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  • 1990-1994  (7,584)
  • Biochemistry and Biotechnology  (4,119)
  • Computational Chemistry and Molecular Modeling  (2,365)
  • Genetics  (1,100)
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  • 1
    Electronic Resource
    Electronic Resource
    Use of doxorubicin and dacarbazine for the management of unresectable intra-abdominal desmoid tumors in Gardner's syndrome (1994)
    Springer
    Diseases of the colon & rectum 37 (1994), S. 260-267 
    Details
    ISSN: 1530-0358
    Keywords: Desmoids ; Genetics ; Chemotherapy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract PURPOSE: The aim of this study was to describe the natural history and management of surgically unresectable intra-abdominal desmoid tumors in two patients with Gardner's syndrome from two unrelated families, where each had failed on conventional therapy. METHODS: Two patients with Gardner's syndrome were placed on a chemotherapy regimen which included doxorubicin (90 mg/m2) and dacarbazine (900 mg/m2) in divided doses over four days of continuous infusion. Their progress on chemotherapy was assessed by abdominal computerized tomography and laparoscopy. RESULTS: The computerized abdominal tomography scans proved difficult to interpret because of adhesions and matted small bowel resulting from the patients original colectomies. These findings made it difficult to differentiate postoperative changes from residual desmoid tumor. Second-look laparotomy in such patients was contraindicated as this may predispose to further desmoid production. Laparoscopy disclosed a complete response to this chemotherapy. Nevertheless, we had an iatrogenic small bowel perforation in one of these patients. Each patient showed a complete response to chemotherapy. CONCLUSION: Surgical resection remains the first-line treatment of intra-abdominal desmoid tumors. However, doxorubicin/ dacarbazine chemotherapy on a clinical trial basis may be indicated in patients whose intra-abdominal desmoid is unresectable, or who have failed to respond to treatment with hormones (tamoxifen, Toremifene), steroids (prednisone), and nonsteroidal anti-inflammatory agents (Clinoril®; Merck & Co., Inc., West Point, PA).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02048164
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  • 2
    Electronic Resource
    Electronic Resource
    Genetic ecology: A new interdisciplinary science, fundamental for evolution, biodiversity and biosafety evaluations (1994)
    Springer
    Cellular and molecular life sciences 50 (1994), S. 429-437 
    Details
    ISSN: 1420-9071
    Keywords: Genetics ; ecology ; DNA-transfer ; conjugation ; transformation ; transduction ; transposons ; dormant cells ; epilithon ; microbial colonisation ; symbiosis ; virus resistance ; biosafety ; release of genes ; insults to humanity ; evolution ; biodiversity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Genetic ecology is the extension of our modern knowledge in molecular genetics to studies of viability, gene expression and gene movements in natural environments like soils, aquifers and digestive tracts. In such milieux, the horizontal transfer of plasmid-borne genes between phylogenetically distant species has already been found to be much more frequent than had been expected from laboratory experience. For the study of exchanges involving chromosomally-located genes, more has to be learned about the behaviour of transposons in such environments. The results expected from studies in genetic ecology are relevant for considerations of evolution, biodiversity and biosafety. The role of this new field of research in restoring popular confidence in science and in its biotechnological applications is stressed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01920741
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  • 3
    Electronic Resource
    Electronic Resource
    HLA class II genes and antibodies against recombinant U1-nRNP proteins in patients with systemic lupus erythematosus (1994)
    Springer
    Rheumatology international 14 (1994), S. 63-69 
    Details
    ISSN: 1437-160X
    Keywords: Systemic lupus erythematosus ; Recombinant U1-nRNP proteins ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract To investigate a possible involvement of HLA-class II alleles in the genetic predisposition for the formation of anti-U1-nRNP antibody in systemic lupus erythematosus (SLE), genomic DNA of 178 patients was typed for the DRB1, DQA1 and DQB1 alleles using a polymerase chain reaction (PCR) and non-radioactive-oligonucleotide typing. Antibodies against recombinant U1-nRNP proteins (U1-A- U1-C-and 70K-protein) were determined by ELISA. Anti-U1-C antibody was found in 26 (14.7%), anti-U1-A in 34 (19.2%) and anti-70K in 17 (9.6%) patients. A joint occurrence was observed for these antibodies against the recombinant U1-nRNP proteins: anti-U1-C and anti-U1-A antibodies occurred together more frequently than alone and than together with anti-U1-70K antibodies. The frequency of DRB1 * 04 was slightly increased in the patients with anti-U1-C as compared to the patients without anti-U1-C (P〈0.05, Pcorr=n.s., RR=2.4). The DQA1 * 0301 allele, which is in linkage disequilibrium with DRB1 * 04, is found more frequently in anti-U1-C-positive than in antibody-negative patients. The DQB1 * 0303 allele, detected in 12 of 176 SLE patients, was absent in the patients with any of the antibodies against the U1-nRNP proteins. All these deviations may be due to chance alone. We concluded that the presence of antibodies against recombinant U1-nRNP proteins was not significantly associated with any HLA DRB1, DQA1 and DQB1 allele in our group of SLE patients.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00300249
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  • 4
    Electronic Resource
    Electronic Resource
    Myotonic dystrophy and limb girdle muscular dystrophy in one family (1994)
    Springer
    Journal of molecular medicine 72 (1994), S. 409-413 
    Details
    ISSN: 1432-1440
    Keywords: Myotonic dystrophy ; Limb girdle muscular dystrophy ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract A family is reported in which a 29-year-old woman showed the clinical features of myotonic dystrophy while her 26-year-old brother presented with the clinical picture of limb girdle syndrome. In the affected female, direct genetic testing for the specific myotonic dystrophy mutation on chromosome 19 revealed abnormal expansion of a repeat unit containing the three nucleotides cytosine, thymine, and guanine (CTG) — typical for myotonic dystrophy — while her diseased brother displayed two normal alleles. This supports the hypothesis of the extremely rare occurrence of two clinically and genetically different myopathies in one family. Genetic analysis of six other family members showed that the father of the diseased siblings as well as all of his three brothers and sisters had a pathological CTG repeat expansion, and that the other two family members tested had a normal allelic pattern. The number of CTG repeats in the diseased women was approximately tenfold higher than in her asymptomatic relatives who revealed an abnormal allelic pattern. The increase in CTG repeats with transmission to a subsequent generation in this family was paralleled by a dramatic increase in the severity of myotonic dystrophy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00252840
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  • 5
    Electronic Resource
    Electronic Resource
    Mixed desmoplastic primitive neuroepithelial tumor of infancy: a light microscopic, immunocytochemical, ultrastructural and genetic study (1994)
    Springer
    Acta neuropathologica 89 (1994), S. 99-104 
    Details
    ISSN: 1432-0533
    Keywords: Key words     Primitive neuroepithelial tumor ; Desmoplastic small cell tumor ; Brain tumor of infancy ; Immunocytochemistry ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract      We describe a case of a desmoplastic brain tumor which was initially resected from the right fronto-temporal region in a 2 year-old boy. This nodular, calcified tumor was vascularized by the internal carotid artery and the middle meningeal artery branches. Grossly, it contained several mucoid cysts. Light microscopy showed cords or nests of small cuboidal cells surrounded by a loose connective tissue and desmoplasic areas containing fibers and spindle cells. The cuboidal cells expressed epithelial, neuronal and neuroendocrine markers. Some foci of spindle cells showed glial differentiation. The tumor recurred 16 months later and displayed some characteristics of the small cell neuroepithelial component, mitoses being conspicuous. Electron microscopy revealed undifferentiated clear cells, some containing neurosecretory granules. Karyotyping demonstrated the following formula: 〈 15 〉 46, t(8;11) (q13; q11). The chromosome 11 breakpoint was different from that described in Ewing's sarcoma. This isolated translocation has not been previously reported to our knowledge. These unusual features lead us to report this case and to discuss its pathogenesis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004010050221
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  • 6
    Electronic Resource
    Electronic Resource
    Familial amyotrophic lateral sclerosis with a mutation in the Cu/Zn superoxide dismutase gene (1994)
    Springer
    Acta neuropathologica 88 (1994), S. 185-188 
    Details
    ISSN: 1432-0533
    Keywords: Amyotrophic lateral sclerosis ; Neuropathology ; Posterior column involvement ; Genetics ; Superoxide dismutase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Several missense mutations within exons 1, 2, 4 and 5 of the gene for Cu/Zn-binding superoxide dismutase (SOD1) have been discovered to be involved in the development of chromosome 21q-linked familial amyotrophic lateral sclerosis (FALS). We describe here an autopsied patient with FALS, in whom we have recently identified a novel missense mutation in exon 1 of the SOD1 gene. The neuropathological findings were compatible with those described previously in patients with FALS with posterior column involvement. This suggests that mutations of the SOD1 gene may be responsible for this form of FALS.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00294513
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  • 7
    Electronic Resource
    Electronic Resource
    Familial amyotrophic lateral sclerosis with a mutation in the Cu/Zn superoxide dismutase gene (1994)
    Springer
    Acta neuropathologica 88 (1994), S. 185-188 
    Details
    ISSN: 1432-0533
    Keywords: Key words: Amyotrophic lateral sclerosis ; Neuropathology ; Posterior column involvement ; Genetics ; Superoxide dismutase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Several missense mutations within exons 1, 2, 4 and 5 of the gene for Cu/Zn-binding superoxide dismutase (SOD1) have been discovered to be involved in the development of chromosome 21q-linked familial amyotrophic lateral sclerosis (FALS). We describe here an autopsied patient with FALS, in whom we have recently identified a novel missense mutation in exon 1 of the SOD1 gene. The neuropathological findings were compatible with those described previously in patients with FALS with posterior column involvement. This suggests that mutations of the SOD1 gene may be responsible for this form of FALS.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00294513
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  • 8
    Electronic Resource
    Electronic Resource
    Mitochondrial gene defects in patients with NIDDM (1994)
    Springer
    Diabetologia 37 (1994), S. 372-376 
    Details
    ISSN: 1432-0428
    Keywords: Genetics ; diabetes mellitus ; mitochondria ; maternal ; deafness
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Non-insulin-dependent diabetes mellitus (NIDDM) has a strong genetic component and maternal factors have recently been implicated in disease inheritance. The mitochondrial myopathies are a group of diseases which often show maternal inheritance as a result of mtDNA defects; some patients have impaired glucose tolerance. Occasional families with maternally inherited diabetes and deafness associated with a deletion or point mutation of mtDNA have been reported. To assess the importance of mitochondrial gene defects in NIDDM, 150 unrelated diabetic subjects from Wales, UK and 68 unrelated patients with diabetes and at least one affected sibling from England, UK were studied. Southern blot analysis did not show any large mtDNA deletions or duplications. One patient had a mutation in the mitochondrial tRNAleu(UUR) gene at bp 3243. This mutation is commonly associated with the syndrome of mitochondrial encephalomyopathy, lactic acidosis and stroke like episodes (MELAS). Study of this patient and his siblings showed a distinct form of late-onset diabetes associated with nerve deafness but no clinical features of the MELAS syndrome. No diabetic subject was shown to have the mtDNA mutation at position 8344 (tRNAlys) which has previously been described in the syndrome of mitochondrial encephalomyopathy and red-ragged fibres (MERRF). The role of other mitochondrial gene defects in diabetes and the pathophysiological basis of glucose intolerance in patients with the MELAS mutation requires further elucidation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00408473
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  • 9
    Electronic Resource
    Electronic Resource
    Renal eicosanoids and blood pressure in genetically hypertensive rats of the lyon strain (1994)
    Springer
    Journal of biomedical science 1 (1994), S. 201-203 
    Details
    ISSN: 1423-0127
    Keywords: Hypertension ; Eicosanoid ; Rat ; Genetics ; Kidney
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The present paper reviews the evidence for a possible involvement of renal eicosanoids in the pathophysiology of high blood pressure in genetically hypertensive rats of the Lyon strain. Both in vivo and in vitro experiments suggest that an increased ability to synthesize the vasoconstrictor prostaglandin H2 and/or thromboxane A2 in renal vessels (1) acts as an autocrine amplifier of pressor agents and (2) may contribute to resetting the pressure natriuresis curve which is a prerequisite for the development and maintenance of hypertension.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02253302
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  • 10
    Electronic Resource
    Electronic Resource
    A gene in the HLA class I region contributes to susceptibility to IDDM in the Finnish population (1994)
    Springer
    Diabetologia 37 (1994), S. 937-944 
    Details
    ISSN: 1432-0428
    Keywords: Genetics ; haplotype ; HLA-A ; HLA-DQ ; HLA-DR ; tumour necrosis factor ; diabetes mellitus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary In Finland the haplotype A2, Cw1, B56, DR4, DQ8 is the third most common haplotype in insulin-dependent diabetic (IDDM) patients and has the highest haplotype-specific absolute risk for IDDM. Cw1, B56, DR4, DQ8 haplotypes containing HLA-A alleles other than A2 are infrequent in the population and are not associated with IDDM. Comparison of the A2 and non-A2 haplotypes at the DNA level showed that they were identical at HLA-B,-DR, and -DQ loci. Evidence that class I alleles confer susceptibility to IDDM was obtained from the two HLA-C, -B, -DR and -DQ haplotypes most frequently found in IDDM patients in Finland. A24, A3 and A2 on the Cw3, B62, DR4, DQ8 haplotype, and A28, A2 and A1 on the Cw7, B8, DR3, DQ2 were all found to be associated with IDDM. In Finland these seven haplotypes, including A2, Cw1, B56, DR4, DQ8, account for 33% of diabetic haplotypes and 10.3% of non-diabetic haplotypes (p〈0.00001). The contribution of the class I region to IDDM susceptibility was also apparent in those IDDM patients lacking the disease-predisposing class II alleles. Significantly more non-DR3/non-DR4 IDDM patients (47 of 55) possessed two of the IDDM-associated HLA-A alleles compared to non-DR3/non-DR4 control subjects (40 of 58; p=0.038). Moreover, IDDM patients confirmed by oligotyping as unable to form a ‘diabetes-susceptibility’ DQ heterodimer, tended to possess two diabetes-associated HLA-A alleles (12 of 13) compared to control subjects (12 of 20; p=0.056).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00400951
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  • 11
    Electronic Resource
    Electronic Resource
    Familial occurrence of discrete subaortic membrane (1994)
    Springer
    Pediatric cardiology 15 (1994), S. 198-200 
    Details
    ISSN: 1432-1971
    Keywords: Subaortic stenosis ; Congenital heart disease ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The first case of multiple family members with discrete subaortic membrane and no other congenital defects is presented. One family member presents with findings suggesting a forme fruste of this disease. Increased surveillance of family members of individuals with discrete subaortic membrane is warranted, as the clinical findings of mild subaortic obstruction may be indistinguishable from those of an innocent flow murmur.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00800675
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  • 12
    Electronic Resource
    Electronic Resource
    Tricuspid atresia and annular hypoplasia: Report of a familial occurrence (1994)
    Springer
    Pediatric cardiology 15 (1994), S. 201-203 
    Details
    ISSN: 1432-1971
    Keywords: Tricuspid atresia ; Tricuspid hypoplasia ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Occurrence of a similar cardiac malformation in multiple family members has been reported for many lesions. Neither tricuspid atresia nor tricuspid annular hypoplasia and tricuspid atresia and one case of tricuspid annular hypoplasia with an atrial septal defect in siblings. The findings in this family suggest an autosomal recessive pattern of inheritance for abnormal tricuspid valve morphogenesis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00800676
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  • 13
    Electronic Resource
    Electronic Resource
    Genetic analysis of a polyembryonic mutant in rye (1994)
    Springer
    Sexual plant reproduction 7 (1994), S. 290-296 
    Details
    ISSN: 1432-2145
    Keywords: Secale cereale ; Polyembryony ; Chromosome mosaics ; Rye ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have obtained one plant regenerated from rye tissue culture which showed a high percentage of polyembryonic seeds in its progeny. The mutation inducing the development of extra embryos is also influencing erroneous cell division, mitosis and meiosis. The genetic analysis indicated that the aptitude for polyembryonic seed formation is a heritable trait controlled by a dominant gene. However, for expression of the phenotype the female parent should have a specific cytoplasm.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00227712
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  • 14
    Electronic Resource
    Electronic Resource
    Absence epilepsy of early childhood —genetic aspects (1994)
    Springer
    European journal of pediatrics 153 (1994), S. 372-377 
    Details
    ISSN: 1432-1076
