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  • 1990-1994  (1,866)
  • 1880-1889
  • Genetics  (1,100)
  • Biochemistry  (766)
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Sexual plant reproduction 7 (1994), S. 290-296 
    ISSN: 1432-2145
    Keywords: Secale cereale ; Polyembryony ; Chromosome mosaics ; Rye ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have obtained one plant regenerated from rye tissue culture which showed a high percentage of polyembryonic seeds in its progeny. The mutation inducing the development of extra embryos is also influencing erroneous cell division, mitosis and meiosis. The genetic analysis indicated that the aptitude for polyembryonic seed formation is a heritable trait controlled by a dominant gene. However, for expression of the phenotype the female parent should have a specific cytoplasm.
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  • 2
    ISSN: 1432-2242
    Keywords: Breeding ; Helminthosporium turcicum ; RFLP ; QTLs ; Disease-resistance ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RFLPs were used to investigate components of host-plant response to Exserohilum turcicum in 150 unselected F2∶3 lines of a B52/Mo17 maize population. Following inoculation with spore suspensions of the pathogen (race 0), components of disease development were measured and then quantitative trait mapping was performed to identify the location and effects of quantitative trait loci (QTLs) determining host-plant response. Components of interest were the average number of lesions per leaf, the average percent leaf tissue diseased (severity) and the average size of lesions (cm2). Based on a LOD threshold of 2.31 (P〈0.05), the number of lesions appears to be associated with QTLs on chromosomes 1S, 3L, 5S. Severity was associated with analogous regions and, in addition, QTLs on chromosomes 7L and 8L. Most QTLs, for either of these two components, involve additive gene action and partial dominance or overdominance. In contrast, lesion size was associated with QTLs on chromosomes 7L and 5L; recessive gene action may be involved at 7L.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 89 (1994), S. 959-963 
    ISSN: 1432-2242
    Keywords: Sugarcane ; Polyploidy ; Genetics ; Evolution ; Breeding ; DNA markers ; Arbitrarily primed PCR ; RAPD markers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Recent work has revealed random chromosome pairing and assortment in Saccharum spontaneum L., the most widely distributed, and morphologically and cytologically variable of the species of Saccharum. This conclusion was based on the analysis of a segregating population from across between S. spontaneum ‘SES 208’ and a spontaneously-doubled haploid of itself, derived from anther culture. To determine whether polysomic inheritance is common in Saccharum and whether it is observed in a typical biparental cross, we studied chromosome pairing and assortment in 44 progeny of a cross between euploid, meiotically regular, 2n=80 forms of Saccharum officinarum ‘LA Purple’ and Saccharum robustum ‘ Mol 5829’. Papuan 2n=80 forms of S. robustum have been suggested as the immediate progenitor species for cultivated sugarcane (S. officinarum). A total of 738 loci in LA Purple and 720 loci in Mol 5829 were amplified and typed in the progeny by arbitrarily primed PCR using 45 primers. Fifty and 33 single-dose polymorphisms were identified in the S. officinarum and S. robustum genomes, respectively (χ 2 at 98%). Linkage analysis of single-dose polymorphisms in both genomes revealed linkages in repulsion and coupling phases. In the S. officinarum genome, a map hypothesis gave 7 linkage groups with 17 linked and 33 unlinked markers. Four of 13 pairwise linkages were in repulsion phase and 9 were in coupling phase. In the S. robustum genome, a map hypothesis gave 5 linkage groups, defined by 12 markers, with 21 markers unlinked, and 2 of 9 pairwise linkages were in repulsion phase. Therefore, complete polysomic inheritance was not observed in either species, suggesting that chromosomal behavior is different from that observed by linkage analysis of over 500 markers in the S. spontaneum map. Implications of this finding for evolution and breeding are discussed.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Pediatric cardiology 15 (1994), S. 198-200 
    ISSN: 1432-1971
    Keywords: Subaortic stenosis ; Congenital heart disease ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The first case of multiple family members with discrete subaortic membrane and no other congenital defects is presented. One family member presents with findings suggesting a forme fruste of this disease. Increased surveillance of family members of individuals with discrete subaortic membrane is warranted, as the clinical findings of mild subaortic obstruction may be indistinguishable from those of an innocent flow murmur.
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Pediatric cardiology 15 (1994), S. 201-203 
    ISSN: 1432-1971
    Keywords: Tricuspid atresia ; Tricuspid hypoplasia ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Occurrence of a similar cardiac malformation in multiple family members has been reported for many lesions. Neither tricuspid atresia nor tricuspid annular hypoplasia and tricuspid atresia and one case of tricuspid annular hypoplasia with an atrial septal defect in siblings. The findings in this family suggest an autosomal recessive pattern of inheritance for abnormal tricuspid valve morphogenesis.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular medicine 72 (1994), S. 409-413 
    ISSN: 1432-1440
    Keywords: Myotonic dystrophy ; Limb girdle muscular dystrophy ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract A family is reported in which a 29-year-old woman showed the clinical features of myotonic dystrophy while her 26-year-old brother presented with the clinical picture of limb girdle syndrome. In the affected female, direct genetic testing for the specific myotonic dystrophy mutation on chromosome 19 revealed abnormal expansion of a repeat unit containing the three nucleotides cytosine, thymine, and guanine (CTG) — typical for myotonic dystrophy — while her diseased brother displayed two normal alleles. This supports the hypothesis of the extremely rare occurrence of two clinically and genetically different myopathies in one family. Genetic analysis of six other family members showed that the father of the diseased siblings as well as all of his three brothers and sisters had a pathological CTG repeat expansion, and that the other two family members tested had a normal allelic pattern. The number of CTG repeats in the diseased women was approximately tenfold higher than in her asymptomatic relatives who revealed an abnormal allelic pattern. The increase in CTG repeats with transmission to a subsequent generation in this family was paralleled by a dramatic increase in the severity of myotonic dystrophy.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Comparative clinical pathology 4 (1994), S. 146-151 
    ISSN: 1433-2981
    Keywords: Biochemistry ; Development ; Haematology ; Koala
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Haematology and biochemistry of captive pouch young and back young koalas from 165 days to one year old were studied. Distinct changes with age were observed. Packed cell volume, haemoglobin, erythrocyte count, MCV and total plasma protein where lowest in the youngest animals less than 180 days old. Reticulocytes were highest in this age group. Haematological values differed from those of adult animals. Lymphocytosis occurred, especially between 210–330 days of age. Intense erythropoiesis was indicated by reticulocytosis and the presence of erythrocyte granular inclusions, anisocytosis and poikilocytosis on blood films, particularly up to 330 days of age. Microcytosis present on blood films throughout the study period could not be explained by iron deficiency.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Cellular and molecular life sciences 50 (1994), S. 429-437 
    ISSN: 1420-9071
    Keywords: Genetics ; ecology ; DNA-transfer ; conjugation ; transformation ; transduction ; transposons ; dormant cells ; epilithon ; microbial colonisation ; symbiosis ; virus resistance ; biosafety ; release of genes ; insults to humanity ; evolution ; biodiversity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Genetic ecology is the extension of our modern knowledge in molecular genetics to studies of viability, gene expression and gene movements in natural environments like soils, aquifers and digestive tracts. In such milieux, the horizontal transfer of plasmid-borne genes between phylogenetically distant species has already been found to be much more frequent than had been expected from laboratory experience. For the study of exchanges involving chromosomally-located genes, more has to be learned about the behaviour of transposons in such environments. The results expected from studies in genetic ecology are relevant for considerations of evolution, biodiversity and biosafety. The role of this new field of research in restoring popular confidence in science and in its biotechnological applications is stressed.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1432-0533
    Keywords: Key words: Amyotrophic lateral sclerosis ; Neuropathology ; Posterior column involvement ; Genetics ; Superoxide dismutase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Several missense mutations within exons 1, 2, 4 and 5 of the gene for Cu/Zn-binding superoxide dismutase (SOD1) have been discovered to be involved in the development of chromosome 21q-linked familial amyotrophic lateral sclerosis (FALS). We describe here an autopsied patient with FALS, in whom we have recently identified a novel missense mutation in exon 1 of the SOD1 gene. The neuropathological findings were compatible with those described previously in patients with FALS with posterior column involvement. This suggests that mutations of the SOD1 gene may be responsible for this form of FALS.
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  • 10
    ISSN: 1432-0533
    Keywords: Key words     Primitive neuroepithelial tumor ; Desmoplastic small cell tumor ; Brain tumor of infancy ; Immunocytochemistry ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract      We describe a case of a desmoplastic brain tumor which was initially resected from the right fronto-temporal region in a 2 year-old boy. This nodular, calcified tumor was vascularized by the internal carotid artery and the middle meningeal artery branches. Grossly, it contained several mucoid cysts. Light microscopy showed cords or nests of small cuboidal cells surrounded by a loose connective tissue and desmoplasic areas containing fibers and spindle cells. The cuboidal cells expressed epithelial, neuronal and neuroendocrine markers. Some foci of spindle cells showed glial differentiation. The tumor recurred 16 months later and displayed some characteristics of the small cell neuroepithelial component, mitoses being conspicuous. Electron microscopy revealed undifferentiated clear cells, some containing neurosecretory granules. Karyotyping demonstrated the following formula: 〈 15 〉 46, t(8;11) (q13; q11). The chromosome 11 breakpoint was different from that described in Ewing's sarcoma. This isolated translocation has not been previously reported to our knowledge. These unusual features lead us to report this case and to discuss its pathogenesis.
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  • 11
    ISSN: 1432-0533
    Keywords: Amyotrophic lateral sclerosis ; Neuropathology ; Posterior column involvement ; Genetics ; Superoxide dismutase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Several missense mutations within exons 1, 2, 4 and 5 of the gene for Cu/Zn-binding superoxide dismutase (SOD1) have been discovered to be involved in the development of chromosome 21q-linked familial amyotrophic lateral sclerosis (FALS). We describe here an autopsied patient with FALS, in whom we have recently identified a novel missense mutation in exon 1 of the SOD1 gene. The neuropathological findings were compatible with those described previously in patients with FALS with posterior column involvement. This suggests that mutations of the SOD1 gene may be responsible for this form of FALS.
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  • 12
    ISSN: 1432-0428
    Keywords: Genetics ; diabetes mellitus ; mitochondria ; maternal ; deafness
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Non-insulin-dependent diabetes mellitus (NIDDM) has a strong genetic component and maternal factors have recently been implicated in disease inheritance. The mitochondrial myopathies are a group of diseases which often show maternal inheritance as a result of mtDNA defects; some patients have impaired glucose tolerance. Occasional families with maternally inherited diabetes and deafness associated with a deletion or point mutation of mtDNA have been reported. To assess the importance of mitochondrial gene defects in NIDDM, 150 unrelated diabetic subjects from Wales, UK and 68 unrelated patients with diabetes and at least one affected sibling from England, UK were studied. Southern blot analysis did not show any large mtDNA deletions or duplications. One patient had a mutation in the mitochondrial tRNAleu(UUR) gene at bp 3243. This mutation is commonly associated with the syndrome of mitochondrial encephalomyopathy, lactic acidosis and stroke like episodes (MELAS). Study of this patient and his siblings showed a distinct form of late-onset diabetes associated with nerve deafness but no clinical features of the MELAS syndrome. No diabetic subject was shown to have the mtDNA mutation at position 8344 (tRNAlys) which has previously been described in the syndrome of mitochondrial encephalomyopathy and red-ragged fibres (MERRF). The role of other mitochondrial gene defects in diabetes and the pathophysiological basis of glucose intolerance in patients with the MELAS mutation requires further elucidation.
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  • 13
    Electronic Resource
    Electronic Resource
    Springer
    Journal of biomedical science 1 (1994), S. 201-203 
    ISSN: 1423-0127
    Keywords: Hypertension ; Eicosanoid ; Rat ; Genetics ; Kidney
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The present paper reviews the evidence for a possible involvement of renal eicosanoids in the pathophysiology of high blood pressure in genetically hypertensive rats of the Lyon strain. Both in vivo and in vitro experiments suggest that an increased ability to synthesize the vasoconstrictor prostaglandin H2 and/or thromboxane A2 in renal vessels (1) acts as an autocrine amplifier of pressor agents and (2) may contribute to resetting the pressure natriuresis curve which is a prerequisite for the development and maintenance of hypertension.
