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1.
Tob Prev Cessat ; 7: 40, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34084979

RESUMO

INTRODUCTION: Outdoor smoke-free policies (SFPs) at sports clubs may contribute to the prevention of smoking among adolescents. Adolescents' support for such policy is important to its success. The aim of this study is to explore adolescents' perceptions with regard to an outdoor SFP at sports clubs in the Netherlands. METHODS: Focus group discussions (n=27) were held with 180 participants (aged 13-18 years) at 16 sports clubs. Thematic analysis was used to analyze the data. RESULTS: Participants generally supported an outdoor SFP at sports clubs. Five reasons for this support were reported: 1) children should not be exposed to smoking, 2) smoking and sports (clubs) do not fit together, 3) secondhand smoke is undesirable, 4) an outdoor SFP may enhance a sports club's image, and 5) an outdoor SFP contributes to the prevention of smoking. Some participants voiced considerations against an outdoor SFP, arguing amongst others, that smokers need to be taken into account, and that problems may occur with compliance and enforcement. Support for an outdoor SFP was stronger among participants at clubs with an outdoor SFP than among those without such policy. CONCLUSIONS: This study shows that adolescents generally support an outdoor smoke-free policy at sports clubs. After implementation, the outdoor SFP was generally experienced as a normal practice. These results could encourage sports clubs without an outdoor SFP to become smoke-free as well.

2.
J Inherit Metab Dis ; 33 Suppl 3: S5-11, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24137762

RESUMO

The urinary creatine:creatinine (Cr:Crn) ratio was measured in males from 49 families with a family history compatible with X-linked mental retardation (XLMR) in order to estimate the prevalence of SLC6A8 deficiency in Estonia. We identified 11 boys from 9 families with an increased urinary Cr:Crn ratio (18%). In three related boys, a hemizygous missense mutation (c.1271G>A; p.Gly424Asp) was identified. Their mother was heterozygous for the same mutation. Although many missense mutations have been described, the p.Gly424Asp mutation has not been previously reported. The clinical expression varied widely among affected males of this family. Patients 1 and 3 had relatively mild clinical expression (mild mental retardation (MR) and attention deficit disorder), but patient 2 had all typical clinical signs of SLC6A8 defect such as moderate MR, autistic features, expressive dysphasia and epilepsy. Among our patients, we saw significant problems in speech and language development combined with attention and behavioural difficulties. The number of false-positive biochemical results with increased urinary Cr:Crn ratio was higher (18%) in our study than in previous reports (1.8­10%). We therefore suggest that repeated biochemical testing should be performed before DNA sequencing analysis. Our study suggests that 2% (95% confidence limits: 0.05­11.1%) of this Estonian XLMR panel are due to mutations in the SLC6A8, which is similar to the prevalence reported in other populations. We therefore conclude that creatine transporter deficiency is a relatively common genetic disorder in males with sporadic or familiar MR and diagnostic screening of them should always include screening for SLC6A8 deficiency.


Assuntos
Encefalopatias Metabólicas Congênitas/diagnóstico , Creatina/deficiência , Análise Mutacional de DNA , Testes Genéticos/métodos , Deficiência Intelectual Ligada ao Cromossomo X/diagnóstico , Mutação de Sentido Incorreto , Proteínas do Tecido Nervoso/genética , Proteínas da Membrana Plasmática de Transporte de Neurotransmissores/deficiência , Adolescente , Adulto , Biomarcadores/urina , Encefalopatias Metabólicas Congênitas/epidemiologia , Encefalopatias Metabólicas Congênitas/genética , Encefalopatias Metabólicas Congênitas/psicologia , Encefalopatias Metabólicas Congênitas/urina , Criança , Creatina/genética , Creatina/urina , Creatinina/urina , Estônia/epidemiologia , Feminino , Predisposição Genética para Doença , Hereditariedade , Heterozigoto , Humanos , Inteligência/genética , Masculino , Deficiência Intelectual Ligada ao Cromossomo X/epidemiologia , Deficiência Intelectual Ligada ao Cromossomo X/genética , Deficiência Intelectual Ligada ao Cromossomo X/psicologia , Deficiência Intelectual Ligada ao Cromossomo X/urina , Pessoa de Meia-Idade , Proteínas do Tecido Nervoso/deficiência , Linhagem , Pessoas com Deficiência Mental , Fenótipo , Proteínas da Membrana Plasmática de Transporte de Neurotransmissores/genética , Proteínas da Membrana Plasmática de Transporte de Neurotransmissores/urina , Valor Preditivo dos Testes , Prevalência , Índice de Gravidade de Doença , Adulto Jovem
3.
Genet Couns ; 13(4): 459-64, 2002.
Artigo em Inglês | MEDLINE | ID: mdl-12558118

RESUMO

We report on the sudden death of a 3.5-year-old girl with Prader-Willi syndrome (PWS) and 15q11-q13 deletion. She suffered from severe chronic breathing disturbances and recurrent bronchitis. During an episode of acute bronchitis she had a cardiac arrest and died two months later of the sequelae. Brain CT imaging three weeks after the arrest showed bilateral symmetrical haemorrhages in the basal ganglia region. The spatial distribution of the haemorrhages can possibly suggest that the basal ganglia in PWS may be especially susceptible to hypoxemia.


