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  • 2005-2009
  • 2000-2004  (29)
  • 1985-1989  (3,620)
  • Biochemistry and Biotechnology  (3,097)
  • Genetics  (552)
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  • 1
    ISSN: 1432-198X
    Keywords: Key words Glomerulocystic kidney disease ; Oligohydramnion ; Renal failure-neonate ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Two newborns with glomerulocystic kidney disease manifesting as late onset oligohydramnion and neonatal anuria, yet without severe respiratory distress, are presented. They had a similar perinatal course and associated clinical manifestations. No associated congenital or inherited malformation syndrome could be defined. Both infants’ parents were first degree cousins and belonged to the same small Bedouin tribe, and neither they nor the infants’ siblings had polycystic kidneys or renal insufficiency, pointing to either a possible genetic etiology or a common external toxic exposure.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Intensive care medicine 26 (2000), S. S057 
    ISSN: 1432-1238
    Keywords: Key words Critical illness ; Intensive care ; Severity of illness ; Scoring systems ; Genetics ; Susceptibility ; Education
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Risk of critical illness is determined both by genetic and environmental influences, particularly those relating to infectious and cardiovascular diseases. Physiologically-based scoring systems cannot measure prior risk because they do not quantify physiological reserve independently of the acute illness. Genetic profiling could be useful for risk assessment. Early detection of critical illness involves identifying physiological ’triggers' for referral; this requires the education of nursing and medical staff in their significance. Analysis of the relationship between risk factors and interventions may need complex modelling techniques. Therapeutic strategies depend on the nature of the underlying problem: the most useful are likely to be those which enhance tissue oxygen delivery and resistance to infection.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    European journal of pediatrics 159 (2000), S. S35 
    ISSN: 1432-1076
    Keywords: Key words Obesity ; Genetics ; Child ; Nutrient balance ; Energy balance ; Environment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The epidemic diffusion of obesity in industrialised countries has promoted research on the aetiopathogenesis of this disorder. The purpose of this review is to focus mainly on the contribution that European research has made to this field. Available evidence suggests that obesity results from multiple interactions between genes and environment. Parents obesity is the most important risk factor for childhood obesity. Twin, adoption, and family studies indicated that inheritance is able to account for 25% to 40% of inter-individual difference in adiposity. Single gene defects leading to obesity have been discovered in animals and, in some cases, confirmed in humans as congenital leptin deficiency or congenital leptin receptor deficiency. However, in most cases, genes involved in weight gain do not directly cause obesity but they increase the susceptibility to fat gain in subjects exposed to a specific environment. Both genetic and environmental factors promote a positive energy balance which cause obesity. The relative inefficiency of self-adapting energy intake to energy requirements is responsible for fat gain in predisposed individuals. The role of the environment in the development of obesity is suggested by the rapid increase of the prevalence of obesity accompanying the rapid changes in the lifestyle of the population in the second half of this century. Early experiences with food, feeding practices and family food choices affect children's nutritional habits. In particular, the parents are responsible for food availability and accessibility in the home and they affect food preferences of their children. Diet composition, in particular fat intake, influences the development of obesity. The high energy density and palatability of fatty foods as well as their less satiating properties promotes food consumption. TV viewing, an inactivity and food intake promoter, was identified as a relevant risk factor for obesity in children. Sedentarity, i.e. a low physical activity level, is accompanied by a low fat oxidation rate in muscle and a low fat oxidation rate is a risk factor of fat gain or fat re-gain after weight loss. Conclusion Further research is needed to identify new risk factors of childhood obesity, both in the genetic and environmental areas, which may help to develop more effective strategies for the prevention and treatment of obesity.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    European journal of pediatrics 159 (2000), S. S183 
    ISSN: 1432-1076
    Keywords: Key words Database ; Genetics ; Information services ; Internet ; Mutation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Thanks to the World Wide Web, most results of research in genetics are made available in public databases. At the present time there are resources on genetic diseases, genes and their location, mutations of already cloned genes and on laboratories performing the mutation analysis. The main resources on phenotypes are On-line Mendelian Inheritance in Man (OMIM), Pedbase, GeneClinics, London Dysmorphology Database (LDDB) and Orphanet. The main resources on human genes are, in addition to OMIM, the Genome Database, Genatlas and Genecard. There are also two major sequence databases. All of them can be queried using the OMIM number of the disease. Central databases of mutations, as well as locus specific databases have been created. Their list is maintained at the Human Genome Organisation mutation database initiative website. Several initiative have been taken to integrate all these data and help the clinician to find out quickly what he/she needs. The website of the National Center for Biotechnology Information is the best example of such an effort with sections on diseases, a genome guide, and locus links. Several databases of genetic testing resources have been established. GeneTests is an on-line genetics resource that contains a directory of North American laboratories providing testing for heritable disorders. Orphanet is a similar database on French services which is in the process of becoming a European database. Conclusion Even if clinicians do not have as many services at their disposal as the molecular geneticists, various useful databases already exist and should no longer be ignored in practice.
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    European journal of pediatrics 159 (2000), S. S208 
    ISSN: 1432-1076
    Keywords: Key words Cardiovascular disease ; Cystathionine β-synthase ; Genetics ; Methylenetetrahydrofolate reductase ; Mild hyperhomocysteinaemia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Over the last decade mild hyperhomocysteinaemia has widely been recognised as a new risk factor for arteriosclerosis and thrombosis. Main regulating enzymes of homocysteine (Hcy) metabolism are cystathionine β-synthase (CBS), methionine synthase and methylenetetrahydrofolate reductase (MTHFR). Early studies on patients with vascular disease described elevated Hcy concentrations after methionine loading and decreased CBS activity, resembling heterozygotes for CBS deficiency. Therefore, heterozygosity for CBS deficiency was proposed as the main cause of mild hyperhomocysteinaemia. However, more recent enzymatic and molecular genetic studies have demonstrated that heterozygosity for CBS deficiency is not or only a very minor cause of mild hyperhomocysteinaemia in vascular disease. We discovered two common genetic causes of mild hyperhomocysteinaemia, the 677C 〉 T and the 1298A 〉 C mutations in the coding region of MTHFR. The 677C 〉 T mutation causes reduced enzyme activity with thermolabile protein properties, elevated Hcy and low-normal or decreased plasma folate levels. The 1298A 〉 C mutation relates also to decreased enzyme activity, but not to thermolabile protein, and Hcy and folate levels are not influenced. However, compound heterozygosity for these two mutations, i.e. individuals with the 677CT/1298AC genotype, have elevated Hcy and decreased plasma folate levels. Gene-enviroment interactions between 677C 〉 T and folate is demonstrated in individuals with the 677TT genotype. Those with low-normal folate have elevated Hcy, whereas those with high-normal folate have normal Hcy concentrations. The elevated Hcy levels due to these mutations can be normalised by administration of folate, but whether folate reduces the risk of cardiovascular disease remains to be established. Conclusion Heterozygosity for cystathionine β-synthase deficiency is a minor cause of hyperhomocysteinaemia. The current data on mutations in the methylenetetrahydrofolate reductase gene do not tell us whether elevated plasma homocysteine plays a causal role in vascular disease. Low cellular vitamin status may be a possible cause and homocysteine may just be a marker for this situation.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1364-6753
    Keywords: Key words Parkinson's disease ; Familial Parkinson's disease ; Synuclein ; Parkin ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: ABSTRACT¶Parkinson's disease (PD) is a neurodegenerative disease with clinical features resulting from deficiency of dopamine in the nigrostriatal system. Most PD cases are sporadic and the primary cause of the disease is still unknown. Recently, familial PD and parkinsonism have received much attention because these forms of the disease might provide clues to the genetic risk factors involved in the pathogenesis of idiopathic PD. To date, two causative genes, α-synuclein and the parkin gene, have been identified. α-Synuclein is involved in the pathogenesis of an autosomal dominant form of PD and constitutes a major component of the Lewy body, which is a pathological hallmark of idiopathic PD. In addition, mutations in the parkin gene have been identified as the cause of autosomal recessive juvenile parkinsonism (AR-JP). AR-JP manifests itself as a highly selective degeneration of the substantia nigra and the locus coeruleus, but without Lewy body formation. In addition to these two genes, four chromosomal loci have been linked to other forms of familial PD. Furthermore, there are a number of other pedigrees of familial PD in which linkage to known genetic loci has been excluded. Molecular cloning of these disease genes and elucidation of the function of their gene products will greatly contribute to our understanding of the pathogenesis of idiopathic PD.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    The journal of headache and pain 1 (2000), S. S147 
    ISSN: 1129-2377
    Keywords: Key words Dopamine ; Migraine ; Genetics ; DRD2
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Molecular genetics offers a novel approach to the understanding and management of migraine since the disorder is known to have a strong genetic component. In recent studies, polymorphisms in the genes for dopamine receptors have been evaluated. Both positive and negative association studies have been reported. In particular, these data suggest that activation of the DRD2 receptor plays a modifying role in the pathophysiology of migraine. As a result, existing data provide a molecular rationale for the documented efficacy of dopamine D2 receptor antagonists in the treatment of migraine. Therefore, at the present time, molecular genetic data provide support for the hypothesis that susceptibility to migraine may be modified, in part, by variations in dopamine DRD2 receptor function.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    The journal of headache and pain 1 (2000), S. S157 
    ISSN: 1129-2377
    Keywords: Key words Migraine ; Chronic tension type headache ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Pathophysiological studies have dominated migraine research for several years. However, these studies are difficult to interpret because it is difficult to decide whether the observed phenomena are primary or secondary to the migraine attack. For that reason it is important that future migraine research focus on studies that concern migrain etiology. Migraine is a paroxysmal disorder. It is most likely and ion-channel disorder like familial hemiplegic migraine. The present paper focuses on genetic factors in migraine and chronic tension-type headache.
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  • 9
    ISSN: 1129-2377
    Keywords: Key words Cluster headache ; Familial occurrence ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract A Danish genetic study showed increased risk of cluster headache (CH) among relatives of CH patients. We studied the families of 191 CH patients (118 males, 73 females; mean age 45.9 years) attending the Milan Headache Center. Information on 3589 relatives was collected by direct interview of the probands (n = 118) or by mailed questionnaire (n = 73). The diagnostic criteria of the IHS were used. A positive family history was found in 19% (37 of 191) of the families. A total of 32 first-degree (32 of 1036, 3.1%) and 15 second-degree (15 of 2553, 0.6%) relatives were affected. The relative risk of CH was 26.89 (95% CI, 17.57–36.21) in the first-degree relatives and 4.35 (95% CI, 2.13–5.21) in second-degree relatives. This study shows increased familial risk of cluster headache in an Italian population and confirms that cluster headache is, in some families, and inherited disorder.
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    The journal of headache and pain 1 (2000), S. S135 
    ISSN: 1129-2377
    Keywords: Key words Migraine ; Headache ; Genetics ; Serotonin ; Dopamine ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Migraine carries a significant hereditary determination. Familial hemiplegic migraine (FHM) has been recently linked to mutations in the CACNA1A gene on chromosome 19. CACNA1A codes for a subunit of a neural calcium channel. Other linkage loci on chromosome 1q21-23 and 1q31 have been reported. Several linkage and association studies have been performed to determine the role of the CACNA1A gene, and of other candidate genes implicated in the metabolism of serotonin and dopamine, in the more common types of migraine. Co-morbidity of migraine with vascular events has been analysed versus genetic prothrombotic factors and mitochondrial DNA, and genes involved in the inflammatory cascade have been explored. Though no definite conclusions have emerged from these studies as yet, molecular genetics of migraine can be expected to unravel the complex aetiologies of these fascinating diseases.
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  • 11
    Electronic Resource
    Electronic Resource
    Springer
    The journal of headache and pain 1 (2000), S. S153 
    ISSN: 1129-2377
    Keywords: Key words Migraine ; Genetics ; Dopamine ; Hypersensitivity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Migraine is a common chronic disorder with an etiology still mostly unknown. Several neurotransmitters such as dopamine and serotonin are considered to be involved in the pathogenesis of the disease and the study of their systems is crucial in the understanding of migraine. Dopaminergic receptors are variously represented in human CNS and periphery. The hypothesis that a hypersensitivity of the dopaminergic system may have a role in migraine is based on clinical and genetic data. Genetic data are represented by association studies using dopaminergic genes as candidate genes which show that the D2 receptor gene appears to be involved in the pathogenesis of migraine.
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  • 12
    Electronic Resource
    Electronic Resource
    Springer
    The journal of headache and pain 1 (2000), S. S141 
    ISSN: 1129-2377
    Keywords: Key words Migraine ; Genetics ; Human leukocyte antigens ; Heredity ; Susceptibility
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Human leukocyte Antigens (HLA) are encoded by genes located on chromosome 6p21. Genes important in migraine are being recognized in two basic ways: association studies and linkage analysis. One of the strongest associations is with the HLA region. Actually, genome scan studies suggest that multiple genes are involved in both migraine without aura (MWoA) and migraine with aura (MWA). However, both MWoA and MWA are disorders in which multiple factors, including environmental and genetic factors, confer disease susceptibility. Linkage analysis is identifying new candidate genes that will help to explain the etiology of migraine. In this review previous studies regarding genetic susceptibility to migraine are analyzed, particularly those related to the HLA region. I discuss evidence that HLA shared-hyplotypes in MWoA-affected pairs in different than that expected, that HLA-DR2 antigen provides additional basis for the proposed genetic heterogeneity between MWoA and MWA, and lastly that TNFB gene studies seem to play an important role in the susceptibility to MWoA. In the past years, major advances hae been made in understanding the genetic foundation of MWoA and MWA. Our reported genome-scan studies support the concept that MWoA/MWA are coinherited with a particular HLA region. However, the examination of candidate genes (Ca2+ channel, vascular, CNS, etc.) in a large migraine population seems to be the correct direction in which we have to move. More MWoA/MWa gene studies are needed to test this developing hypothesis and to further establish the complete genetic scenario of migraine.