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  • 14
    Electronic Resource
    Electronic Resource
    Springer
    European journal of pediatrics 153 (1994), S. 372-377 
    ISSN: 1432-1076
    Keywords: Epilepsy ; Absences ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Clinical and EEG family data of 140 cases with early childhood epilepsy with absences are presented. The aim of the study was to evaluate, whether the occurrence of generalized tonic clonic seizures (GTCS) as a presenting symptom might correlate with family data, i.e. whether there are indications of heterogeneity. One hundred and forty cases were selected from the epilepsy family data base of the Neuropaediatric Department. The selection parameter was epilepsy with absences manifesting between the 1 st and 5th year of age. The incidence of seizures was evaluated in siblings, parents and parents' siblings. EEG records were available from 103 parents and 106 siblings. The analysis supports the assumption of heterogeneity within early childhood absence epilepsy. Parents and their sibs of cases manifesting with GTCS had seizures twice as often than parents and their sibs in the non-GTCS group. In the affected relatives of the GTCS group early onset GTCS prevailed, whereas in the relatives of the non-GTCS group absences were found more frequently. The EEG of relatives showed elevated incidences of spikes and waves and photosensitivity in both groups, indicating common genetic factors. In parents of the non-GTCS group, however, EEG pathology was significantly more frequent than in parents of the GTCS group. Comparing EEG pathology in parents with seizure risk in siblings, evidence for maternal preponderance in transmission of the seizure liability was found. Mothers' EEG seems to be the best predictor of the seizure risk in probands' siblings. Early childhood epilepsy with absences can be regarded as an intermediate type, showing overlap with early onset GTCS and myoclonic astatic epilepsy on the one side and with childhood absence epilepsy on the other.
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  • 15
    ISSN: 1432-0428
    Keywords: Genetics ; haplotype ; HLA-A ; HLA-DQ ; HLA-DR ; tumour necrosis factor ; diabetes mellitus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary In Finland the haplotype A2, Cw1, B56, DR4, DQ8 is the third most common haplotype in insulin-dependent diabetic (IDDM) patients and has the highest haplotype-specific absolute risk for IDDM. Cw1, B56, DR4, DQ8 haplotypes containing HLA-A alleles other than A2 are infrequent in the population and are not associated with IDDM. Comparison of the A2 and non-A2 haplotypes at the DNA level showed that they were identical at HLA-B,-DR, and -DQ loci. Evidence that class I alleles confer susceptibility to IDDM was obtained from the two HLA-C, -B, -DR and -DQ haplotypes most frequently found in IDDM patients in Finland. A24, A3 and A2 on the Cw3, B62, DR4, DQ8 haplotype, and A28, A2 and A1 on the Cw7, B8, DR3, DQ2 were all found to be associated with IDDM. In Finland these seven haplotypes, including A2, Cw1, B56, DR4, DQ8, account for 33% of diabetic haplotypes and 10.3% of non-diabetic haplotypes (p〈0.00001). The contribution of the class I region to IDDM susceptibility was also apparent in those IDDM patients lacking the disease-predisposing class II alleles. Significantly more non-DR3/non-DR4 IDDM patients (47 of 55) possessed two of the IDDM-associated HLA-A alleles compared to non-DR3/non-DR4 control subjects (40 of 58; p=0.038). Moreover, IDDM patients confirmed by oligotyping as unable to form a ‘diabetes-susceptibility’ DQ heterodimer, tended to possess two diabetes-associated HLA-A alleles (12 of 13) compared to control subjects (12 of 20; p=0.056).
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  • 16
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 88 (1994), S. 754-758 
    ISSN: 1432-2242
    Keywords: Potato breeding ; Potato leaf roll virus ; Virus resistance ; Major gene resistance ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The concentration of potato leaf roll virus (PLRV), as measured by a quantitative enzyme-linked immunosorbent assay, in the foliage of potato plants (Solanum tuberosum) of cv ‘Maris Piper’ with secondary infection was 2900 ng/g leaf, whereas in clones G7445(1) and G7032(5) it was 180 ng/g leaf and 120 ng/g leaf, respectively. To examine the genetic control of resistance to PLRV multiplication, reciprocal crosses were made between the susceptible cultivar ‘Maris Piper’ and the two resistant clones, and the three parents were selfed. Seedling progenies of these families were grown to generate tubers of individual genotypes (clones). Clonally propagated plants were graft-inoculated, and their daughter tubers were collected and used to grow plants with secondary infection in which PLRV concentration was estimated. The expression of resistance to PLRV multiplication had a bimodal distribution in progenies from crosses between ‘Maris Piper’ and either resistant clone, and also in progeny from selfing the resistant parents, with genotypes segregating into high and low virus titre groups. Only the progeny obtained from selfing ‘Maris Piper’ did not segregate, all genotypes being susceptible to PLRV multiplication. The pattern of segregation obtained from these progenies fits more closely with the genetical hypothesis that resistance to PLRV multiplication is controlled by two unlinked dominant complementary genes, both of which are required for resistance, than with the simpler hypothesis that resistance is conferred by a single dominant gene, as published previously.
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  • 17
    ISSN: 1432-2242
    Keywords: Genetics ; Disease resistance ; Monocots
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An F2 oat population was produced by crossing the diploid (n=7) species Avena strigosa (CI 3815) with A. wiestii (CI 1994), resistant and susceptible, respectively, to 40 isolates of Puccinia coronata, the causal agent of crown rust. Eighty-eight F2 individuals were used to construct an RFLP linkage map representing the A genome of cultivated hexaploid oat. Two hundred and eight RFLP loci have been placed into 10 linkage groups. This map covers 2416 cM, with an average of 12 cM between RFLP loci. Eighty-eight F3 lines, derived from F2 individuals used to construct the map, were screened for resistance to 9 isolates of P. coronata. One locus, Pca, was found to confer a dominant resistance phenotype to isolates 203, 258, 263, 264B, 290, 298, 325A, and 345. Pca also conferred resistance to isolate 276; however, an unlinked second gene may also be involved.
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  • 18
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 89 (1994), S. 313-317 
    ISSN: 1432-2242
    Keywords: Genetics ; Rice ; Phosphorousefficiency ; Diallel analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The inheritance of phosphorous (P) — deficiency tolerance in rice was investigated by a sevenparent diallel. The parent materials involved were four P-efficient (IR20, IR54, IR28, and Mahsuri), one moderately P-efficient (TN1), and two P-inefficient (IR31406333-1 and IR34686-179-1-2-1), genotypes. Relative tilering ability (RTA) under P-deficient and P-supplemented soil conditions was the parameter used in determining the tolerance level of the different genotypes. Diallel graph analysis revealed that tolerant parents have an excess of recessive genes, while moderate and susceptible parents possess more dominant genes. Genetic-component analysis suggested that both additive and dominance gene effects are involved in the inheritance of P-deficiency tolerance in rice. The trait exhibited over doiminance as confirmed by the graphical analysis. Narrow-sense heritability of the trait was moderate (0.50) and environmental effects were low. Both the general combining ability (GCA) and the specific combining ability (SCA) were significant, but GCA was more prevalent than SCA. Tolerant parents exhibited a high GCA whereas susceptibles have a very poor GCA, suggesting that tolerant parents were mostly enriched in additive genes and susceptible parents in non-additive genes. Crosses involving two high general combiners showed low SCA effects whereas crosses between poor general combiners manifested highly-significant SCA values.
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  • 19
    ISSN: 1432-2072
    Keywords: Risperidone ; Antipsychotics ; 5-HT2 antagonism ; D2 antagonism ; Pharmacology ; Receptor binding ; Biochemistry ; Review
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract This review reports on the pharmacodynamics of the new antipsychotic risperidone. The primary action of risperidone is serotonin 5-HT2 receptor blockade as shown by displacement of radioligand binding (Ki: 0.16 nM), activity on isolated tissues (EC50:0.5 nM), and antagonism of peripherally (ED50: 0.0011 mg/kg) and centrally (ED50:0.014 mg/kg) acting 5-HT2 receptor agonists in rats. Risperidone is at least as potent as the specific 5-HT2 receptor antagonist ritanserin in these tests. Risperidone is also a potent dopamine D2 receptor antagonist as indicated by displacement of radioligand binding (Ki: 1.4 nM), activity in isolated striatal slices (IC50: 0.89 nM), and antagonism of peripherally (ED50: 0.0057 mg/kg in dogs) and centrally acting D2 receptor agonists (ED50: 0.056–0.15 mg/kg in rats). Risperidone shows all effects common to D2 antagonists, including enhancement of prolactin release. However, some central effects such as catalepsy and blockade of motor activity occur at high doses only. Risperidone is 4–10 times less potent than haloperidol as a central D2 antagonist in rats and it differs from haloperidol by the following characteristics: predominant 5-HT2 antagonism; LSD antagonism; effects on sleep; smooth dose-response curves for D2 antagonism; synergism of combined 5-HT2/D2 antagonism; pronounced effects on amphetamine-induced oxygen consumption; increased social interaction; and pronounced effects on dopamine (DA) turnover. Risperidone displays similar activity at pre- and postsynaptic D2 receptors and at D2 receptors from various rat brain regions. The binding affinity for D4 and D3 receptors is 5 and 9 times weaker, respectively, than for D2 receptors; interaction with D1 receptors occurs only at very high concentrations. The pharmacological profile of risperidone includes interaction with histamine H1 and α-adrenergic receptors but the compound is devoid of significant interaction with cholinergic and a variety of other types of receptors. Risperidone has excellent oral activity, a rapid onset, and a 24-h duration of action. Its major metabolite, 9-hydroxyrisperidone, closely mimics risperidone in pharmacodynamics. Risperidone can be characterized as a potent D2 antagonist with predominant 5HT2 antagonistic activity and optimal pharmacokinetic properties.
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  • 20
    ISSN: 1530-0358
    Keywords: Desmoids ; Genetics ; Chemotherapy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract PURPOSE: The aim of this study was to describe the natural history and management of surgically unresectable intra-abdominal desmoid tumors in two patients with Gardner's syndrome from two unrelated families, where each had failed on conventional therapy. METHODS: Two patients with Gardner's syndrome were placed on a chemotherapy regimen which included doxorubicin (90 mg/m2) and dacarbazine (900 mg/m2) in divided doses over four days of continuous infusion. Their progress on chemotherapy was assessed by abdominal computerized tomography and laparoscopy. RESULTS: The computerized abdominal tomography scans proved difficult to interpret because of adhesions and matted small bowel resulting from the patients original colectomies. These findings made it difficult to differentiate postoperative changes from residual desmoid tumor. Second-look laparotomy in such patients was contraindicated as this may predispose to further desmoid production. Laparoscopy disclosed a complete response to this chemotherapy. Nevertheless, we had an iatrogenic small bowel perforation in one of these patients. Each patient showed a complete response to chemotherapy. CONCLUSION: Surgical resection remains the first-line treatment of intra-abdominal desmoid tumors. However, doxorubicin/ dacarbazine chemotherapy on a clinical trial basis may be indicated in patients whose intra-abdominal desmoid is unresectable, or who have failed to respond to treatment with hormones (tamoxifen, Toremifene), steroids (prednisone), and nonsteroidal anti-inflammatory agents (Clinoril®; Merck & Co., Inc., West Point, PA).
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  • 21
    ISSN: 1437-160X
    Keywords: Systemic lupus erythematosus ; Recombinant U1-nRNP proteins ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract To investigate a possible involvement of HLA-class II alleles in the genetic predisposition for the formation of anti-U1-nRNP antibody in systemic lupus erythematosus (SLE), genomic DNA of 178 patients was typed for the DRB1, DQA1 and DQB1 alleles using a polymerase chain reaction (PCR) and non-radioactive-oligonucleotide typing. Antibodies against recombinant U1-nRNP proteins (U1-A- U1-C-and 70K-protein) were determined by ELISA. Anti-U1-C antibody was found in 26 (14.7%), anti-U1-A in 34 (19.2%) and anti-70K in 17 (9.6%) patients. A joint occurrence was observed for these antibodies against the recombinant U1-nRNP proteins: anti-U1-C and anti-U1-A antibodies occurred together more frequently than alone and than together with anti-U1-70K antibodies. The frequency of DRB1 * 04 was slightly increased in the patients with anti-U1-C as compared to the patients without anti-U1-C (P〈0.05, Pcorr=n.s., RR=2.4). The DQA1 * 0301 allele, which is in linkage disequilibrium with DRB1 * 04, is found more frequently in anti-U1-C-positive than in antibody-negative patients. The DQB1 * 0303 allele, detected in 12 of 176 SLE patients, was absent in the patients with any of the antibodies against the U1-nRNP proteins. All these deviations may be due to chance alone. We concluded that the presence of antibodies against recombinant U1-nRNP proteins was not significantly associated with any HLA DRB1, DQA1 and DQB1 allele in our group of SLE patients.