    Keywords: Epilepsy ; Absences ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Clinical and EEG family data of 140 cases with early childhood epilepsy with absences are presented. The aim of the study was to evaluate, whether the occurrence of generalized tonic clonic seizures (GTCS) as a presenting symptom might correlate with family data, i.e. whether there are indications of heterogeneity. One hundred and forty cases were selected from the epilepsy family data base of the Neuropaediatric Department. The selection parameter was epilepsy with absences manifesting between the 1 st and 5th year of age. The incidence of seizures was evaluated in siblings, parents and parents' siblings. EEG records were available from 103 parents and 106 siblings. The analysis supports the assumption of heterogeneity within early childhood absence epilepsy. Parents and their sibs of cases manifesting with GTCS had seizures twice as often than parents and their sibs in the non-GTCS group. In the affected relatives of the GTCS group early onset GTCS prevailed, whereas in the relatives of the non-GTCS group absences were found more frequently. The EEG of relatives showed elevated incidences of spikes and waves and photosensitivity in both groups, indicating common genetic factors. In parents of the non-GTCS group, however, EEG pathology was significantly more frequent than in parents of the GTCS group. Comparing EEG pathology in parents with seizure risk in siblings, evidence for maternal preponderance in transmission of the seizure liability was found. Mothers' EEG seems to be the best predictor of the seizure risk in probands' siblings. Early childhood epilepsy with absences can be regarded as an intermediate type, showing overlap with early onset GTCS and myoclonic astatic epilepsy on the one side and with childhood absence epilepsy on the other.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01956423
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  • 15
    Electronic Resource
    Electronic Resource
    Multiple sclerosis: genetic versus environmental aetiology: epidemiology in Israel updated (1994)
    Springer
    Journal of neurology 241 (1994), S. 341-346 
    Details
    ISSN: 1432-1459
    Keywords: Multiple sclerosis Epidemiology ; Immigrants Environment ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The incidence and prevalence of multiple sclerosis (MS) were compared, controlling for age, in native-born Israelis of different origins and in immigrants to Israel. This comparison was carried out in two populations, countrywide and in Jerusalem. In the countrywide population, ascertainment was based mainly on hospitalizations; it included 252 patients who were native-born and 150 who had immigrated from Africa-Asia (AA immigrants). The 89 MS patients of Jerusalem also included patients diagnosed in outpatient clinics. In native-born Israelis whose father was born in Europe-America (I-EA), the incidence and prevalence of MS were found to be as high as or even higher than that found previously in immigrants from Europe-America. Among native-born Israelis whose father was born in Africa or Asia (I-AA), the yearly age-adjusted incidence and prevalence rates were found to be 1.4- to 1.8-fold higher than among AA immigrants, pointing to environmental factors. The incidence and prevalence rates in the I-EA were 1.2- to 1.6-fold higher than in the I-AA, pointing to genetic factors. These results seem to point to both environmental and genetic factors in the aetiology of MS. Further research is needed, however, to disentangle the genetic factors from possible environmental differences in the two ethnic groups.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00868444
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  • 16
    Electronic Resource
    Electronic Resource
    Follow-up and family study of postpartum psychoses (1994)
    Springer
    European archives of psychiatry and clinical neuroscience 244 (1994), S. 138-140 
    Details
    ISSN: 1433-8491
    Keywords: Parity ; Genetics ; Diathesis-stress model
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract As part of a follow-up and family study of post-partum psychoses, this episode of illness being the first leading to psychiatric hospitalisation, patients with puerperal episodes (PE) and nonpuerperal episodes (NPE) of illness in the long-term course (n=79) were compared to patients with PE only (n=40). Few differences were found. Relatives of patients with PE only had a lower morbidity risk for functional psychoses than relatives of patients with PE and NPE. A favourable course of illness in the presence of a low genetic predisposition may be expected, according to the diathesis-stress model of functional psychoses.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02191888
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  • 17
    Electronic Resource
    Electronic Resource
    Clinical and genetic aspects of juvenile absence epilepsy (1994)
    Springer
    Journal of neurology 241 (1994), S. 487-491 
    Details
    ISSN: 1432-1459
    Keywords: Juvenile absence epilepsy ; Valproate ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Fifteen patients aged 11–25 years (mean 15.37, SD 3.89) suffering from juvenile absence epilepsy are presented. Only 3 (20%) had absences (AS) as the only seizure type, 12 (80%) had associated generalized tonic-clinic seizures (GTCS) and in the remaining 3 with absences and GTCS there was also sporadic myoclonus. We found a higher frequency of AS in our patients by clinical history and video-EEG than has been previously reported. In our patients the mean age of onset in years was 11.4, SD 1.24 for AS, 13.12, SD 2.31 for GTCS and 12.5, SD 2.18 for myoclonus. The correct diagnosis was not made on referrals for any of the patients. It took an average of 3–5.5 years from the onset of the AS (range: 6–120 months) and 2 years from the occurrence of GTCS (average: 1–72 months) to make the correct diagnosis and institute proper treatment, which was valproic acid (VPA). The GTCS were controlled in all patients whereas AS continued in 6 (40%), but to a significantly lesser degree. The frequency and the duration of the GTCS before the start of VPA treatment seemed to have an adverse effect on AS control. We documented no circadian rhythm in either AS or the GTCS, except in 2 patients who had AS and GTCS mainly when they awoke in the morning. The sample size was too small to perform a proper genetic study, though a positive history of epilepsies of mixed types was obtained in 35.7% of the parents and the siblings of the probands.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00919710
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  • 18
    Electronic Resource
    Electronic Resource
    Molecular marker-facilitated studies in an elite maize population: I. Linkage analysis and determination of QTL for morphological traits (1994)
    Springer
    Theoretical and applied genetics 88 (1994), S. 7-16 
    Details
    ISSN: 1432-2242
    Keywords: Maize ; Restriction fragment length polymorphisms (RFLPs) ; Qualitative and quantitative inheritance ; Plant breeding ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Restriction fragment length polymorphisms (RFLPs) and one morphological marker were used to investigate quantitative trait loci (QTL) for morphological and physiological traits evaluated on 150 F2∶3 maize (Zea mays L.) lines derived from the cross of elite U.S. Corn Belt inbreds Mo17 and H99. F2∶3 lines were grown in a replicated experiment and evaluated for plant and ear heights and flowering traits. QTL were identified for each trait, and genetic effects were determined. Estimated gene action for the flowering traits was predominantly overdominance. Both parents contributed toward increased values for anthesis and silk emergence. QTL for increased plant and ear heights were usually contributed by the taller parent, Mo17. Estimated gene action for these traits was mainly partial to overdominance. QTL for plant height were located in the vicinity of loci defined by alleles with qualitative effects on plant height.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00222387
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  • 19
    Electronic Resource
    Electronic Resource
    Chromosome assortment in Saccharum (1994)
    Springer
    Theoretical and applied genetics 89 (1994), S. 959-963 
    Details
    ISSN: 1432-2242
    Keywords: Sugarcane ; Polyploidy ; Genetics ; Evolution ; Breeding ; DNA markers ; Arbitrarily primed PCR ; RAPD markers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Recent work has revealed random chromosome pairing and assortment in Saccharum spontaneum L., the most widely distributed, and morphologically and cytologically variable of the species of Saccharum. This conclusion was based on the analysis of a segregating population from across between S. spontaneum ‘SES 208’ and a spontaneously-doubled haploid of itself, derived from anther culture. To determine whether polysomic inheritance is common in Saccharum and whether it is observed in a typical biparental cross, we studied chromosome pairing and assortment in 44 progeny of a cross between euploid, meiotically regular, 2n=80 forms of Saccharum officinarum ‘LA Purple’ and Saccharum robustum ‘ Mol 5829’. Papuan 2n=80 forms of S. robustum have been suggested as the immediate progenitor species for cultivated sugarcane (S. officinarum). A total of 738 loci in LA Purple and 720 loci in Mol 5829 were amplified and typed in the progeny by arbitrarily primed PCR using 45 primers. Fifty and 33 single-dose polymorphisms were identified in the S. officinarum and S. robustum genomes, respectively (χ 2 at 98%). Linkage analysis of single-dose polymorphisms in both genomes revealed linkages in repulsion and coupling phases. In the S. officinarum genome, a map hypothesis gave 7 linkage groups with 17 linked and 33 unlinked markers. Four of 13 pairwise linkages were in repulsion phase and 9 were in coupling phase. In the S. robustum genome, a map hypothesis gave 5 linkage groups, defined by 12 markers, with 21 markers unlinked, and 2 of 9 pairwise linkages were in repulsion phase. Therefore, complete polysomic inheritance was not observed in either species, suggesting that chromosomal behavior is different from that observed by linkage analysis of over 500 markers in the S. spontaneum map. Implications of this finding for evolution and breeding are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00224524
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  • 20
    Electronic Resource
    Electronic Resource
    Genetic analysis of tolerance for phosphorous deficiency in rice (Oryza sativa L.) (1994)
    Springer
    Theoretical and applied genetics 89 (1994), S. 313-317 
    Details
    ISSN: 1432-2242
    Keywords: Genetics ; Rice ; Phosphorousefficiency ; Diallel analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The inheritance of phosphorous (P) — deficiency tolerance in rice was investigated by a sevenparent diallel. The parent materials involved were four P-efficient (IR20, IR54, IR28, and Mahsuri), one moderately P-efficient (TN1), and two P-inefficient (IR31406333-1 and IR34686-179-1-2-1), genotypes. Relative tilering ability (RTA) under P-deficient and P-supplemented soil conditions was the parameter used in determining the tolerance level of the different genotypes. Diallel graph analysis revealed that tolerant parents have an excess of recessive genes, while moderate and susceptible parents possess more dominant genes. Genetic-component analysis suggested that both additive and dominance gene effects are involved in the inheritance of P-deficiency tolerance in rice. The trait exhibited over doiminance as confirmed by the graphical analysis. Narrow-sense heritability of the trait was moderate (0.50) and environmental effects were low. Both the general combining ability (GCA) and the specific combining ability (SCA) were significant, but GCA was more prevalent than SCA. Tolerant parents exhibited a high GCA whereas susceptibles have a very poor GCA, suggesting that tolerant parents were mostly enriched in additive genes and susceptible parents in non-additive genes. Crosses involving two high general combiners showed low SCA effects whereas crosses between poor general combiners manifested highly-significant SCA values.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00225160
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  • 21
    Electronic Resource
    Electronic Resource
    Resistance to potato leaf roll virus multiplication in potato is under major gene control (1994)
    Springer
    Theoretical and applied genetics 88 (1994), S. 754-758 
    Details
    ISSN: 1432-2242
    Keywords: Potato breeding ; Potato leaf roll virus ; Virus resistance ; Major gene resistance ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The concentration of potato leaf roll virus (PLRV), as measured by a quantitative enzyme-linked immunosorbent assay, in the foliage of potato plants (Solanum tuberosum) of cv ‘Maris Piper’ with secondary infection was 2900 ng/g leaf, whereas in clones G7445(1) and G7032(5) it was 180 ng/g leaf and 120 ng/g leaf, respectively. To examine the genetic control of resistance to PLRV multiplication, reciprocal crosses were made between the susceptible cultivar ‘Maris Piper’ and the two resistant clones, and the three parents were selfed. Seedling progenies of these families were grown to generate tubers of individual genotypes (clones). Clonally propagated plants were graft-inoculated, and their daughter tubers were collected and used to grow plants with secondary infection in which PLRV concentration was estimated. The expression of resistance to PLRV multiplication had a bimodal distribution in progenies from crosses between ‘Maris Piper’ and either resistant clone, and also in progeny from selfing the resistant parents, with genotypes segregating into high and low virus titre groups. Only the progeny obtained from selfing ‘Maris Piper’ did not segregate, all genotypes being susceptible to PLRV multiplication. The pattern of segregation obtained from these progenies fits more closely with the genetical hypothesis that resistance to PLRV multiplication is controlled by two unlinked dominant complementary genes, both of which are required for resistance, than with the simpler hypothesis that resistance is conferred by a single dominant gene, as published previously.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01253981
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  • 22
    Electronic Resource
    Electronic Resource
    Molecular-marker-facilitated investigation of host-plant response to Exserohilum turcicum in maize (Zea mays L.): components of resistance (1994)
    Springer
    Theoretical and applied genetics 88 (1994), S. 305-313 
    Details
    ISSN: 1432-2242
    Keywords: Breeding ; Helminthosporium turcicum ; RFLP ; QTLs ; Disease-resistance ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RFLPs were used to investigate components of host-plant response to Exserohilum turcicum in 150 unselected F2∶3 lines of a B52/Mo17 maize population. Following inoculation with spore suspensions of the pathogen (race 0), components of disease development were measured and then quantitative trait mapping was performed to identify the location and effects of quantitative trait loci (QTLs) determining host-plant response. Components of interest were the average number of lesions per leaf, the average percent leaf tissue diseased (severity) and the average size of lesions (cm2). Based on a LOD threshold of 2.31 (P〈0.05), the number of lesions appears to be associated with QTLs on chromosomes 1S, 3L, 5S. Severity was associated with analogous regions and, in addition, QTLs on chromosomes 7L and 8L. Most QTLs, for either of these two components, involve additive gene action and partial dominance or overdominance. In contrast, lesion size was associated with QTLs on chromosomes 7L and 5L; recessive gene action may be involved at 7L.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00223637
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  • 23
    Electronic Resource
    Electronic Resource
    A linkage map of diploid Avena based on RFLP loci and a locus conferring resistance to nine isolates of Puccinia coronata var. ‘avenae’ (1994)
    Springer
    Theoretical and applied genetics 89 (1994), S. 831-837 
    Details
    ISSN: 1432-2242
    Keywords: Genetics ; Disease resistance ; Monocots
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An F2 oat population was produced by crossing the diploid (n=7) species Avena strigosa (CI 3815) with A. wiestii (CI 1994), resistant and susceptible, respectively, to 40 isolates of Puccinia coronata, the causal agent of crown rust. Eighty-eight F2 individuals were used to construct an RFLP linkage map representing the A genome of cultivated hexaploid oat. Two hundred and eight RFLP loci have been placed into 10 linkage groups. This map covers 2416 cM, with an average of 12 cM between RFLP loci. Eighty-eight F3 lines, derived from F2 individuals used to construct the map, were screened for resistance to 9 isolates of P. coronata. One locus, Pca, was found to confer a dominant resistance phenotype to isolates 203, 258, 263, 264B, 290, 298, 325A, and 345. Pca also conferred resistance to isolate 276; however, an unlinked second gene may also be involved.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00224505
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  • 24
    Electronic Resource
    Electronic Resource
    Behavioral and life-history components of division of labor in honey bees (Apis mellifera L.) (1994)
    Springer
    Behavioral ecology and sociobiology 34 (1994), S. 117-409 
    Details
    ISSN: 1432-0762
    Keywords: Social insects ; Apis mellifera ; Division of labor ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Variability exists among worker honey bees for components of division of labor. These components are of two types, those that affect foraging behavior and those that affect life-history characteristics of workers. Variable foraging behavior components are: the probability that foraging workers collect (1) pollen only; (2) nectar only; and (3) pollen and nectar on the same trip. Life history components are: (1) the age the workers initiate foraging behavior; (2) the length of the foraging life of a worker; and (3) worker length of life. We show how these components may interact to change the social organization of honey bee colonies and the lifetime foraging productivity of individual workers. Selection acting on foraging behavior components may result in changes in the proportion of workers collecting pollen and nectar. Selection acting on life-history components may affect the size of the foraging population and the distribution of workers between within nest and foraging activities. We suggest that these components define possible sociogenic “pathways” through which colony-level natural selection can change social organization. These pathways may be analogous to developmental pathways in the morphogenesis of individual organisms because small changes in behavioral or life history components of individual workers may lead to major changes in the organizational structure of colonies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00167332
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  • 25
    Electronic Resource
    Electronic Resource
    Reproductive competition in queenless honey bee colonies (Apis mellifera L.) (1994)
    Springer
    Behavioral ecology and sociobiology 35 (1994), S. 99-107 
    Details
    ISSN: 1432-0762
    Keywords: Key words Apis mellifera ; Genetics ; Drone production ; Allozymes ; Reproductive conflict
