presented that the local energy minima of a ligand in a binding site are arranged in a hierarchical fashion. This observation motivates the construction of a hierarchical docking algorithm that substantially enriches the population of ligand conformations close to the crystal conformation. The algorithm is also adapted to permit docking into a flexible binding site and preliminary tests of this method are presented. Proteins 33:475-495, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 24 Ill.
    Materialart: Digitale Medien
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  • 90
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 496-517 
    ISSN: 0887-3585
    Schlagwort(e): energy landscape ; hierarchical conformational substates ; molecular dynamics ; normal mode analysis ; principal component analysis ; jumping-among-minima model ; human lysozyme ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We have investigated energy landscape of human lysozyme in its native state by using principal component analysis and a model, jumping-among-minima (JAM) model. These analyses are applied to 1 nsec molecular dynamics trajectory of the protein in water. An assumption embodied in the JAM model allows us to divide protein motions into intra-substate and inter-substate motions. By examining intra-substate motions, it is shown that energy surfaces of individual conformational substates are nearly harmonic and mutually similar. As a result of principal component analysis and JAM model analysis, protein motions are shown to consist of three types of collective modes, multiply hierarchical modes, singly hierarchical modes, and harmonic modes. Multiply hierarchical modes, the number of which accounts only for 0.5% of all modes, dominate contributions to total mean-square atomic fluctuation. Inter-substate motions are observed only in a small-dimensional subspace spanned by the axes of multiplyhierarchical and singly hierarchical modes. Inter-substate motions have two notable time components: faster component seen within 200 psec and slower component. The former involves transitions among the conformational substates of the low-level hierarchy, whereas the latter involves transitions of the higher level substates observed along the first four multiply hierarchical modes. We also discuss dependence of the subspace, which contains conformational substates, on time duration of simulation. Proteins 33:496-517, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 13 Ill.
    Materialart: Digitale Medien
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  • 91
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 518-534 
    ISSN: 0887-3585
    Schlagwort(e): structure databank ; superfold ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Eight microbial genomes are compared in terms of protein structure. Specifically, yeast, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, M. pneumoniae, H. pylori, and E. coli are compared in terms of patterns of fold usage - whether a given fold occurs in a particular organism. Of the ∼340 soluble protein folds currently in the structure databank (PDB), 240 occur in at least one of the eight genomes, and 30 are shared amongst all eight. The shared folds are depleted in all-helical structure and enriched in mixed helix-sheet structure compared to the folds in the PDB. The top-10 most common of the shared 30 are enriched in superfolds, uniting many non-homologous sequence families, and are especially similar in overall architecture - eight having helices packed onto a central sheet. They are also very different from the common folds in the PBD, highlighting databank biases. Folds can be ranked in terms of expression as well as genome duplication. In yeast the top-10 most highly expressed folds are considerably different from the most highly duplicated folds. A tree can be constructed grouping genomes in terms of their shared folds. This has a remarkably similar topology to more conventional classifications, based on very different measures of relatedness. Finally, folds of membrane proteins can be analyzed through transmembrane-helix (TM) prediction. All the genomes appear to have similar usage patterns for these folds, with the occurrence of a particular fold falling off rapidly with increasing numbers of TM-elements, according to a “Zipf-like” law. This implies there are no marked preferences for proteins with particular numbers of TM-helices (e.g. 7-TM) in microbial genomes. Further information pertinent to this analysis is available at http://bioinfo.mbb.yale.edu/genome. Proteins 33:518-534, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 92
    ISSN: 0887-3585
    Schlagwort(e): mutagenesis ; c.d. spectroscopy ; unfolding ; Ω-loop ; molten-globule ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We wished to test the hypothesis that the non proline cis to trans isomerization of the peptide bond at position 167 in the S. aureus β-lactamase PC1 exerts a significant controlling effect on the folding pathway of this enzyme. The previous data presented in support of this hypothesis could not rule out the effect of factors unrelated to non-proline cis/trans isomerization. We have used the plasmid pET9d to direct soluble overproduction of the S. aureus β-lactamase PC1 and a site-directed mutant (Ile 167 to Pro) in Escherichia coli. Following purification the proteins were subjected to a comparative analysis of the kinetics of unfolding and refolding using the techniques of near- and far-UV circular dichroism spectroscopy and fluorescence spectroscopy in conjunction with “double-jump” experiments. Results show that the fully-unfolded I167P mutant enzyme retains 20% of molecules in a fast-refolding form and that slower-refolding molecules fold faster than the recombinant wild-type enzyme. The final stage of folding involves folding of the Ω-loop into a conformation essential for enzymatic activity. In support of the original hypothesis, the folding of this Ω-loop is rate limited by the isomerization of the Glu 166-Ile 167 peptide bond. Proteins 33:550-557, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 93
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 116-127 
    ISSN: 0887-3585