    Type of Medium: Electronic Resource
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  • 13
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 100 (2000), S. 401-408 
    ISSN: 1432-2242
    Keywords: Key words Complementary genes ; Extreme virus resistance ; Genetics ; Necrotic tubers ; Restricted virus distribution ; Solanum tuberosum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The potato cultivar ’Shepody’ is susceptible to a number of potato viruses including potato virus Y (PVY, potyvirus) but was found to possess extreme resistance to another potyvirus, potato virus A (PVA). ’Shepody’ plants were resistant to PVA infection in manual and graft inoculations. PVA replication was not detected in any of the inoculated plants by ELISA, an infectivity assay and RT-PCR. However, ’Shepody’ plants grafted with shoots containing PVA developed a novel symptomology which resembled a virus infection in appearance and in rate of translocation to the entire plant. Efforts to transmit the symptom-inducing agent manually failed. Graft-inoculation to potato virus indicator plants and PVA-susceptible potato plants showed that the symptom inducer was PVA at an extremely low concentration, detected using RT-PCR followed by Southern blot assay. Tubers from grafted but resistant ’Shepody’ plants had necrotic surfaces and internal spots. PVA was detected from necrotic areas but not from the non-necrotic ones. However, plants resulting from necrotic tubers were free from aerial leaf symptoms observed in grafted plants and produced non-necrotic normal tubers. A trace-back of the parental lineage of ’Shepody’ indicated that the resistance had been introgressed from the cultivar ’Bake King’. Analysis of progeny of a cross of resistant ’Shepody’ to the susceptible ’Goldrus’ indicated that this resistance is controlled by two independent dominant complementary genes in contrast to monogenic resistance reported for other potato viruses.
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  • 14
    ISSN: 1432-2242
    Keywords: Key words Avicennia marina ; Microsatellite ; Mangrove ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  An enriched microsatellite library of the mangrove species Avicennia marina was constructed, in which 85.8% of the clones contained microsatellite sequences. Of the microsatellite repeat sequences isolated, 55.0% were di-nucleotides, 34.2% were tri-nucleotides, 50.0% were perfect, 24.2% were imperfect, and 15.0% were compound. Four different di-nucleotide repeats were isolated with repeat lengths ranging from 5 to 33; ten different tri-nucleotide repeats were isolated with repeat lengths ranging from 3 to 25. The most common di-nucleotide was the AC/TG repeat; the most common tri-nucleotide was the CCG/GGC repeat. Sixteen microsatellite sequences were selected for primer design, and 6 primers were selected to investigate the polymorphism detected among 15 individuals of A. marina from three natural populations in Australia. A total of 40 alleles were detected at 6 microsatellite loci. The number of alleles per microsatellite locus ranged from 5 to 13. On average, 7 alleles were detected per locus. All microsatellite loci showed high levels of gene diversity (heterozygosity), with values ranging from 0.53 to 0.88; the mean value of gene diversity was 0.70. Microsatellite loci were also tested for conservation across Avicennia species. There was a decline in amplification success with increasing divergence between Avicennia species. The results indicate that microsatellites are abundant in the Avicennia genome and can be valuable genetic markers for assessing the effects of deforestation and forest fragmentation in mangrove communities, which is an important issue for mangrove conservation and afforestation schemes.
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  • 15
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 101 (2000), S. 234-240 
    ISSN: 1432-2242
    Keywords: Key words Cherry ; Genetics ; Compatibility ; Incompatibility ; Isoelectric focusing ; Prunus avium ; Ribonuclease
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The (in)compatibility genotypes of two self-compatible sweet cherry selections, JI 2420 and JI 2434, originating from the John Innes Institute were re-examined. The selections and seedlings derived from them were analysed for stylar ribonucleases, which are known to correlate with S alleles, and the outcome of test crosses was recorded. JI 2420, which had been reported previously as S 3 S 4 ", where " indicates loss of pollen activity, was deduced to have the genotype S 4 S 4 ’. For JI 2434, which had been reported previously as S 3 S 4 0 , S 3 S 3 0 or S 3 S 3 ", where 0 indicates loss of pollen and stylar activity, two different clones were identified. One, at East Malling, was deduced to be S 3 "S 4 ; the other, at Ahrensburg, appeared to be S 3 S 3 " or S 3 S 3 0 .
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  • 16
    ISSN: 1432-1211
    Keywords: Key words Skin ; Genetics ; TNFA ; ¶Inflammation ; PCR-RFLP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Mechanisms underlying susceptibility to skin irritants are not clearly understood. Cytokines play a key role in inflammation, and functional polymorphisms in cytokine genes may affect responses to irritants. We investigated the relationship between polymorphism in the tumor necrosis factor (TNF) α-chain gene and responses to irritants. Volunteers (n=221) tested with sodium dodecyl sulfate (SDS) and benzalkonium chloride (BKC) were divided into responders and nonresponders and high and low irritant-threshold groups. DNA was assayed for the TNF-308 polymorphism by a polymerase chain reaction-restriction fragment length polymorphism method. There was a significant increase in the A allele (P=0.030) and AA genotype (P=0.023) in both the SDS low irritant-threshold group and in SDS responders (A allele P=0.022, AA genotype P=0.048). In the BKC low irritant-threshold group, we found a significant increase in the A allele (P=0.002) and AA genotype (P=0.016). Individuals with a low threshold to both irritants demonstrated a significant increase (P=0.002) in the A allele. This is the first description of a nonatopic genetic marker for irritant susceptibility in normal individuals. Genotyping for theTNF-308 polymorphism may thus contribute to screening of individuals deemed at risk of developing irritant contact dermatitis.
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  • 17
    ISSN: 1432-1459
    Keywords: Key words Progressive ¶supranuclear palsy ; Genetics ; Clinical characteristics ; Parkinsonism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Genetic studies have detected an association between the presence of the τ gene A0 allele and patients with progressive supranuclear palsy (PSP). This study examined whether patients with this polymorphism exhibit distinct demographic or clinical characteristics. We studied 26 patients who fulfilled clinical criteria for the diagnosis of PSP, 20 who had the A0/A0 genotype and 6 who had other genotypes. A questionnaire on demographic data, past medical history, familial history, and initial symptoms was completed as part of the consultation. A complete neurological examination was performed and PSP symptoms were quantified following Golbe’s PSP disability scale. We found a significant difference in the age at onset of PSP symptoms, which was 65.9 ± 5.3 years in the A0/A0 group and 71.2 ± 5.6 in the non-A0/A0 group (P = 0.016). There were no significant differences in the years from disease onset between the two groups. Symptom severity did not differ significantly in patients with the different A0/A0 genotypes. The detection of significantly lower age at onset with the A0/A0 alleles is consistent with the known association of this genotype as a risk factor for PSP. No significant differences were detected in symptom severity between the two groups of patients.
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  • 18
    ISSN: 1432-1459
    Keywords: Key words Amyotrophic lateral sclerosis ; Genetics ; Presenilin-1 intron 8 polymorphism ; Apoptosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The mechanisms underlying motor neuron degeneration in amyotrophic lateral sclerosis are not fully understood. Recent studies suggest that apoptosis is involved in the abnormal neural death that occurs in this devastating disease. Presenilin-1, a transmembrane protein, seems to be implicated in apoptosis. To determine whether presenilin-1 intron 8 polymorphism has an influence in the course of amyotrophic lateral sclerosis, we examined this polymorphism genotypes in a large group of patients (n=72) with amyotrophic lateral sclerosis and in a random sample of 213 healthy individuals. The results showed a significant difference in genotype (P 〈 0.04) and allele (P 〈 0.03) distribution between patients and controls. These results suggest a possible intervention of presenilin-1 in the pathogenesis of amyotrophic lateral sclerosis.
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  • 19
    ISSN: 1432-1459
    Keywords: Key words Parkinson’s disease ; Monoamine oxidase B ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Monoamine oxidase B (MAOB) metabolises dopamine and activates neurotoxins known to induce parkinsonism in humans and primates. Therefore the MAOB gene (MAOB; Xp15.21–4) is a candidate gene for Parkinson’s disease (PD). Longer length dinucleotide repeat sequences in a highly polymorphic GT repeat region of intron 2 of this gene showed an association with PD in an Australian cohort. We repeated this allele-association study in a population of 176 Chinese PD patients ¶(90 men, 86 women) and 203 age-matched controls (99 men, 104 women). Genomic DNA was extracted from venous blood and the polymerase chain reaction was used to amplify the appropriate regions of the MAOB gene. The length of each (GT) repeat sequence was determined by 5% polyacrylamide denaturing gel electrophoresis. There was no significant difference in allele frequencies of the (GT) repeat allelic variation between patients and controls (χ2 = 2.48; df = 5, P 〈 0.75). Therefore the longer length GT repeat alleles are not associated with PD in this Chinese population. Possible reasons for the discrepancy between Chinese and Australian populations include a different interaction between this genetic factor and environmental factors in the two populations and the possibility that the long length GT repeat alleles may represent a marker mutation, genetically linked to another susceptibility allele in whites but not in Chinese. Methodological differences in the ascertainment of cases and controls in this cohort could also explain the observed differences. Further study is required to determine whether the longer length GT repeat alleles are true susceptibility alleles in PD.
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  • 20
    ISSN: 1432-1459
    Keywords: Key words Multiple sclerosis ; Genetics ; ICAM-1 gene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract An increased amount of the intercellular adhesion molecule (ICAM) 1 molecule has been found in the blood of actively relapsing multiple sclerosis (MS) patients, but is unclear whether this enhanced expression is partially causative of the MS process, or whether it is merely an epiphenomenon of the inflammatory-immunological reaction. Using the transmission disequilibrium test (TDT), we studied exon 4 and exon 6 polymorphism of the ICAM-1 gene from 157 families with both parents, one affected and one healthy sib coming from Sardinia, an Italian island having a high incidence and prevalence of MS. TDT did not show variation in the expected 50:50 frequency in transmission in either healthy or affected sibs, using phenotypic or genotypic analysis. Moreover, independence from the predisposing HLA-DRB1-DQA1-DQB1 haplotype was confirmed by TDT analysis performed on the patients stratified according to the presence or absence of the HLA-DRB1, DQA1, DQB1 Sardinian predisposing haplotypes. Our data suggest that the increased expression of the ICAM-1 molecule observed in both blood and periplaque microvessels may be considered a consequence of the inflammatory process rather than the result of a genetic variation.
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  • 21
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    Electronic Resource
    Springer
    Journal of neurology 247 (2000), S. 81-87 
    ISSN: 1432-1459
    Keywords: Key words Dementia ; Vascular ¶dementia ; Alzheimer’s disease ; Risk factors, stroke ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract This review describes differing profiles of vascular risk factors in different types of dementia. Although vascular risk factors are related to various types of strokes, their independent effect on the occurrence of poststroke dementia appears to be small. Various risk factors have been identified for microangiopathy-related cerebral abnormalities, such as white matter changes and lacunae, which are the core lesions for the development of a vascular dementia syndrome without stroke symptoms. Most consistently, arterial hypertension and diabetes mellitus have been found to be associated with such brain abnormalities. Diastolic blood pressure seems to be of particular importance as recent investigations demonstrate that this factor is related to the course of multiple lacunar strokes and the progression of white matter disease. Epidemiological studies report that various vascular risk factors including arterial hypertension, diabetes mellitus, and atrial fibrillation may also be associated with Alzheimer’s disease. There is also evidence of a direct relationship between Alzheimer’s disease and general atherosclerosis. Further investigations are needed to determine whether these associations are due to the weakness of diagnostic criteria, or whether vascular risk factors indeed modulate the clinical expression of primary degenerative dementia. Common susceptibility genes leading to shared risk factors may be one of the reasons for a higher coincidence of Alzheimer’s disease and vascular dementia than can be expected by chance. A modulatory effect of vascular risk factors in the development of primary degenerative dementia may extend treatment options.
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  • 22
    ISSN: 1432-1459
    Keywords: Key words Multiple sclerosis ; Siblings ; Genetics ; Oligoclonal bands ; Measles
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We found that 19% (9/47) of healthy siblings of patients with clinically definite multiple sclerosis had an intrathecal immunological reaction with two or more 2 CSF-enriched oligoclonal bands (OCBs), in contrast to (4%) (2/50) unrelated healthy controls. Furthermore, in this group of nine healthy sibs the measles CSF IgG antibody titers were higher than that of the other sibs and that of controls. There were also differences in the serum titers for measles IgG antibody, which were higher in the group of all healthy sibs than in healthy volunteers, and (as with CSF titers) higher in the subgroup of healthy sibs with two or more 2 CSF-enriched OCBs than the other sibs. Thus a significant proportion of healthy siblings to MS patients have a partially hyperimmune condition similar to that occurring in MS, which in 19% manifested itself as an OCB reaction, in 9% as increased CSF measles IgG antibody titers, and in 21% as increased serum measles IgG antibody titers, these phenomena tending to occur in the same individuals. This condition is characterized by CSF-enriched OCBs with undefined specificity, although some increased antiviral reactivity is found both in the serum and CSF. While it needs further characterization, a genetic trait interacting with common infections is suggested. The recurrence risk of this condition is approximately five times higher than the 3–4% recurrence risk for manifest MS reported for sibs.