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Previously we reported that there are subfamily differences in drone production in queenless honey bee colonies, but these biases are not always explained by subfamily differences in oviposition behavior. Here we determine whether these puzzling results are best explained by either inadequate sampling of the laying worker population or reproductive conflict among workers resulting in differential treatment of eggs and larvae. Using colonies composed of workers from electrophoretically distinct subfamilies, we collected samples of adult bees engaged in the following behavior: “true” egg laying, “false” egg laying, indeterminate egg laying, egg cannibalism, or nursing (contact with larvae). We also collected samples of drone brood at four different ages: 0 to 2.5-h-old eggs, 0 to 24-h-old eggs, 3 to 8-day-old larvae, and 9 to 14-day-old larvae and pupae. Allozyme analyses revealed significant subfamily differences in the likelihood of exhibiting egg laying, egg cannibalism, and nursing behavior, as well as significant subfamily differences in drone production. There were no subfamily differences among the different types of laying workers collected from each colony, suggesting that discrepancies between subfamily biases in egg-laying behavior and drone production are not due to inadequate sampling of the laying worker population. Subfamily biases in drone brood production within a colony changed significantly with brood age. Laying workers had significantly more developed ovaries than either egg cannibals or nurses, establishing a physiological correlate for the observed behavioral genetic differences. These results suggest there is reproductive conflict among subfamilies and individuals within queenless colonies of honey bees. The implications of these results for the evolution of reproductive conflict, in both queenright and queenless contexts, are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002650050075
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  • 26
    Electronic Resource
    Electronic Resource
    Genotypic differences in brood rearing in honey bee colonies: context-specific? (1994)
    Springer
    Behavioral ecology and sociobiology 34 (1994), S. 125-137 
    Details
    ISSN: 1432-0762
    Keywords: Social insects ; Apis mellifera ; Division of labor ; Genetics ; Nepotism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Three experiments were performed to determine whether brood care in honey bee colonies is influenced by colony genetic structure and by social context. In experiment 1, there were significant genotypic biases in the relative likelihood of rearing queens or workers, based on observations of individually labeled workers of known age belonging to two visually distinguishable subfamilies. In experiment 2, no genotypic biases in the relative likelihood of rearing drones or workers was detected, in the same colonies that were used in experiment 1. In experiment 3, there again were significant genotypic differences in the likelihood of rearing queens or workers, based on electrophoretic analyses of workers from a set of colonies with allozyme subfamily markers. There also was an overall significant trend for colonies to show greater subfamily differences in queen rearing when the queens were sisters (half- and super-sisters) rather than unrelated, but these differences were not consistent from trial to trial for some colonies. Results of experiments 1 and 3 demonstrate genotypic differences in queen rearing, which has been reported previously based on more limited behavioral observations. Results from all three experiments suggest that genotypic differences in brood care are influenced by social context and may be more pronounced when workers have a theoretical opportunity to practice nepotism. Finally, we failed to detect persistent interindividual differences in bees from either subfamily in the tendency to rear queen brood, using two different statistical tests. This indicates that the probability of queen rearing was influenced by genotypic differences but not by the effect of prior queen-rearing experience. These results suggest that subfamilies within a colony can specialize on a particular task, such as queen rearing, without individual workers performing that task for extended periods of time.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00164183
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  • 27
    Electronic Resource
    Electronic Resource
    Reproductive competition in queenless honey bee colonies (Apis mellifera L.) (1994)
    Springer
    Behavioral ecology and sociobiology 35 (1994), S. 99-107 
    Details
    ISSN: 1432-0762
    Keywords: Apis mellifera ; Genetics ; Drone production ; Allozymes ; Reproductive conflict
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Previously we reported that there are subfamily differences in drone production in queenless honey bee colonies, but these biases are not always explained by subfamily differences in oviposition behavior. Here we determine whether these puzzling results are best explained by either inadequate sampling of the laying worker population or reproductive conflict among workers resulting in differential treatment of eggs and larvae. Using colonies composed of workers from electrophoretically distinct subfamilies, we collected samples of adult bees engaged in the following behavior: “true” egg laying, “false” egg laying, indeterminate egg laying, egg cannibalism, or nursing (contact with larvae). We also collected samples of drone brood at four different ages: 0 to 2.5-h-old eggs, 0 to 24-h-old eggs, 3 to 8-day-old larvae, and 9 to 14-day-old larvae and pupae. Allozyme analyses revealed significant subfamily differences in the likelihood of exhibiting egg laying, egg cannibalism, and nursing behavior, as well as significant subfamily differences in drone production. There were no subfamily differences among the different types of laying workers collected from each colony, suggesting that discrepancies between subfamily biases in egg-laying behavior and drone production are not due to inadequate sampling of the laying worker population. Subfamily biases in drone brood production within a colony changed significantly with brood age. Laying workers had significantly more developed ovaries than either egg cannibals or nurses, establishing a physiological correlate for the observed behavioral genetic differences. These results suggest there is reproductive conflict among subfamilies and individuals within queenless colonies of honey bees. The implications of these results for the evolution of reproductive conflict, in both queenright and queenless contexts, are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00171499
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  • 28
    Electronic Resource
    Electronic Resource
    Genetics of alcoholism: Role of the endogenous opioid system (1994)
    Springer
    Metabolic brain disease 9 (1994), S. 105-131 
    Details
    ISSN: 1573-7365
    Keywords: Alcoholism ; Genetics ; Endorphins ; Enkephalins ; Dynorphins ; Opioid ; Receptors
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract At the present time alcoholism is recognized as a metabolic disease exhibiting the clinical features of craving for alcohol, loss of control over drinking, tolerance and physical dependence on alcohol, while both epidemiological and experimental studies have demonstrated that genetic factors may be important in determining whether an individual has a high or low vulnerability to develop alcoholism. Evidence also indicates that alcoholism is not characterized by a single gene single allele inheritance. Instead it seems that multiple genes and environmental factors interact to increase or decrease an individual's vulnerability to become an alcoholic. Current research is aimed at investigating whether certain behavioral, physiological and biochemical markers are highly associated with the incidence of alcoholism. Among the biochemical markers currently under investigation is the endogenous opioid system and its implication in mediating the reinforcing effects of ethanol. It is the objective of this manuscript to review current research on: (a) the interactions of ethanol with the endogenous opioid system at the molecular level; (b) the existence of genetically determined differences in the response of the endogenous opioid system to ethanol between subjects at high and low risk for excessive ethanol consumption, as well as between lines of animals showing preference or aversion for ethanol solutions; (c) the decrease of alcohol consumption following pretreatment with opioid antagonists; and (d) the possible use of specific opioid receptor antagonists together with behavioral therapy to modify drinking behavior, to control craving and to prevent relapse.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01999765
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  • 29
    Electronic Resource
    Electronic Resource
    Expression of a reporter gene is reduced by a ribozyme in transgenic plants (1994)
    Springer
    Molecular genetics and genomics 245 (1994), S. 465-470 
    Details
    ISSN: 1617-4623
    Keywords: Gene regulation ; Ribozyme ; npt-gene ; Transgenic tobacco ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A chimeric gene encoding a ribozyme under the control of the cauliflower mosaic virus (CaMV) 35S promoter was introduced into transgenic tobacco plants. In vivo activity of this ribozyme, which was designed to cleave npt mRNA, was previously demonstrated by transient expression assays in plant protoplasts. The ribozyme gene was transferred into transgenic tobacco plants expressing an rbcS-npt chimeric gene as an indicator. Five double transformants out of sixteen exhibited a reduction in the amount of active NPT enzyme. To measure the amount of ribozyme produced, in the absence of its target, the ribozyme and target genes were separated by genetic segregation. The steady-state concentrations of ribozyme and target RNA were shown to be similar in the resulting single transformants. Direct evidence for a correlation between reduced npt gene expression and ribozyme expression was provided by crossing a plant containing only the ribozyme gene with a transgenic plant expressing the npt gene under control of the 35S promoter, i.e. the same promoter used to direct ribozyme expression. The expression of npt was reduced in all progeny containing both transgenes. Both steady-state levels of npt mRNA and amounts of active NPT enzyme are decreased. In addition, our data indicate that, at least in stable transformants, a large excess of ribozyme over target is not a prerequisite for achieving a significant reduction in target gene expression.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00302259
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  • 30
    Electronic Resource
    Electronic Resource
    766 cases of oral cleft in Italy (1994)
    Springer
    European journal of epidemiology 10 (1994), S. 317-324 
    Details
    ISSN: 1573-7284
    Keywords: Epidemiology ; Genetics ; Oral clefts ; Registers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Epidemiological and genetic variables for oral clefts were analysed for the years 1981–1989 in a case-control study of congenital malformations in the Emilia Romagna, Veneto, and Friuli regions, and in the Trento and Bolzano hospitals. Birth prevalence for all cases of cleft lip with or without cleft palate (CL(P)) was 8.2 per 10,000 births, and that for cleft palate only (CP) was 6.1 per 10,000. Coexisting abnormalities were found in 23% of CL(P) cases and in 43% of CP. No clusters in time or space were detected. For isolated clefts, a predominance of males among CL(P) and of females among CP was found; epilepsy was the only maternal risk factor correlated with clefts, and an association between clefting and consanguinity was found. Empirical recurrence risks were calculated in both isolated CL(P) and CP.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01719356
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  • 31
    Electronic Resource
    Electronic Resource
    Solution structure of a core peptide derived from scyllatoxin (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 205-215 
    Details
    ISSN: 0887-3585
    Keywords: peptide folding ; disulfide framework ; insect toxins ; NMR ; distance geometry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An analysis of the sequences of scyllatoxin and charybdotoxin suggested that it would be possible to design a core peptide sequence which would still fold to give the β-hairpin and helix seen in the toxins, but which would eliminate one disulfide and connecting residues. The core sequence was modeled, then synthesized and purified. The cysteines oxidize in air to give the same disulfide pairings as seen in the parent toxins as the major product. The three-dimensional structure of the core sequence peptide, termed Max, was determined using proton NMR spectroscopy and found to be identical in secondary structure to the toxins. However differences were found in the relative orientation of the β-hairpin and helix. The use of this structural motif, found in many insect toxins, as a disulfide framework for exploring sequence/structure/activity relationships is discussed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180302
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  • 32
    Electronic Resource
    Electronic Resource
    Thermodynamics of ubiquitin unfolding (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 246-253 
    Details
    ISSN: 0887-3585
    Keywords: microcalorimetry ; heat capacity ; enthalpy ; hydrogen bonding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The energetics of ubiquitin unfolding have been studied using differential scanning microcalorimetry. For the first time it has been shown directly that the enthalpy of protein unfolding is a nonlinear function of temperature. Thermodynamic parameters of ubiquitin unfolding were correlated with the structure of the protein. The enthalpy of hydrogen bonding in ubiquitin was calculated and compared to that obtained for other proteins. It appears that the energy of hydrogen bonding correlates with the average length of the hydrogen bond in a given protein structure. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180305
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  • 33
    Electronic Resource
    Electronic Resource
    Hydrogen bond strength and β-sheet propensities: The role of a side chain blocking effect (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 262-266 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; protein stability ; hydrogen bond ; β-sheet ; amino acid propensity ; steric effect ; hydrogen exchange ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Amino acid side chains can enhance peptide group hydrogen bond strength in protein structures by obstructing the competing hydrogen bond to solvent in the unfolded state. Available data indicate that the steric blocking effect contributes an average of 0.5 kJ per residue to protein hydrogen bond strength and accounts for the intrinsic α-sheet propensities of the amino acids. In available data for helical models, the contribution to α-helix propensities is obscured especially by large context-dependent effects. These issues are all related by a common side chain-dependent steric clash which disfavors peptide to water H-bond formation, peptide to catalyst complexation in hydrogen exchange reactions (Bai et al., Proteins 17:75-86, 1993), and peptide to peptide H-bonding in the helical main chain conformation (Creamer and Rose, Proc. Natl. Acad. Sci. U.S.A. 89:5937-5941, 1992) but not in α-strands. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180307
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  • 34
    Electronic Resource
    Electronic Resource
    A method for α-helical integral membrane protein fold prediction (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 281-294 
    Details
    ISSN: 0887-3585
    Keywords: membrane ; protein ; structure ; prediction ; G-protein coupled receptor ; rhodopsin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Integral membrane proteins (of the α-helical class) are of central importance in a wide variety of vital cellular functions. Despite considerable effort on methods to predict the location of the helices, little attention has been directed toward developing an automatic method to pack the helices together. In principle, the prediction of membrane proteins should be easier than the prediction of globular proteins: there is only one type of secondary structure and all helices pack with a common alignment across the membrane. This allows all possible structures to be represented on a simple lattice and exhaustively enumerated. Prediction success lies not in generating many possible folds but in recognizing which corresponds to the native. Our evaluation of each fold is based on how well the exposed surface predicted from a multiple sequence alignment fits its allocated position. Just as exposure to solvent in globular proteins can be predicted from sequence variation, so exposure to lipid can be recognized by variable-hydrophobic (variphobic) positions. Application to both bacteriorhodopsin and the eukaryotic rhodopsin/opsin families revealed that the angular size of the lipid-exposed faces must be predicted accurately to allow selection of the correct fold. With the inherent uncertainties in helix prediction and parameter choice, this accuracy could not be guaranteed but the correct fold was typically found in the top six candidates. Our method provides the first completely automatic method that can proceed from a scan of the protein sequence databanks to a predicted three-dimensional structure with no intervention required from the investigator. Within the limited domain of the seven helix bundle proteins, a good chance can be given of selecting the correct structure. However, the limited number of sequences available with a corresponding known structure makes further characterization of the method difficult. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180309
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  • 35
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary crystallographic studies of the precursor and mature forms of a neutral lipase from the fungus Rhizopus delemar (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 301-306 
    Details
    ISSN: 0887-3585
    Keywords: triglyceride lipase ; proenzyme ; molecular replacement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A neutral lipase from the filamentous fungus Rhizopus delemar has been crystallized in both its proenzyme and mature forms. Although the latter crystallizes readily and produces a variety of crystal forms, only one was found to be suitable for X-ray studies. It is monoclinic (C2, a = 92.8 Å, b = 128.9 Å, c = 78.3 Å, β = 135.8) with two molecules in the asymmetric unit related by a noncrystallographic diad. The prolipase crystals are orthorhombic (P212121, with a = 79.8 Å, b = 115.2 Å, c = 73.0 Å) and also contain a pair of molecules in the asymmetric unit. Initial results of molecular replacement calculations using the refined coordinates of the related lipase from Rhizomucor miehei identified the correct orientations and positions of the protein molecules in the unit cells of crystals of both proenzyme and the mature form. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180311
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  • 36
    Electronic Resource
    Electronic Resource