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  • 22
    ISSN: 1432-1459
    Keywords: PGAM deficiency ; Myopathy ; Biochemistry ; Muscle culture ; 31P-MR spectroscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Muscle phosphoglycerate mutase (PGAM) deficiency has been so far identified in only six patients, five of these being African Americans. We report the results of clinical, morphological, biochemical, muscle culture and31P-MR spectroscopy studies in the first Caucasian patient with muscle PGAM deficiency. A 23-year-old man had a 10-year history of cramps after physical exertion with one episode of pigmenturia. Neurological examination and EMG study were normal. ECG and echocardiography revealed hypertrophy of the interventricular septum and slight dilatation of the left chambers of the heart. Muscle biopsy revealed increased glycogen content and some accumulation of mitochondria. Muscle PGAM activity was markedly decreased (6.5% and 9.7% of control value in two different biopsies). Citrate synthase and other mitochondrial respiratory chain enzyme activities were much higher than normal. In contrast to the marked decrease of PGAM activity observed in muscle biopsy, total enzyme activity in the patient's aneural muscle culture was normal, being represented exclusively by BB isoenzyme. The deficiency of PGAM-MM isoenzyme was reproduced in the patient's innervated muscle culture. Muscle31P-MR spectroscopy showed accumulation of phosphomonoesters only on fast “glycolytic” exercise. On “aerobic” exercise, Vmax, calculated from the work-energy cost transfer function, showed an increase consistent with the morphological and biochemical evidence of mitochondrial proliferation. This might represent a sort of compensatory aerobic effort in an attempt to restore muscle power.
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  • 23
    ISSN: 1432-1459
    Keywords: Multiple sclerosis Epidemiology ; Immigrants Environment ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The incidence and prevalence of multiple sclerosis (MS) were compared, controlling for age, in native-born Israelis of different origins and in immigrants to Israel. This comparison was carried out in two populations, countrywide and in Jerusalem. In the countrywide population, ascertainment was based mainly on hospitalizations; it included 252 patients who were native-born and 150 who had immigrated from Africa-Asia (AA immigrants). The 89 MS patients of Jerusalem also included patients diagnosed in outpatient clinics. In native-born Israelis whose father was born in Europe-America (I-EA), the incidence and prevalence of MS were found to be as high as or even higher than that found previously in immigrants from Europe-America. Among native-born Israelis whose father was born in Africa or Asia (I-AA), the yearly age-adjusted incidence and prevalence rates were found to be 1.4- to 1.8-fold higher than among AA immigrants, pointing to environmental factors. The incidence and prevalence rates in the I-EA were 1.2- to 1.6-fold higher than in the I-AA, pointing to genetic factors. These results seem to point to both environmental and genetic factors in the aetiology of MS. Further research is needed, however, to disentangle the genetic factors from possible environmental differences in the two ethnic groups.
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  • 24
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    Journal of neurology 241 (1994), S. 487-491 
    ISSN: 1432-1459
    Keywords: Juvenile absence epilepsy ; Valproate ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Fifteen patients aged 11–25 years (mean 15.37, SD 3.89) suffering from juvenile absence epilepsy are presented. Only 3 (20%) had absences (AS) as the only seizure type, 12 (80%) had associated generalized tonic-clinic seizures (GTCS) and in the remaining 3 with absences and GTCS there was also sporadic myoclonus. We found a higher frequency of AS in our patients by clinical history and video-EEG than has been previously reported. In our patients the mean age of onset in years was 11.4, SD 1.24 for AS, 13.12, SD 2.31 for GTCS and 12.5, SD 2.18 for myoclonus. The correct diagnosis was not made on referrals for any of the patients. It took an average of 3–5.5 years from the onset of the AS (range: 6–120 months) and 2 years from the occurrence of GTCS (average: 1–72 months) to make the correct diagnosis and institute proper treatment, which was valproic acid (VPA). The GTCS were controlled in all patients whereas AS continued in 6 (40%), but to a significantly lesser degree. The frequency and the duration of the GTCS before the start of VPA treatment seemed to have an adverse effect on AS control. We documented no circadian rhythm in either AS or the GTCS, except in 2 patients who had AS and GTCS mainly when they awoke in the morning. The sample size was too small to perform a proper genetic study, though a positive history of epilepsies of mixed types was obtained in 35.7% of the parents and the siblings of the probands.
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  • 25
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    European archives of psychiatry and clinical neuroscience 244 (1994), S. 138-140 
    ISSN: 1433-8491
    Keywords: Parity ; Genetics ; Diathesis-stress model
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract As part of a follow-up and family study of post-partum psychoses, this episode of illness being the first leading to psychiatric hospitalisation, patients with puerperal episodes (PE) and nonpuerperal episodes (NPE) of illness in the long-term course (n=79) were compared to patients with PE only (n=40). Few differences were found. Relatives of patients with PE only had a lower morbidity risk for functional psychoses than relatives of patients with PE and NPE. A favourable course of illness in the presence of a low genetic predisposition may be expected, according to the diathesis-stress model of functional psychoses.
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  • 26
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    European journal of epidemiology 10 (1994), S. 317-324 
    ISSN: 1573-7284
    Keywords: Epidemiology ; Genetics ; Oral clefts ; Registers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Epidemiological and genetic variables for oral clefts were analysed for the years 1981–1989 in a case-control study of congenital malformations in the Emilia Romagna, Veneto, and Friuli regions, and in the Trento and Bolzano hospitals. Birth prevalence for all cases of cleft lip with or without cleft palate (CL(P)) was 8.2 per 10,000 births, and that for cleft palate only (CP) was 6.1 per 10,000. Coexisting abnormalities were found in 23% of CL(P) cases and in 43% of CP. No clusters in time or space were detected. For isolated clefts, a predominance of males among CL(P) and of females among CP was found; epilepsy was the only maternal risk factor correlated with clefts, and an association between clefting and consanguinity was found. Empirical recurrence risks were calculated in both isolated CL(P) and CP.
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  • 27
    ISSN: 1432-2242
    Keywords: Maize ; Restriction fragment length polymorphisms (RFLPs) ; Qualitative and quantitative inheritance ; Plant breeding ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Restriction fragment length polymorphisms (RFLPs) and one morphological marker were used to investigate quantitative trait loci (QTL) for morphological and physiological traits evaluated on 150 F2∶3 maize (Zea mays L.) lines derived from the cross of elite U.S. Corn Belt inbreds Mo17 and H99. F2∶3 lines were grown in a replicated experiment and evaluated for plant and ear heights and flowering traits. QTL were identified for each trait, and genetic effects were determined. Estimated gene action for the flowering traits was predominantly overdominance. Both parents contributed toward increased values for anthesis and silk emergence. QTL for increased plant and ear heights were usually contributed by the taller parent, Mo17. Estimated gene action for these traits was mainly partial to overdominance. QTL for plant height were located in the vicinity of loci defined by alleles with qualitative effects on plant height.
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  • 28
    ISSN: 1617-4623
    Keywords: Gene regulation ; Ribozyme ; npt-gene ; Transgenic tobacco ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A chimeric gene encoding a ribozyme under the control of the cauliflower mosaic virus (CaMV) 35S promoter was introduced into transgenic tobacco plants. In vivo activity of this ribozyme, which was designed to cleave npt mRNA, was previously demonstrated by transient expression assays in plant protoplasts. The ribozyme gene was transferred into transgenic tobacco plants expressing an rbcS-npt chimeric gene as an indicator. Five double transformants out of sixteen exhibited a reduction in the amount of active NPT enzyme. To measure the amount of ribozyme produced, in the absence of its target, the ribozyme and target genes were separated by genetic segregation. The steady-state concentrations of ribozyme and target RNA were shown to be similar in the resulting single transformants. Direct evidence for a correlation between reduced npt gene expression and ribozyme expression was provided by crossing a plant containing only the ribozyme gene with a transgenic plant expressing the npt gene under control of the 35S promoter, i.e. the same promoter used to direct ribozyme expression. The expression of npt was reduced in all progeny containing both transgenes. Both steady-state levels of npt mRNA and amounts of active NPT enzyme are decreased. In addition, our data indicate that, at least in stable transformants, a large excess of ribozyme over target is not a prerequisite for achieving a significant reduction in target gene expression.
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  • 29
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    Behavioral ecology and sociobiology 35 (1994), S. 99-107 
    ISSN: 1432-0762
    Keywords: Key words Apis mellifera ; Genetics ; Drone production ; Allozymes ; Reproductive conflict
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Previously we reported that there are subfamily differences in drone production in queenless honey bee colonies, but these biases are not always explained by subfamily differences in oviposition behavior. Here we determine whether these puzzling results are best explained by either inadequate sampling of the laying worker population or reproductive conflict among workers resulting in differential treatment of eggs and larvae. Using colonies composed of workers from electrophoretically distinct subfamilies, we collected samples of adult bees engaged in the following behavior: “true” egg laying, “false” egg laying, indeterminate egg laying, egg cannibalism, or nursing (contact with larvae). We also collected samples of drone brood at four different ages: 0 to 2.5-h-old eggs, 0 to 24-h-old eggs, 3 to 8-day-old larvae, and 9 to 14-day-old larvae and pupae. Allozyme analyses revealed significant subfamily differences in the likelihood of exhibiting egg laying, egg cannibalism, and nursing behavior, as well as significant subfamily differences in drone production. There were no subfamily differences among the different types of laying workers collected from each colony, suggesting that discrepancies between subfamily biases in egg-laying behavior and drone production are not due to inadequate sampling of the laying worker population. Subfamily biases in drone brood production within a colony changed significantly with brood age. Laying workers had significantly more developed ovaries than either egg cannibals or nurses, establishing a physiological correlate for the observed behavioral genetic differences. These results suggest there is reproductive conflict among subfamilies and individuals within queenless colonies of honey bees. The implications of these results for the evolution of reproductive conflict, in both queenright and queenless contexts, are discussed.
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  • 30
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    Metabolic brain disease 9 (1994), S. 105-131 
    ISSN: 1573-7365
    Keywords: Alcoholism ; Genetics ; Endorphins ; Enkephalins ; Dynorphins ; Opioid ; Receptors
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract At the present time alcoholism is recognized as a metabolic disease exhibiting the clinical features of craving for alcohol, loss of control over drinking, tolerance and physical dependence on alcohol, while both epidemiological and experimental studies have demonstrated that genetic factors may be important in determining whether an individual has a high or low vulnerability to develop alcoholism. Evidence also indicates that alcoholism is not characterized by a single gene single allele inheritance. Instead it seems that multiple genes and environmental factors interact to increase or decrease an individual's vulnerability to become an alcoholic. Current research is aimed at investigating whether certain behavioral, physiological and biochemical markers are highly associated with the incidence of alcoholism. Among the biochemical markers currently under investigation is the endogenous opioid system and its implication in mediating the reinforcing effects of ethanol. It is the objective of this manuscript to review current research on: (a) the interactions of ethanol with the endogenous opioid system at the molecular level; (b) the existence of genetically determined differences in the response of the endogenous opioid system to ethanol between subjects at high and low risk for excessive ethanol consumption, as well as between lines of animals showing preference or aversion for ethanol solutions; (c) the decrease of alcohol consumption following pretreatment with opioid antagonists; and (d) the possible use of specific opioid receptor antagonists together with behavioral therapy to modify drinking behavior, to control craving and to prevent relapse.