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  • 23
    ISSN: 1433-8491
    Keywords: Key words Dopamine receptor D4 ; Genetics ; Personality inventory ; Polymorphism ; Excitement-Seeking
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract An association between long alleles of a variable number tandem repeat (VNTR) polymorphism in the dopamine receptor D4 gene and the extraversion related personality traits Excitement and Novelty Seeking has been reported in healthy subjects. In an attempt to replicate the previous findings, 256 healthy Caucasian volunteers were analysed for a potential relationship between the dopamine receptor D4 exon III VNTR polymorphism and Extraversion as assessed by the Revised Neo Personality Inventory (NEO PI-R). The present study did not yield evidence for an association between Extraversion and the dopamine receptor D4 polymorphism.
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  • 24
    ISSN: 1433-8491
    Keywords: Key words Pharmacogenetics ; Genetics ; Risk factor ; Choreoathetotic movements
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract In the search for genetic factors contributing to tardive dyskinesia, dopamine receptor genes are considered major candidates. The dopamine D3 receptor is of primary interest as dopamine D3 receptor knock-out mice show locomotor hyperactivation resembling extrapyramidal side-effects of neuroleptic treatment. Furthermore, Steen and colleagues (1997) recently reported an association between tardive dyskinesia and a dopamine D3 receptor gene variant. In the present study we tried to replicate this finding. We investigated 157 patients with schizophrenia or schizoaffective disorder receiving long-term neuroleptic medication who never or persistently displayed tardive dyskinesia. As advanced age is a main risk factor for tardive dyskinesia, we also compared older patients with a long duration of schizophrenia not displaying tardive dyskinesia to younger patients with a shorter duration of the illness displaying tardive dyskinesia. However, we found no evidence that the dopamine D3 receptor gene is likely to confer susceptibility to the development of tardive dyskinesia.
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  • 25
    ISSN: 1590-3478
    Keywords: Key words Nervous system ; Cavernous angiomas ; Genetics ; Onset symptoms
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We performed a clinical and genetic study of patients affected by cavernous angiomas (CA) of the nervous system. We examined initial signs and symptoms in sporadic and familial cases. We obtained clinical, neuroimaging and genetic data on 15 Italian patients with CA of the nervous system with positive, doubtful or apparently negative family history. Genetic markers surrounding three different gene regions (7q, 3q and 7p) were analysed. In one small family, genetic linkage was consistent with all chromosome loci. In another family with the unusual association of cerebral and spinal CA, linkage with chromosome 7q and, likely, 7p was excluded, while linkage with locus 3q was possible. Our results indicate that Italian families with CA may show genetic heterogeneity. Non-specific and subtle onset symptoms hide the presence of CA within families. Patients with multiple CA may have silent cerebral lesions confirming the low penetrance of clinical signs in spite of radiological ones.
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  • 26
    ISSN: 1590-3478
    Keywords: Key words Evoked potentials ; Ceroid lipofuscinoses ; Mutation ; Classification ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The importance of visual evoked potential (VEPs) and electroencephalography for diagnosing and distinghishing the infantile (INCL), late-infantile (LINCL) and juvenile (JNCL) forms of neuronal ceroid lipofuscinoses (NCL) is well established. Variant forms with protracted clinical courses and atypical symptoms have been described recently, whose neurophysiological characteristics sometimes overlap those of LINCL and JNCL. It is unclear whether these variant forms are due to phenotypic variability of known genetic defects, or represent new mutations. Twenty-eight NCL patients have been diagnosed at our institute; a proportion of them were investigated genetically. In 17 we performed neurophysiological investigations including VEPs, brainstem auditory (BAEP) and upper limb somatosensory (SEP) evoked potentials. We found typical and diagnostic electrophysiological involvement of the visual system in 8 patients with classic forms of NCL. Furthermore, the distinctive features of the multimodal evoked potentials in most of the six patients with variant NCL suggest that these are distinct genetic entities.
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  • 27
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    Neurological sciences 21 (2000), S. 373-377 
    ISSN: 1590-3478
    Keywords: Key words Myoclonus-dystonia ; Essential myoclonus ; Dystonia ; Alcohol ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We present the clinical profile of a group of patients with myoclonus and dystonia sensitive to alcohol and address these cases in the context of essential myoclonus. Six patients from 4 families were selected: 4 men and 2 women with myoclonus affecting predominantly the arms. Active movements of these segments elicited the dystonic and myoclonic movements. A marked improvement with alcohol intake was seen. Laboratory findings including EEG, SSEP, and cranial CT and MRI were normal. Surface EMG recording showed bursts with duration of 30–112 ms in 3 patients. One patient showed a triphasic recording pattern (agonist-antagonist-agonist) of ballistic type. Our findings suggest that the myoclonus-dystonia disorder is present in Brazilian patients.
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  • 28
    ISSN: 1437-2320
    Keywords: Key words Von Hippel-Lindau disease ; Hemangioblastoma ; Endolymphatic sac tumor ; Angiogenesis ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Von Hippel-Lindau disease (VHL) is a hereditary cancer syndrome caused by germline mutations of the VHL tumor suppressor gene. Major progress has been made in the last decade in both clinical and fundamental aspects of VHL. The VHL gene product, pVHL, has major and multiple functions: pVHL regulates not only first angiogenesis but also extracellular matrix formation and the cell cycle. A molecular diagnosis of VHL is now available, leading to a transformation in clinical management of patients and their families. Diagnosis of VHL has to be suspected in patients with a VHL-related tumor without familial history and especially in case of hemangioblastoma or endolymphatic sac tumors. Such patients should be systematically investigated for clinical and molecular evidence of VHL disease. Treatment of symptomatic hemangioblastomas remains mainly neurosurgical, often in emergency, but stereotactic radiosurgery is emerging as an alternative therapeutic procedure. In the future, antiangiogenic drugs could represent a potential medical treatment of CNS hemangioblastomas in view of their highly vascular structure. Lastly, visceral manifestations of VHL disease are also of critical importance and require early detection for effective treatment.
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  • 29
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    Child's nervous system 16 (2000), S. 809-820 
    ISSN: 1433-0350
    Keywords: Keywords Pediatric neurosurgery ; Molecular biology ; Genetics ; Novel therapeutics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  The new millennium beckons for novel advances in the diagnosis and treatment of pediatric neurosurgical conditions. Almost every aspect of pediatric neurosurgery has changed over the last decade. Undoubtedly with the application of knowledge in molecular biology to human disease many aspects of neurosurgery, especially neuro-oncology and the field of neuro-developmental anomalies, will change appreciably over the next decade. Overall, the trend in surgery in general and neurosurgery in particular is toward less invasive procedures and possibly non-surgical interventions. This review will briefly cover many of the important areas of pediatric neurosurgery. We will describe the state-of-the-art of our subspecialty and discuss possible future directions.
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  • 30
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    Psychopharmacology 99 (1989), S. 147-150 
    ISSN: 1432-2072
    Keywords: Locomotor activity ; CNS depression ; Cocaine ; Mice ; Behavior ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Cocaine produces several behavioral effects, most notably locomotor stimulation. Biochemically, cocaine is known to inhibit reuptake at the three monoamine transporter sites, and may have highest affinity at the serotonin transporter. Serotonin augmentation has been associated with decreases in behavioral activity, but cocaine has not been reported to produce behavioral depressant effects except at high doses which cause stereotypy and disruption of behavior. This study examined the effects of relatively low doses of cocaine, in the range of 0.1–10 mg/kg, on locomotor activity in C57BL/6J and DBA/2J mice. A biphasic dose-response curve was seen for both strains. At the lowest doses, activity was depressed. As the dose of cocaine increased, activity returned to baseline, and at the highest doses, increases in locomotor activity were found. DBA/2J mice were depressed at a lower dose of cocaine than were C57BL/6J mice; however, C57BL/6J mice showed locomotor depression over a broader range of doses. Activity was maximally depressed at 0.1 mg/kg for DBA/2J mice, and maximally depressed at 0.3 mg/kg for C57BL/6J mice. Thus, low doses of cocaine are shown to produce significant decreases in locomotor activity in two strains of mice. It is postulated that these low doses of cocaine which depress locomotor activity do so via inhibition of serotonin uptake, resulting in potentiation of serotonergic activity.
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  • 31
    ISSN: 1432-2072
    Keywords: Ethanol ; Bicuculline ; Picrotoxin ; Seizures ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The convulsant potency of bicuculline, a GABA antagonist, was shown to be greater in Short-Sleep (SS) mice than in Long-Sleep (LS) mice. LS mice, selectively bred for lengthy ethanol-induced narcosis, had longer latencies to myoclonus and clonus following administration of bicuculline and picrotoxin than did ethanol-resistant SS mice. SS mice were also more susceptible to pentylenetetrazol-induced myoclonus, but not clonus. F1 hybrids showed bicuculline seizure sensitivity intermediate to the two parent lines. Ethanol weakly inhibited bicuculline-induced myoclonus in both LS and SS mice. Clonus was clearly antagonized by ethanol in both lines, but to a similar degree. These data provide evidence for a GABAergic role in geno-type-dependent sensitivity to ethanol.
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  • 32
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    Psychopharmacology 98 (1989), S. 518-523 
    ISSN: 1432-2072
    Keywords: Ethanol ; GABA ; Bicuculline ; Sedation ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Two lines of mice, selectively bred for differential sensitivity to the soporific effects of ethanol (ETOH), were administered GABAergic drugs in an effort to evaluate a role for GABA in ETOH sensitivity. ETOH sensitive Long-Sleep mice (LS) showed potentiated ETOH sedation when administered bicuculline, muscimol and aminooxyacetic acid (AOAA). ETOH-insensitive SS mice exhibited reduced ETOH sedation in the presence of the antagonists, bicuculline and picrotoxin, and potentiated sedation in the presence of muscimol and AOAA. These changes in narcosis duration were interpreted as central effects, since blood ethanol levels at waking from ETOH sedation varied with GABAergic drug treatment. Picrotoxin antagonized pentobarbital-induced nacrosis in both lines, but to a greater extent in SS mice. These and other experiments with a genetically heterogeneous stock suggest GABA involvement in genotype-dependent ETOH sensitivity, but do not support a simple role of GABA receptor involvement.
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  • 33
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    Psychopharmacology 98 (1989), S. 549-555 
    ISSN: 1432-2072
    Keywords: Ethanol (ETOH) ; GABA ; Bicuculline ; Sedation ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Genetic influences on the interaction between ethanol (ETOH) and gamma-aminobutyric acid (GABA) neurotransmitter systems were eveluated with a survey of responses to coadministration of ETOH and a GABA antagonist, bicuculline, in a battery of inbred mouse strains. The selectively bred ETOH-sensitive Long-Sleep (LS) mice, the relatively ETOH-resistant Short-Sleep (SS) mice, and a genetically heterogeneous stock (GHS) were also evaluated. The effect of bicuculline on ETOH-induced sedation, hypothermia, and blood ethanol content upon recovery from sedation was assessed. Inheritance of these responses was also examined using F1 hybrids. The effect of bicuculline on ETOH-produced narcosis varied widely among stocks and included antagonism, potentiation, and no effect. Changes in ETOH-induced narcosis produced by bicuculline were accompanied by changes in blood ethanol concentrations consistent with an hypothesis of altered central nervous system sensitivity to ETOH. Knowledge of a strain's seizure susceptibility to the GABA antagonist or of its sensitivity to the hypnotic effects of ETOH were of no predictive value in estimating the outcome of coadministration studies, suggesting at least partially separate genetic influences on each phenotype. In cross-breeding studies there was commonly dominance toward a profile of bicuculline antagonism of ETOH narcosis but different patterns of dominance were observed for seizure susceptibility, again inicating separate genetic control. The results suggest considerable complexity of GABAergic involvement in genotype-dependent ETOH sensitivity.
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  • 34
    ISSN: 1432-2242
    Keywords: Solanum tuberosum ; Genetics ; Breeding ; Plant appearance ; Economy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In 1985, 1986 and 1987, 600 clones were visually assessed at harvest on plant appearance. The clones were harvested 80 days after planting in the first year, in the following years after approximately 80 days as well as after 145 days. The correlation coefficients between years and between harvest times were low to medium. Simulating different selection intensities using the performance of these 600 clones in two successive years, the relation between selection pressure in the first year and the retained proportion of well performing clones in the second year was described. Including the costs of testing, the most economic selection procedure was calculated. This procedure consisted in testing 1,579 first-year clones and 499 second-year clones for every 100 third-year clones required. The optimal period of the main evaluation in the second clonal year is at ware potato harvest time. This selection procedure also provides good selection possibilities for underwater weight and foliage maturity.
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  • 35
    ISSN: 1432-1939
    Keywords: Logging disturbance ; Land gastropods ; Ecology ; Genetics ; Population
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Ecological and genetic properties of two North American terrestrial gastropods (Mesomphix spp.) were characterized in paired control and previously logged watersheds in two North Carolina forests (Coweeta and the Great Smoky Mountains National Park) of the Southern Appalachian Biosphere Reserve Cluster. Shell growth was greater in the control sites, but density and mortality were largely independent of prior logging history and forest reserve. Based on starch gel electrophoresis data, both species showed their highest levels of genetic diversity in the Coweeta forest, the component of the reserve cluster which had the most extensive and variable history of logging disturbance. M. subplanus also exhibited higher levels of heterozygosity in logged than in control watersheds, and M. andrewsae showed over twice as many rare alleles in disturbed sites as in control sites. F-statistic analysis depicted both excess levels of homozygosity and moderate genetic differentiation among the populations, reflecting the effects of small population size and perhaps drift and inbreeding. Estimated gene flow was relatively low. These results correspond to the recent finding by Bryant et al. (1987) and others on the effects of bottlenecks, and to the contrasting history of habitat instability of the two major study forests.