    Schlagwort(e): molecular dynamics ; X-ray crystallography ; essential dynamics ; lysozyme ; hinge bending ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A comparison of a series of extended molecular dynamics (MD) simulations of bacteriophage T4 lysozyme in solvent with X-ray data is presented. Essential dynamics analyses were used to derive collective fluctuations from both the simulated trajectories and a distribution of crystallographic conformations. In both cases the main collective fluctuations describe domain motions. The protein consists of an N- and C-terminal domain connected by a long helix. The analysis of the distribution of crystallographic conformations reveals that the N-terminal helix rotates together with either of these two domains. The main domain fluctuation describes a closure mode of the two domains in which the N-terminal helix rotates concertedly with the C-terminal domain, while the domain fluctuation with second largest amplitude corresponds to a twisting mode of the two domains, with the N-terminal helix rotating concertedly with the N-terminal domain. For the closure mode, the difference in hinge-bending angle between the most open and most closed X-ray structure along this mode is 49 degrees. In the MD simulation that shows the largest fluctuation along this mode, a rotation of 45 degrees was observed. Although the twisting mode has much less freedom than the closure mode in the distribution of crystallographic conformations, experimental results suggest that it might be functionally important. Interestingly, the twisting mode is sampled more extensively in all MD simulations than it is in the distribution of X-ray conformations. Proteins 31:116-127, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
    Materialart: Digitale Medien
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  • 94
    ISSN: 0887-3585
    Schlagwort(e): Drosophila melanogaster couch potato protein ; Werner's syndrome ; restrained molecular dynamics ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We have recently described an automated approach for homology modeling using restrained molecular dynamics and simulated annealing procedures (Li et al, Protein Sci., 6:956-970,1997). We have employed this approach for constructing a homology model of the putative RNA-binding domain of the human RNA-binding protein with multiple splice sites (RBP-MS). The regions of RBP-MS which are homologous to the template protein snRNP U1A were constrained by “homology distance constraints,” while the conformation of the non-homologous regions were defined only by a potential energy function. A full energy function without explicit solvent was employed to ensure that the calculated structures have good conformational energies and are physically reasonable. The effects of misalignment of the unknown and the template sequences were also explored in order to determine the feasibility of this homology modeling method for distinguishing possible sequence alignments based on considerations of the resulting conformational energies of modeled structures. Differences in the alignments of the unknown and the template sequences result in significant differences in the conformational energies of the calculated homology models. These results suggest that conformational energies and residual constraint violations in these homology-constrained simulated annealing calculations can be used as criteria to distinguish between correct and incorrect sequence alignments and chain folds. Proteins 33:558-566, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
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  • 95
    ISSN: 0887-3585
    Schlagwort(e): bacterial cellobiase ; mutated β-glucosidase ; family 1 ; thermoresistance ; X-ray structure ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The increasing development of the biotechnology industry demands the design of enzymes suitable to be used in conditions that often require broad resistance against adverse conditions. β-glucosidase A from Bacillus polymyxa is an interesting model for studies of protein engineering. This is a well-characterized enzyme, belonging to glycosyl hydrolase family 1. Its natural substrate is cellobiose, but is also active against various artificial substrates. In its native state has an octameric structure. Its subunit conserves the general (α/β)8 barrel topology of its family, with the active site being in a cavity defined along the axis of the barrel. Using random-mutagenesis, we have identified several mutations enhancing its stability and it was found that one them, the E96K substitution, involved structural changes. The crystal structure of this mutant has been determined by X-ray diffraction and compared with the native structure. The only difference founded between both structures is a new ion pair linking Lys96 introduced at the N-terminus of helix α2, to Asp28, located in one of the loops surrounding the active-site cavity. The new ion pair binds two segments of the chain that are distant in sequence and, therefore, this favorable interaction must exert a determinant influence in stabilizing the tertiary structure. Furthermore, analysis of the crystallographic isotropic temperature factors reveals that, as a direct consequence of the introduced ion pair, an unexpected decreased mobility of secondary structure units of the barrel which are proximal to the site of mutation is observed. However, this effect is observed only in the surrounding of one of the partners forming the salt bridge and not around the other. These results show that far-reaching effects can be achieved by a single amino acid replacement within the protein structure. Consequently, the identification and combination of a few single substitutions affecting stability may be sufficient to obtain a highly resistant enzyme, suitable to be used under extreme conditions. Proteins 33:567-576, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 96
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 1-2 
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 97
    ISSN: 0887-3585