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    Behavioral ecology and sociobiology 34 (1994), S. 117-409 
    ISSN: 1432-0762
    Keywords: Social insects ; Apis mellifera ; Division of labor ; Genetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Variability exists among worker honey bees for components of division of labor. These components are of two types, those that affect foraging behavior and those that affect life-history characteristics of workers. Variable foraging behavior components are: the probability that foraging workers collect (1) pollen only; (2) nectar only; and (3) pollen and nectar on the same trip. Life history components are: (1) the age the workers initiate foraging behavior; (2) the length of the foraging life of a worker; and (3) worker length of life. We show how these components may interact to change the social organization of honey bee colonies and the lifetime foraging productivity of individual workers. Selection acting on foraging behavior components may result in changes in the proportion of workers collecting pollen and nectar. Selection acting on life-history components may affect the size of the foraging population and the distribution of workers between within nest and foraging activities. We suggest that these components define possible sociogenic “pathways” through which colony-level natural selection can change social organization. These pathways may be analogous to developmental pathways in the morphogenesis of individual organisms because small changes in behavioral or life history components of individual workers may lead to major changes in the organizational structure of colonies.
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  • 32
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    Behavioral ecology and sociobiology 35 (1994), S. 99-107 
    ISSN: 1432-0762
    Keywords: Apis mellifera ; Genetics ; Drone production ; Allozymes ; Reproductive conflict
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Previously we reported that there are subfamily differences in drone production in queenless honey bee colonies, but these biases are not always explained by subfamily differences in oviposition behavior. Here we determine whether these puzzling results are best explained by either inadequate sampling of the laying worker population or reproductive conflict among workers resulting in differential treatment of eggs and larvae. Using colonies composed of workers from electrophoretically distinct subfamilies, we collected samples of adult bees engaged in the following behavior: “true” egg laying, “false” egg laying, indeterminate egg laying, egg cannibalism, or nursing (contact with larvae). We also collected samples of drone brood at four different ages: 0 to 2.5-h-old eggs, 0 to 24-h-old eggs, 3 to 8-day-old larvae, and 9 to 14-day-old larvae and pupae. Allozyme analyses revealed significant subfamily differences in the likelihood of exhibiting egg laying, egg cannibalism, and nursing behavior, as well as significant subfamily differences in drone production. There were no subfamily differences among the different types of laying workers collected from each colony, suggesting that discrepancies between subfamily biases in egg-laying behavior and drone production are not due to inadequate sampling of the laying worker population. Subfamily biases in drone brood production within a colony changed significantly with brood age. Laying workers had significantly more developed ovaries than either egg cannibals or nurses, establishing a physiological correlate for the observed behavioral genetic differences. These results suggest there is reproductive conflict among subfamilies and individuals within queenless colonies of honey bees. The implications of these results for the evolution of reproductive conflict, in both queenright and queenless contexts, are discussed.
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  • 33
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    Behavioral ecology and sociobiology 34 (1994), S. 125-137 
    ISSN: 1432-0762
    Keywords: Social insects ; Apis mellifera ; Division of labor ; Genetics ; Nepotism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Three experiments were performed to determine whether brood care in honey bee colonies is influenced by colony genetic structure and by social context. In experiment 1, there were significant genotypic biases in the relative likelihood of rearing queens or workers, based on observations of individually labeled workers of known age belonging to two visually distinguishable subfamilies. In experiment 2, no genotypic biases in the relative likelihood of rearing drones or workers was detected, in the same colonies that were used in experiment 1. In experiment 3, there again were significant genotypic differences in the likelihood of rearing queens or workers, based on electrophoretic analyses of workers from a set of colonies with allozyme subfamily markers. There also was an overall significant trend for colonies to show greater subfamily differences in queen rearing when the queens were sisters (half- and super-sisters) rather than unrelated, but these differences were not consistent from trial to trial for some colonies. Results of experiments 1 and 3 demonstrate genotypic differences in queen rearing, which has been reported previously based on more limited behavioral observations. Results from all three experiments suggest that genotypic differences in brood care are influenced by social context and may be more pronounced when workers have a theoretical opportunity to practice nepotism. Finally, we failed to detect persistent interindividual differences in bees from either subfamily in the tendency to rear queen brood, using two different statistical tests. This indicates that the probability of queen rearing was influenced by genotypic differences but not by the effect of prior queen-rearing experience. These results suggest that subfamilies within a colony can specialize on a particular task, such as queen rearing, without individual workers performing that task for extended periods of time.
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  • 34
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    Journal of Computational Chemistry 15 (1994), S. 12-22 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. © 1994 by John Wiley & Sons, Inc.
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  • 35
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    Journal of Computational Chemistry 15 (1994), S. 54-60 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicitly correlated Gaussian functions have been used in variational calculations on the ground state of the helium atom. The major problem of this application, as well as in other applications of the explicitly correlated Gaussian functions to compute electronic energies of atoms and molecules, is the optimization of the nonlinear parameters involved in the variational wave function. An effective Newton-Raphson optimization procedure is proposed based on analytic first and second derivatives of the variational functional with respect to the Gaussian exponents. The algorithm of the method and its computational implementation is described. The application of the method to the helium atom shows that the Newton-Raphson procedure leads to a good convergence of the optimization process. © 1994 by John Wiley & Sons, Inc.
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  • 36
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    Journal of Computational Chemistry 15 (1994), S. 90-104 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We described various technical aspects in applying reaction field theories using continuum models to practical problems. It was investigated how solvent-dependent properties of solute molecules are influenced by the following factors: difference in quantum-chemical description of solute-solvent (continuum dielectric) interaction, difference in values of empirically determinable parameters such as atomic radii to define a size of a cavity created in a dielectric to accommodate a solute, and difference in the sophistication level of molecular orbital calculation, including electron correlation and different parameter sets (MNDO, AM1, and PM3). Through these investigations, the better parameter sets were found to evaluate accurately physicochemically important parameters such as hydration enthalpy. © 1994 by John Wiley & Sons, Inc.
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  • 37
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    Journal of Computational Chemistry 15 (1994), S. 132-143 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio MP2/6-31G*//MP2/6-31G* and semiempirical AM1 and PM3 calculations on a series of differently substituted α-oxo-ketenes are used to investigate E/Z-isomerism and rotational barriers in these molecules. Sterically crowded derivatives are found to exist solely as s-E conformers. The unusual stability of these derivatives thus can be attributed to their inability to adopt the s-Z conformation required for the normal α-oxo-ketene reactions. With respect to structures and energies, the PM3 method (especially in the case of highly crowded molecules) is found to be less reliable than AM1. Ab initio HF/3-21G and PM3 vibrational frequencies appear to be of sufficient accuracy for a distinction between s-Z and s-E conformers. In this respect, the AM1 method appears less reliable. © 1994 by John Wiley & Sons, Inc.
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  • 38
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    Journal of Computational Chemistry 15 (1994), S. 155-161 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is described for refining the populations of a set of multiple-solution conformers using experimental nuclear Overhauser effects (nOes). The method is based upon representing the effective relaxation matrix for the set of interconverting proposed conformers as a linear combination of relaxation matrices (LCORMs) due to each conformer. The conformer population derivative of the nOe is derived from a Taylor series expression for the calculated nOe. This derivative may then be used in a standard nonlinear least-squares refinement procedure. The LCORM nOe procedure is tested using a monosaccharide system, 1-O-methyl-α-L-iduronate, that is known to exhibit conformational variability. The measured nOes for this system are used to refine the populations of a set of three static conformers, namely, the 1C4, 4C1, and 2S0 ring conformers. The populations thus derived are compared to those previously obtained using nuclear magnetic resonance proton-proton coupling constant information. Two possible extensions to the method are discussed: The first uses combined nOe and coupling constant data while the second removes the restrictions that the conformers used for fitting be rigid entities. © 1994 by John Wiley & Sons, Inc.
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  • 39
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    Journal of Computational Chemistry 15 (1994), S. 190-199 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article introduces a novel potential function that allows the use of topographical information in molecular modeling. Quantitative shape data are provided by techniques such as electron-microscopy-based three-dimensional image reconstruction for large macromolecular assemblies. Such data can provide important constraints for molecular mechanics. We represent topographical data by spherical harmonic surfaces, first used by Max and Getzoff21 for displaying molecular surfaces. A simple harmonic potential is used to constrain atoms within these spherical harmonic surfaces. This potential was implemented in the yammp molecular mechanics package.27 Implementation details and results of several test cases are discussed here. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 249-249 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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    Journal of Computational Chemistry 15 (1994), S. 283-299 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM3 force field has been extended to cover alkyl radicals. Structures, conformational energies, vibrational spectra, and heats of formation have been well fit, mostly to ab initio data. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 269-282 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum chemical computations on a subset of a large molecule can be performed, at the neglect of diatomic differential overlap (NDDO) level, without further approximation provided that the atomic orbitals of the frontier atoms are replaced by parametrized orthogonal hybrid orbitals. The electrostatic interaction with the rest of the molecule, treated classically by the usual molecular mechanical approximations, is included into the self-consistent field (SCF) equations. The first and second derivatives of energy are obtained analytically, allowing the search for energy minima and transition states as well as the resolution of Newton equations in molecular dynamics simulations. The local self-consistent field (LSCF) method based on these approximations is tested by studying the intramolecular proton transfer in a Gly-Arg-Glu-Gly model tetrapeptide, which reveals an excellent agreement between a computation performed on the whole molecule and the results obtained by the present method, especially if the quantum subsystem includes the side chains and the peptidic unit in between. The merits of the LSCF method are examplified by a study of proton transfer in the Asp69 - Arg71 salt bridge in dihydrofolate reductase. Simulations of large systems, involving local changes of electronic structure, are therefore possible at a good degree of approximation by introducing a quantum chemical part in molecular dynamics studies. This methodology is expected to be very useful for reactivity studies in biomolecules or at the surface of covalent solids. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 333-345 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The alkyl boronic acid moiety is incorporated into many biologically interesting structures. To provide parameters for molecular mechanics and dynamics studies of compounds containing this group, we performed ab initio calculations at the 6-31G* level to obtain bond stretching, bending, and torsion constants. The hydrodynamic formulation of the time-dependent density functional theory was used to calculate the attractive part of van der Waals (VDW) 6-12 potential. The geometry of boronic acid moiety of the 6-31G* optimized methyl boronic acid was similar to that of the X-ray crystal structure of phenyl boronic acid. To test the reliability of nonbonded parameters, Monte Carlo free energy perturbation simulations and the thermodynamic cycle approach were used to estimate the differences in solvation free energy between alkyl alcohol and alkyl boronic acid, both in water and in chloroform. These free energy differences were also obtained experimentally by measuring the vapor-water and water-chloroform partition coefficients. The close agreement between experimental values and the results of our simulations suggests the reliability of new molecular mechanics force-field parameters for alkyl boronic acids. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 45
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    Journal of Computational Chemistry 15 (1994), S. 395-404 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The kinetics and thermodynamics of lactam/lactim tautomerization in 2-pyridone have been investigated, with special attention to direct and assisted proton transfer mechanisms in the ground and first excited electronic state. Specific interactions with a single water molecule strongly enhance the reaction rate and shift the equilibrium toward the lactam form. The effect of bulk solvent is comparatively negligible, although the lactam form is further stabilized. Electron excitation strongly destabilizes the saddle point for proton transfer and, especially, the lactim form with respect to the lactam species. As a consequence, the direct reaction barrier is increased, but the reverse barrier is lowered. Nonpotential energy effects are relatively small and do not modify the aforementioned general trends. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 374-374 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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    Journal of Computational Chemistry 15 (1994), S. 377-384 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical and numerical results related to the calculation of multidimensional vibrational levels are presented. A description of the methodological details of a very general method (normal coordinates-finite elements, NC-FEM) is provided. Several representative three-dimensional (3D) systems (Henon-Heiles and Eckart potentials, and the H3+ molecule) are studied, and NC-FEM results are compared with those published by other authors. For the H3+, a vibrational Hamiltonian expressed in terms of the three internuclear distances is integrated, and the results obtained are compared with the experimental ones. © 1994 by John Wiley & Sons, Inc.