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  • 36
    ISSN: 1432-0428
    Keywords: Genetics ; insulin gene ; DQβ gene ; fibrocalculous pancreatic diabetes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Fibrocalculous pancreatic diabetes (previously known as tropical pancreatic diabetes) is a rare cause of diabetes confined to countries within the tropical belt. The aetiology of fibrocalculous pancreatic diabetes is thought to be environmental although the agent(s) is unknown. We have investigated a possible genetic basis of this disease by looking for restriction fragment length polymorphisms of genes implicated in the aetiology of diabetes mellitus. Seventy-six Dravidian patients with fibrocalculous pancreatic diabetes were studied, and the restriction fragment length polymorphisms obtained compared to racially matched control subjects (n=94), patients with Type 2 (non-insulin-dependent) diabetes (n=87) and Type 1 (insulin-dependent) diabetes (n=58). No association of fibrocalculous pancreatic diabetes was found with restriction fragment length polymorphisms of the insulin receptor gene. Although no association of fibrocalculous pancreatic diabetes was found with polymorphism of the HLA DRα/DQα/DXα genes, an association was found with the Taq 1 restriction fragment length polymorphisms of the DQβ gene (DQβ T2/T6 present in 39% of patients with fibrocalculous pancreatic diabetes compared to 19% in control subjects; p=0.01; corrected p value=0.04) which is similar to that found in Type 1 but not Type 2 diabetes. An association of fibrocalculous pancreatic diabetes was also found with the hypervariable region in the 5-prime flanking region of the insulin gene; 40% of patients possessed the class 3 allele compared to 9.5% of control subjects p=0.0001; corrected p value=0.0008). In Type 2 diabetes, similar results were obtained with 33% subjects possessing the class 3 allele (p value compared to control subjects=0.0005; corrected p value=0.004). This study suggests that fibrocalculous pancreatic diabetes has a genetic component in its aetiology. Furthermore, its origin might be related to an individual with part of the genetic predisposition to diabetes (Type 1 or Type 2) who additionally has evidence of chronic calcific pancreatitis.
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  • 37
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    Archives of microbiology 152 (1989), S. 335-341 
    ISSN: 1432-072X
    Keywords: Carboxydotrophic bacteria ; Plasmids ; CO dehydrogenase subunits ; N-terminal sequences ; Oligonucleotides ; Hybridization ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The 17 (S), 30 (M) and 87 kDa (L) subunits of CO dehydrogenases from the CO-oxidizing bacteria Pseudomonas carboxydoflava, Pseudomonas carboxydohydrogena and Pseudomonas carboxydovorans OM5 were isolated and purified. The N-terminal sequences of same subunits from different bacteria showed distinct homologies. Dot blot hybridization employing oligonucleotide probes derived from the sequences of the S-subunit of P. carboxydovorans OM5 and the M-subunit of P. carboxydohydrogena and DNA of the plasmid-containing CO-oxidizing bacteria Alcaligenes carboxydus, Azomonas B1, P. carboxydoflava, P. carboxydovorans OM2, OM4 and OM5 indicated that all genes encoding these subunits reside on plasmids. That in P. carboxydovorans OM5 CO dehydrogenase structural genes are located entirely on plasmid pHCG3 was evident from the absence of hybridization employing DNA from the cured mutant strain OM5-12. CO dehydrogenase structural genes could be identified on the chromosome of the plasmid-free bacteria Arthrobacter 11/x, Bacillus schlegelii, P. carboxydohydrogena and P. carboxydovorans OM3. There was no example of a plasmid-harboring carboxydotrophic bacterium that did not carry CO dehydrogenase structural genes on the plasmid. The N-terminal sequences of CO dehydrogenase structural genes were found to be conserved among carboxydotrophic bacteria of distinct taxonomic position, independent of the presence of plasmids. It is discussed whether this might be the consequence of horizontal gene transfer.
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  • 38
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    Theoretical and applied genetics 78 (1989), S. 97-104 
    ISSN: 1432-2242
    Keywords: Beta vulgaris ; Sugar beet ; Isozymes ; Genetics ; Linkage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Five isozyme systems were genetically investigated. The different separation techniques, the developmental expression and the use as marker system in sugar beet genetics and breeding is discussed. Isocitrate dehydrogenase was controlled by two genes. The gene products form inter- as well as intralocus dimers, even with the gene products of the Icd gene in B. procumbens and B. patellaris. Adenylate kinase was controlled by one gene. Three different allelic forms were detected, which were active as monomeric proteins. Glucose phosphate isomerase showed two zones of activity. One zone was polymorphic. Three allelic variants, active as dimers, were found. Phosphoglucomutase also showed two major zones of activity. One zone was polymorphic and coded for monomeric enzymes. Two allelic forms were found in the accessions studied. The cathodal peroxidase system was controlled by two independent genes, of which only one was polymorphic. The gene products are active as monomers. Linkage was found between red hypocotyl color (R) and Icd 2. Pgm 1, Gpi 2, Ak 1 and the Icd 2-R linkage group segregated independently.
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  • 39
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    Journal of molecular medicine 67 (1989), S. 225-237 
    ISSN: 1432-1440
    Keywords: Atherosclerosis ; Apolipoprotein ; Gene expression ; Genetics ; Evolution ; Gene duplication ; Lipid binding ; DNA polymorphism ; Hypercholesterolemia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The plasma apolipoproteins can be classified into two subgroups: the soluble apolipoproteins including apolipoprotein (apo) A-I, A-II, A-IV, C-I, C-II, C-III, and E, and the apoBs including apoB-100 and apoB-48. The soluble apolipoproteins have very similar genomic structures, each having a total of three introns at the same locations; apoA-IV is an exception in that it has lost its first intron. Using the exon/intron junctions as reference points, we can obtain an alignment of the coding regions of all the soluble apolipoprotein genes. The mature peptide regions of the genes are almost completely made up of tandem repeats of 11 codons. The part of mature peptide region encoded by exon 3 contains a common block of 33 codons, whereas the part encoded by exon 4 contains a much more variable number of internal repeats of 11 codons. On the basis of the degree of homology of the various sequences, and the pattern of the internal repeats in these genes, an evolutionary tree has been proposed for the soluble apolipoprotein genes. ApoB-100 differs considerably from the soluble apolipoproteins. It is the largest apolipoprotein containing 4536 amino acid residues. Two types of internal repeats are identified in apoB-100: amphipathic α-helical repeats and proline-containing repeats with high β-sheet content. The apoB gene contains 29 exons and 28 introns. Its evolutionary relationship to the soluble apolipoprotein genes is unclear. The 3′ end of the apoB gene contains a region of variable number of tandem 12–16-base pair repeats. We have applied the polymerase chain reaction technique to characterize this highly polymorphic locus. The same technique can be used to accurately type other variable number of tandem repeats loci. Finally, apoB-48 was shown to be the product of an RNA editing mechanism involving an intestinal mRNA that has an in-frame UAA stop codon resulting from a C→U change in the codon CAA encoding Gln-2153 in apoB-100 mRNA. Using a molecular approach to apolipoprotein synthesis, structure and genetic analysis, we have generated information important to our understanding of lipoprotein metabolism; we also uncovered unexpected experimental results that are relevant to general cell and molecular biology and molecular evolution.
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  • 40
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    European archives of psychiatry and clinical neuroscience 239 (1989), S. 43-48 
    ISSN: 1433-8491
    Keywords: Schizophrenia ; Eye movements ; Genetics ; Twins ; Latent trait
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Eye movement dysfunctions have been found in a large number of schizophrenic patients and in about half of their first-degree relatives. The distribution of these traits within the families of schizophrenic patients suggests a model of genetic transmission that fits an autosomal dominant model, which we have called the “genetic latent trait model.” The model, with seven parameters, was fitted to a U.S. population and the model was cross-validated on an independent Norwegian sample. Although the model does not invalidate other, more conventional solutions to the puzzle of schizophrenic transmission, such as multifactorial transmission, the latent trait model does more easily permit linkage studies and therefore will allow refutation or support from the use of molecular genetics techniques.
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  • 41
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 125-131 
    ISSN: 0887-3585
    Keywords: protein conformation ; dynamics ; Monte Carlo simulation ; conformational energy ; minimization ; plastic deformation ; conformational heterogeneity ; hierarchy in dynamics ; trypsin inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Differences in atom packing are studied in the minimum energy conformations derived from the record of the Monte Carlo simulation of conformational fluctuation in the native state of a globular protein, bovine pancreatic trypsin inhibitor. It is found that local deformations observed among the minima which are found in the previous paper are accompanied by rearrangement of atom packing. Spatial locations of the local deformations in the three-dimensional folded structure are also studied. It is foundthat the local deformations are distributed in space in several clusters inthe folded structure. The size and location of the clusters characterize the respective fluctuations of the first and the second levels observed in the simulation. In the fluctuations of the first level local deformations, each of which usually involves a few side chains and one main chain local segment, are thermally exited independently of each other near thesurface of the molecule. The observed fluctuation of the second level involves a cooperative deformation involving many side chains and local main chain segments all in one cluster, which goes though the core of the molecule. The collective local deformations observed both in the first and second levels are plastic in the sense that they are accompanied with rearrangement of atom packing.
    Additional Material: 3 Ill.
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  • 42
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 139-148 
    ISSN: 0887-3585
    Keywords: protein architecture ; packing ; evolutionary relationships ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: α/β barrel structures very similar to that first observed in triose phosphate isomerase are now known to occur in 14 enzymes. To understand the origin of this fold, we analyzed in three of these proteins the geometry of the eight-stranded β-sheets and the packing of the residues at the center of the barrel. The Packingin thisregion is seen in its simplest form in glycolate oxidase. It consists of 12 residues arranged in three layers. Each layer contains four side chains. The packing of RubisCO and TIM can be understood in terms of distortions of this simple pattern, caused by residues with small side chains at someof the positions inside the barrel. Two classes of packing are found. In one class, to which RubisCO and TIM belong, the central layer is formed by a residue from the first, third, fifth, and seventh strands; the upper and lower layers are formed by residues fromthe second, fourth, sixth, and eighth strands. In the second class, to which GAO belongs, this is reversed: it is side chains from the even-numbered strands that form the central layer, and side chains from the oddnumbered strands that form the outer layers. Our results suggest that not all proteins with this fold are related by evolution, but that they represent a common favorable solution to the structural problems involved in the creation of a closed β barrel.
    Additional Material: 8 Ill.
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  • 43
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    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 170-182 
    ISSN: 0887-3585
    Keywords: modeling ; flavodoxin ; structure prediction ; side chains ; database ; structure analysis ; protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The tertiary structure of flavodoxin has been model build from only the X-ray crystallographic α-carbon coordinates. Main-Chain atoms were generated from a dictionary of backbone structures. Side-chain conformations were initially set according to observed statistical distributions, clashes were resolved with reference to other knowledge-based parameters, and finally, energy minimization was applied. The RMSD of the model was 1.7 Å across all atoms to the native structure. Regular secondary structural elements were modeledmore accurately than other regions. About 40%of the ξ1 torsional angles were modeled correctly. Packing of side chains in the core was energetically stable but diverged significantly from the native structure in some regions.The modeling of protein structures is increasing in popularity but relatively few checks have been applied to determine the accuracy of the approach. In this work a variety of parameters have been examined. It was found that close contact, and hydrogen-bonding patterns could identifypoorly packed residues. These tests, however, did not indicate which residues had a conformation different from the native structure or how to move such residues to bring them into agreement. To assist in the modeling of interacting side chains a database of known interactions has been prepared.
    Additional Material: 8 Ill.
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  • 44
    ISSN: 0887-3585
    Keywords: yeast hexokinase II ; dimerization ; in vivo functions ; glucose repression ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The function of the N-terminal amino acids of Saccharomyces cerevisiae hexokinase II was studied in vivo using strains producing a form of hexokinase II lacking its first 15 amino acids (short form).This short form of hexokinase II was produced from a fusion between the promoter region of the PGK1 gene and the HXK2 coding sequence except the first 15 codons. As expected, the in vitro analysis of the short from protein by gel filtration chromatography indicates that the short protein does not form dimers under conditions where the wild-type protein dimerizes. Kinetic studies show that the enzymatic activities are very similarto wild-type behavior. The physiological experiments performed on the strains containing the fusion allele demonstrate that the short form ofthe enzyme is similar to the wild-type both in terms of phosphorylation of hexoses and glucose repression. We conclude that the N-terminalamino acids of hexokinase II are not required in vivo either for phosporylation of hexoses or for glucose repression.
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  • 45
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 289-312 
    ISSN: 0887-3585
    Keywords: aconitase ; iron-sulfur enzyme ; crystal structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of the 80,000 Da Fe—S enzyme aconitase has been solved and refined at 2.1 Å resolution. The protein contains four domains; the first three from the N-terminus are closely associated around the [3Fe-4S] cluster with all three cysteine ligands to the cluster being provided by the third domain. Associationof the larger C-terminal domain with the first three domains createsan extensive cleft leading to the Fe—S cluster. Residues from all four domains contribute to the active site region, which is defined by the Fe—S cluster and a bound SO42-ion. This region of the structure contains 4 Arg, 3 His, 3 Ser, 2 Asp, 1 Glu, 3 Asn, and 1 Gln residues, as well asseveral bound water molecules. Three of these side chains reside on a threeturn 310 helix in the first domain. The SO42-ion is bound 9.3 Å from the center of the [3Fe-4S] cluster by the side chains of 2 Arg and 1 Gln rsidues. Each of 3 His side chains in the putative active site is paired with Asp or Glu side chains.