    Correlated mutations and residue contacts in proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 309-317 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; predicted contact maps ; correlated mutations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The maintenance of protein function and structure constrains the evolution of amino acid sequences. This fact can be exploited to interpret correlated mutations observed in a sequence family as an indication of probable physical contact in three dimensions. Here we present a simple and general method to analyze correlations in mutational behavior between different positions in a multiple sequence alignment. We then use these correlations to predict contact maps for each of 11 protein families and compare the result with the contacts determined by crystallography. For the most strongly correlated residue pairs predicted to be in contact, the prediction accuracy ranges from 37 to 68% and the improvement ratio relative to a random prediction from 1.4 to 5.1. Predicted contact maps can be used as input for the calculation of protein tertiary structure, either from sequence information alone or in combination with experimental information. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180402
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  • 37
    Electronic Resource
    Electronic Resource
    Analysis of Cα geometry in protein structures (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 324-337 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; secondary structure ; peptide geometry ; Ramachandran plot ; β-turns ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The polypeptide of a protein molecule can be considered as a chain of Cα atoms linked by pseudobonds between the Cα atoms of successive amino acid residues. This paper presents an analysis of the angle and dihedral angles made by these pseudobonds in protein structures determined at high resolution by X-ray crystallography. This analysis reveals a strong correlation between Cα geometry and the protein fold. The regular features of protein secondary structure such as α-helix and α-sheet are very clearly defined. In addition, it is possible to identify with some confidence the discrete populations of particular conformations of α-turn. Comparison with the traditional Ramachandran type of plot demonstrates that an analysis of protein structure on the basis of Cα geometry provides a richer description of protein conformation. In addition, the characteristics of this geometry could be a useful guide in model building of protein structure. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180404
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    Crystallization of a fragment of human fibronectin: Introduction of methionine by site-directed mutagenesis to allow phasing via selenomethionine (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 48-54 
    Details
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; extracellular matrix ; multiwavelength anomalous diffraction (MAD) ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of a fragment of human fibronectin encompassing the 7th through the RGD-containing 10th type III repeats (FN7-10) have been produced with protein expressed in E. coli. The crystals are monoclinic with one molecule in the asymmetric unit and diffract to beyond 2.0 Å Bragg spacings. A mutant FN7-10 was produced in which three methionines, in addition to the single native methionine already present, have been introduced by site-directed mutagenesis. Diffraction-quality crystals of this mutant protein have been grown in which methionine was replaced with selenomethionine. The introduction of methionine by site-directed mutagenesis to allow phasing from selenomethionyl-substituted crystals is shown to be feasible by this example and is proposed as a general approach to solving the crystallographic phase problem. Strategies for selecting propitious sites for methionine mutations are discussed. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190107
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    Combining evolutionary information and neural networks to predict protein secondary structure (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 55-72 
    Details
    ISSN: 0887-3585
    Keywords: secondary structure prediction ; prediction of secondary structure class ; prediction of secondary structure content ; evolutionary information ; multiple alignment profiles ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using evolutionary information contained in multiple sequence alignments as input to neural networks, secondary structure can be predicted at significantly increased accuracy. Here, we extend our previous three-level system of neural networks by using additional input information derived from multiple alignments. Using a position-specific conservation weight as part of the input increases performance. Using the number of insertions and deletions reduces the tendency for overprediction and increases overall accuracy. Addition of the global amino acid content yields a further improvement, mainly in predicting structural class. The final network system has a sustained overall accuracy of 71.6% in a multiple cross-validation test on 126 unique protein chains. A test on a new set of 124 recently solved protein structures that have no significant sequence similarity to the learning set confirms the high level of accuracy. The average cross-validated accuracy for all 250 sequence-unique chains is above 72%. Using various data sets, the method is compared to alternative prediction methods, some of which also use multiple alignments: the performance advantage of the network system is at least 6 percentage points in three-state accuracy. In addition, the network estimates secondary structure content from multiple sequence alignments about as well as circular dichroism spectroscopy on a single protein and classifies 75% of the 250 proteins correctly into one of four protein structural classes. Of particular practical importance is the definition of a position-specific reliability index. For 40% of all residues the method has a sustained three-state accuracy of 88%, as high as the overall average for homology modelling. A further strength of the method is greatly increased accuracy in predicting the placement of secondary structure segments. © 1994 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190108
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    Expression, purification, and crystallization of restriction endonuclease PvuII with DNA containing its recognition site (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 77-79 
    Details
    ISSN: 0887-3585
    Keywords: endonuclease overexpression ; crystallization ; X-ray diffraction ; protein-DNA complex ; Type II restriction enzyme ; vapor diffusion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have overexpressed the type II restriction endonuclease PvuII (R.PvuII) in E. coli, prepared large amounts of the homogeneous enzyme, and crystallized it with an oligonucleotide carrying a PvuII recognition site. The cocrystals are orthorhombic space group P212121 with cell constants a = 95.8 Å, b = 86.3 Å, c = 48.5 Å, and diffract X-rays to at least 2.7 Å. There is a complex of two protein subunits and one oligonucleotide duplex in the asymmetric unit. © 1994 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190110
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190201
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    Crystallization and preliminary X-ray crystallographic analysis of phospholipid transfer protein from maize seedlings (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 80-83 
    Details
    ISSN: 0887-3585
    Keywords: maize protein ; crystals ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Phospholipid transfer protein from maize seedlings has been crystallized using trisodium citrate as precipitant. The crystal belongs to the orthorhombic space group P212121 with unit cell dimensions of a = 24.46 Å, b = 49.97 Å, and c = 69.99 Å. The presence of one molecule in the asymmetric unit gives a crystal volume per protein mass (Vm) of 2.36 Å 3/Da and a solvent content of 48% by volume. The X-ray diffraction pattern extends at least to 1.6 Å Bragg spacing when exposed to both CuKα and synchrotron X-rays. A set of X-ray data to approximately 1.9 Å Bragg spacing has been collected from a native crystal. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190111
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    α-Helix-forming propensities in peptides and proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 85-97 
    Details
    ISSN: 0887-3585
    Keywords: protein conformation ; secondary structure ; protein folding ; helix stability ; helix formation ; conformational entropy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Much effort has been invested in seeking to understand the thermodynamic basis of helix stability in both peptides and proteins. Recently, several groups have measured the helix-forming propensities of individual residues (Lyu, P. C., Liff, M. I., Marky, L. A., Kallenbach, N. R. Science 250:669-673, 1990; O'Neil, K. T., DeGrado, W. F. Science 250:646-651, 1990; Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T. M., Baldwin, R. L. Nature (London) 344:268-270, 1990). Using Monte Carlo computer simulations, we tested the hypothesis that these differences in measured helix-forming propensity are due primarily to loss of side chain conformational entropy upon helix formation (Creamer, T. P., Rose, G. D. Proc. Natl. Acad. Sci. U.S.A. 89:5937-5941, 1992). Our previous study employed a rigid helix backbone, which is here generalized to a completely flexible helix model in order to ensure that earlier results were not a methodological artifact. Using this flexible model, side chain rotamer distributions and entropy losses are calculated and shown to agree with those obtained earlier. We note that the side chain conformational entropy calculated for Trp in our previous study was in error; a corrected value is presented. Extending earlier work, calculated entropy losses are found to correlate strongly with recent helix propensity scales derived from substitutions made within protein helices (Horovitz, A., Matthews, J. M., Fersht, A. R. J. Mol. Biol. 227:560-568, 1992; Blaber, M., Zhang, X.-J., Matthews, B. M. Science 260:1637-1640, 1993). In contrast, little correlation is found between these helix propensity scales and the accessible surface area buried upon formation of a model polyalanyl α-helix. Taken in sum, our results indicate that loss of side chain entropy is a major determinant of the helix-forming tendency of residues in both peptide and protein helices. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190202
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    1.56 Å structure of mature truncated human fibroblast collagenase (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 98-109 
    Details
    ISSN: 0887-3585
    Keywords: crystallography ; hydroxamate ; high resolution ; metalloproteinase ; zinc ; X-ray ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray crystal structure of a 19 kDa active fragment of human fibroblast collagenase has been determined by the multiple isomorphous replacement method and refined at 1.56 Å resolution to an R-factor of 17.4%. The current structure includes a bound hydroxamate inhibitor, 88 waters and three metal atoms (two zincs and a calcium). The overall topology of the enzyme, comprised of a five stranded β-sheet and three α-helices, is similar to the thermolysin-like metalloproteinases. There are some important differences between the collagenase and thermolysin families of enzymes. The active site zinc ligands are all histidines (His-218, His-222, and His-228). The presence of a second zinc ion in a structural role is a unique feature of the matrix metalloproteinases. The binding properties of the active site cleft are more dependent on the main chain conformation of the enzyme (and substrate) compared with thermolysin. A mechanism of action for peptide cleavage similar to that of thermolysin is proposed for fibroblast collagenase. © 1994 Wiley-Liss, Inc.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190203
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    Kinetic study on myoglobin refolding monitored by five optical probe stopped-flow methods (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 110-119 
    Details
    ISSN: 0887-3585
    Keywords: folding intermediate ; urea denaturation ; stopped-flow circular dichroism ; molten globule ; hemindicyanide ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The refolding kinetics of horse cyanometmyoglobin induced by concentration jump of urea was investigated by five optical probe stopped-flow methods: absorption at 422 nm, tryptophyl fluorescence at around 340 nm, circular dichroism (CD) at 222 nm, CD at 260 nm, and CD at 422 nm. In the refolding process, we detected three phases with rate constants of 〉 1 × 102 s-1, (4.5-9.3) S-1, and (2-5) × 10-3 s-1. In the fastest phase, a substantial amount of secondary structure (40%) is formed within the dead time of the CD stopped-flow apparatus (10.7 ms). The kinetic intermediate populated in the fastest phase is shown to capture a hemindicyanide, suggesting that a “heme pocket precursor” recognized by hemindicyanide must be constructed within the dead time. In the middle phase, most of secondary and tertiary structures, especially around the captured hemindicyanide, have been constructed. In the slowest phase, we detected a minor structural rearrangement accompanying the ligand-exchange reaction in the fifth coordination of ferric iron. We present a possible model for the refolding process of myoglobin in the presence of the heme group. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190204
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    Decoupling of melting domains in immobilized ribonuclease A (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 120-131 
    Details
    ISSN: 0887-3585
    Keywords: enzymes ; protein immobilization ; microcalorimetry ; protein melting domains ; protein DSC ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ribonuclease A has been immobilized on silica beads through glutaraldeyde-mediated chemical coupling in order to improve the stability of the protein against thermal denaturation. The thermodynamic and binding properties of the immobilized enzyme have been studied and compared with those of the free enzyme. The parameters describing the binding of the inhibitor 3′ -CMP (Ka and ΔH) as monitored by spectrophotometry and calorimetry were not significantly affected after immobilization. Conversely both the stability and unfolding mechanism drastically changed. Thermodynamic analysis of the DSC data suggests that uncoupling of protein domains has occurred as a consequence of the immobilization. The two state approximation of the protein unfolding process is not longer valid for the immobilized RNase. Protein stability strongly depends on the hydrophobicity properties of the support surface as well as on the presence of the inhibitor and pH. For example, after immobilization on a highly hydrophobic surface, the enzyme is partially in the unfolded state. The binding of a ligand is able to reorganize the protein structure into a native-like conformation. The refolding rates are different for the two protein domains and vary as a function of pH and presence of the inhibitor 3′-CMP. © 1994 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190205
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    Temperature-induced complementarity as a mechanism for biomolecular assembly (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 73-76 
    Details
    ISSN: 0887-3585
    Keywords: molecular recognition ; protein assembly ; protein folding ; protein interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent advances in the measurement and theory of “hydration” interactions between biomolecules provide a basis on which to formulate mechanisms of biomolecular recognition. In this paper we have developed a mathematical formalism for analyzing specificity encoded in dynamic distributions of surface polar groups, a formalism that incorporates newly recognized properties of directly measured “hydration” forces. As expected, attraction between surfaces requires complementary patterns of surface polar groups. In contrast to usual expectations, thermal motion can create these complementary surface configurations. We have demonstrated that assembly can occur with an increase in conformational entropy of polar residues. Elevated temperature then facilitates recognition rather than hinders it. This mechanism might underlie some temperature-favored assembly reactions common in biological systems that are usually associated with the “hydrophobic effect” only. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190109
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    Coiled-coil stutter and link segments in keratin and other intermediate filament molecules: A computer modeling study (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 174-184 
    Details
    ISSN: 0887-3585
    Keywords: coiled-coils ; keratin ; intermediate filament proteins ; link segments ; heptad phasing ; computer modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural discontinuities have previously been identified in four regions of the coiled-coil rod domain structure present in intermediate filament (IF) protein molecules. These include a point at which a phase shift occurs in the heptad periodicity characteristic of the sequence of polar and apolar residues in α-helical coiled-coils, and three links that lack a heptad substructure. We have studied these regions by computer-based molecular modeling and comparative sequence analysis and conclude that the phasing discontinuity can be accommodated without significant distortion of the overall double-helical chain conformation; the L2 link has a similar conformation in all different types of IF molecules, a favorable conformation being one in which the two strands wrap tightly around each other; the L12 links vary in length between different IF types but contain important sequence similarities suggestive of a partial β structure; the L1 links show larger variations in length, a lower degree of similarity, and probably diverse structures. Variations in the overall charges of the different links suggest that ionic interactions may playa significant role in filament assembly. The results also have general significance for other α-fibrous proteins in which either the characteristic heptad phasing undergoes a discontinuity or where a short non-coiled-coil sequence occurs within a coiled-coil rod domain structure. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340200207
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    Crystallization and characterization of the recombinant human Clara cell 10-kDa protein (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 191-196 
    Details
    ISSN: 0887-3585
    Keywords: human Clara cell 10-kDa protein ; X-ray diffraction ; phospholipase A2 inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of recombinant human Clara cell 10-kDa protein were grown both from ammonium sulfate and polyethylene glycol (PEG) solutions. Crystals grown from ammonium sulfate solution have been characterized by X-ray diffraction studies as monoclinic with the space group C2 and lattice constants a = 69.2 Å, b = 83.0 Å, c = 58.3 Å, and β = 99.7°. The monoclinic crystals diffract to beyond 2.5 Å. Some of the crystals grown from PEG were of a similar habit to those grown from ammonium sulfate, but others were triclinic with the space group P1 and cell constants a = 40.3 Å, b = 46.3 Å, c = 51.3 Å, α = 117.7°, β = 102.3°, and γ = 71.4°. These crystals diffract to beyond 3.2 Å. © 1994 Wiley-Liss, Inc.