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  • 48
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    Journal of Computational Chemistry 15 (1994), S. 466-474 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new code has been written to perform relativistic Dirac-Fock self-consistent field (SCF) calculations on closed-shell molecules of any symmetry. The choice of the basis set allows us to work at different levels of approximation depending on the precision required. Calculations on the H2Po molecule show that accurate results on specific problems like geometry optimization can be obtained by evaluating the two-electron integrals on half the basis spinors. © 1994 by John Wiley & Sons, Inc.
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  • 49
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    Journal of Computational Chemistry 15 (1994), S. 455-465 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A molecular mechanics force field for studying some beta-lactams was developed from ab initio and experimental data. The optimized parameters allowed accurate calculation of the geometries of both the compounds on which the parametrization was based and others on which the validity of the predictions was checked. © 1994 by John Wiley & Sons, Inc.
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  • 50
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    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 51
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    Journal of Computational Chemistry 15 (1994), S. 524-531 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Starting from the bond polarization theory (BPT), a new semiempirical method for the calculation of net atomic charges is developed. The bond polarization theory establishes a linear dependence of atomic charges from the bond polarization energy. This energy is calculated from the hybrid orbitals forming a bond and the point charges within the neighborhood. Empirical parameters are introduced for the polarity of an unpolarized bond and for the change of the atomic charge with σ- and π-bond polarization. Because these parameters are linear, they can be calibrated directly using net atomic charges from ab initio calculations. This procedure was performed using the charges from STO3G calculations on a set of 18 amino acids. Using the two parameters for CH, OH, σ-CO, and NH bonds and the three parameters for CC, CO, and CN bonds, the 350 ab initio charges can be reproduced with high accuracy by solving sets of linear equations for the charges. The calculation of charges for large molecular systems including all inter- and intramolecular mutual polarizations requires only a few seconds (up to 100 atoms) or minutes (700 atoms) on a PC. This procedure is well suited for the application in molecular mechanics or molecular dynamics programs to overcome the limitations of most force fields used up to now. One of the weakest points in these programs is the use of fixed or topological charges to define the electrostatic potential. As an application of the new method, we calculated the interaction energy of an ion with valinomycin. This ring molecule forms octahedral oxygen cages around ions like potassium and acts thereby as selective ion carrier. To accomplish this function, valinomycin has to strip off the hydratization spheres of the ions, and therefore its preference for certain types of ions could be deduced from the interaction energies. © 1994 by John Wiley & Sons, Inc.
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  • 52
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    Journal of Computational Chemistry 15 (1994), S. 488-506 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It is aimed at protein structure prediction, homology modeling, molecular docking, nuclear magnetic resonance (NMR) structure determination, and protein design. The method uses and further develops a previously introduced approach to model biomolecular structures in which bond lengths, bond angles, and torsion angles are considered as independent variables, any subset of them being fixed. Here we simplify and generalize the basic description of the system, introduce the variable dihedral phase angle, and allow arbitrary connections of the molecules and conventional definition of the torsion angles. Algorithms for calculation of energy derivatives with respect to internal variables in the topological tree of the system and for rapid evaluation of accessible surface are presented. Multidimensional variable restraints are proposed to represent the statistical information about the torsion angle distributions in proteins. To incorporate complex energy terms as solvation energy and electrostatics into a structure prediction procedure, a “double-energy” Monte Carlo minimization procedure in which these terms are omitted during the minimization stage of the random step and included for the comparison with the previous conformation in a Markov chain is proposed and justified. The ICM method is applied successfully to a molecular docking problem. The procedure finds the correct parallel arrangement of two rigid helixes from a leucine zipper domain as the lowest-energy conformation (0.5 Å root mean square, rms, deviation from the native structure) starting from completely random configuration. Structures with antiparallel helixes or helixes staggered by one helix turn had energies higher by about 7 or 9 kcal/mol, respectively. Soft docking was also attempted. A docking procedure allowing side-chain flexibility also converged to the parallel configuration starting from the helixes optimized individually. To justdy an internal coordinate approach to the structure prediction as opposed to a Cartesian one, energy hypersurfaces around the native structure of the squash seeds trypsin inhibitor were studied. Torsion angle minimization from the optimal conformation randomly distorted up to the rms deviation of 2.2 Å or angular rms deviation of l0° restored the native conformation in most cases. In contrast, Cartesian coordinate minimization did not reach the minimum from deviations as small as 0.3 Å or 2°. We conclude that the most promising detailed approach to the protein-folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space. © 1994 by John Wiley & Sons, Inc.
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  • 53
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    Journal of Computational Chemistry 15 (1994) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 54
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    Journal of Computational Chemistry 15 (1994), S. 627-632 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An important area of research in computational biochemistry is the design of molecules for specific applications. The design of these molecules, which depends on the accurate determination of their three-dimensional structure, can be formulated as a global optimization problem. In this article, we present results from the application of a new conformation searching method based on direct search methods. We compare these results to some earlier results using genetic algorithms and simulated annealing. © 1994 by John Wiley & Sons, Inc.
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  • 55
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    Journal of Computational Chemistry 15 (1994), S. 719-732 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Traditional net atomic charge models were found unsatisfactory for representing the molecular electric potential (MEP) of n-alkanes ethane through decane in their van der Waals envelopes. The MEP of these molecules was calculated by ab initio methods. Mulliken atomic charges were erratic and gave root mean square (rms) relative errors of fit to the MEP ranging from 152 to 607% with the 6-31 + + g** basis set. Fitting the MEP with potential-derived net atomic charges (PD charges) gave errors ranging from 51 to 62% with the same basis set. The use of larger basis sets, inclusion of electron correlation, use of more MEP data points, or relaxation to optimal structural geometry did not improve significantly the representation of the MEP by net atomic charges. In many cases PD charges of hydrogen atoms were negative, and carbon atoms were positive. To improve the representation of the MEP of n-alkanes, augmentation of the model with nonatomic sites was investigated with the program PDM93. Models with additional charge sites located between hydrogens, on a line bisecting the CH2 group, achieved fits to the MEP with errors reduced to 8% or less, except for n-butane, where the fitting error was 16%. The PD models augmented with methylene bisector sites generally show positive hydrogen charges. They also show CH2 group charge alternation along the n-alkane chains. The augmented charge models were consistent with the observed quadrupole moment of ethane and gave satisfactory predictions for the crystal structures of pentane and octane. © 1994 by John Wiley & Sons, Inc.
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  • 56
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    Journal of Computational Chemistry 15 (1994), S. 733-746 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A semiempirically parameterized version of the extended Hückel molecular orbital method has been combined with an efficient quasi-Newton Broyden-Fletcher-Goldfarb-Shannon (BFGS) optimization algorithm to obtain accurate geometries for compounds containing H, C, N, O, and F. The requirement of only one matrix diagonalization per energy evaluation makes the EHNDO (Extended Hückel Neglect of Differential Overlap) method faster than semiempirical Hartree-Fock NDDO methods such as MNDO, AM1, and PM3. Geometrical results for EHNDO appear to be as good as or better than results for the widely used AM1 technique, and geometry optimization for EHNDO also requires only a fraction of the time. © 1994 by John Wiley & Sons, Inc.
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  • 57
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    Journal of Computational Chemistry 15 (1994), S. 782-790 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have applied the FEM-MP2 method (an implementation of the p-version finite element technique within the framework of second-order Møller-Plesset perturbation theory, [J. Chem. Phys., 98, 5642 (1993), and references therein]) to calculate second-order correlation energies for the atoms Be, Ca, Sr, Ba, Yb, Cd, and Hg and thus to complete our studies on closed-shell elements. The FEM-MP2 method permits the use of virtual orbitals of very high angular momentum (lmax = 12) in combination with radial basis sets which are very close to completeness, in such a way that we are able to obtain results that could be the most accurate published so far and, in some cases, the only values available in the literature. We hope they may be useful as a reference for basis set saturation tests and for new methods to calculate correlation energies. © 1994 by John Wiley & Sons, Inc.
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  • 58
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    Journal of Computational Chemistry 15 (1994), S. 820-837 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is presented to reduce the memory requirement of normal mode analysis applied to systems containing two or more large proteins when these systems exhibit symmetry properties. We use a rigid geometry model (i.e., only the dihedral angles of the polypeptide chain are considered as variables). This model allows a reduction by a factor of 8 on average of the number of variables with a concomitant freezing of the high-frequency modes. The symmetry properties of the system are used to reduce further the number of variables that must be considered in the computation. Application of group theory leads to a factorization of the matrices of interest (the coefficient and the Hessian matrices) into independent blocks along the diagonal. The initial, reducible representation is thus transformed into a number of irreducible representations of smaller dimensions. In the case of the C2 symmetry group, the method leads to a reduction of the size of the matrices that must be manipulated during the computation (coefficient matrix, Hessian matrix, and eigenvectors matrix) by a factor of 256 compared with the usual normal mode analysis in Cartesian coordinate space. The method is particularly well adapted to the study of the dynamics of oligomeric proteins because these proteins often display symmetry properties (e.g., virus coat proteins, immunoglobulins, hemoglobin, etc.). In favorable cases, in conjunction with X-ray diffuse scattering data, the study of systems showing allosteric properties might be considered. © 1994 by John Wiley & Sons, Inc.
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  • 59
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    Journal of Computational Chemistry 15 (1994), S. 561-570 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: By nuclear magnetic resonance (NMR), the four ring forms of psicose, α-and β-pyranose and α- and β-furanose, have almost equal concentrations in aqueous solution. Prediction of this equilibrium by molecular mechanics tests both the balance within the force field and the methods for including the many degrees of freedom in the system. For both the α- and β-furanoses, each of 410 different ring shapes was studied in combination with 37 combinations of staggered side-group orientations. Of these, 48 and 57 initial combinations of side-group orientations contributed to the α- and β-furanose energy surfaces. The pyranoses were analyzed in two steps. First, the 38 characteristic ring conformations were optimized with the 63 staggered side-group combinations. All combinations that gave the lowest energy at one or more of the 38 shapes (20 combinations for α-pyranose, 15 for β-pyranose) were then optimized with 4912 different ring forms. Ring conformations were generated by fixing nonadjacent ring atoms (two for furanose rings, three for pyranoses) at increments of 0.1 Å from the plane of the remaining three atoms. At a dielectric constant of 4.0, prediction was in fair agreement with the NMR results. Model northern and southern conformers contribute to the furanose equilibrium, and both chairs are important for α-psicopyranose. © 1994 by John Wiley & Sons, Inc.
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  • 60
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    Journal of Computational Chemistry 15 (1994), S. 588-595 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A genetic algorithm has been developed for molecular mechanics calculations. It has been proved to be a robust and efficient structure optimization technique. Because it uses randomly generated starting structures and stochastic operators, the resulting structures are not subjected to the chemist's bias. © 1994 by John Wiley & Sons, Inc.
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  • 61
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    Journal of Computational Chemistry 15 (1994), S. 644-652 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have studied the effect of excess charge on the bond strength in the silanes SiH4 and Si2H6 to assess whether charge trapping in a solid-state lattice might promote the technologically important photodegradation of amorphous silicon alloys (the Staebler-Wronski effect). The calculations indicate that both positive and negative charges reduce the strength of Si—H and Si—Si bonds considerably, to the point where they may be broken easily by visible or even infrared light. © 1994 by John Wiley & Sons, Inc.
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  • 62
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    Journal of Computational Chemistry 15 (1994), S. 596-626 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The effects of substituents (X) on the structures and stabilities of CH2X- anions for groups comprised of fourth- and fifth-period main group elements (X = K, CaH, GaH2, GeH3, AsH2, SeH, Br, Rb, SrH, InH2, SnH3, SbH2, TeH, and I) have been investigated by ab initio pseudopotential calculations. Full geometry optimizations have been carried out on the CH2X- anions and the corresponding neutral parent molecules, CH3X, at HF/DZP + and MP2/DZP + levels. Results for substituents from the second (X = Li—F) and third (X = Na—Cl) periods provide comparisons of substituent effects of the main group elements of the first four rows of the periodic table on methyl anions. Frequency calculations characterize the nature of stationary points and show pyramidal CH2X- anion structures to be the most stable unless π acceptor interactions (e.g., with BH2, AlH2, GaH2, and InH2 favor planar geometries. The CH2X- stabilization energies [at QCISD(T)/DZP + /MP2/DZP + + ZPE level for X = K—I and QCISD(T)/6-31 + G*/MP2/6-31 + G* + ZPE level] for X = Li—Cl) also show strong π-stabilizing effects for the same substituents. With the exception of CH3 and NH2, all substituents stabilize methyl anions, although the σ stabilization by OH and F is small. The SiH3—PH2—SH—Cl, GeH3—AsH2—SeH—Br, and SnH3—SbH2—TeH—I sets of substituents give stabilization energies between 19 and 30 kcal/mol. The stability of methyl anions substituted by the halogens and the chalcogens (X = OH, SH, SeH, and TeH) increases down a group in accord with the increasing substituent polarizability, while for π acceptors (BH2, AlH2, GaH2, and InH2) the stability decreases down a group in line with their π-accepting ability. © 1994 by John Wiley & Sons, Inc.