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  • 46
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 271-280 
    ISSN: 0887-3585
    Keywords: antifluorescyl monoclonal antibody ; high-affinity binding site ; effects of MPD on hapten binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of a fluorescein-Fab (4-4-20) complex was determined at 2.7 Å resolution by molecularreplacement methods. The starting model was the refined 2.7 Å structure of unliganded Fab from an autoantibody (BV04-01) with specificity for single-stranded DNA. In the 4-4-20 complex fluorescein fits tightly into a relatively deep slot formed by a network of tryptophan and tyrosine side chains. The planar xanthonyl ring of the hapten is accommodated at the bottom of the slot while the phenylcarboxyl group interfaces with solvent. Tyrosine 37 (light chain) and tryptophan 33 (heavy chain) flank the xanthonyl group and tryptophan 101 (light chain) provides the floor of the combining site. Tyrosine 103 (heavy chain) is situated near the phenyl ring of the hapten and tyrosine 102 (heavy chain) forms part of the boundary of the slot. Histidine 31 and arginine 39 of the light chain are located in positions adjacent to the two enolic groups at opposite ends of the xanthonyl ring, and thus account for neutralization of one of two negative charges in the haptenic dianion. Formation of an enol-arginine ion pair in a region of low dielectric constant may account for an incremental increase in affinity of 2-3 orders of magnitude in the 4-4-20 molecules relative to other members of an idiotypic family of monoclonalantifluorescyl antibodies. The phenyl carboxyl group of fluorescein appearsto be hydrogen bonded to the phenolic hydroxyl group of tyrosine 37 of the light chain. A molecule of 2-methyl-2,4-pentanediol (MPD), trapped in the interface of the variable domainsjust below the fluorescein binding site, may be partly responsible for the decrease in affinity for the hapten in MPD.
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  • 47
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 355-373 
    ISSN: 0887-3585
    Keywords: protein ; structure ; prediction ; primary ; secondary ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new approach is introduced for analyzing and ultimately predicting protein structures, defined at the level of Cα coordinates. We analyze hexamers (oligopeptides of six amino acid residues) and show that their structure tends to concentrate in specific clusters rather than vary continuously. Thus, we can use a limited set ofstandard structural building blocks taken from these clusters as representatives of the repertoire of observed hexamers. We demonstrate that protein structures can be approximated by concatenating such building blocks. We have identified about 100 building blocks by applying clustering algorithms, and have shown that they can “replace” about 76% ofall hexamers in well-refined known proteins with an error of less than 1 Å, and can be joined together to cover 99% of the residues. After replacing each hexamer by a standard building block with similar conformation, we can approximately reconstruct the actual structure by smoothly joining the overlapping building blocks into a full protein. The reconstructed structures show, in most cases, high resemblance to the original structure, although using a limited number of building blocks and local criteria of concatenating them is not likely to produce a very precise global match. Since these building blocks reflect, in many cases, some sequence dependency, it may be possible to use the results of this study as a basis for a protein structure prediction procedure.
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  • 48
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 20-31 
    ISSN: 0887-3585
    Keywords: ribonuclease ; active site ; conformational change ; protein-nucleic ; acid interactions ; fluorescence depolarization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations were performed on free RNase T1 and the 2′GMP-RNase T1 complex in vacuum and with water in the active site along with crystallographically identified waters, allowing analysis of both active site and overall structural and dynamics changes due to the presence of 2′GMP. Difference in the active site include a closing in the presence of 2′GMP, which is accompanied by a decrease in mobility of active site residues. The functional relevance of the active site fluctuations is discussed. 2′GMP alters the motion of Tyr-45, suggesting a role for that residue in providing a hydrophobic environment for the protein-nucleic acid interactions responsible for the specificity of RNase T1. The presence of 2′GMP causes a structural change of the C-terminus of the α-helix, indicating the transmission of structural changes from the active site through the protein matrix. Overall fluctuations of both the free and 2′GMP enzyme forms are in good agreement with X-ray temperature factors. The motion of Trp-59 is influenced by 2′GMP, indicating difference in enzyme dynamics away from the active site, with the calculated changes following those previously seen in time-resolved fluorescence experiments.
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  • 49
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 324-337 
    ISSN: 0887-3585
    Keywords: aspartyl protease ; HIV/AIDS ; yeast expression ; polyprotein processing ; α-factor ; secretion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The protease of the human immunodeficiency virus type I (HIV1) was expressed both intracellularly and extracellularly in Saccharomyces cerevisiae. Intracellular expression of the protease was achieved by fusing a 179 amino acid precursor form of the protease to human superoxide dismutase (hSOD). Self-processing of the viral enzyme from the hybrid precursor was demonstrated to ocur within the yeast host. Secretion of the protease was achieved by fusing the leader sequence of yeast α-factor to the precursor form of the protrease or to the 99 amino acid mature form of the protease. Authentic and active forms of the retroviral enzyme were detected in yeast supernatants of cells expressing the precursor or the mature form of the protease. A D25E active site variant of the retroviral enzyme exhibited diminished autocatalytic activity when expressed intracellularly or secreted from yeast. The wild-type protease was active in an in vitro assay on the natural substrate, myristylated gag precursor, Pr53gag. Correct processing of Pr53gag at the Tyr 138-Pro 139 junction was confirmed by amino terminal sequence analysis of the resulting capsid protein (CA, p24). The secreted protease was purified to homogeneity from yeast media using preparative isoelectric focusing and reverse-phase HPLC. Amino terminal sequence analysis showed a sequence beginning at amino acid 1 of the mature enzyme (Pro) and another sequence beginning at amino acid 6 (Trp). This shorter sequence may represent a natural autolytic product of the proteaseaspartyl protease.
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  • 50
    ISSN: 0887-3585
    Keywords: protein tertiary structure ; incorrect and correct folding ; molecular surfaces ; solvation free energy ; solution and crystal structure ; disulfide connectivity determination ; squash inhibitor family ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Refinement of distance geometry (DG) structures of EETI-II (Heitz et al.:Biochemistry 28:2392-2398, 1989), a member of the squash family trypsin inhibitor, have been carried out by restrained molecular dynamics (RMD) in water. The resulting models show better side chain apolar/polar surface ratio and estimated solvation free energy than structures refined “in cacuo.” The consistent lower values of residual NMR constraint violations, apolar/polar surface ration and solvation free energy of one of these refined structures allowed prediction of the 3D folding and disulfide connectivity of EETI-II. Except for the few first residues for which no NMR constraints were available, this computer model fully agree with X-ray structures of CMTI-I (Boe et al.: FEBS Lett. 242:285-292, 1989) and EETI-II complexed with trypsin that appeared after the RMD simulation was completed. Restrained molecular dynamics n water is thus proved to highly valuable for refinement of DG structures Also, the successful use of apolar/polar surface ratio and solvation free energy reinforce the analysis of Novotny et al. (Proteins 4: 19-30, 1988) and shows that these criteria are useful indicators of correct versus misfolded models.
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  • 51
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    Proteins: Structure, Function, and Genetics 5 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 52
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 155-167 
    ISSN: 0887-3585
    Keywords: protein structure comparison ; dihedral angles ; protein conformation ; hemoglobin structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An efficient algorithm was characterized that determines the similarity in main chain conformation between short protein substructures. The algorithm computes Δt, the root mean square difference in φ and ψ torsion angles over a small number of amino acids (typically 3-5). Using this algorithm, large number of protein substrates comparisons were feasible. The parameter Δt was sensitive to variations in local protein conformation, and it correlates with Δr, the root mean square deviation in atomic coordinates. Values for Δt were obtained that define similarity thresholds, which determine whether two substructure are considered structurally similar. To set a lower bound on the similarity threshold, we estimated the component of Δt due to measurement noise fromcomparisons of independently refined coordinates of the same protein. A sample distribution of Δt from nonhomologous protein comparisons identified an upper bound on the similarity threshold, one that refrains from incorporating large numbers of nonmatching comparisons large numbers of nonmatching comparisons. Unlike methods based on Cα atoms alone, Δt was sensitive to rotations in the peptide plane, shown to occur in several proteins. Comparisons of homologus proteins by Δt showed that the active site torsion angles are highly conserved. The Δt method was applied to the α-chain of human hemoglobin, where it readily demonstrated the local differences in the structures of different ligation states.
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  • 53
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 193-209 
    ISSN: 0887-3585
    Keywords: protein folding ; simulated annealing ; empirical potentials ; Monte Carlo dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The current work describes a simplified representation of protein structure with uses in the simulation of protein folding. The model assumes that a protein can be represented by a freely rotating rigid chain with a single atom approximately the effect of each side chains. Potentials describing the attraction or repulsion between different types of amino acids are determined directly from the distribution of amino acids in the database of known protein structures. The optimization technique of simulated annealinghas been used to dynamically sample the conformations available to this sample model, allowing the protein to evolve from an extended, random coil into a compact globular structure. Many characteristics expected of true proteins, such as the sequence-dependent formation of secondary structure, the partitioning of hydrophobic residues, and specific disulfide, suggestion the model may accurately simulate the folding process.
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  • 54
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 249-258 
    ISSN: 0887-3585
    Keywords: DNA binding domain ; etheno-M13 DNA ; single-stranded DNA affinity chromatography ; proteolytic fragments ; truncated topoisomerase ; protein-DNA interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Limited digestion of E. coli DNA topoisomerase I with trypsin or papain generated a DNA-binding domain of MW 14,000 corresponding to the carboxyl terminal of the enzyme. This fragment binds to single-stranded DNA agarose as tightly as the intact enzyme. It required around 400 mM NaCl for elution. A truncated topoisomerase that lacks this C-terminal domain was purified. It was eluted from the single-stranded DNA agarose column at around 150 mM NaCl. Although the truncated enzyme could relax negatively supercoiled DNA as efficiently as the intact enzyme at low ionic strength, its processivity was more sensitive to increasing salt concentration. Measurement of binding to fluorescent etheno-M13 DNA also demonstrated that the presence of the C-terminal domain confers higher affinity to DNA for the enzyme.
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  • 55
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 275-283 
    ISSN: 0887-3585
    Keywords: mutagenesis ; structure-function relationships ; enzymatic catalysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Site saturation mutagenesis has been carried out at Ala-237 in RTEM-1 β-lactamase to assess the role of this site in modulating differences in specificity of β-lactamases for penams vs. cephams as substrates. (An Ala-237 Thr mutation had previously been shown to increase activity on cephems by about 30-80%.1,2) Screening of all 19 possibles mutants on penams and cephems revealed the even more active Ala-237 Asn mutant. Detailed kinnetic analysis showns that this mutant has about four times the activity toward cephalothin and cephalosporin C as the wild-type enzyme. Both mutations reduce the activity toward penams to about 10% that of RETM-1 β-lactamase and lower by about 5°C the tempreature at which the enzyme denatures. Functional properties of the other mutants have also been surveyed. The most intresting aspect of these results is that two quite disparate amino acids, theronine and asparagine, when intorduced for Ala-237, cause such similar changes in enzyme specificity while more similar residues do not alter the catalytic properties of the enzyme to such a significant degree.
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  • 56
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 338-340 
    ISSN: 0887-3585
    Keywords: cytochrome c ; axial ligand ; semisynthesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Semisynthesis has been employed to replace the axial methionine in horse heart cytochrome c with histidine. The reduction potential of the His-80 protein (cyt c-His-80) is 41 mV vs NHE (0.1 M phosphate; pH 7.0; 25°C). The absorption spectra of oxidized and reduced cyt c-His-80 are very similar to those of the native protein in the porphyrin region, but the 695 nm band is absent in the oxidized His-80 protein.
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  • 57
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    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 58
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 372-381 
    ISSN: 0887-3585
    Keywords: cytochromec ; Saccharomyces cerevisiae ; protein secondary structures ; protein design ; protein engineering ; protein folding ; protein evolution ; modular exchange ; loop swap ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ω(Omega)-loops are protein secondary structural elements having small distance between segment termini. It should be possible to delete or replace certain of these Ω-loops without greatly distorting the overall structure of the remaining portion of the molecule. Functional requirements of regions of iso-1-cytochrome c from the yeast Saccharomyces cerevisiae were in investigated by determining the biosynthesis and activity in vivo of mutant forms in which four different Ω-loops were individually deleted, or in which one Ω-loop was replaced with five different segments. Deletion encompassing amino acid positions 27-33 and79-83 either prevented synthesis of the holoprotein, or produced highly labile iso-1-cytochromes c, whereas deletions encompassing position 42-45 and 48-55 allowed partial synthesis and activity. These two latter regions, therefore, are not absolutely required for any biosynthetic process such as heme attachment, mitochondrial import, or for enzymatic interactions. All replacements in Loop A (residue position 24-33) with the same size (10 amino acid residues), longer (13 and 15 amino acid residues), or shorter segments (6 amino acid residues), resulted in strains having at least partial levels of iso-1-cytochrome c; however, the relative activities ranged from zero to almost the normal level. Thus, Loop A does not appear to be essential for such biosynthetic steps as heme attachment and mitochondrial import. In contrast, the full range of relative activities suggest that this region interacts with physiological partners to carry out efficient electron transport.
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  • 59
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 418-423 
    ISSN: 0887-3585
    Keywords: accessible area ; power law fit ; bootstrap analyses ; fractal structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The coefficients in a power low fit of accessible area versus molecular weight for high-reslution monomeric protein structures are assessed with respect to statistical accuracy using bootstrap analyses, and with respect to physical significance using model systems and the concept of roughness or fractal structure of the protein surface.