Assuntos
Morte Súbita , Síndrome de Prader-Willi/fisiopatologia , Pré-Escolar , Deleção Cromossômica , Cromossomos Humanos Par 15 , Feminino , Humanos , Síndrome de Prader-Willi/genética , Tomografia Computadorizada por Raios X
4.
Unfallchirurg ; 104(5): 392-8, 2001 May.
Artigo em Alemão | MEDLINE | ID: mdl-11413954

RESUMO

The aim of this study was to analyze meniscal sutures under cyclic loading conditions for different suture types (vertical and horizontal mattress sutures) and suture materials (absorbable monofilament sutures: PDS 2-0; PDS-0, and PDS-1 USP). Testing was performed on medial porcine menisci, using a well-established biomechanical testing model with a complete longitudinal tear 3 mm from the periphery of the meniscus. Sixty specimens were used. One suture was tested at a time. During cyclic testing 100 load cycles were applied with a crosshead speed of 50 mm/min. Three different maximum loads (10 N, 20 N, and 40 N) were used. The preload was set at 5 N. After cyclic loading, the specimens were loaded until failure. During cyclic loading, a gap appeared between the two parts of the meniscus, and partial tissue failures were observed at the surface of the meniscus. Gapping was more marked with higher loads and with the weaker suture material (p < 0.001). Using PDS 0 and PDS 1 sutures, less partial tissue failures were observed compared to PDS 2-0 (p < 0.001). The ultimate failure loads after cyclic loading were higher with PDS-0 and PDS-1 sutures. With these suture materials vertical sutures were stronger than horizontal sutures (p < 0.05). Using PDS 2-0 this difference could not be found. These results show that the primary strength of meniscal sutures depends on the suture material. The frequency and the amount of gapping and partial tissue failures, which can be observed under cyclic loading, are less distinct with PDS-0 and PDS-1 compared to PDS 2-0. From a biomechanical point of view, PDS 0 and PDS 1 sutures are recommended for meniscal sutures to guarantee a high primary stability, a small amount of gapping, and few partial tissue failures.


Assuntos
Meniscos Tibiais/cirurgia , Polidioxanona , Suturas , Suporte de Carga/fisiologia , Animais , Fenômenos Biomecânicos , Meniscos Tibiais/fisiopatologia , Técnicas de Sutura , Suínos , Resistência à Tração
5.
Am J Med Genet ; 80(5): 491-3, 1998 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-9880214

RESUMO

Williams-Beuren syndrome (WBS) occurs sporadically; however, at least four familial cases of WBS have been described previously. We describe a mother and her son with typical WBS. The diagnosis of WBS in the son was confirmed by molecular cytogenetic analysis fluorescence in situ hybridization. He had a deletion of 7q11.23 at the ELN locus. The mother was diagnosed after the identification of WBS in her affected son. She is deceased and was thus not studied by FISH. However, her combined symptoms make it very clear that she had WBS. Two traits uncommon in WBS were observed, unilateral renal hypoplasia in the mother and a hemivertebra at L5 in the son.


Assuntos
Cromossomos Humanos Par 7/genética , Síndrome de Williams/genética , Adulto , Criança , Feminino , Humanos , Hibridização in Situ Fluorescente , Masculino
6.
Angiogenesis ; 2(2): 183-99, 1998.
Artigo em Inglês | MEDLINE | ID: mdl-14517473

RESUMO

The conformational requirements of suramin for its binding to basic fibroblast growth factor (bFGF) and platelet-derived growth factor (PDGF) were examined by molecular modeling and docking simulations using the conformational features of suramin determined by the present proton nuclear magnetic resonance (1H-NMR) studies and the crystal structures of growth factors reported previously. The assignment of resonances of suramin to individual protons was accomplished by the combined analysis of the coupling constants, two-dimensional correlated spectroscopy (COSY) and nuclear Overhauser effect spectroscopy (NOESY). The NOESY data obtained for suramin were utilized in a conformational search algorithm with constraints to generate a family of conformers which were further refined by restrained energy minimization. A family of nine conformers generated by restrained modeling falls primarily into one of two categories, either the conformer's two naphthyl rings are far apart, approximately 28-30 A, from one another or the conformer's two naphthyl rings are relatively close, approximately 16-18 A. The NMR data provide evidence for the presence of more than one conformer in solution. The modeling and docking simulation studies suggest that suramin binds efficiently to bFGF and PDGF by an induced-fit mechanism, wherein suramin complements bFGF or PDGF by adjusting its conformational freedom around the two pairs of single bonds that link the middle phenyl rings to the secondary amide backbone. The interaction of suramin with bFGF or PDGF primarily involves ion-pair, hydrophobic and hydrogen bonding interactions, in addition to van der Waals' contacts. The results indicate that suramin not only sterically blocks the receptor binding loop of the growth factors, but also competes for the binding sites of agonists such as heparin. The results suggest that suramin's propensity to bind to several polypeptides of varying size and structure is due to its conformational flexibility. Collectively, the data emphasize that conformationally constrained suramin analogs that selectively and competitively target angiogenic growth factors could be designed to reduce non-specific binding and, accordingly, toxicity.