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  • 63
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    Journal of Computational Chemistry 15 (1994), S. 633-643 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure is developed and applied to characterize the global shape of the hydrogen-bonded networks formed in solvent and solute-solvent clusters. The methodology combines elements of geometry and topology of molecular chains, and it provides a description of the compactness and complexity of the entanglements formed by the network of hydrogen bonds between solute and solvent molecules. This approach complements others in the literature, where the hydrogen bonding is described in terms of the spatial distribution of bonds, their energetics and lifetimes, or the length hydrogen-bonded walks in space. The results of the present technique do not depend too strongly on the details of the molecular geometry. Therefore, one can assess the extent to which large-scale architecture is modified by rearrangements in the nuclear configuration, information which is important in molecular dynamics when estimating the persistence of essential structural features along dynamic trajectories. In this article we discuss the methodology and illustrate its application to the study of water clusters and solvated clusters of acetic acid. Expected qualitative features in the change of shape descriptors in actual reorganizations of hydrogen-bonding patterns are discussed briefly. © 1994 by John Wiley & Sons, Inc.
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  • 64
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    Journal of Computational Chemistry 15 (1994), S. 662-665 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An X-PLOR scheme for imitating the action of ribosomes in aiding synthesizing peptides to find their ultimate conformations is introduced. The scheme is tested with an example from the Delta-Sleep-Inducing-Peptide mutant family. © 1994 by John Wiley & Sons, Inc.
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  • 65
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    Journal of Computational Chemistry 15 (1994), S. 667-683 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: New atom- and group-based spherical-cutoff methods have been developed for the treatment of nonbonded interactions in molecular dynamics (MD) simulation. A new atom-based method, force switching, leaves short-range forces unaltered by adding a constant to the potential energy, switching forces smoothly to zero over a specified range. A simple improvement to group-based cutoffs is presented: Switched group-shifting shifts the group-group potential energy by a constant before being switched smoothly to zero. Also introduced are generalizations of atom-based force shifting, which adds a constant to the Coulomb force between two charges. These new approaches are compared to existing methods by evaluating the energy of a model hydrogen-bonding system consisting of two N-methyl acetamide molecules and by full MD simulation. Thirty-five 150 ps simulations of carboxymyoglobin (MbCO) hydrated by 350 water molecules indicate that the new methods and atom-based shifting are each able to approximate no-cutoff results when a cutoff at or beyond 12 Å is used. However, atom-based potential-energy switching and truncation unacceptably contaminate group-group electrostatic interactions. Group-based potential truncation should not be used in the presence of explicit water or other mobile electrostatic dipoles because energy is not a state function with this method, resulting in severe heating (about 4 K/ps in the simulations of hydrated MbCO). The distance-dependent dielectric (∊ ∝ r) is found to alter the temperature dependence of protein dynamics, suppressing anharmonic motion at high temperatures. Force switching and force shifting are the best atom-based spherical cutoffs, whereas switched group-shifting is the preferred group-based method. To achieve realistic simulations, increasing the cutoff distance from 7.5 to 12 Å or beyond is much more important than the differences among the three best cutoff methods. © 1994 by John Wiley & Sons, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
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  • 66
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    Journal of Computational Chemistry 15 (1994), S. 704-718 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics (MD) simulation and thermodynamic integration (TI) techniques have been used to study the relative free energies of the 8-methyl-N5-deazapterin and 8-methyl-pterin cations (N3 protonated) in aqueous solution. The MD simulations were performed at constant temperature and volume, and the mutations between the cations were carried out by changing the coupling parameter continuously and linearly with the MD simulation time (continuous coupling or slow growth method). The free energy changes have been calculated using both linear and nonlinear couplings of the potential energy functions. Free energy changes have also been computed using the perturbation method for comparison. After separation into electrostatic and van der Waals mutations, most (ca. 80%) of the total free energy change is found to be due to mutation of the electrostatic terms. The free energy change is found to be sensitive to the cutoff radii for interactions between solvent molecules, but rather insensitive to the cutoff radii for interactions between cation and solvent. The free energy changes have also been calculated using various cation and solvent models. Atomic charges for the cations were derived from the molecular electrostatic potential at the semiempirical AM1 and ab initio self-consistent field (SCF) (3-21G, 6-31G, 6-31G*, 6-311G**) levels using AM1 and 3-21G optimized geometries. The TIP3P and SPC models were adopted for the solvent. For the TIP3P solvent model, the order of the free energy change is 6-31G 〉 3-21G 〉 6-31G* ≈ 6-311G** 〉 AM1, where the difference between 6-31G and AM1 is approximately 1 kcal/mol. The free energies obtained using 3-21G optimized geometries are approximately 0.7 kcal/mol larger than those obtained using AM1 geometries for the cations. The free energy change computed using the TIP3P/6-311G* model is 0.3 kcal/mol larger than that obtained for the SPC/6-311G* model. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 752-768 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A CFF931 all-atom force field for aromatic polyesters based on ab initio calculations is reported. The force field parameters are derived by fitting to quantum mechanical data which include total energies, first and second derivatives of the total energies, and electrostatic potentials. The valence parameters and the ab initio electrostatic potential (ESP) derived charges are then scaled to correct the systematic errors originating from the truncation of the basis functions and the neglect of electron correlation in the HF/6-31G* calculations. Based on the force field, molecular mechanics calculations are performed for homologues of poly(p-hydroxybenzoic acid) (PHBA) and poly(ethylene terephthalate) (PET). The force field results are compared with available experimental data and the ab initio results. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 769-781 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A molecular dynamics (MD) simulation of 35,000 picoseconds (ps) has been carried out to study the conformational interconversions of 1,1-difluoro-4,4-dimethylcycloheptane at room temperature using the MM3 force field. The exchange between axial and equatorial fluorine atoms was the only conformational interconversion that occurred, and it took place via the process of pseudorotation. Ring inversions (twist-chair 〈 twist-boat 〈 twist-chair) were not observed. The axial-equatorial exchange of the two fluorine atoms took place five times during the MD trajectory of 35,000 ps. The two CH3 groups occupied symmetrical positions (exchangeable by a C2-like rotations, where C2-like means it would be C2 if the fluorines were not present) in the MM3 structures, and during most of the time of the MD trajectory. The methyls occasionally moved off the C2-like axis in the simulated process, mostly because the C2-like axis was momentarily moved so that it did not pass through the ring atom to which the two CH3 groups are bonded. A C2-like symmetry of the twist-chair conformation was maintained approximately during most of the MD simulation. The conformational geometry with the highest energy obtained during the axial-equatorial exchange process was found and used to locate the transition state. The energy barrier for this axial-equatorial exchange was calculated to be 4.7 kcal/mol, and it compares with the value (5.0 kcal/mol) determined by dynamic nuclear magnetic resonance (NMR). © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 838-846 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A detailed comparison has been made of the performance of molecular dynamics and hybrid Monte Carlo simulation algorithms for calculating thermodynamic properties of 2D Lennard-Jonesium. The hybrid Monte Carlo simulation required an order of magnitude fewer steps than the molecular dynamics simulation to calculate reproducible values of the specific heat. The ergodicity of the two algorithms was compared via the use of intermediate scattering functions. For classical systems the intermediate scattering functions should be real; however, a simple analysis demonstrates that this function will have a significant imaginary component when ergodicity breaks down. For q vectors near the zone boundary, the scattering functions are real for both algorithms. However, for q vectors near the zone center (i.e., harmonic, weakly coupled modes), the scattering function calculated via molecular dynamics had a significantly larger imaginary component than that calculated using hybrid Monte Carlo. Therefore, the hybrid Monte Carlo algorithm is more ergodic and samples phase space more efficiently than molecular dynamics for simulations of 2D Lennard-Jonesium. © 1994 by John Wiley & Sons, Inc.
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  • 70
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    Journal of Computational Chemistry 15 (1994), S. 847-857 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The AM1/MST strategy for the computation of hydrated neutral molecules has been optimized. For this purpose, we have systematically explored the best cavity definition, the most suitable strategy to compute the molecular electrostatic potential (MEP), and the use of MEP scaling factors to correct the semiempirical MEPs. As a result, we have developed an optimized version of the AM1/MST method, which allows us to reproduce well the experimental free energies of hydration (root mean square, rms, deviation in the range of 1 kcal/mol) as well as the water-induced dipoles computed at the 6-31G*/MST level (rms deviations in the range of 0.3 D). © 1994 by John Wiley & Sons, Inc.
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  • 71
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    Journal of Computational Chemistry 15 (1994), S. 866-874 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Based on results of electron diffraction, gas phase infrared spectroscopy (IR), and MP2/6-31 + G* ab initio calculations, a set of molecular mechanics (MM3) parameters was developed for molecules containing the N(sp3) - O(sp3) moiety. Using this set of parameters, MM3 is able to reproduce structures (bond lengths and bond angles) and vibrational spectra satisfactorily. © 1994 by John Wiley & Sons, Inc.
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  • 72
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    Journal of Computational Chemistry 15 (1994), S. 919-924 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations are used to test the ability of various representations to reproduce bond energies. It is found that expansion in 1/R, where R is the bond length, is remarkably efficient and is consistently better than the usual R expansion. A quadratic form in 1/R is better than a cubic representation in R and sometimes even as good as a quartic representation. A cubic function in 1/R is, in all cases studied, better performing than the quartic expansion in R. It is also found that parameters derived with the 1/R expansion are defined more sharply than those derived for the R expansion. It is suggested that the 1/R expansion may be computationally more efficient for simulations of large biomolecules and for constructions of reactive force fields than the standard bond functions. © 1994 by John Wiley & Sons, Inc.
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  • 73
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    Journal of Computational Chemistry 15 (1994), S. 947-962 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article studies the backbone influence on the side chains of N-methyl N′-acetyl amides (dipeptides) of alanine, valine, phenylalanine, leucine, isoleucine, glutamine, and lysine. Several local minima corresponding to protein φ, ψ, and χ values for each dipeptide are determined through optimization in the MM2 force field. These local minima are located in various regions on the Ramachandran map related to particular protein secondary structures. The dipeptide backbone influence on the side chain is explored via the sensitivity of the side chain torsion angles χ with respect to the backbone φ and ψ angles. Sensitivity coefficients are calculated, describing the χ response to an externally imposed change in φ or ψ. The χ response, which depends on the backbone conformation in a particular region, is induced primarily by the van der Waals and dipole interactions between the backbone and the side chain, which change with a deviation in φ or ψ. Various sensitivity trends are observed in the particular Ramachandran regions, revealing the subtle relationships between the dipeptide backbone and the side chain. © 1994 by John Wiley & Sons, Inc.
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  • 74
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    Journal of Computational Chemistry 15 (1994), S. 1053-1063 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present potential energy surfaces for Rh—CO obtained from density functional theory for two electronic states of Rh—CO. We have performed local spin-density calculations including relativistic as well as gradient corrections. The construction of a reasonably accurate atom-atom potential for Rh—CO is not possible. We were much more successful in constructing the potential energy surfaces by representing the potential as a spherical expansion. The expansion coefficients, which are functions of the distance between the rhodium atom and the carbon monoxide center of mass, can be represented by Lennard-Jones, Buckingham, or Morse functions, with an error of the fit within 10 kJ/mol. The potential energy surfaces, using Morse functions, predict that the electronic ground state of Rh—CO is 2Σ+ or 2Δ. This is a linear structure with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.253 nm. The bonding energy is -184 kJ/mol. Further, Morse functions predict that the first exicted state is 4A′. This is a bent structure (∠Rh—CO = 14°) with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.298 nm. The bonding energy of this state is -60 kJ/mol. Both these predictions are in good agreement with the actual density functional calculations. We found 0.250 nm with -205 kJ/mol for 2Σ+ and 0.253 nm with -199 kJ/mol for 2Δ. For 4A′, we found 0.271 nm, ∠Rh—CO = 30°, with -63 kJ/mol. The larger deviation for 4A′ than for 2Σ+ or 2Δ is a consequence of the fact that the minimum for 4A′ is a very shallow well. © 1994 by John Wiley & Sons, Inc.