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  • 60
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 38-46 
    ISSN: 0887-3585
    Keywords: reconstitution ; membrane protein folding/unfolding ; pH effects ; differential scanning calorimetry ; circular dichroism ; electron microscopy ; HPLC ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Thermal unfolding experiments on bacteriorhodopsin in mixed Phospholipid/detergent micelles were performed. Bacteriorhodopsin was extracted from the purple membrane in a denatured state and then renatured in the micellar system. The purpose of this study was to compare the changes, if any, in the structure and stability of a membrane protein that has folded in a nonnative environment with results obtained on the native system, i.e., the purple membrane. The purple membrane crystalline lattice is an added factor that may influence the structural stability of bacteriorhodopsin. Micelles containing bacteriorhodopsin are uniformly sized disks 105 ± 13 Å in diameter (by electron microscopy) and have an estimated molecular mass of 210 kDa (by gel filtration HPLC). The near-UV CD spectra (which is indicative of tertiary structure) for micellar bacteriorhodopsin and the purple membrane are very similar. In the visible CD region of retinal absorption, the double band seen in the spectrum of the purple membrane is replaced with a broad positive band for micellar bacteriorhodopsin, indicating that in micelles, bacteriorhodopsin is monomeric. The plot of denaturational temperature vs. pH for micellar bacteriorhodopsin is displaced downward on the temperature axis, illustrating the lower thermal stability of micellar bacteriorhodopsin when compared to the purple membrane at the same pH. Even though micellar bacteriorhodopsin is less stable, similar changes in response to pH and temperature are seen in the visible absorption spectra of micellar bacteriorhodopsin and the purple membrane. This demonstrates that changes in the protonation state or temperature have a similar affect on the local environment of the chromophore and the protein conformation. We conclude that the tertiary structure of the bacteriorhodopsin monomer is essentially the same in micelles and the purple membrane. On the other hand, in the synthetic mixed micelle system, the packing between the nonnative amphiphiles and bacteriorhodopsin is probably not optimal, protein-protein interactions have been lost, and thehelical packing may be looser because the crystalline lattice is absent. Itis likely that a combination of these effects leads to the decreased stability of micellar bacteriorhodopsin.
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  • 61
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 22-37 
    ISSN: 0887-3585
    Keywords: sequence homology ; tertiary structure prediction ; molecular dynamics ; energy minimization ; hydrophobic interactions ; aromatic ring-ring interactions ; salt bridges ; calcium binding ; thermoactinomyces vulgaris ; extracellular protease ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Subtilisin family of proteases has four members of known sequence and structure: subtilisin Carlsberg, Subtilisin novo, proteinase K, and thermitase. Using thermitase as a test case, we ask two questions. How good are methods for model building a three-dimensional structure of a protein based on sequence homology to a known structure? And what are the molecular causes of thermostability? First, we compare predicted models of thermitase, refined by energy minimization and varied by molecular dynamics, with the preliminary crystal structure. The predictions work best in the conserve structural core and less well in seven loop regions involving insertions and deletions relative to Subtilisin. Here, variation of loop regions by molecular dynamics simulation in vacuo followed by energy minimization does not improve the prediction since we find no correlation between in vacuo energy and correctness of structure when comparing local energy minima. Second, in order to identify the molecular case of thermostability we confront hypotheses erived by calculation of the details of interatomic interactions with inactivation experiments. As a result, we can exclude salt bridges and hydrophobic interactions as main cause of thermostability. Based on a combination of theoretical and experimental evidence, the unusually tight binding of calcium by thermitase emerges as the most likely single influence responsible for its increased thermostability.
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  • 62
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 166-169 
    ISSN: 0887-3585
    Keywords: α-crystallin ; enthalpy ; entropy of solution ; light scattering ; second virial coefficient ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Light scattering studies were performed on bovine α-crystallin measuring the scattering intensities as a function of scattering angle, concentration, and temperature. The data yielded the molecular weight, radius of gyration, and second virial coefficient of α-crystallin at different temperatures. The second virial coefficient increased with increasing temperature. Both the enthalpy and entropy of solution of α-crystallin are positive. The Flory thetatemperature was found to be 271 K.
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  • 63
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 202-210 
    ISSN: 0887-3585
    Keywords: enhanced stability ; λCro ; genetic suppression ; intracellular proteolysis ; antibody screen ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A mutant Cro protein, which bears the Ile-30→ Leu substitution, is thermally unstable and degraded more rapidly than wildtype Cro in vivo. Using an antibody screen, we have isolated five different second site suppressor substitutions that reduce the proteolytic hypersensitivity of this mutant Cro protein. Two of the suppressor substitutions increase the thermal stability of Cro by 12°C to 14°C. These amino acid substitutions affect residues 16 and 26, which are substitutions affect residues 16 and 26, which are substantially exposed to solvent in the crystal structure of wild-type Cro.
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  • 64
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 211-217 
    ISSN: 0887-3585
    Keywords: tyrosin ; mutant protein ; amino acid substitution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: CD spectra in the aromatic region of a series of the mutant α-subunits of tryptophan synthase from Escherichia coli, substituted at position 49 buried in the interior of the molecule, were measured at pH 7.0 and 25°C. The measurements were taken to gain information on conformational change produced by single amino acid substitutions. The CD spectra of the mutant proteins, substituted by Tyr or Trp residue in place of Glu residue at position 49, showed more intense positive bands due to one additional Tyr or Trp residue at position 49. The CD spectra of other mutant proteins also differed from that of the wild-type protein, despite the fact that the substituted residues at position 49 were not aromatic. Using the spectrum of the wild-type protein (Glu49) as a standard, the spectra of the other mutants were classified into three major groups. For 10 mutant proteins substituted by Ile, Ala, Leu, Met, Val, Cys, Pro, Ser, His, or Gly, their CD values of bands (due to Tyr residues) decreased in comparison with those of thewild-type protein. The mutant protein substituted by Phe also belonged to this group. These substituted amino acid residues are more hydrophobic than the original residue, Glu. In the second group, three mutant proteins were substituted by Lys, Gln, or Asn, and the CD values of tyrosyl bands increased compared to those of the wild-type proteins. These residues are polar. In the third group, the CDvalues of tyrosyl bands of two mutant proteins substituted by Asp or Thr were similar to those of the wild-type protein, except for oneband at 276.5 nm. these results suggested that the changes in the CD spectra for the mutant proteins were affected by the hydrophobicity of the residuesat position 49.
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  • 65
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    Proteins: Structure, Function, and Genetics 5 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 66
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 266-270 
    ISSN: 0887-3585
    Keywords: crystallization ; purification ; crystals ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Single crystals of T7 RNA polymerase have been grown to a maximum size of 1.8 × 0.3 × 0.3 mm. The crystals are composed of fully intact T7 RNA polymerase which in enzymatically active upon dissolution. These crystals belong to the monoclinic space group P21 and have unit cell parameters a =114.5 Å, b=139.6 Å, c=125.7 Å, β=98.1° Self-rotation function studies indicate that there are three molecules per asymmetricunit. The crystals diffract to at least 3.0 Å resolution. These are the first crystals of a DNA-dependent RNA polymerase suitable for high-resolution X-ray structure determination.
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 233-247 
    ISSN: 0887-3585
    Keywords: protein folding ; crystallographic data base ; structural analysis ; computer program system ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: PKB is a computer program system that combines a data base of three-dimensional protein structures with a series of algorithms for pattern recognition, data analysis, and graphics. By typing relatively simple commands the user may search the data base for instances of a structural motif and analyze in detail the set of individual structures that are found. The application of PKB to the study of protein folding is illustrated in three examples. The first analysis compares the conformations observed for a short sequential motif, sequences similar to the cell-attachment signal Arg-Gly-Asp. The second compares sequences observed for a conformational motif, a 16-residue βαβ unit. The third analysis considers a population of substructures containing ion-pair interaction, examining the relationship offrequency of occurrence to calculated electrostatic energy.
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  • 68
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    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 69
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 46-60 
    ISSN: 0887-3585
    Keywords: macromolecular conformation ; protein folding ; helical axis ; secondary structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present a general and mathematically rigorous algorithm which allows the helicoidal structure of a protein to be calculated starting from the atomic coordinated of its peptide backbone. This algorithm yields a unique curved axis which quantifies the folding of the backbone and a full set of helicoidal parameters describing the location of each peptide unit. The parameters obtained form a complete and independent set and can therefore be used for analyzing, comparing, or reconstructing protein backbone geometry. This algorithm has been implemented in a computer program named P-Curve. Several examples of its possible applications are discussed.
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  • 70
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 61-69 
    ISSN: 0887-3585
    Keywords: peptides ; hormones ; amphipathic helix ; hydrophobic moment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Eisenberg's helical hydrophobic moment (〈μH〉) algorithm was applied to the analysis of the primary structure of amphipathic α-helical peptide hormones and an optimal method for identifying other peptides of this class determined. We quantitate and compare known amphipathic helical peptide hormones with a second group of peptides with proven nonamphipathic properties and determine the best method of distinguishing between them. The respective means of the maximum 11 residue 〈μH〉 for the amphipathic helical and control peptides were 0.46 (±/-0.07) and 0.33 (0.07) (P+0.004). To better reflect the amphipathic potential of the entire peptide, the percent of 11 residue segments in each peptide above a particular 〈μH〉 was plotted vs 〈μH〉. The resulting curves are referred to as HM-C. The mean HM-C (of the two groups) was highly significantly different such that the HM-C method was superior to others in its ability to distinguish amphipathic from nonamphipathic peptides. Several potential new members of this structural class were identified using this approach. Molecular modeling of a portion of one of these, prolactin inhibitory factor, reveals a strongly amphipathic α helix at residues 4-21. This computer-based method may enable rapid identification of peptide of the amphipathic α-helix class.
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  • 71
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 128-138 
    ISSN: 0887-3585
    Keywords: DNA repair ; ultravioletlight ; pyrimidine dimers ; glycosylase ; apurinic/apyrimidinic endonuclease ; DNA repair enzymology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Previous structure/function analyses of the DNA repairenzyme, T4 endonuclease V, have suggested that the extreme carboxyl portion of the enzyme is associated with pyrimidine dimer-specific binding (Recinos and Lloyd, and Stump and Lloyd, Biochemistry 27:1832-1838 and 1839-1843, 1988, respectively). Within the final 11 amino acids there are 5 aromatic, 2 basic, and no acidic residues and it has been proposed that these residues stack with and electrostatically interact with the kinked DNA at the site of a pyrimidine dimer. The role of the tyrosine residue at position 129 has beeninvestigated by oligonucleotide site-directed mutagenesis in which the codon for Tyr-129 has been altered to reflect conservative changesof Trp and Phe and more dramatic changes of Ser- a stop, codon, deletion of the codon or introduction of a frameshift. Both changesto the aromatic amino acids resulted in proteins which accumulated will in E. coli and not only significantly enhanced the UV survival of repair, deficient cells but also complemented a defective denV gene within UV-irradiated T4 phage. Partially purified preparations of the Tyr-129 → Trp and Tyr-129 → Phe mutants were assayed for their ability to processively incise UV-irradiated plasmid DNA (a nicking reaction carried out at low 25 mM salt concentrations). The mutant enzymes Tyr-129 → Phe and Tyr-129 → Trp displayed a 1000% and 500% enhanced specific nicking activity, respectively. These reactions were also shown to be completely processive. Assays performed at higher (100 mM) salt concentrations reduced the specific activities of the mutant enzymes approximately to that of wild type for the Tyr-129 → Phe mutant and to 20% that of wild type for the Tyr1-29 → Trp mutant.
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  • 72
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 168-192 
    ISSN: 0887-3585
    Keywords: salt bridge ; ab initio ; calcium ; magnesium ; carboxylate ; phosphate ; ammonium ; guanidinium ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Equilibrium geometries and binding energies of model “salt” or “ion” bridge systems have been computed by ab initio quantum chemistry techniques (GAUSSIAN82) and by empirical techniques (AMBER2.0). Formate and dimethyl phosphate served as anions in the model compounds while interacting with several organic cations, including methyl ammonium, methyl guanidinium, and divalent metal ion (either Mg2+ or Ca2+) without and with an additional chloride; and a divalent metal ion (either Mg2+ or Ca2+), chloride, and four water molecules of hydration about the metal ion. The majority of the quantum chemical computations were performed using a split-valence basis set. For the model compounds studied we find that the ab initio geometries are in remarkably goodagreement with the molecular mechanics geometries.Several Calculations werealso performed using diffuse fractions. The formate anion binds these modelcations more strongly than does dimethyl phosphate, while the organiccation methyl ammonium binds model anions more strongly than does methyl guanidinium. Finally, in model compounds including organic anions, Mg2+ or Ca2+ and four molecules of water, and a chloride anion, we find that the equilibrium structure of the magnesium complex involves a solvent separated ion pair (the magnesium ion is six coordinate), whereas the calcium ion complex remains seven coordinate. Molecular mechanics overestimates binding energies, but the estimates may be close enough to actual binding energies togive useful insight into the details energies to give useful insight into the details of salt bridges in biological systems.
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  • 73
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 306-315 
    ISSN: 0887-3585
    Keywords: oncogene ; GTP-binding protein ; cancer ; S. cerevisiae adenylyl cyclase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Biologically active forms of Ras complexed to GTP can bind to the GTP ase-activating protein (GAP), which has been implicated as a possible target of Ras in mammalian cells. In order to study the structural features of Ras required for this interaction, we have evaluated a series of mutant ras proteins for the ability to bind GAP and a series of Ras peptides for the ability to interfere with this interaction. Point mutations in the putative effector region of Ras (residues 32-40) that inhibit biological activity also impair Ras binding to GAP. An apparent exception is the Thr to Ser substitution at residue 35; [Ser-35]Ras binds to GAP as effectively as wild-type Ras even though this mutant is biologically weak in both mammalian and S. cerevisiae cells. In vitro, [Ser-35]Ras can also efficiently stimulate the S. cerevisiae target of Ras adenylyl cyclase, indicating that other factors may influence Ras/protein interactions in vivo. Peptides having Ras residues 17-44 and 17-32 competed with the binding of RAS to E. coli-expressed GAP with IC50 values of 2.4 and 0.9 μM, respectively, whereas Ras peptide 17-26 was without effect up to 400 μM. A related peptide from the yeast GTP-binding protein YPT1 analogous to Ras peptide 17-32 competed with an IC50 value of 19 μM even though the YPT1 protein itself is unable to bind to GAP. These results suggest that determinants within Ras peptide 17-32 may be important for Ras binding to GAP.