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    Conformational analysis of hemopexin by fourier-transform infrared and circular dichroism spectroscopy (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 185-190 
    Details
    ISSN: 0887-3585
    Keywords: heme ; secondary structure ; conformation ; hemopexin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hemopexin is a serum glyco-protein that binds heme with the highest known affinity of any characterized heme-binding protein and plays an important role in receptormediated cellular heme uptake. Complete understanding of the function of hemopexin will require the elucidation of its molecular structure. Previous analysis of the secondary structure of hemopexin by far-UV circular dichroism (CD) failed due to the unusual positive ellipticity of this protein at 233 nm. In this paper, we present an examination of the structure of hemopexin by both Fourier-transform infrared (FTIR) and circular dichroism spectroscopy. Our studies show that hemopexin contains about 55% β-structure, 15% α-helix, and 20% turns. The two isolated structural domains of hemopexin each have secondary structures similar to hemopexin. Although there are significant tertiary conformational changes indicated by the CD spectra, the overall secondary structure of hemopexin is not affected by binding heme. However, moderate changes in secondary structure do occur when the heme-binding domain of hemopexin associates with heme. In spite of the exceptionally tight binding at neutral pH, heme is released from the bis-histidyl heme-hemopexin complex at pH 5.0. Under this acidic condition, hemopexin maintains the same overall secondary structure as the native protein and is able to resume the heme-binding function and the native structure of the hemeprotein (as indicated by the CD spectra) when returned to neutral pH. We propose that the state of hemopexin identified in vitro at pH 5.0 resembles that of this protein in the acidic environment of the endosomes in vivo when hemopexin releases heme during receptor-mediated endocytosis. © 1994 Wiley-Liss, Inc.
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340200301
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    Preliminary crystallographic analysis of an enzyme involved in erythromycin biosynthesis: Cytochrome P450eryF (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 197-201 
    Details
    ISSN: 0887-3585
    Keywords: cytochrome P450 ; erythromycin ; P450eryF ; crystallization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cytochrome P450eryF was overexpressed in Escherichia coli and purified in high yield. Crystals of the protein in the presence of the substrate, 6-deoxyerythronolide B, have been obtained by the hanging drop vapor diffusion method, using polyethylene glycol 4000 as a precipitant. The crystals belong to the orthorhombic space group P212121 with unit cell dimensions of a = 54.16 Å, b = 79.67 Å, and c = 99.48 Å and one molecule per asymmetric unit. A complete native data set has been collected to a resolution of 2.1 Å, and anomalous dispersion difference Patterson maps have revealed the location of the single heme iron atom. © 1994 Wiley-Liss, Inc.
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    Homology modeling of the Abl-SH3 domain (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 203-215 
    Details
    ISSN: 0887-3585
    Keywords: SH3 ; Abl ; molecular modeling ; homology modeling ; molecular dynamics ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A tertiary structure model of the Abl-SH3 domain is predicted by using homology modeling techniques coupled to molecular dynamics simulations. Two template proteins were used, Fyn-SH3 and Spc-SH3. The refined model was extensively checked for errors using criteria based on stereochemistry, packing, solvation free-energy, accessible surface areas, and contact analyses. The different checking methods do not totally agree, as each one evaluates a different characteristic of protein structures. Several zones of the protein are more susceptible to incorporating errors. These include residues 13, 15, 35, 39, 45, 46, 50, and 60. An interesting finding is that the measurement of the Cα chirality correlated well with the rest of the criteria, suggesting that this parameter might be a good indicator of correct local conformation. Deviations of more than 4 degrees may be indicative of poor local structure. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340200302
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    Homologous modeling of the lysosomal protective protein/carboxypeptidase L: Structural and functional implications of mutations identified in galactosialidosis patients (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 81-93 
    Details
    ISSN: 0887-3585
    Keywords: serine carboxypeptidase ; protein modeling ; mutation analysis ; comparative modeling ; cathepsin A ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The deficiency of the lysosomal protective protein/carboxypeptidase L (CARB L) causes the lysosomal storage disorder, galactosialidosis, characterized by neuraminidase and β-galactosidase deficiencies in patients' cells. The three enzymes form a complex inside the lysosome, and the neuraminidase and β-galactosidase deficiencies are secondary to CARB L deficiency. Sequence similarity and common enzymological properties suggest that the protomeric tertiary structure of CARB L is conserved within a family of serine carboxypeptidases which includes the yeast carboxypeptidase Y, killer expression I gene product and several plant carboxypeptidases. We used this homology to build a model of the CARB L structure based on the recently published X-ray atomic coordinates of the wheat carboxypeptidase II (CPDW-II) which shares 32% primary structure identity with CARB L. Small insertions and deletions were accommodated into the model structure by energy minimization using the DREIDING II force field. The Cα atomic-coordinates of the final CARB L model have a RMS shift of 1.01 Å compared to the corresponding conserved residues in the CPDW-II template structure. The correct orientation of the homologous catalytic triad residues Ser150, His429 and Asp392, the potential energy calculations and the distribution of hydrophobic and hydrophillic residues in the structure all support the validity of the CARB L model. Most missense mutations identified in galactosialidosis patients were located in secondary structural elements except for the Tyr211→Asn mutation which is in a loop. The other mutant residues have their side chains deeply buried in the central β-sheet of the model structure except for the Phe412→Val mutation which is located in the dimer interface. The predicted effects of specific mutations on CARB L structural stability correlates well with recently published transient expression studies of mutant CARB L (Shimmoto, M. et al., J. Clin. Invest., 91:2393-2399, 1993). © 1994 John Wiley & Sons, Inc.
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    Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 227-247 
    Details
    ISSN: 0887-3585
    Keywords: cell multipole method ; Newton-Euler inverse mass operator ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two new methods developed for molecular dynamics simulations of very large proteins are applied to a series of proteins ranging up to the protein capsid of tomato bushy stunt virus (TBSV).For molecular dynamics of very large proteins and polymers, it is useful to carry out the dynamics using internal coordinates (say, torsions only) rather than Cartesian coordinates. This allows larger time steps, eliminates problems with the classical description of high energy modes, and focuses on the important degrees of freedom. The resulting equation of motion has the form where for T is the vector of generalized forces, M(θ) is the moments of inertia tensor, is the vector of torsions, and C is a vector containing Coriolis forces and nonbond forces. The problem is that to calculate the acceleration vector from M, C, and Trequires inverting. M(θ), an order N3calculation. Since the number of degrees of freedom might be 300,000 for a million atom system, solving these equations every time step is impractical, restricting internal coordinate methods to small systems. The new method, Newton-Euler Inverse Mass Operator (NEIMO) dynamics, constructs the torsional accelerations vector directly by an order N process, allowing internal-coordinate dynamics to be solved for super larger (million atom) systems, The first use of the NEIMO method for molecular dynamics of proteins is presented here.A second serious difficulty for large proteins is calculation of the nonbond forces. We report here the first application to proteins of the new Cell Multipole Method (CMM) to evaluate the Coulomb and van der Waals interactions. The cost of CMM scales linearly with the number of particles while retaining an accuracy significantly better than standard non bond methods (involving cutoffs).Results for NEIMO and CMM are given for simulations of a wide range of peptide and protein systems, including the protein capsid of TBSV with 488,000 atoms. The computational times for NEIMO and CMM are demonstrated to scale linearly with size. With NEIMO the dynamics time steps can be as large as 20 fs (for small peptides), much larger than possible with standard Cartesian coordinate dynamics.For TBSV we considered both the normal form and the high pH form, in which the Ca2+ ions are removed. These calculations lead to a contraction of the protein for both forms (probably because of ignoring the RNA core not observed in the X-ray). © 1994 Wiley-Liss, Inc.