    Schlagwort(e): [Fe] hydrogenase ; protein-protein interaction ; BIAcore analysis ; crystallization ; cooperativity ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Hydrogenases from Desulfovibrio are found to catalyze hydrogen uptake with low potential multiheme cytochromes, such as cytochrome c3, acting as acceptors. The production of Fe-only hydrogenase from Desulfovibrio vulgaris Hildenborough was improved with respect to the growth phase and media to determine the best large-scale bacteria growth conditions. The interaction and electron transfer from Fe-only hydrogenase to multiheme cytochrome has been studied in detail by both BIAcore and steady-state measurements. The electron transfer between [Fe] hydrogenase and cytochrome c3 appears to be a cooperative phenomenon (h = 1.37). This behavior could be related to the conductivity properties of multihemic cytochromes. An apparent dissociation constant was determined (2 × 10-7 M). The importance of the cooperativity for contrasting models proposed to describe the functional role of the hydrogenase/cytochrome c3 complex is discussed. Presently, the only determined structure is from [NiFe] hydrogenase and there are no obvious similarities between [NiFe] and [Fe] hydrogenase. Furthermore, no crystallographic data are available concerning [Fe] hydrogenase. The first results on crystallization and X-ray crystallography are reported. Proteins 33:590-600, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
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  • 98
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 577-589 
    ISSN: 0887-3585
    Schlagwort(e): electrostatics ; accessible surface area ; fatty acid binding proteins ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Adipocyte lipid-binding protein (ALBP) is one of a family of intracellular lipid-binding proteins (iLBPs) that bind fatty acids, retinoids, and other hydrophobic ligands. The different members of this family exhibit a highly conserved three-dimensional structure; and where structures have been determined both with (holo) and without (apo) bound lipid, observed conformational changes are extremely small (Banaszak, et al., 1994, Adv. Prot. Chem. 45, 89; Bernlohr, et al., 1997, Annu. Rev. Nutr. 17, 277). We have examined the electrostatic, hydrophobic, and water accessible surfaces of ALBP in the apo form and of holo forms with a variety of bound ligands. These calculations reveal a number of previously unrecognized changes between apo and holo ALBP, including: 1) an increase in the overall protein surface area when ligand binds, 2) expansion of the binding cavity when ligand is bound, 3) clustering of individual residue exposure increases in the area surrounding the proposed ligand entry portal, and 4) ligand-binding dependent variation in the topology of the electrostatic potential in the area surrounding the ligand entry portal. These focused analyses of the crystallographic structures thus reveal a number of subtle but consistent conformational and surface changes that might serve as markers for differential targeting of protein-lipid complexes within the cell. Most changes are consistent from ligand to ligand, however there are some ligand-specific changes. Comparable calculations with intestinal fatty-acid-binding protein and other vertebrate iLBPs show differences in the electrostatic topology, hydrophobic topology, and in localized changes in solvent exposure near the ligand entry portal. These results provide a basis toward understanding the functional and mechanistic differences among these highly structurally homologous proteins. Further, they suggest that iLBPs from different tissues exhibit one of two predominant end-state structural distributions of the ligand entry portal. Proteins 33:577-589, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
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  • 99
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 601-612 
    ISSN: 0887-3585
    Schlagwort(e): platelet-derived growth factor receptor ; E5 protein ; bovine papillomavirus ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The bovine papillomavirus E5 protein is thought to be a type II integral membrane protein that exists as a disulfide-linked homodimer in transformed cells. Polarized-infrared measurements show that the E5 dimer in membrane bilayers is largely α-helical and has a transmembrane orientation. Computational searches of helix-helix conformations reveal two possible low-energy dimer structures. Correlation of these results with previous mutagenesis studies on the E5 protein suggests how the E5 dimer may serve as a molecular scaffold for dimerization and ligand-independent activation of the PDGF-β receptor. We propose that on each face of the E5 dimer a PDGF-β receptor molecule interacts directly with Gln17 from one E5 monomer and with Asp33 from the other E5 monomer. This model accounts for the requirement of Gln17 and Asp33 for complex formation and explains genetic results that dimerization of the E5 protein is essential for cell transformation. Proteins 33:601-612, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 100
    ISSN: 0887-3585
    Schlagwort(e): mass spectrometry ; time-of-flight ; nanoflow electrospray ; transthyretin ; retinol binding protein ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Complexes formed between transthyretin and retinol-binding protein prevent loss of retinol from the body through glomerular filtration. The interactions between these proteins have been examined by electrospray ionization combined with time-of-flight mass analysis. Conditions were found whereby complexes of these proteins, containing from four to six protein molecules with up to two ligands, are preserved in the gas phase. Analysis of the mass spectra of these multimeric species gives the overall stoichiometry of the protein subunits and provides estimates for solution dissociation constants of 1.9 ± 1.0 × 10-7 M for the first and 3.5 ± 1.0 × 10-5 M for the second retinol-binding protein molecule bound to a transthyretin tetramer. Dissociation of these protein assemblies within the gas phase of the mass spectrometer shows that each retinol-binding protein molecule interacts with three transthyretin molecules. Mass spectral analysis illustrates not only a correlation with solution behavior and crystallographic data of a closely related protein complex but also exemplifies a general method for analysis of multi-protein assemblies. Proteins Suppl. 2:3-11, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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