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  • 74
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 357-371 
    ISSN: 0887-3585
    Keywords: sea anemone toxin ; NMR ; distance geometry ; restrained energy minimization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: With the aid of 1H nuclear magnetic resonance (NMR) spectroscopy, the three-dimensional structure in aqueous solution was determined for ATX Ia, which is a 46 residue polypeptide neurotoxin of the sea anemone Anemonia sulcata. The input for the structure calculations consisted of 263 distance constraints from nuclear Overhauser effects (NOE) and 76 vicinal coupling constants. For the structure calculation several new or ammended programs were used in a revised strategy consisting of five successive computational steps. First, the program HABAS was used for a complete search of all backbone and χ1 conformations that are compatible with the intraresidual and sequential NMR constraints. Second, using the program DISMAN, we extended this approach to pentapeptides by extensive sapling of al conformations that are consistent with the local and medium-range NMR constraints. Both steps resulted in the definition of additional dihedral angle constraints and in stereospecific assignments for a number of β-methylene groups. In the next two steps DISMAN was used to obtain a group of eight conformers that contain no significant residual violations of the NMR constraints or van der Waals contacts. Finally, these structures were subjected to restrained energy refinement with a modified version of the molecular mechanics module of AMBER, which in addition to the energy force field includes potentials for the NOCE distance constraints and the dihedral angle constraints. The average of the pairwise minimal RMS distances between the resulting refined conformers calculated for the well defined molecular core, which contains the backbone atoms of 35 residues and 20 interior side chains, is 1.5 ± 0.3 Å. This core is formed by a four-stranded β-sheet connected by two well-defined loops, and there is an additional flexible loop consisting of the eleven residues 8-18. The core of the protein is stabilized by three disulfide bridges, which are surrounded by hydrophobic residues and shielded on one side by hydrophilic residues.
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  • 75
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 424-430 
    ISSN: 0887-3585
    Keywords: ultracentrifugation ; calcium-binding proteins ; fluorescence resonance energy transfer ; pH effect ; hydrophobic interactions ; troponin C dimer ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have investigated pH-dependent changes of the properties of troponin C from rabbit skeletal muscle. At pH 7.5 this protein is a monomer and at pH 5.2 it is a dimer. In contrast, bovine cardiac troponin C remains essentially monomeric at pH 5.2. Bovine brain calmodulin is not a dimer, but significantly aggregated at the same acidic pH. The dimerization of skeletal troponin C was demonstrated by low-speed (16,000 rpm) sedimentation equilibrium measurements carried out at 20°C and by polyacrylamide gel electrophoresis under nondenaturing conditions. Dimer formation was significantly inhibited in the ultracentrifuge at rotor speeds of 30,000 and 40,000 rpm at 20°C, and was completely prevented at a rotor speed of 40,000 rpm and 4°C. This temperature and pressure dependence of dimerization strongly suggests that hydrophobic bonding is a major factor in promoting skeletal troponin C association at pH 5.2. The intramolecular distance between Met-25 and Cys-98 of rabbit skeletal troponin C deduced from fluorescence resonance energy transfer measurements increased by a factor of two upon lowering the pH from 7.5 to 5.2, indicating a pH-dependent transition in which the protein changed from a relatively compact conformation to an elongated conformation. The protein-induced increase in the energy transfer distance is related to the acid-induced dimerization of the protein. The extended conformation observed at pH 5.2 is compatible with the dumbbell-shaped structure of skeletal troponin C crystals obtained from turkey at pH 5.0 [Herzberg, O., James, M. N. G. Nature (London) 313:653-659, 1985] and chicken at pH 5.1 (Sundaralingam, M., Bergstrome, R., Strasburg, G., Rao, S. T., Roychowdhury, P., Greaser, M., Wang, B. C. Science 227:945-948, 1985). However, the conformation in neural solution deviates form that predicted by crystallography. Intermolecular interactions leading to dimer formation likely play an important role in promoting the extended conformation that exists at acidic pH.
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  • 76
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 8-12 
    ISSN: 0887-3585
    Keywords: ribonuclease A ; protein deamidation ; protein conformation ; disulfide bonds ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The effect of the folded conformation of a protein on the rate of deamidation of a specific asparaginyl residue has been determine. Native and unfolded ribonuclease A (RNase A) could be compared under identical conditions, because stable unfolded protein was generated by breaking irreversibly the protein disulfide bonds.Deamidation of the labile Asn-67 residue of RNase A was followedelectrophoretically and chromatographically. At 80°C, similar rates of deamidation were observed for the disulfidebonded form, which is thermally unfolded, and the reduced form. At 37°C and pH 8, however, the rate of deamidation of native RNase A was negligible, and was more than 30-fold slower than that of reduced, unfolded RNase A. This demonstrates that the Asn-67 residue is located in a local conformation in the native protein that greatly inhibits deamidation. This conformation is the β-turn of residues 66-68.
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  • 77
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 1-7 
    ISSN: 0887-3585
    Keywords: helix stabilization ; helix dipole ; charged group ; pH titration ; electrostatic interaction ; hydrogen bonding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Interactions between the α-helix peptide dipoles and charged groups close to the ends of the helix were found to be an important determinant of α-helix stability in a previous study.1 The charge on the N-terminal residue of the C-peptide from ribonuclease A was varied chiefly by changing the α-NH2 blocking group, and the correlation of helix stability with N-terminal charge was demonstrated. An alternative explanation for some of those results is that the succinyl and acetyl blocking groups stabilize the helix by hydrogen bonding to an unsatisfied main-chain NH group. The helix dipole model is tested here with peptides that contain either a free α-NH3+ α-COO- groups, and no other charged groups that would titrate with similar pKa's. This model predicts that α-NH3α-COO- groups are helix-destabilizingand that the destabilizing interactions are electrostatic in origin. The hydrogen bonding model predicts that α-NH3 and α-COO- groups are not themselves helix-destabilizing, but that an acetyl or amide blocking group at the N- or C- terminus, respectively, stabilizes the helix by hydrogen bonding to an unsatisfied main-chain NH or CO group.The results are as follows: (1) Removal of the charge from α-NH3 and α-COO- groups by pH titration stabilizes an α-helix. (2) The increase in helix stability on pH titration of these groups is close to the increase produced by adding an acetyl or amide blocking group. (3) The helix-stabilizing effect of removing the charge from α-NH3 and α-COO- groups by pH titration is screened by increasing the NaCl concentration, and therefore the effect is electrostatic in origin. (4) Replacing the C-terminal amide blocking group with a methylester blocking group, which cannot donate a hydrogen bond, causes little change in helix stability.
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  • 78
    ISSN: 0887-3585
    Keywords: template-assembled synthetic protein (TASP) ; 4-helix bundle ; β-barrel structure ; protein de novo design ; peptide synthesis ; peptide conformation ; orthogonal protection ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The construction of a template-assembled synthetic protein (TASP) designed to contain both a 4-helix bundle and a β-barrel as two folding “domains” is described. For the de novo design of proteins, amphiphilic helices (α) and β-sheets (β) are covalently attached to a template peptide (T) carrying functional side chains suitably oriented to promote intarmolecular folding of the secondary structure blocks into a characteristic packing arrangement, i.e., T8-(4α)(4β). The design of this new macromolecule was assisted by computer modeling, which suggested a low-energy conformation with tight hydrophobic packing of the secondary structure subunits. Solid-phase synthesis of the “two-domain” TASP molecule was achieved using orthogonal protection techniques. The solution properties as well as circular dichroism (CD) and infrared spectroscopy (IR) data under various experimental conditions are consistent with the folded conformation suggested by modeling.
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  • 79
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 313-321 
    ISSN: 0887-3585
    Keywords: protein ; electron transfer ; molecular dynamic simulations ; dielectric ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Electrostatic calculations have been carried out on a number of structural conformers of tuna cytochrome c Conformers were generated using molecular dynamics simulations with a range of solvent simulating, macroscopic dielectric formalisms, and one solvent model that explicitly included solvent water molecules. Structures generated using the lowest dielectric models were relatively tight, with-side chains collapsed on the surface, while those from the higher dielectric modelshad more internal and external fluidity, with surface side chains exploring a fuller range of conformational space. The average structure generated with the explicitly solvated model corresponded most closely with the crystal structure. Individual pK values, overall titration curves, and electrostatic potential surfaces were calculated for average structures and along each simulation. Differences between structural conformers within each simulation give rise to substantial changes in calculated local electrostatic interactions, resulting in pK value fluctuations for individual sites in the protein that very by 0.3-2.0 pK units from the calculated time average. These variations are due to the thermal side chain reorientations that produce fluctuations in charge site separations. Properties like overall titration curves and pH dependent stability are not as sensitive to side chain fluctuations within a simulation, but there are substantial effects between simulation due to markeddifferences in average side chain behavior. These findings underscore the importance of proper dielectric formalism in molecular dynamics simulations when used to generate alternate solution structures from a crystal structure, and suggest that conformers significantly removed from the averagestructure have altered electrostatic properties that may prove important inepisodic protein properties such as catalysis.
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  • 80
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 78-92 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 81
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 97-103 
    ISSN: 0887-3585
    Keywords: protein conformation ; dynamics ; Monte Carlo simulation ; conformational energy ; minimization ; spin glass ; conformational substates ; conformational heterogeneity ; hierarchy in dynamics ; trypsin inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A computer experiment of protein dynamics is carried out, which consists of two steps: (1) A Monte Carlo simulation of thermal fluctuations in the native state of a globular protein, bovinepancreatic trypsin inhibitor; and (2) a simulation of the quick freezingof fluctuating conformations into energy minima by minimization of the energy of a number of conformations sampled in the Monte Carlo simulations sampled in the Monte Carlo simulation. From the analysis of results of the computer experiment is obtained the following picture of protein dynamics:multiple energy minima exist in the native state, and they are distributedin clusters in the conformational space. The dynamics has a hierarchical structure which has at least two levels. In the first level, dynamics is restricted within one of the clusters of minima. In the second, transitions occur among the clusters. Local parts of a protein molecule, side chains and local main chain segments, can take multiple locally stable conformations in the native state. Many minima result from combinations of these multiple local conformations. The hierarchical structure in the dynamics comes from interactions among the local parts. Protein moleculeshave two types of flexibility, each associated with elastic and plastic deformations, respectively.
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  • 82
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 149-155 
    ISSN: 0887-3585
    Keywords: solution scattering ; low-angle scattering ; spherical averaging ; spherical harmonics ; spherical Fourier transform ; bound water ; solvent structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: If one expands the structure factor equation in spherical coordinates, rotational averaging of the molecular Fourier transform, which leads directly to the solution scattering profile, is greatly simplified. It becomes a projection in the polar and azimuthal angular variables. The profile is given by The index j runs over all atoms; r, θ, φ are atomic coordinates and ε and N are constants; the Ym,n are complex spherical harmonics, and Jn are spherical Bessel functions; R = 2 sin θ/λ. The effects of solvent have been modeled by subtracting from each protein atom a properly weighted water. Hydrogens have been included by using scattering curves fj derived from the spherical averaging ofprotein atoms with their attached hydrogens. This approach may also be satisfactory for neutron scattering. Published scattering profiles2 for lysozyme and BPTI have been accurately matched in less than one-tenth the time required by other methods. Separate, adjustable temperature factors for the protein, solvent waters, and bound watersare used, and appear to be needed. In the case of BPTI, as suggested by NMR observations, the observed diffraction pattern was much better accounted for by including only 4 tightly bound waters rather than the roughly 60 seen by crystallography.
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  • 83
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 156-165 
    ISSN: 0887-3585
    Keywords: retrovirus integrase ; circular dichroism ; homologous proteins ; secondary structural predictions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The retrovirus integrase (IN) protein is essentialfor integration of viral DNA into host DNA. The secondary structure of thepurified IN protein from avian myeloblastosis virus was investigated by bothcircular dichroism (CD) spectroscopy and five empirical prediction methods. The secondary structures determined from the resolving of CD spectra through a least-squares curve fitting procedure were compared with those predicted from four statistical methods, e.g., the Chou-Fasman, arnier-Osguthorpe-Robson, Nishikawa-Ooi, and a JOINT scheme which combined all three of these methods, plus a pure a priori one, the Ptitsyn-Finkelstein method. Among all of the methods used, the Nishikawa-Ooiprediction gave the closest match in the composition of secondary structureto the CD result, although the other methods each correctly predictedoneor more secondary structural group. Most of the α-helix and β-sheet states predicted by the Ptitsyn-Finkelstein methodwere in accord with the Nishikawa-Ooi method. Secondary structural predictions by the Nishikawa-Ooi method were extended further toinclude IN proteins from four phylogenetic distinct retroviruses. The structuralrelationships between the four most conserved amino acid blocks of these IN proteins were compared using sequence homology and secondary structure predictions.
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  • 84
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 183-201 
    ISSN: 0887-3585
    Keywords: crystallographic refinement ; restrained least-squares refinement ; Konnert-Hendrickson refinement ; phosphodiesterase ; protein structure ; enzyme mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of a complex of staphylococcal nuclease with Ca2+ and deoxythymidine 3′,5′-biophosphate (pdTp) has been refined by stereochemically restrained leastsquares minimization to a crystallographic R value of 0.161 at Å resolution. The estimated root-mean-square (rms) error in the coordinates in 0.16 Å. The final model comprises 1082 protein atoms, onecalcium ion, the pdTp molecule, and 82 protein atoms, onecalcium ion, the pdTp molecule, and 82 solvent water molecules;it displays an rms deviation from ideality of 0.017 Å for bond distances and 1.8° for bond angles.The mean distance between corresponding α carbons in the refined and unrefined structures is 0.6 Å we observe small but significant differences between the refined and unrefined models in the turn between residues 27 and 30, the loop between residues 44 and 50, the first helix, and the extended strand between residues 112 and 117 which forms part of the active site binding pocket.The details of the calcium liganding and solvent structure in the activesite are clearly shown in the final electron density map. The structure ofthe catalytic site is consistent with mechanism that has been proposed for this enzyme. However, we note that two lysines from a symmetry-related molecule in the crystal lattice may play an important role in determining the geometry of inhibitor binding, and that only one of the two required calcium ions is observed in the crystal structure; thus, caution is advised in extrapolating from the structure of the complex of enzyme and inhibitor to that enzyme and substrate.