    Additional Material: 21 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200304
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    Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 68-84 
    Details
    ISSN: 0887-3585
    Keywords: side chain conformation ; protein folding ; protein binding ; helix formation ; helix stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Theoretical estimations of changes in side chain configurational entropy are essential for understanding the different contributions to the overall thermodynamic behavior of important biological processes like folding and binding. The configurational entropy of any given side chain in any particular protein can be evaluated from the complete energy profile of the side chain. Calculations of the energy profiles can be performed using the side chain single bond dihedrals as the only independent variables as long as the structures at each value of the dihedrals are allowed to relax through small changes in the valence bond angles. The probabilities of different side chain conformers obtained from these energy profiles are very similar to the conformer populations obtained by analysis of side chain preferences in the proteins of the Protein Data Bank. Also, side chain conformational entropies obtained from the energy profiles agree extremely well with those obtained from the Protein Data Bank conformer populations. Changes in side chain configurational entropy in binding and folding can be computed as differences in conformational entropy because, in most cases, the frequency of the rotational oscillation around the energy minimum of any given conformer does not appear to change significantly in the reaction. Changes of side chain conformational entropy calculated in this way were compared with experimental values. The only available experimental data-the effect of side chain substitution on the stability of α-helices-were used for this comparison. The experimental values were corrected to subtract the solvent contributions. This comparison yields an excellent agreement between calculated and experimental values, validating not only the theoretical estimates but also the separability of the entropic contributions into configurational terms and solvation related terms. © 1994 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200108
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    Microtube batch protein crystallization: Applications to human immunodeficiency virus type 2 (HIV-2) protease and human renin (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 98-102 
    Details
    ISSN: 0887-3585
    Keywords: X-ray diffraction ; aspartic protease ; AIDS ; recombinant protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: For therapeutically relevant targets, the evaluation of enzymes in complex with their inhibitors by cocrystallization and high resolution structural analysis has become a vital component of structure-driven drug design and development. Two approaches, hanging drop vapor diffusion and a novel microtube batch method, were utilized in parallel to grow crystals of recombinant HIV -2 protease and recombinant human renin in complex with inhibitors. In the case of HIV -2 protease in complex with a reduced amide inhibitor, crystallization was achieved only by the microbatch method. In the case of human renin, the addition of precipitant was required for crystal growth. The microbatch method described here is a useful supplementary or alternative approach for screening parameters and generating crystals suitable for high resolution structural analysis. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200110
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    Solvent-induced organization: A physical model of folding myoglobin (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 124-138 
    Details
    ISSN: 0887-3585
    Keywords: leghemoglobin ; hydrophobic ; interactions ; hydrophobicity ; protein folding ; structure prediction ; protein dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The essential features of the in vitro refolding of myoglobin are expressed in a solvable physical model. Alpha helices are taken as the fundamental collective coordinates of the system, while the refolding is assumed to be mainly driven by solvent-induced hydrophobic forces. A quantitative model of these forces is developed and compared with experimental and theoretical results. The model is then tested by being employed in a simulation scheme designed to mimic solvent effects. Realistic dynamic trajectories of myoglobin are shown as it folds from an extended conformation to a close approximation of the native state. Various suggestive features of the process are discussed. The tenets of the model are further tested by folding the single-chain plant protein leghemoglobin. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200203
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    An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 19-33 
    Details
    ISSN: 0887-3585
    Keywords: Discover program ; protein dynamics ; computer simulation ; protein motions ; counterions ; dielectric ; protein electrostatics ; aqueous simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this report we examine several solvent models for use in molecular dynamics simulations of protein molecules with the Discover program from Biosym Technologies. Our goal was to find a solvent system which strikes a reasonable balance among theoretical rigor, computational efficiency, and experimental reality. We chose phage T4 lysozyme as our model protein and analyzed 14 simulations using different solvent models. We tested both implicit and explicit solvent models using either a linear distance-dependent dielectric or a constant dielectric. Use of a linear distance-dependent dielectric with implicit solvent significantly diminished atomic fluctuations in the protein and kept the protein close to the starting crystal structure. In systems using a constant dielectric and explicit solvent, atomic fluctuations were much greater and the protein was able to sample a larger portion of conformational space. A series of nonbonded cutoff distances (9.0, 11.5, 15.0, 20.0 Å) using both abrupt and smooth truncation of the nonbonded cutoff distances were tested. The method of dual cutoffs was also tested. We found that a minimum nonbonded cutoff distance of 15.0 Å was needed in order to properly couple solvent and solute. Distances shorter than 15.0 Å resulted in a significant temperature gradient between the solvent and solute. In all trajectories using the proprietary Discover switching function, we found significant denaturation in the protein backbone; we were able to run successful trajectories only in those simulations that used no switching function. We were able to significantly reduce the computational burden by using dual cutoffs and still calculate a quality trajectory. In this method, we found that an outer cutoff distance of 15.0 Å and an inner cutoff distance of 11.5 worked well. While a 10 Å shell of explicit water yielded the best results, a 6 A shell of water yielded satisfactory results with nearly a 40% reduction in computational cost. © 1994 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180105
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    Molecular surface representations by sparse critical points (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 94-101 
    Details
    ISSN: 0887-3585
    Keywords: surface representation ; molecular recognition ; protein docking ; surface triangulation ; molecular graphics ; molecular visualization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have defined a molecular surface representation that describes precisely and concisely the complete molecular surface. The representation consists of a limited number of critical points disposed at key locations over the surface. These points adequately represent the shape and the important characteristics of the surface, despite the fact that they are modest in number. We expect the representation to be useful in areas such as molecular recognition and visualization. In particular, using this representation, we are able to achieve accurate and efficient protein-protein and protein-small molecule docking. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180111
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    Lobster enolase crystallized by serendipity (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 390-393 
    Details
    ISSN: 0887-3585
    Keywords: protein crystallization ; enzyme copurification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An unknown protein crystallized from a lobster muscle preparation in which arginine kinase was the majority component. It was identified as enolase by peptide sequencing and activity testing, and a SIRAS electron density map showed its three-dimensional structure to be very similar to that of yeast enolase. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180409
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    Crystallographic analysis of oxygenated and deoxygenated states of arthropod hemocyanin shows unusual differences (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 302-309 
    Details
    ISSN: 0887-3585
    Keywords: dinuclear copper site ; hemocyanin ; oxygen binding ; allosteric regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray structure of an oxygenated hemocyanin molecule, subunit II of Limulus polyphemus hemocyanin, was determined at 2.4 Å resolution and refined to a crystallographic R-factor of 17.1%. The 73-kDa subunit crystallizes with the symmetry of the space group R32 with one subunit per asymmetric unit forming hexamers with 32 point group symmetry. Molecular oxygen is bound to a dinuclear copper center in the protein's second domain, symmetrically between and equidistant from the two copper atoms. The copper-copper distance in oxygenated Limulus hemocyanin is 3.6 ± 0.2 Å, which is surprisingly 1 Å less than that seen previously in deoxygenated Limulus polyphemus subunit II hemocyanin (Hazes et al., Protein Sci. 2:597, 1993). Away from the oxygen binding sites, the tertiary and quaternary structures of oxygenated and deoxygenated Limulus subunit II hemocyanins are quite similar. A major difference in tertiary structures is seen, however, when the Limulus structures are compared with deoxygenated Panulirus interruptus hemocyanin (Volbeda, A., Hol, W. G. J. J. Mol. Biol. 209:249, 1989) where the position of domain 1 is rotated by 8° with respect to domains 2 and 3. We postulate this rotation plays an important role in cooperativity and regulation of oxygen affinity in all arthropod hemocyanins. © 1994 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190405
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    Conservation and prediction of solvent accessibility in protein families (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 216-226 
    Details
    ISSN: 0887-3585
    Keywords: evolutionary information ; multiple alignments ; neural networks ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Currently, the prediction of three-dimensional (3D) protein structure from sequence alone is an exceedingly difficult task. As an intermediate step, a much simpler task has been pursued extensively: predicting 1D strings of secondary structure. Here, we present an analysis of another 1D projection from 3D structure: the relative solvent accessibility of each residue. We show that solvent accessibility is less conserved in 3D homologues than is secondary structure, and hence is predicted less accurately from automatic homology modeling; the correlation coefficient of relative solvent accessibility between 3D homologues is only 0.77, and the average accuracy of predictions based on sequence alignments is only 0.68. The latter number provides an effective upper limit on the accuracy of predicting accessibility from sequence when homology modeling is not possible. We introduce a neural network system that predicts relative solvent accessibility (projected onto ten discrete states) using evolutionary profiles of amino acid substitutions derived from multiple sequence alignments. Evaluated in a cross-validation test on 238 unique proteins, the correlation between predicted and observed relative accessibility is 0.54. Interpreted in terms of a three-state (buried, intermediate, exposed) description of relative accessibility, the fraction of correctly predicted residue states is about 58%. In absolute terms this accuracy appears poor, but given the relatively low conservation of accessibility in 3D families, the network system is not far from its likely optimal performance. The most reliably predicted fraction of the residues (50%) is predicted as accurately as by automatic homology modeling. Prediction is best for buried residues, e.g., 86% of the completely buried sites are correctly predicted as having 0% relative accessibility. © 1994 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200303
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    Molecular dynamics simulations of trp apo-and holorepressors: Domain structure and ligand-protein interaction (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 248-258 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; trp-repressor ; ligand ; domain ; dynamic cross-correlation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations of the apo- and holo-forms of thetrp-repressor protein were performed under extensively solvated conditions in order to elucidate their dynamic structures and ligand-protein interactions. The root mean square fluctuations calculated from the trajectories agreed with those calculated from X-ray temperature factors. Distance, distance fluctuation, and dynamic cross-correlation maps were drawn to provide information on the dynamic structures and communications among the domains. A three-domain format has been proposed for the crystal structure (Zhang et at., Nature 327:591-597, 1987) namely, helices A-C and F of both subunits make up a central core, and D and E of each subunit forms a DNA binding head. The results of the simulations were mostly consistent with the three-domain format. However, helix F was more flexible and freer than other parts of the central core. The turn DE, the helix-turn-helix DNA binding motif, was free from interactions and correlations with other domains in both forms of the repressor. A comparison of the simulations of the aporepressor and holorepressor showed that tryptophan binding made the DNA-binding helix D more flexible but helix F less flexible. Several amino acid residues in contact with the bound tryptophan were identified as making concerted motions with it. Interaction energies between the corepressor and the amino acid residues of the protein were analyzed; the results were mostly consistent with the mutational experiments. © 1994 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200305
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    Magnetic resonance studies of the binding of oligonucleotide substrates to mutants of staphylococcal nuclease (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 68-80 
    Details
    ISSN: 0887-3585
    Keywords: staphylococcal nuclease ; nonproductive substrate binding to ; subsites of ; active site mutants of ; oligonucleotide binding to ; Ca2+ binding to ; Mn2+ binding to ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: By a combination of NMR docking and model building, the substrate binding site on staphylococcal nuclease was found to accommodate a trinucleotide and to consist of three subsites, each interacting with a single nucleotidyl unit of DNA. Binding of the essential Ca2+ activator and substrate cleavage occur between subsites 1 and 2. Hence, catalytically productive binding would span subsites 1 and 2 while nonproductive binding would span subsites 2 and 3. Lys-49 is near subsite 1, and Lys-84 and Tyr-115 interact with substrates at sub site 3 [Weber, D. J., Gittis, A. G., Mullen, G. P., Abeygunawardana, C., Lattman, E. E., Mildvan, A. S. Proteins 13:275-287, 1992]. The proposed locations of these subsites were independently tested by the effects of the K49A, K84A, and Y115A mutations of staphylococcal nuclease on the binding of Mn2+, Ca2+, and the dinucleotide and trinucleotide substrates, 5′-pdTdA, dTdA, and dTdAdG. These three mutants have previously been shown to be fully active and to have CD and 2D NMR spectra very similar to those of the wild-type enzyme (Chuang, W.-J., Weber, D. J., Gittis, A. G., Mildvan, A. S. Proteins 17:36-48, 1993). All three mutant enzymes and their pdTdA and dTdA complexes (but not their dTdAdG complex) bind Mn2+ and Ca2+ more weakly than the wild-type enzyme by factors ranging from 2 to 11. The presence of a terminal phosphate as in 5′-pdTdA raises the affinity of the substrate for staphylococcal nuclease and its three mutants by two orders of magnitude and for the corresponding enzyme-metal complexes by three to four orders of magnitude, suggesting that the terminal phosphate is coordinated by the enzyme-bound divalent cation. Such complexation would result in the nonproductive binding of 5′-pdTdA at subsites 2 and 3. Accordingly, the K84A and Y115A mutations significantly weaken the binding of 5′-pdTdA and its metal to staphylococcal nuclease by factors of 2.2 to 37.8, while the K49A mutation has much smaller or no effect. Such nonproductive binding explains the low activity of staphylococcal nuclease with small substrates, especially those With a terminal phosphate. Similarly, the K84A and Y115A mutations weaken the binding of dTdA and its metal complexes to the enzyme by factors of 3.4 to 13.1 while the K49A mutation has smaller effects indicating significant nonproductive binding of dTdA. The trinucleotide dTdAdG binds more tightly to wild-type and mutant staphylococcal nuclease and to its metal complexes than does the dinucleotide dTdA by factors of 2.4 to 12.2, reflecting the occupancy of an additional subsite. Predominantly productive binding of dTdAdG is indicated by the 1.7- to 8.3-fold lower affinities of the K49A, K84A, and Y115A mutants for the trinucleotide and its metal complexes. The largest effects on dTdAdG binding are seen with the Y115A mutation presumably reflecting the dual role of Tyr-115 both in donating a hydrogen bond to a phosphodiester oxygen between subsites 2 and 3 and in stacking onto the guanine base at subsite 3. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180109
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    New Developments at PROTEINS (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180102
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    Rigid-body docking with mutant constraints of influenza hemagglutinin with antibody HC19 (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 8-18 
    Details
    ISSN: 0887-3585
    Keywords: docking algorithm ; antigen-antibody complex ; epitope ; influenza virus hemagglutinin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An automatic docking algorithm has been applied to the modeling of the complex between hemagglutinin from influenza virus and the Fab fragment of a monoclonal antibody raised against this antigen. We have introduced here the use of biochemical information provided by mutants of hemagglutinin. The docking procedure finds a small number of candidate solutions where three sites of escape mutations are buried and form hydrogen bonds in the interface. The localization of the epitope is improved by additional biochemical data about mutants that do not affect antibody binding. Five candidate solutions with low energy, reasonably well-packed interfaces, and six to ten hydrogen bonds are compatible with mutant information. One of the five stands out as generally better than the others from these points of views. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180104
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    Alpha helix capping in synthetic model peptides by reciprocal side chain-main chain interactions: Evidence for an N terminal “capping box” (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 1-7 
    Details
    ISSN: 0887-3585
    Keywords: α-helix capping ; α-helix initiation ; α-helix termination ; synthetic peptides ; protein folding ; circular dichroism ; 1H nmr ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A significant fraction of the amino acids in proteins are alpha helical in conformation. Alpha helices in globular proteins are short, with an average length of about twelve residues, so that residues at the ends of helices make up an important fraction of all helical residues. In the middle of a helix, H-bonds connect the NH and CO groups of each residue to partners four residues along the chain. At the ends of a helix, the H-bond potential of the main chain remains unfulfilled, and helix capping interactions involving bonds from polar side chains to the NH or CO of the backbone have been proposed and detected. In a study of synthetic helical peptides, we have found that the sequence Ser-Glu-Asp-Glu stabilizes the alpha helix in a series of helical peptides with consensus sequences. Following the report by Harper and Rose, which identifies SerXaaXaaGlu as a member of a class of common motifs at the N termini of alpha helices in proteins that they refer to as “capping boxes,” we have reexamined the side chain-main chain interactions in a varient sequence using 1H NMR, and find that the postulated reciprocal side chain-backbone bonding between the first Ser and last Glu side chains and their peptide NH partners can be resolved: Deletion of two residues N terminal to the Ser-Glu-Asp-Glu sequence in these peptides has no effect on the initiation of helical structure, as defined by two-dimensional (2D) NMR experiments on this variant. Thus the capping box sequence Ser-Glu-Asp-Glu inhibits N terminal fraying of the N terminus of alpha helix in these peptides, and shows the side chain-main chain interactions proposed by Harper and Rose. It thus acts as a helix initiating signal. Since normal a helix cannot propagate beyond the N terminus of this structure, the box acts as a termination signal in this direction as well. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180103
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    Cold adaption of enzymes: Structural comparison between salmon and bovine trypsins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 149-166 
    Details
    ISSN: 0887-3585
    Keywords: crystal structure ; cold adaption ; catalytic efficiency ; protein stability ; anionic ; ectotherm ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of an anionic form of salmon trypsin has been determined at 1.82 Å resolution. We report the first structure of a trypsin from a phoikilothermic organism in a detailed comparison to mammalian trypsins in order to look for structural rationalizations for the cold-adaption features of salmon trypsin. This form of salmon trypsin (T II) comprises 222 residues, and is homologous to bovine trypsin (BT) in about 65% of the primary structure. The tertiary structures are similar, with an overall displacement in main chain atomic positions between salmon trypsin and various crystal structures of bovine trypsin of about 0.8 Å. Intramolecular hydrogen bonds and hydrophobic interactions are compared and discussed in order to estimate possible differences in molecular flexibility which might explain the higher catalytic efficiency and lower thermostability of salmon trypsin compared to bovine trypsin. No overall differences in intramolecular interactions are detected between the two structures, but there are differences in certain regions of the structures which may explain some of the observed differences in physical properties. The distribution of charged residues is different in the two trypsins, and the impact this might have on substrate affinity has been discussed. © 1994 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200205
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    Collective motions in proteins investigated by X-ray diffuse scattering (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 34-48 
    Details
    ISSN: 0887-3585