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  • 75
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    Journal of Computational Chemistry 15 (1994), S. 1105-1112 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient algorithm for parallelization of a molecular mechanics program operating in the space of internal coordinates such as dihedral angles, bond angles, and bond lengths is described. The iterative procedure to calculate analytical energy derivatives with respect to the internal coordinates was modified to allow parallelization. Computationally intensive modules that calculate energy and its derivatives, solvent-accessible surface, electrostatic polarization energy and that update lists of interactions were parallelized with nearly 100% efficiency. The proposed strategy for the shared-memory computer architecture is easily scalable and requires minimum changes in a program code. The overall speedup for a realistic calculation minimizing the energy of a myoglobin reaches a factor of 3 for 4 processors. © 1994 by John Wiley & Sons, Inc.
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  • 76
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    Journal of Computational Chemistry 15 (1994), S. 1437-1445 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A bond and group equivalent scheme that allows the calculation of heats of formation of alkenes from ab initio 6-31G* energies has been developed. For a group of 26 compounds, the root mean square (rms) error for the calculated heat of formation was 0.78 kcal/mol. Heats of formation have been predicted for an additional nine compounds for which the experimental values are either unknown or suspect. The heats of hydrogenation of barrelene and related compounds are discussed. © 1994 by John Wiley & Sons, Inc.
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  • 77
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    Journal of Computational Chemistry 15 (1994), S. 1127-1138 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To understand and calculate the interactions of a solute with a solvent, a good method of computing the molecular surface is needed. Three kinds of surfaces may be used: the van der Waals Surface, the Accessible Surface, and the Molecular Surface. The latter is redefined in this article as the Solvent-Excluding Surface. The new algorithm for computing the Solvent-Excluding Surface included in the GEPOL93 program is described. GEPOL93 follows the same concept as former versions of GEPOL but with a full new algorithm. Thus, it computes the Solvent-Excluding Surface by filling the spaces not accessible to the solvent with a set of new spheres. The computation is controlled by three parameters: the number of triangles per sphere, controlled by NDIV; the maximum overlap among the new spheres (OFAC); and the size of the smallest sphere that can be created (RMIN). The changes introduced for the computation of the ESURF make GEPOL93 not just a new version but a new program. An estimation is made of the error in the area and volume obtained in the function of the parameters. © 1994 by John Wiley & Sons, Inc.
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  • 78
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    Journal of Computational Chemistry 15 (1994), S. 1176-1185 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article presents the results of an extensive examination of the stable conformations of CH3CH2OCH2CH2OH at various levels of theory. In particular, 41 initial conformations are optimized using the MM2 force field in BIGSTRN-3; the MINDO/3, MNDO, and AM1 Hamiltonians in AMPAC 2.2; the PM3 Hamiltonian in MOPAC 7.0; and at the HF/STO-3G and HF/3-21G levels using Gaussian 92. The optimized HF/3-21G structures are reoptimized at the HF/6-31G(d) level, and the unique structures are optimized again at the MP2 = FULL/6-31G(d) level. In addition, single-point MP2/6-31G(d) calculations are performed using the HF/6-31G(d) geometries. The goal is to determine the relative accuracy of each method and discuss their strengths and weaknesses. © 1994 by John Wiley & Sons, Inc.
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  • 79
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    Journal of Computational Chemistry 15 (1994), S. 1199-1216 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A previously proposed method of modeling force field transition structures as the lowest energy structure on the seam of two intersecting potential energy surfaces is improved with respect to the force field expression and the efficiency of the optimization algorithm. Comparison with ab initio and experimental results show that the force field method may have the potential of achieving almost quantitative results. It appears that the results from transition state modeling are currently limited by the accuracy of the underlying force field. © 1994 by John Wiley & Sons, Inc.
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  • 80
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    Journal of Computational Chemistry 15 (1994), S. 1217-1227 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report on an implementation of quantum mechanical density functional calculations carried out in a dielectric medium. The dielectric medium is introduced by integrating the solution of the Poisson-Boltzmann equations into the density functional calculation. The calculations are carried out for a simple amide in vacuum, in the field of an ion, and in the ion field in several dielectric environments. The environment was constructed to include a low dielectric interior embedded in a high dielectric continuum of dielectric 80 (corresponding to aqueous solution). The energies and electron densities of formamide in the ion field were calculated at various configurations in this system, including at the low dielectric-high dielectric interface. The systems were designed to simulate situations which are similar to those that occur in proteins (i.e., the protein constitutes the low dielectric medium surrounded by aqueous solution). The system mimics situations in which charges in such proteins located in various regions interact with other parts of the protein and with ligands which mainly bind to the surface. © 1994 by John Wiley & Sons, Inc.
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  • 81
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method using molecular mechanics to calculate internal energies and the generalized Born/surface area (GB/SA) method for calculating solvation free energy has been compared with the corresponding terms obtained from ab initio quantum chemical calculations in the gas phase and the free energy perturbation method implemented in Monte Carlo (MC) simulations to study conformational equilibria in solution. 1,2-Ethanediol, 2-hydroxybenzoic acid, the neutral and protonated histamine, were considered in aqueous solution as systems capable of intramolecular hydrogen bonding. The molecular mechanics method with all atom and united atom models, using the AMBER* force field and the parameterization as implemented in the MacroModel modeling package and the GB/SA continuum solvation model, produces smaller separation in relative conformer free energies than does the ab initio + MC method in aqueous solution. The GB/SA relative solvation free energies using the charges from the AMBER* force fields were consistently smaller than the values obtained in Monte Carlo simulations. Using the charge sets from the Monte Carlo simulations and considering solute geometries with torsional angles fixed at the optimized ab initio values, the relative solvation free energies remained underestimated by up to 30% as compared to the Monte Carlo values. The AMBER*//GB/SA predicted most stable conformer for the 1,2-ethandiol system in aqueous solution is in contrast with the ab initio + MC finding and the available experimental results. For the histamine system predictions by only the united atom AMBER*//GB/SA model agree with those by ab initio + MC and with data derived from nuclear magnetic resonance (NMR) experiments. Differences in the two methods are considered mainly due to the application of torsional parameters and atomic charges developed in the AMBER* parameter set for monofunctional polar systems. New parameters seem to be needed for quantitative description of the in-solution conformational equilibria for organic compounds with a possible intramolecular hydrogen bond. © 1994 by John Wiley & Sons, Inc.
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  • 82
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    Journal of Computational Chemistry 15 (1994), S. 1278-1290 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two-dimensional protein (ferritin) aggregates with a square lattice symmetry, which were formed within a thin liquid layer on a mercury surface, were studied by molecular dynamics (MD) simulation. For the simulation, the ferritin molecule was modeled by an assembly of 49 spheres, and the intermolecular interactions were given by simple formulae. During the simulation, molecules were confined within a layer, which corresponds to the thin liquid layer. An annealing MD simulation was done starting from a random molecular configuration within the layer, and aggregates with the square lattice symmetry were also obtained. To study the stability of aggregates, dissociation processes of the aggregates were analyzed using MD simulations at room temperature. Interactions between the nearest-neighbor molecules were regarded as bonds. Mean bond energies and correlation coefficients between the bond energies were calculated from the MD trajectories. A decay profile according to the dissociation was obtained, yielding a dissociation rate constant. Buried bonds were stronger than peripheral bonds. The larger the aggregate size, the stronger the bond for each of the buried and peripheral bonds. A simple theoretical account, which is applicable to a general bonded network, was introduced to analyze the dynamics of the aggregates. © 1994 by John Wiley & Sons, Inc.
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  • 83
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The special-purpose computer GRAPE-2A accelerates the calculation of pairwise interactions in many-body systems. This computer is a back-end processor connected to a host computer through a Versa Module Europe (VME) bus. GRAPE-2A receives coordinates and other physical data for particles from the host and then calculates the pairwise interactions. The host then integrates an equation of motion by using these interactions. We did molecular dynamics simulations for two systems of liquid water: System 1 (1000 molecules), and System 2 (1728 molecules). The time spent for one step of molecular dynamics was 3.9 s (System l), and 10.2 s (System 2). The larger the molecular system, the higher the performance. The speed of GRAPE-2A did not depend on the formula describing the pairwise interaction. The cost performance was about 20 times better than that of the fastest workstations available today, and GRAPE-2A cost only $22,000. © 1994 by John Wiley & Sons, Inc.
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  • 84
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    Yeast 10 (1994), S. 1-11 
    ISSN: 0749-503X
    Keywords: Schizosaccharomyces pombe ; Golgi body ; protein transport ; secretion ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Schizosaccharomyces pombe was treated with either cycloheximide or anisomycin at levels sufficient to inhibit 〉95% of protein synthesis for periods upon to 3 h, equivalent to one cell cycle. Treatment for as little as 1 h caused significant loss of the Golgi apparatus by both immunofluorescence and electron microscopy. The loss was quantitated by stereology on electron micrographs. Nearly 90% of the stacked Golgi was lost over a 3 h period. No other intracellular membrane compartment seemed to be affected. Measurement of enzyme activities confirmed these observations. The activity of a resident of the Golgi apparatus, α-1,2 galactosyltransferase, was reduced over this time, whereas the endoplasmic reticulum marker, BiP, and the cytoplasmic enzyme, hexokinase, were unaffected. The morphological changes associated with cycloheximide addition were reversed on its removal, though there was a lag before cells recommenced growth or secretion of the enzyme, acid phosphatase.
    Additional Material: 8 Ill.
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  • 85
    ISSN: 0749-503X
    Keywords: Genome sequencing ; Saccharomyces cerevisiae ; chromosome XI ; MBR1 ; GTPase-activating protein ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We present the DNA sequence analysis of a region covering a 3·5 kb EcoRI fragment from the left arm of chromosome XI from Saccharomyces cerevisiae. This region contains five open reading frames (ORFs) which code for proteins of greater than 100 amino acids. ORF YKL425 codes for the previously sequenced Mbr1 (Valens et al., 1991; Daignan-Fornier et al., 1993) which participates in mitochondrial biogenesis. YKL424 has identity with a GTPase-activating protein of higher eukaryotes. The three remaining ORFs have no identity to known proteins within the databases screened and are not assigned ORF numbers as they are completely contained with ORFs YKL424 and YKL425. This sequence has been entered in the EMBL Data Library under Accession Number X75561.
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  • 86
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    Yeast 10 (1994) 
    ISSN: 0749-503X
    Keywords: Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
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  • 87
    ISSN: 0749-503X
    Keywords: Heterologous gene expression ; levansucrase precursor ; Bacillus subtilis ; yeast ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Levansucrase, a Bacillus subtilis extracellular enzyme, was not secreted in the culture medium when produced in yeast. The protein accumulated inside the cell in its precursor form which represented 0·3% of total proteins. The absence of any post-translational modifications, such as signal sequence cleavage or addition of N-linked sugars, indicated that this protein did not enter the reticulum secretion pathway.Direct observation of the cells by confocal laser scanning microscopy showed that levansucrase was associated with the cytoplasmic membrane. Subcellular fractionation experiments revealed that levansucrase precursor form is associated with membranes through weak ionic interactions. The purified precursor displayed the same catalytic properties as levansucrase secreted by B. subtilis. Thus yeast could be used as a source of levansucrase precursor allowing its isolation as a pure form on a milligram scale.