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  • 85
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    Proteins: Structure, Function, and Genetics 5 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 86
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 224-232 
    ISSN: 0887-3585
    Keywords: effective pore's radius ; α-ketoglutarate dehydrogenase complex ; branched chain α-keto acid dehydrogenase complex ; electron microscopy ; multienzyme complex ; two-dimensional ; electrophoresis ; multienzyme complex ; aggregation of Pyruvate dehydrogenase complex ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In the studies of the size and structure of multienzyme complexes, a procedure complementary to electron microscopy for determining the molecular dimensions of hydrated multisubunit complexes is needed. For some applications this procedure must be capable of detecting aggregation of complexes and must be applicable to impure preparations. In the present study, a procedure of two-dimensional agarose gel electrophoresis (2d-AGE) (Serwer, P. et al. Anal. Biochem. 152: 339-345, 1986) was modified and employed to provide accurate sizemeasurements of several classical multienzyme complexes. To improve band clarity and to achieve required gel pore sizes, a hydroxyethylated agarose was used. The effective pore's radius (PE) as a function of gel concentration was determined for this agarose inthe range of PE value needed for multienzyme complexes (effective radius, R = 10-30 nm). Appropriate conditions wereestablished to measure R value ± 1% of the pyruvate (PDC), α-ketoglutarate (α-KGDC), and the branched chain α-keto acid (BCDC) dehydrogenase multienzyme complexes; the accuracy of R was limited by the accuracy of the determinations of the R value for the sizestandards. The PDC from bovine heart was found to have an R = 22.4 ± 0.2 nm following cross-linking with glutaraldehyde that was necessary for stabilization of the complex. Dimers and trimers of PDC, present in the preparations used, were separated from monomeric PDCduring 2d-AGE. All R values for the enzyme complexes studied were agreement with, though more accurate than, R valuesobtained by use of electron microscopy. In contrast to this statement, the internal dihydrolipoyl transacetylase core of PDC (E2) had an R of 18.8 ± 0.2 nm using 2d-AGE, but 10.5 nm by electron microscopy. This observation confirms the proposal that the core of the PDC has externally projecting fibrous domains invisibleto electron microscopy.
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  • 87
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 259-265 
    ISSN: 0887-3585
    Keywords: cDNA expression ; deletion mutagenesis ; zymogen activation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cultured mouse myeloma cells were transfected with expression vectors encoding the aspartyl proteinase, human renin. The full construct, encoding the renin precursor prorenin, allows transfected cellsto secrete the enzymically inactive pro-protein. Activity is detectable only following trypsin treatment which mimics the physiological activation step. Accordingly, it appears that myeloma cells do not contain detectable levels of an appropriate activating proteinase. However, when these cells are transfected with a construct from which the pro-peptide coding sequence has been deleted, they secrete an apparently fully active enzyme which is indistinguishable from mature renin. We conclude that expression of the pro-peptide is not necessary to allow correct folding of the molecule and its passage through the secretory pathway.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 88
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 281-288 
    ISSN: 0887-3585
    Keywords: Hu protein ; integration host factor ; transcription factor 1 ; DNA bending protein ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The prokaryotic protein HU, integration host factor (IHF) from Escherichia coli and transcription factor 1 (TF1) from bacteriophage SPO1 are closely related molecules. Biochemical results suggest that the role of these proteins is to bind and bend DNA. From the high-resolution structure of HU, we propose a model for thisinteraction with DNA. Crucial amino acid differences between the proteins can be rationalized in terms of their different specific functions.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 89
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 322-336 
    ISSN: 0887-3585
    Keywords: sequence conservation ; exon ; gene duplication ; protein folding ; structure-function ; X-ray structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Detailed analysis of the CuZn superoxide dismutase (SOD) structure provides new results concerning the significance and molecular basis for sequence conservation, intron-exon boundary locations, gene duplication, and Greek key β-barrel evolution. Using 15 aligned sequences, including a new mouse sequence, specific roles have been assigned to all 23 invariant residues and additional residues exhibiting functional equivalence. Sequence invariance is dominated by 15 residues that form the active site stereochemistry, supporting a primary biological function of uperoxide dismutation. The β-strands have no sequence insertions and deletions, whereas insertions occur within the loops connecting the β-strands and at both termini. Thus, the β-barrel with only four invariant residues is apparently over determined, but dependent on multiple cooperative side chain interactions. The regions encoded by exon I, a proposed nucleation site for protein folding, and exon III, the Zn loop involved in stability and catalysis, are the major structural subdomains not included in the internal twofold axis of symmetry passing near the catalytic Cu ion. This provides strong confirmatory evidence for gene evolution by duplication and fusion followed by the addition of these two exons. The proposed evolutionary pathway explains the structural versatility ofthe Greek key β-barrel through functional specialization and subdomain insertions in new loop connections, and provides a rationale for the size of the present day enzyme.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 90
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 1-19 
    ISSN: 0887-3585
    Keywords: virus crystallography ; molecular dynamics ; hydrophobic pockets ; antiviral agents ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: X-Ray diffraction data have been obtained for nine related antiviral agents (“WIN compounds”) while bound to human rhinovirus 14 (HRV14).These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (∼60percnt;) occupancies of these compounds in the crystal, (2) the large (up to 7.9 Å) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps.The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the β-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the β-barrel.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 91
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 92
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 104-127 
    ISSN: 0887-3585
    Keywords: lac repressor; lac operator ; lac headpiece-operator complex ; protein-DNA specificity ; molecular dynamics ; computer simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The results of a 125 psec molecular dynamics simulation of a lac headpiece-operator complex in aqueous solution are reported. The complexsatisfies essentially all experimental distance information derived from two-dimensional nuclear magnetic resonance (2-D-NMR) studies. The interaction between lac repressor headpiece and its operator based on many direct- and water-mediated hydrogenbonds and nonpolar contacts which allow the formation of a tight complex. Nostable hydrogen bonds between side chains and bases and found, while specific contacts occur between both nonpolar groups and, to a lesserextent, through water-mediated hydrogen bonds. The simulated complex structure in water is intrinsically stable without application of nuclear Overhauser effect (NOE) distance restraints, while being compatible with most of the available biochemical, genetic, andchemically induced dynamic nuclear polarization (CIDNP) data.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 93
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 94
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 217-221 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
    Type of Medium: Electronic Resource
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  • 95
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 240-248 
    ISSN: 0887-3585
    Keywords: substrate-assisted catalysis ; serine protease ; fusion proteins ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A combination of protein engineering and substrate optimization was used to create variants of the serine protease, subtilisin BPN′, which efficiently and specifically cleave a designed target sequence in a fusion protein. The broad substrate specificity of wildtype subtilisin BPN′ is greatly restricted by substitution of the catalytic histidine 64 with alanine (H64A) so that certain histidine-containing substrates are preferentially hydrolysed (Carter, P., Wells, J. A. Science 237:394-399, 1987). The catalytic efficiency, (kcat/Km), of this H64A variant was increased almost 20-fold by judicious choice of substrate and by installing three additional mutations which increase the activity of wild-type subtilisin. The most favorable substrate sequence identified was introduced as a linker in a fusion protein between a synthetic IgG binding domain of Staphylococcus aureus protein A and Escherichia coli alkaline phosphatase. The fusion protein (affinity purified on an IgG column) was cleaved by the prototype H64A enzyme and its improved variant, efficiently and exclusively at the target site, to liberate an alkaline phosphatase product of the expected size and N-terminal sequence. Several features of H64A variants of subtilisin make them attractive for site-specific proteolysis of fusion proteins: they have exquisite substrate specificity on the N-terminal side of the cleavage site and yet are broadly specific on the C-terminal side; they can be produced in large quantities and remain highly active even in the presence of detergents, reductants (modest concentrations), protease inhibitors, at high temperatures, or when specifically immobilized on a solid support.
    Additional Material: 4 Ill.
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  • 96
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 284-293 
    ISSN: 0887-3585
    Keywords: calmodulin ; peptides ; fluorescence spectroscopy ; photoaffinity labeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Calmodulin is known to bind target enzymes and basic, amphiphilic peptides in a Ca2+-dependent manner. Recently, we introduced a photoaffinity label, p-benzoylphenylalanine (Bpa), into the sequence of a model, α-helical, calmodulin-binding peptide. When the Bpa residue was introduced at the third position of the peptide, Met-144 on the C-terminal domain of calmodulin was labeled, whereas when the photolabel was placed at the thirteenth position, Met-71 on the N-terminal do main was labeled. Assuming that both peptides bind in similar orientations, these results are not consistent with the crystal structure of calmodulin, in which the domains are held at a significant distance from one another by a long α-helical segment. To test the assumption that both peptides bind in similar orientations, we have synthesized a calmodulin-binding peptide with the photolabel in both the third and the thirteenth positions. Upon photolysis, this peptide forms a cross-link between Met-71 and Met 124 on the N- and C-terminal domains, respectively. Furthermore, a peptide with a Bpa in the thirteenth position and a Trp residue in the third position was also synthsized. After photocross-linking the Bpa redidue of this peptide to Met-71 of calmodulin, it could be shown that the fluorescence properties of the Trp residue were consistent with its side chain being buried in a hydrophobic pocket on the C-terminal domain of calmodulin. These data indicate that, when complexed with basic, amphiphi peptides, calmodulin can adopt a conformation in which its two domains are significantly closer than in the crystal sturcture of the uncommplexed protein.
    Additional Material: 6 Ill.
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  • 97
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 231-239 
    ISSN: 0887-3585
    Keywords: phosphotyrosine linkage ; protein-DNA transesterification ; enzyme mechanism ; DNA-protein covalent complex ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Tyrosine 319 of E. coli topoisomerase I is shown to be the activesite tyrosine that becomes covalently attached to a DNA 5′ phosphoryl group during the transient breakage of a DNA internucleotide bond by the enzyme. The tyrosine was mapped by trapping the covalent complex between the DNA and DNA topoisomerase I, digesting the complex exhaustively with trypsin, and sequencing the DNA-linked tryptic peptide. Site-directed mutagenesis converting Tyr-319 to a serine or phenylalanine completely inactivates the enzyme. The structure of the enzyme andits catalysis of DNA strand breakage, passage, and rejoining are discussed in terms of the available information.
    Additional Material: 4 Ill.
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  • 98
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 259-266 
    ISSN: 0887-3585
    Keywords: protein folding ; folding intermediate ; hydrophobic effect ; tryptophan fluorescence ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The rapid kinetic phase that leads from unfolded species to transient folding intermediates in dihydrofolate reductase from Escherichia coli was examined by site-directed mutagenesis and by physicochemical means. The absence of this fluorescence-detected phase in the refolding of the Trp-74Phe mutant protein strongly implies that this early phase in refolding can be assigned to just one of the five Trp residues in the protein, Trp-74. In addition, water-soluble fluorescence quenching agents, iodide and cesium, have a much less significant effect on this early step in refolding than on the slower phases that lead to native and nativelike conformers. These and other data imply that an important early event in the folding of dihydrofolate reductase is the formation of a hydrophobic cluster which protects Trp-74 fromsolvent.
    Additional Material: 3 Ill.
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  • 99
    ISSN: 0887-3585
    Keywords: α-helix ; EPR ; trypsinolysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Colicin E1 is an E. coli plasmid-lencoded water-soluble protein that spontaneously inserts into lipid membranes to form a voltage-gated ion channel. We have employed a novel approach is which site-directed mutagenesis is used to provide highly specific attachment points for nitroxide spin labels. A series of colicin mutants, differing only by the position of a single cysteine residue, were prepared and selectively labeled at that cysteine. A hydrophilic sequence (398-406) within the C-terminal domain of the water-soluble form of the protein was investigated and exhibited an electron paramagnetic resonancc (EPR) spectral periodicity strongly suggesting an amphiphilic α-helix. After removal of the N—terminus of the protein with trypsin, the spectra for this sequence indicate increased label mobility and a more flexible structure.
    Additional Material: 7 Ill.
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  • 100
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 382-394 
    ISSN: 0887-3585
    Keywords: immunoglobulins ; hydrogen bonding ; hairpin loops ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Loops are integral components of protein structures, providing links between elements of secondary structure, and in many cases contributing to catalytic and binding sites.The conformations of short loops are now understood to depend primarily on their amino acid sequences. In contrast, the structural determinants of longer loops involve hydrogen-bonding and packing interactions within the loop and with other parts of the protein. By searching solved protein structures for regions similar in main chain conformation to the antigen-binding loops in immunoglobulins, we identified medium-sized loops of similar structure in unrelated proteins, and compared the determinants of their conformations.For loops that form compact substructures the major determinant of the conformation is the formation of hydrogen bonds to inward-pointing main chain atoms. For oops that have more extended conformations, the major determinant of their structure is the packing of a particular residue or residues against the rest of the protein.The following picture emerges: Medium-sized lops of similar conformation are stabilized by similar interaction. The groups that interact with the loop have very similar spatial dispositions with respect to the loop. However, the residues that provide these interactions may arise from dissimilar parts of the protein: The conformation of the loop requires certain interactions that the protein may provide in a variety of ways.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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