    Keywords: normal mode refinement ; correlation function ; intra- and intermolecular correlation ; higher order scattering ; human lysozyme ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have developed theoretical models for analysis of X-ray diffuse scattering from protein crystals. A series of models are proposed to be used for experimental data with different degrees of precision. First, we propose the normal mode model, where conformational dynamics of a protein is assumed to occur mostly in a limited conformational subspace spanned by a small number of low-frequency normal modes in the protein. When high precision data are available, variances and covariances of the normal mode variables can be determined from experimental data using this model. For experimental data with lower degrees of precision, we introduce a series of simpler models. These models express the covariance matrix using relatively simple empirical correlation functions by assuming the correlation between a pair of atoms to be isotropic. As an application of these simpler models, we calculate diffuse-scattering patterns from a human lysozyme crystal to examine how each adjustable parameter in the models affects general features of the resulting patterns. The results of the calculation are summarized as follows. (1) The higher order scattering makes a significant contribution at high resolutions. (2) The resulting simulated patterns are sensitive to changes in correlation lengths of about 1 Å, as well as to changes of the functional form of the correlation function. (3) But only the “average” value of the intra- and intermolecular correlation lengths seems to determine the gross features of the pattern. (4) The effect of the atom-dependent amplitude of fluctuations is difficult to observe. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180106
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    The enzymatic mechanism of carboxypeptidase: A molecular dynamics study (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 186-197 
    Details
    ISSN: 0887-3585
    Keywords: carboxypeptidas ; molecular dynamics ; enzymatic mechanisms ; peptidase mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An MD simulation of the system carboxypeptidase A (CPA) with the tetrapeptide Val-Leu-Phe-Phe has been performed in order to learn about the substrate disposition just prior to nucleophilic attack. We have explored the model in which the substrate does not substitute the zinc-coordinated water (the “water” mechanism). The simulations do suggest as feasible that the Zn-OH2 group performs a nucleophilic attack on the Phe-Phe peptidic bond. We have also investigated the model in which the carbonyl oxygen displaces the zinc-coordinated water. In this case the substrate and Glu-270 orient themselves to allow an anhydride intermediate during the peptidic bond cleavage (the “anhydride” mechanism). Based on the results of the simulations, both “water” and “anhydride” mechanisms are structurally feasible, although the former model seems more probable on chemical grounds. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180210
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    A molecular dynamics approach for the generation of complete protein structures from limited coordinate data (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 174-185 
    Details
    ISSN: 0887-3585
    Keywords: computer modeling ; protein structure prediction ; α-carbons ; structure evaluation ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Generation of full protein coordinates from limited information, e.g., the Cα coordinates, is an important step in protein homology modeling and structure determination, and molecular dynamics (MD) simulations may prove to be important in this task. We describe a new method, in which the protein backbone is built quickly in a rather crude way and then refined by minimization techniques. Subsequently, the side chains are positioned using extensive MD calculations. The method is tested on two proteins, and results compared to proteins constructed using two other MD-based methods. In the first method, we supplemented an existing backbone building method with a new procedure to add side chains. The second one largely consists of available methodology. The constructed proteins are compared to the corresponding X-ray structures, which became available during this study, and they are in good agreement (backbone RMS values of 0.5-0.7 Å, and all-atom RMS values of 1.5-1.9 Å). This comparative study indicates that extensive MD simulations are able, to some extent, to generate details of the native protein structure, and may contribute to the development of a standardized methodology to predict reliably (parts of) protein structures when only partial coordinate data are available. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340180209
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    Introducing “Future Directions” (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180202
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    Crystallization and characterization of colicin E1 channel-forming polypeptides (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 150-157 
    Details
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; membrane protein ; ion channels ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of the channel-forming domain of colicin E1 from E. coli were grown by vapor diffusion at pH 6.4 and higher pH values. Cleavage of the colicin molecule with trypsin or thermolysin produced two of the pore-forming polypeptides used in these experiments. The third polypeptide was purified from a constructed plasmid that overexpresses only the C-terminal domain of colicin E1. Polypeptide crystals are tetragonal with space group I4, have one monomer in the asymmetric unit, and diffract to 2.2-2.4 Å. Unit cell parameters for the tryptic and thermolytic polypeptides are a = 102.9 Å and c = 35.6 Å. Crystals of the overexpressed polypeptide have unit cell parameters of a =87.2 Å and c =59.1 Å. The crystals were characterized by precession photography, and native data sets of each channel-forming fragment were collected on a Siemens-Nicolet area detector. The crystallization and characterization of these polypeptides are the first steps in the structure determination of the channel-forming domain of colicin E1. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190208
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    A model for the structure of a homodimeric prohormone: The precursor to the locust neuropeptide AKH I (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 356-366 
    Details
    ISSN: 0887-3585
    Keywords: NMR ; structure determination ; coiled coil ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have determined the structure in solution of a homodimeric protein that is a precursor to the locust neuropeptide adipokinetic hormone I using nuclear magnetic resonance spectroscopy. This precursor, called P1, is comprised of two 41 residue strands joined by a single inter-chain disulphide at Cys39. We have also determined the structure of an end product of P1 processing, called APRP1; this is a homodimer comprised of residues 14-41 of PI. Nuclear Overhauser Effect (nOe) data indicate that in both P1 and APRP1, residues 22-37 (numbered with respect to P1) form pairs of α-helices, with no evidence for any other secondary structure. © 1994 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340200408
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    Molecular dynamics simulation of the docking of substrates to proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 174-182 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; docking ; computer simulation ; substrate docking ; immunoglobulin ; rational drug design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A simple method is described to perform docking of subtrates to proteins or probes to receptor molecules by a modification of molecular dynamics simulations. The method consists of a separation of the center-of-mass motion of the substrate from its internal and rotational motions, and a separate coupling to different thermal baths for both types of motion of the substrate and for the motion of the receptor. Thus the temperatures and the time constants of coupling to the baths can be arbitrarily varied for these three types of motion, allowing either a frozen or a flexible receptor and allowing control of search rate without disturbance of internal structure. In addition, an extra repulsive term between substrate and protein was applied to smooth the interaction. The method was applied to a model substrate docking onto a model surface, and to the docking of phosphocholine onto immunoglobulin McPC603, in both cases with a frozen receptor. Using transrational temperatures of the substrate in the range of 1300-1700 K and room temperature for the internal degrees of freedom of the substrate, an efficient nontrapping exploratory search (“helicopter view”) is obtained, which visits the correct binding sites. Low energy conformations can then be further investigated by separate search or by dynamic simulated annealing. In both cases the correct minima were identified. The possibility to work with flexible receptors is discussed. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190303
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    Spatial optimization of electrostatic interactions between the ionized groups in globular proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 222-229 
    Details
    ISSN: 0887-3585
    Keywords: protein electrostatics ; energy calculations ; ion pairs ; Monte-Carlo simulations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model approach is suggested to estimate the degree of spatial optimization of the electrostatic interactions in protein molecules. The method is tested on a set of 44 globular proteins, representative of the available crystallographic data. The theoretical model is based on macroscopic computation of the contribution of charge-charge interactions to the electrostatic term of the free energy for the native proteins and for a big number of virtual structures with randomly distributed on protein surface charge consetellations (generated by a Monte-Carlo technique). The statistical probability of occurrence of random structures with electrostatic energies lower than the energy of the native protein is suggested as a criterion for spatial optimization of the electrostatic interactions. The results support the hypothesis that the folding process optimizes the stabilizing effect of electrostatic interactions, but to very different degree for different proteins. A parallel analysis of ion pairs shows that the optimization of the electrostatic term in globular proteins has increasingly gone in the direction of rejecting the repulsive short contacts between charges of equal sign than of creating of more salt bridges (in comparison with the statistically expected number of shortrange ion pairs in the simulated random structures). It is observed that the decrease in the spatial optimization of the electrostatic interactions is usually compensated for by an appearance of disulfide bridges in the covalent structure of the examined proteins. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190306
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    Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 244-255 
    Details
    ISSN: 0887-3585
    Keywords: energy minimization ; rotamers ; automaton ; de novo design ; sequence prediction ; side-chain conformation prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Globular proteins have high packing densities as a result of residue side chains in the core achieving a tight, complementary packing. The internal packing is considered the main determinant of native protein structure. From that point of view, we present here a method of energy minimization using an automata network to predict a set of amino acid sequences and their side-chain conformations from a desired backbone geometry for de novo design of proteins. Using discrete side-chain conformations, that is, rotamers, the sequence generation problem from a given backbone geometry becomes one of combinatorial problems. We focused on the residues composing the interior core region and predicted a set of amino acid Sequences and their side-chain conformations only from a given backbone geometry. The kinds of residues were restricted to six hydrophobic amino acids (Ala, Ile, Met, Leu, Phe, and Val) because the core regions are almost always composed of hydrophobic residues. The obtained sequences were well packed as was the native sequence. The method can be used for automated sequence generation in the de novo design of proteins. © 1994 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190308
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  • 79
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    Parser for protein folding units (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 256-268 
    Details
    ISSN: 0887-3585
    Keywords: unfolding ; solvation ; contact maps ; protein design ; structural domains ; normal modes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: General patterns of protein structural organization have emerged from studies of hundreds of structures elucidated by X-ray crystallography and nuclear magnetic resonance. Structural units are commonly identified by visual inspection of molecular models using qualitative criteria. Here, we propose an algorithm for identification of structural units by objective, quantitative criteria based on atomic interactions. The underlying physical concept is maximal interactions within each unit and minimal interaction between units (domains). In a simple harmonic approximation, interdomain dynamics is determined by the strength of the interface and the distribution of masses. The most likely domain decomposition involves units with the most correlated motion, or largest interdomain fluctuation time. The decomposition of a convoluted 3-D structure is complicated by the possibility that the chain can cross over several times between units. Grouping the residues by solving an eigenvalue problem for the contact matrix reduces the problem to a one-dimensional search for all reasonable trial bisections. Recursive bisection yields a tree of putative folding units. Simple physical criteria are used to identify units that could exist by themselves. The units so defined closely correspond to crystallographers' notion of structural domains. The results are useful for the analysis of folding principles, for modular protein design and for protein engineering. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190309
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  • 80
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    Crystallization and preliminary X-ray diffraction study of the green flavoenzyme 5-Hydroxyvaleryl-CoA dehydratase/dehydrogenase from Clostridium aminovalericum (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 269-271 
    Details
    ISSN: 0887-3585
    Keywords: acyl-CoA dehydrogenase ; bifunctional enzyme ; charge-transfer complex ; clostridial metabolism ; FAD, x-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The bifunctional flavoenzyme 5-hydroxyvaleryl-CoA dehydratase/ dehydrogenase has been crystallized from solutions containing ammonium sulfate (form I) or polyethylene glycol (form II) as precipitant. In both cases, the crystals grew in the monoclinic space group C2. The unit cell dimensions for form I crystals were determined as a = 162.8 Å, b = 71.8 Å, c = 83.5 Å, β = 109.1°. Corresponding values for form II crystals were a = 161.2 Å, b = 71.6 Å, c = 82.2 Å, β = 109.3°. In both cases most probably there are two monomers per asymmetric unit. The crystals diffract to about 2 Å resolution and are rather stable in the X-ray beam. © 1994 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190310
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    Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 277-290 
    Details
    ISSN: 0887-3585
    Keywords: simulated annealing ; molecular dynamics ; torsion angle dynamics ; conformational sampling ; X-ray crystallography ; refinement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A reduced variable conformational sampling strategy for macromolecules based on molecular dynamics in torsion angle space is evaluated using crystallographic refinement as a prototypical search problem. Bae and Haug's algorithm for constrained dynamics [Bae, D. S., Haug, E. J. A recursive formulation for constrained mechanical system dynamics. Mech. Struct. Mach. 15:359-382, 1987], originally developed for robotics, was used. Their formulation solves the equations of motion exactly for arbitrary holonomic constraints, and hence differs from commonly used approximation algorithms. It uses gradients calculated in Cartesian coordinates, and thus also differs from internal coordinate formulations. Molecular dynamics can be carried out at significantly higher temperatures due to the elimination of the high frequency bond and angle vibrations. The sampling strategy presented here combines high temperature torsion angle dynamics with repeated trajectories using different initial velocities. The best solutions can be identified by the free R value, or the R value if experimental phase information is appropriately included in the refinement. Applications to crystallographic refinement show a significantly increased radius of convergence over conventional techniques. For a test system with diffraction data to 2 Å resolution, slow-cooling protocols fail to converge if the backbone atom root mean square (rms) coordinate deviation from the crystal structure is greater than 1.25 Å, but torsion angle refinement can correct backbone atom rms coordinate deviations up to approximately 1.7 Å. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190403
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    Helix-capping interaction in λ cro protein: A free energy simulation analysis (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 310-323 
    Details
    ISSN: 0887-3585
    Keywords: protein stability ; free energy simulations ; molecular dynamics calculations ; helix-capping interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The stability mutant Tyr-26 → Asp was studied in the Cro protein from bacteriophage λ using free energy molecular dynamics simulations. The mutant was calculated to be more stable than the wild type by 3.0 ± 1.7 kcal/mol/monomer, in reasonable agreement with experiment (1.4 kcal/mol/monomer). Moreover, the aspartic acid in the mutant was found to form a capping interation with the amino terminus of the third α-helix of Cro. The simulations were analyzed to understand better the source of the stability of this helix-capping interaction and to examine the results in light of previous explanations of stabilizing helix caps-namely, a model of local unsatisfied hydrogen bonds at the helix termini and the helix macro dipole model. Analysis of the simulations shows that the stabilizing effect of this charged helical cap is due both to favorable hydrogen bonds with backbone NH groups at the helix terminus and to favorable electrostatic interactions (but not hydrogen bonds) with their carbonyls (effectively the next row of local dipoles in the helix). However, electrostatic interactions are weak or negligible with backbone dipolar groups in the helix further away from the terminus. Moreover, the importance of other local electrostatic interactions with polar side chains near the helix terminus, which are neglected in most treatments of this effect, are shown to be important. Thus, the results support a model that is intermediate between the two previous explanations: both unsatisfied hydrogen bonds at the helix terminus and other, local preoriented dipolar groups stabilize the helix cap. These findings suggest that similar interactions with preoriented dipolar groups may be important for cooperativity in other charge-dipole interactions and may be employed to advantage for molecular design. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190406
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    Multiple copy sampling: Rigid versus flexible protein (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 324-329 
    Details
    ISSN: 0887-3585
    Keywords: multiple copy conformational sampling ; protein flexibility ; sampling convergence ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Effects of protein flexibility on multiple copy conformational sampling were systematically evaluated by studying the side-chain placement of Phe-14 in protein Zif268. The multiple copy sampling is shown to be significantly more efficient when a flexible but harmonically constrained protein is used instead of a rigid protein. A range of constraint force from 1 to 25 kcal/mol. Å per atom is determined to be sufficient to prevent the protein from distortion while allowing the protein to fluctuate for enhanced sampling. The protein fluctuations are essential in smoothing the effective energy surface as shown by the opening-closing of a protein hydrophobic pocket during a multiple copy energy minimization, a phenomenon that has been previously observed only in molecular dynamics. These results provide a practical guidance for applying the multiple copy techniques to molecular modeling and computer-aided drug design. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190407
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    Protein stability parameters measured by hydrogen exchange (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994), S. 4-14 
    Details
    ISSN: 0887-3585
    Keywords: thermodynamic parameters ; cytochrome c ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The hydrogen exchange (HX) rates of the slowest peptide group NH hydrogens in oxidized cytochrome c (equine) are controlled by the transient global unfolding equilibrium. These rates can be measured by one-dimensional nuclear magnetic resonance and used to determine the thermodynamic parameters of global unfolding at mild solution conditions well below the melting transition. The free energy for global unfolding measured by hydrogen exchange can differ from values found by standard denaturation methods, most notably due to the slow cis-trans isomerization of the prolyl peptide bond. This difference can be quantitatively calculated from basic principles. Even with these corrections, HX experiments at low denaturant concentration measure a free energy of protein stability that rises above the usual linear extrapolation from denaturation data, as predicted by the denaturant binding model of Tanford. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340200103
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    Protein folding: Predicting predicting (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 1-3 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; protein conformation ; Paracelsus award ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190102
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    Structure of trichosanthin at 1.88 Å resolution (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 4-13 
    Details
    ISSN: 0887-3585
    Keywords: trichosanthin ; ribosome-inactivating proteins ; crystal structure ; orthorhombic ; molecular replacement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Trichosanthin (TCS) is one of the single chain ribosome-inactivating proteins (RIPs). The crystals of the orthorhombic form of trichosanthin have been obtained from a citrate buffer (pH 5.4) with KC1 as the precipitant. The crystal belongs to the space group P212121 with a = 38.31, b = 76.22, c = 79.21 Å. The structure was solved by molecular replacement method and refined using the programs XPLOR and PROLSQ to an R-factor of 0.191 for the reflections within the 6-1.88 Å resolution range. The bond length and bond angle in the protein molecule have root-mean-square deviations from ideal value of 0.013 Å and 3.3°, respectively. The refined model includes 247 residues and 197 water molecules. The TCS molecule consists of two structural domains. The large domain contains six α-helices, a six stranded sheet, and an antiparallel β-sheet. The small domain has a largest α-helix, which shows a distinct bend. The possible active site of the molecule located on the cleft between two domains was proposed. In the active site Arg-163 and Glu-160, Glu-189 and Arg-122 form two ion pairs, Glu-189 and Gln-156 are hydrogen bonded to each other. Three water molecules are bonded to the residues in the active site region. The structures of TCS molecule and ricin A-chain (RTA) superimpose quite well, showing that the structures of the two protein molecules are homologous. Comparison of the structures of the TCS molecule in this orthorhombic crystal with that in the monoclinic crystal indicates that there are no essential differences of the structures between the two protein crystals. © 1994 Wiley-Liss, Inc.