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  • 88
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    Yeast 10 (1994), S. 271-274 
    ISSN: 0749-503X
    Keywords: Genome sequencing ; Saccharomyces cerevisiae ; chromosome III ; telomeres ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: A comparison of the sequences of telomere regions from several yeast chromosomes revealed an apparent cloning artifact for the right end of chromosome III. An integrating vector containing G1-3T telomere sequences was used to clone the right end of chromosome III from a strain related to S288C. The sequence of this clone confirmed that the published sequence was incorrect and demonstrated that the right telomere region of chromosome III is similar to other telomeres.
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  • 89
    ISSN: 0749-503X
    Keywords: Saccharomyces cerevisiae ; Saccharomyces douglasii ; evolution ; ARG4 ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: A 3·6 kb DNA fragment from Saccharomyces douglasii, containing the ARG4 gene, has been cloned, sequenced and compared to the corresponding region from Saccharomyces cerevisiae. The organization of this region is identical in both yeasts. It contains besides the ARG4 gene, another complete open reading frame (ORF) (YSD83) and a third incomplete one (DED81). The ARG4 and the YSD83 coding regions differ from their S. cerevisiae homologs by 8.1% and 12·5%, respectively, of base substitutions. The encoded proteins have evolved differently: amino acid replacements are significantly less frequent in Arg4 (2·8%) than in Ysc83 (12·4%) and most of the changes in Arg4 are conservative, which is not the case for Ysc83. The non-coding regions are less conserved, with small AT-rich insertions/deletions and 20% base substitutions. However, the level of divergence is smaller in the aligned sequences of these regions than in silent sites of the ORFs, probably revealing a higher degree of constraints. The Gcn4 binding site and the region where meiotic double-strand breaks occur, are fully conserved. The data confirm that these two yeasts are evolutionarily closely related and that comparisons of their sequences might reveal conserved protein and DNA domains not expected to be found in sequence comparisons between more diverged organisms.
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  • 90
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    Yeast 10 (1994), S. 371-376 
    ISSN: 0749-503X
    Keywords: Saccharomyces cerevisiae ; NES24 ; chromosome XIII ; neomycin ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We have cloned NES24 using a temperature-sensitive nes24-1 mutant as a host and sequenced a 3162 bp XhoI-EcoRI DNA fragment containing the NES24 gene. Computer analysis revealed that this segment contains a 1806 bp open reading frame which is needed for complementation of the nes24-1 mutation. We found SUP8 in the region upstream of the NES24 gene, placing the NES24 gene on chromosome XIII. A protein homology search indicated that NES24 encodes a new protein. The disruption of the NES24 gene resulted in temperature-sensitive growth. The sequence has been deposited in DDBJ/EmBL/GenBank data bases under Accession Number D15052.
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  • 91
    ISSN: 0749-503X
    Keywords: Saccharomyces cerevisiae ; Chromosome V ; Monomeric G-protein ; Rab protein ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: A Saccharomyces cerevisiae sequence cloned by serendipity was found to encode a protein that is a new member of the Ypt/Rab monomeric G-protein family. This sequence shows high homology to the yeast genes SEC4 and YPT1 and, like SEC4 and YPT1, is essential for viability. The sequence was localized to chromosome V based upon hybridization to pulse-field gel-separated yeast chromosomes. The sequence has been deposited in the GenBank data library under Accession Number L17070.
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  • 92
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    Yeast 10 (1994) 
    ISSN: 0749-503X
    Keywords: Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
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  • 93
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    Yeast 10 (1994), S. 451-461 
    ISSN: 0749-503X
    Keywords: RAS-cAMP pathway ; CDC25 family ; cell division cycle mutation ; S. cerevisiae ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We have identified MS12 as a gene of Saccharomyces cerevisiae which, when on a multicopy vector, suppresses the heat shock sensitivity caused by the loss of the IRA1 product, a negative regulator of the RAS protein. The multicopy MSI2 also suppresses the heat shock sensitivity of cells with the RAS2val19 mutation but not those with the bcy1 mutation, suggesting that the MSI2 protein may interfere with the activity of the RAS protein. The sequence analysis of MSI2 reveals that it is identical to LTE1 belonging to the CDC25 family: CDC25, SCD25 and BUD5, each of which encodes a guanine nucleotide exchange factor for the ras superfamily gene products. Deletion of the entire MSI2 coding region reveals that MSI2 is not essential but the disruptant shows a cold-sensitive phenotype. Under the non-permissive conditions, more than 70% of the msi2 disruptants arrested at telophase as large budded cells with two nuclei divided completely and elongated spindles, indicating that the msi2 deletion is a cell division cycle mutation. These results suggest that MSI2 is involved in the termination of M phase and that this process is regulated by a ras superfamily gene product.
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  • 94
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    Yeast 10 (1994), S. 463-474 
    ISSN: 0749-503X
    Keywords: Saccharomyces cerevisiae ; cell polarity ; cellular morphogenesis ; GTPases ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: Cdc24p and Cdc42p are involved in the control of cell polarity during the Saccharomyces cerevisiae cell cycle. Cdc42p is a member of the Ras superfamily of GTPases and Cdc24p displays limited amino-acid sequence similarity with the Dbl proto-oncoprotein, which acts to stimulate guanine-nucleotide exchange on human Cdc42p. We have performed several genetic experiments to test whether Cdc24p and Cdc42p interact within the cell. First, overexpression of Cdc24p suppressed the dominant-negative cdc42D118A allele. Second, overexpression of wild-type CDC24 and CDC42 genes together was a lethal event resulting in a morphological phenotype of large, round, unbudded cells, indicating a loss of cell polarity. Third, a cdc24ts cdc42ts double mutant exhibited a synthetic-lethal phenotype at the semi-permissive temperature of 30°C. These data suggest that Cdc24p and Cdc42p interact within the cell and that Cdc24p may be involved in the regulation of Cdc42p activity.
    Additional Material: 4 Ill.
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  • 95
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 10 (1994), S. 497-508 
    ISSN: 0749-503X
    Keywords: Protein secretion and processing ; gene expression ; killer toxin ; Kex2 protease ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: K1 preprotoxin is the 316 residue precursor of the K1 killer toxin secreted by the yeast Saccharomyces cerevisiae. The SPβla reporter consists of the mature, secreted form of β-lactamase (βla) fused to S and P, two fragments of preprotoxin. S is the N-terminal 34 residues, including the secretion signal. P, a 67 residue ‘processing’ segment with three sites for N-glycosylation, terminates in a Lys Arg site for cleavage by the Kex2 protease. Expression of SPβla in yeast results in efficient secretion, processing by signal peptidase and glycosylation in the endoplasmic reticulum, producing proßla. Kex2 cleavage of proßla in the lumen of a late Golgi compartment releases βla, which accumulates stably in culture media buffered at pH 5·8-7. The half-life of secretion is 11 min at 30°C; 10-12% of the total activity in exponential-phase cells is intracellular, mostly in the form of proßla, indicating that transit from the endoplasmic reticulum to the Golgi is rate limiting. We have used SPβla expression in single- and multi-copy vectors to compare the PGK, GAL1, GAL10, PHO5 and CUP1 promoters under varying nutritional conditions. In exponential-phase cells, secretion of βla over a 40-fold range and up to several μg/ml was proportional to transcript level, demonstrating that SPβla can be employed as a convenient secreted reporter of promoter function in yeast.
    Additional Material: 7 Ill.
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  • 96
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 10 (1994), S. 415-415 
    ISSN: 0749-503X
    Keywords: Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Type of Medium: Electronic Resource
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  • 97
    ISSN: 0749-503X
    Keywords: Yeast ; fungi ; zymocin ; promoter ; pGKL1 ; pGKL2 ; pSKL ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The toxin-encoding linear plasmid systems found in Pichia acaciae and Kluyveromyces lactis yeasts appear to be quite similar, both in function and structural organization. By Southern hybridization, a linear plasmid of P. acaciae, pPac1-2, was found to hybridize to the second open reading frame (ORF2) of K. lactis plasmid pGKL1, known to encode the α and β subunits of the K. lactis toxin. A 1·7 kbp segment of pPac1-2 DNA was cloned, sequenced and shown to contain four regions of strong homology to four similarly oriented regions of K. lactis ORF2. This 1·7 kbp fragment also contained an ORF of 1473 bp that could encode a protein of ∼ 55·8 kDa. Like the α subunit gene of K. lactis ORF2, a very hydrophobic region occurs at the N-terminus, perhaps representing a signal sequence for transport out of the cell. Unlike K. lactis ORF2, however, the encoded polypeptide is much smaller and lacks a recognizable domain common to chitinases. The structure of a toxin that includes the translation product of this P. acaciae ORF would likely be quite different from that of the K. lactis toxin. Analysis of the upstream region of the P. acaciae ORF revealed an upstream conserved sequence identical to that found before ORFs 8 and 9 of pGKL2. A possible hairpin loop structure, as has been described for each of the four K. lactis pGKL1 ORFs, was found just upstream of the presumed start codon. The similarity of the promoter-like elements found in the linear plasmid genes of these diverse yeasts reinforces the idea of the existence of a unique, but highly conserved, expression system for these novel plasmids. The sequence has been deposited in the GenBank data library under Accession Number U02596.
    Additional Material: 6 Ill.
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  • 98
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 10 (1994), S. 491-496 
    ISSN: 0749-503X
    Keywords: Saccharomyces cerevisiae ; ARS1 ; DNA replication, mitotic ; DNA replication, premeiotic ; plasmid integration ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We have investigated the significance of the chromosomal replication origin, ARS1, during the entire life cycle of yeast. This was done by substituting the chromosomal copy with a series of ars1 deletion mutants. It was shown that the ARS1 replication origin is not essential for mitotic or premeiotic DNA replication since no effect on growth, chromosomal loss rate and spore viability was observed in the ars1 mutant strains. We conclude that replication origins are abundantly, present in the yeast genome and that the removal of a single replication origin is compensated for by replication forks emanating from neighbouring origins.
    Additional Material: 2 Ill.
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  • 99
    ISSN: 0749-503X
    Keywords: Mitochondrial carriers ; duplication ; citrate synthase ; RNA binding ; ribosomes ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: A 15·1 kb fragment of the yeast genome was allocated to the centromeric region of chromosome XIV by genetic mapping. It contained six bona fide genes, RPC34, FUN34, CIT1 (Suissa et al., 1984), RLP7, PET8 and MRP7 (Fearon and Mason, 1988) and two large open reading frames, DOM34 and TOM34, RPC34 and RLP7 define strictly essential functions, whereas CIT1, PET8 and MRP7 encode mitochondrial proteins. The PET8 product belongs to a family of mitochondrial carrier proteins. FUN34 encodes a putative transmembraneous protein that is non-essential as judged from the normal growth of the fun34-::L̈K18 (URA3) allele, even on respirable substrates. TOM34 codes for a putative RNA binding protein, and DOM34 defines a hypothetical polypeptide of 35 kDa, with no significant homology to known proteins. The region under study also contains two divergently transcribed tDNAs, separated only by a chimeric transposable element. This tight tDNA linkage pattern is commonly encountered in yeast, and a general hypothesis is proposed for its emergence on the Saccharomyces cerevisiae genome. RPC34, RLP7, PET8 and MRP7 are unique on the yeast genome, but the remaining genes belong to an extant centromeric duplication between chromosome III and XIV. The sequences have been deposited in the EMBL/GenBank data libraries under Accession Numbers L11277, L19167, M11344, M22116, V02536, X00782 and X63746.
    Additional Material: 6 Ill.
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  • 100
    ISSN: 0749-503X
    Keywords: Random-breakage mapping ; yeast ; APN1 ; YUH1 ; chromosome XI ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We have used the previously described technique of random-breakage mapping to locate the two yeast genes APN1 and YUH1. The APN1 locus is located ∼235 kb from the left telomere of chromosome XI, and shows weak (∼53 cM) genetic linkage to ura1. The YUH1 locus is located ∼140 kb from the right telomere of chromosome X, and genetically maps 3·6 cM distal to cdc11. In addition, we show by random-breakage mapping that TRP3 is located ∼45 kb from the left telomere of chromosome XI, whereas FAS1 is ∼110 kb from the same telomere. This supports a gene order on the left distal portion of chromosome XI that agrees with other physical reports but is inverted with respect to Edition 11 of the published genetic map. This report confirms that random-breakage mapping is a rapid and convenient method of locating cloned genes.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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