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    Monte carlo simulations of protein folding. I. Lattice model and interaction scheme (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 338-352 
    Details
    ISSN: 0887-3585
    Keywords: tertiary structure prediction ; reduced protein model ; lattice protein models ; dynamic Monte Carlo simulations ; potentials of mean force ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new hierarchical method for the simulation of the protein folding process and the de novo prediction of protein three-dimensional structure is proposed. The reduced representation of the protein α-carbon backbone employs lattice discretizations of increasing geometrical resolution and a single ball representation of side chain rotamers. In particular, coarser and finer lattice backbone descriptions are used. The coarser (finer) lattice represents Cα traces of native proteins with an accuracy of 1.0 (0.7) Å rms. Folding is simulated by means of very fast Monte Carlo lattice dynamics. The potential of mean force, predominantly of statistical origin, contains several novel terms that facilitate the cooperative assembly of secondary structure elements and the cooperative packing of the side chains. Particular contributions to the interaction scheme are discussed in detail. In the accompanying paper (Kolinski, A., Skolnick, J. Monte Carlo simulation of protein folding. II. Application to protein A, ROP, and crambin. Proteins 18:353-366, 1994), the method is applied to three small globular proteins. © 1994 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340180405
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    Investigation of the functional interplay between the primary site and the subsite of RNase T1: Kinetic analysis of single and multiple mutants for modified substrates (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 318-323 
    Details
    ISSN: 0887-3585
    Keywords: ribonuclease T1 ; functional cooperativity ; double mutant cycle ; subsite ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We report on the functional cooperativity of the primary site and the sub-site of ribonuclease T1 (RNase T1; EC 3.1.27.3). The kinetic properties of the single Tyr-38-Phe and Asn-98-Ala mutants have been compared with those of the corresponding double mutant. The Tyr-38-Phe mutation has been used to probe enzyme-substrate interactions at the primary site; the Asn-98-Ala mutation monitors subsite interactions.1 In addition to the dinucleoside phosphate substrate GpC, we measured the kinetics for GpMe, a synthetic substrate in which the leaving nucleoside cytosine has been replaced by methanol. All data were combined in a triple mutant box to analyze the interplay between Tyr-38, Asn-98, and the leaving group. The free energy barriers to kcat, introduced by the single Tyr-38-Phe and Asn-98-Ala mutations are not additive in the corresponding double mutant. The energetic coupling between both mutations is independent of the binding of the leaving cytosine at the subsite. We conclude that the coupling of the Tyr-38-Phe and Asn-98-Ala mutations arises through distortion or reorientation of the 3′-guanylic acid moiety bound at the primary site. The experimental data indicate that the enzyme-substrate interactions beyond the scissile phosphodiester bond contribute to catalysis through the formation of new or improved contacts in going from ground state to transition state, which are functionally independent of primary site interactions. © 1994 John Wiley & Sons, Inc.
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    Recognition of distantly related proteins through energy calculations (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 132-140 
    Details
    ISSN: 0887-3585
    Keywords: distant protein folds ; sequence homology ; database searching ; profile analysis ; protein structure comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new method to detect remote relationships between protein sequences and known three-dimensional structures based on direct energy calculations and without reliance on statistics has been developed. The likelihood of a residue to occupy a given position on the structural template was represented by an estimate of the stabilization free energy made after explicit prediction of the substituted side chain conformation. The profile matrix derived from these energy values and modified by increasing the residue self-exchange values successfully predicted compatibility of heatshock protein and globin sequences with the three-dimensional structures of actin and phycocyanin, respectively, from a full protein sequence databank search. The high sensitivity of the method makes it a unique tool for predicting the three-dimensional fold for the rapidly growing number of protein sequences. © 1994 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.340190206
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    Characterization of two crystal forms of Clostridium thermocellum endoglucanase CelC (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 158-160 
    Details
    ISSN: 0887-3585
    Keywords: crystallization ; cellulases ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Endoglucanase CelC from Clostridium thermocellum expressed in Escherichia coli has been crystallized in two different crystal forms by the hanging drop method. Crystals of form I were grown with polyethylene glycol as a precipitant. They are orthorhombic, space group P212121, with cell dimensions a =51.4 Å, b =84.3 Å, and c =87.5 Å. Crystals of form II, obtained in ammonium sulfate solutions, belong to the tetragonal space group P41212 (or P43212) with cell dimensions of a = b = 130.7 Å and c = 69.6 Å. Diffraction data to 2.8 Å resolution were observed for both crystal forms with a rotating anode generator. Preliminary oscillation images of the orthorhombic form I crystals using a synchrotron radiation source show diffraction to 2.2 Å resolution, indicating that these crystals are suitable for high resolution crystallographic analysis. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190209
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  • 91
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190301
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  • 92
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    Searching protein structure databases has come of age (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 165-173 
    Details
    ISSN: 0887-3585
    Keywords: algoriths ; structure alignment ; Protein Data Bank ; protein superfamilies ; structural homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The number of protein structures known in atomic detail has increased from one in 1960 (Kendrew, J. C., Strandberg, B. E., Hart, R. G., Davies, D. R., Phillips, D. C., Shore, V. C. Nature (London) 185:422-427, 1960) to more than 1000 in 1994. The rate at which new structures are being published exceeds one a day as a result of recent advances in protein engineering, crystallography, and spectroscopy. More and more frequently, a newly determined structure is similar in fold to a known one, even when no sequence similarity is detectable. A new generation of computer algorithms has now been developed that allows routine comparison of a protein structure with the database of all known structures. Such structure database searches are already used daily and they are beginning to rival sequence database searches as a tool for discovering biologically interesting relationships. © 1994 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190302
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  • 93
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    The closed conformation of a highly flexible protein: The structure of E. coli adenylate kinase with bound AMP and AMPPNPThe structure is listed as 1ANK in the Brookhaven Protein Data Bank. (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 183-198 
    Details
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; Rfree ; ATP and AMP binding sites ; Mg2+ coordination ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of E. coli adenylate kinase with bound AMP and AMPPNP at 2.0 Å resolution is presented. The protein crystallizes in space group C2 with two molecules in the asymmetric unit, and has been refined to an R factor of 20.1% and an Rfree of 31.6%. In the present structure, the protein is in the closed (globular) form with the large flexible lid domain covering the AMPPNP molecule. Within the protein, AMP and AMPPNP, an ATP analog, occupy the AMP and ATP sites respectively, which had been suggested by the most recent crystal structure of E. coli adenylate kinase with AP5A bound (Müller and Schulz, 1992, ref. 1) and prior fluorescence studies (Liang et al., 1991, ref. 2). The binding of substrates and the positions of the active site residues are compared between the present structure and the E. coli adenylate kinase/Ap5A structure. We failed to detect a peak in the density map corresponding to the Mg2+ ion which is required for catalysis, and its absence has been attributed to the use of ammonium sulfate in the crystallization solution. Finally, a comparison is made between the present structure and the structure of the heavy chain of muscle myosin. © 1994 Wiley-Liss, Inc.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190304
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  • 94
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    HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 199-221 
    Details
    ISSN: 0887-3585
    Keywords: multicopy simulation search ; rational drug design ; database search ; computer-aided design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A program (HOOK) is described for generating potential ligands that satisfy the chemical and steric requirements of the binding region of a macromolecule. Functional group sites with defined positions and orientations are derived from known ligand structures or the multicopy simulation search (MCSS) method (Miranker, A., Karplus, M. Proteins 11:29-34, 1991). HOOK places molecular “skeletons” from a database into the protein binding region by making bonds between sites (“hooks”) on the skeleton and functional groups. The nonpolar interactions with the binding region of candidate molecules are assessed by use of a simplified van der Waals potential. The method is illustrated by constructing ligands for the sialic acid binding site of the hemagglutinin from the influenza A virus and the active site of chloramphenicol acetyltransferase. Aspects of the HOOK program that lead to a highly efficient search of 105 or more skeletons for binding to 102 or more functional group minima are outlined. © 1994 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190305
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  • 95
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    Structural modeling and electrostatic properties of aspartate transcarbamylase from Saccharomyces cerevisiae (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 230-243 
    Details
    ISSN: 0887-3585
    Keywords: aspartate transcarbamylase ; multienzyme complex ; comparative structure modeling ; allosteric enzymes ; molecular evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In Saccharomyces cerevisiae the first two reactions of the pyrimidine pathway are catalyzed by a multifunctional protein which possesses carbamylphosphate synthetase and aspartate transcarbamylase activities. Genetic and proteolysis studies suggested that the ATCase activity is carried out by an independently folded domain. In order to provide structural information for ongoing mutagenesis studies, a model of the three-dimensional structure of this domain was generated on the basis of the known X-ray structure of the related catalytic subunit from E. coli ATCase. First, a model of the catalytic monomer was built and refined by energy minimization. In this structure, the conserved residues between the two proteins were found to constitute the hydrophobic core whereas almost all the mutated residues are located at the surface. Then, a trimeric structure was generated in order to build the active site as it lies at the interface between adjacent chains in the E. coli catalytic trimer. After docking a bisubstrate analog into the active site, the whole structure was energy minimized to regularize the interactions at the contact areas between subunits. The resulting model is very similar to that obtained for the E. coli catalytic trimer by X-ray crystallography, with a remarkable conservation of the structure of the active site and its vicinity. Most of the interdomain and intersubunit interactions that are essential for the stability of the E. coli catalytic trimer are maintained in the yeast enzyme even though there is only 42% identity between the two sequences. Free energy calculations indicate that the trimeric assembly is more stable than the monomeric form. Moreover an insertion of four amino acids is localized in a loop which, in E. coli ATCase, is at the surface of the protein. This insertion exposes hydrophobic residues to the solvent. Interestingly, such an insertion is present in all the eukaryotic ATCase genes sequenced so far, suggesting that this region is interacting with another domain of the multifunctional protein. © 1994 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190307
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  • 96
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190401
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  • 97
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    Where is NMR taking us?This article is a US Government work and, as such, is in the public domain in the United States of America. (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 273-276 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340190402
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  • 98
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    Molecular basis of cooperativity in protein folding. V. Thermodynamic and structural conditions for the stabilization of compact denatured states (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 19 (1994), S. 291-301 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; cooperativity ; folding intermediates ; protein thermodynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The heat-denatured state of proteins has been usually assumed to be a fully hydrated random coil. It is now evident that under certain solvent conditions or after chemical or genetic modifications, the protein molecule may exhibit a hydrophobic core and residual secondary structure after thermal denaturation. This state of the protein has been called the “compact denatured” or “molten globule” state. Recently is has been shown that α-lactalbumin at pH 〈 5 denatures into a molten globule state upon increasing the temperature (Griko, Y., Freire, E., Privalov, P. L. Biochemistry 33:1889-1899, 1994). This state has a lower heat capacity and a higher enthalpy at low temperatures than the unfolded state. At those temperatures the stabilization of the molten globule state is of an entropic origin since the enthalpy contributes unfavorably to the Gibbs free energy. Since the molten globule is more structured than the unfolded state and, therefore, is expected to have a lower configurational entropy, the net entropic gain must originate primarily from solvent related entropy arising from the hydrophobic effect, and to a lesser extent from protonation or electrostatic effects. In this work, we have examined a large ensemble of partly folded states derived from the native structure of α-lactalbumin in order to identify those states that satisfy the energetic criteria of the molten globule. It was found that only few states satisfied the experimental constraints and that, furthermore, those states were part of the same structural family. In particular, the regions corresponding to the A, B, and C helices were found to be folded, while the β sheet and the D helix were found to be unfolded. At temperatures below 45°C the states exhibiting those structural characteristics are enthalpically higher than the unfolded state in agreement with the experimental data. Interestingly, those states have a heat capacity close to that observed for the acid pH compact denatured state of α-lactalbumin [980 cal (mol.K)-l]. In addition, the folded regions of these states include those residues found to be highly protected by NMR hydrogen exchange experiments. This work represents an initial attempt to model the structural origin of the thermodynamic properties of partly folded states. The results suggest a number of structural features that are consistent with experimental data. © 1994 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340190404
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  • 99
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 20 (1994) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340200101
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  • 100
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180101
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