7.
J Biomol Struct Dyn ; 15(2): 185-215, 1997 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-9399149

RESUMO

The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex between the anti HIV-1 gag ribozyme and its abortive DNA substrate manifests in the detection of a continuous track of A.T base pairs; this suggests that the interaction between the ribozyme and its DNA substrate is stronger than the one observed in the case of the free ribozyme where the bases in stem I and stem III regions interact strongly with the ribozyme core region (Sarma, R. H., et al. FEBS Letters 375, 317-23, 1995). The complex formation provides certain guidelines in the design of suitable therapeutic ribozymes. If the residues in the ribozyme stem regions interact with the conserved core, it may either prevent or interfere with the formation of a catalytically active tertiary structure.


Assuntos
DNA Viral/química , Genes gag , HIV-1/química , Modelos Químicos , RNA Catalítico/química , Catálise , Simulação por Computador , DNA Recombinante/síntese química , Modelos Moleculares , Ressonância Magnética Nuclear Biomolecular , Conformação de Ácido Nucleico , RNA/síntese química , RNA Viral/química
8.
Herz ; 21(3): 192-7, 1996 Jun.
Artigo em Alemão | MEDLINE | ID: mdl-8767863

RESUMO

Human disease caused by echinococcus granulosus is rare in Northern Europe, but is seen increasingly due to migration of labour and of tourism to endemic areas e. g. Southern Europe and the Middle East. Echinococcosis of the heart occurs in only 0.5 to 2% of cases of echinococcosis. Diagnosis is difficult because of the long latency between infection and manifestation of disease, and also because symptoms are unspecific. It is a diagnosis "to think of". Apart from a thorough history serological tests and medical imaging (ultrasound, X-rays, computed tomography) are used in the diagnosis of echinococcosis. Surgery is the preferred therapy, if not feasible medical treatment with benzimidazoles (Albendazole and Mebendazole) is effective. We describe a case of echinococcosis of the heart as the only manifestation of the disease: a 34-year-old male Turkish patient came in severe cardiac shock due to cardiac tamponade to the emergency department. Immediate heart surgery revealed a pericardium filled with cysts of echinococcus granulosus, infiltrating the left ventricle of the heart (Figure 1). The cysts were removed and the patient was put on a 2-year course of Mebendazole. The patient is free of relapse for more than 6 years now and he is considered to be cured.


Assuntos
Cardiomiopatias/cirurgia , Equinococose/cirurgia , Pericárdio/cirurgia , Adulto , Antinematódeos/administração & dosagem , Tamponamento Cardíaco/patologia , Tamponamento Cardíaco/cirurgia , Cardiomiopatias/patologia , Terapia Combinada , Diagnóstico Diferencial , Equinococose/patologia , Humanos , Masculino , Mebendazol/administração & dosagem , Pericárdio/patologia , Choque Cardiogênico/patologia , Choque Cardiogênico/cirurgia
9.
J Biomol Struct Dyn ; 13(4): 717-26, 1996 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-8906892

RESUMO

Hydration properties of individual nucleic acid bases were calculated and compared with the available experimental data. Three sets of classical potential functions (PF) used in simulations of nucleic acid hydration were juxtaposed: (i) the PF developed by Poltev and Malenkov (PM), (ii) the PF of Weiner and Kollman (WK), which together with Jorgensen's TIP3P water model are widely used in the AMBER program, and (iii) OPLS (optimized potentials for liquid simulations) developed by Jorgensen (J). The global minima of interaction energy of single water molecules with all the natural nucleic acid bases correspond to the formation of two water-base hydrogen bonds (water bridging of two hydrophilic atoms of the base). The energy values of these minima calculated via PM potentials are in somewhat better conformity with mass-spectrometric data than the values calculated via WK PF. OPLS gave much weaker water-base interactions for all compounds considered, thus these PF were not used in further computations. Monte Carlo simulations of the hydration of 9-methyladenine, 1-methyluracil and 1-methylthymine were performed in systems with 400 water molecules and periodic boundary conditions. Results of simulations with PM potentials give better agreement with experimental data on hydration energies than WK PF. Computations with PM PF of the hydration energy of keto and enol tautomers of 9-methylguanine can account for the shift in the tautomeric equilibrium of guanine in aqueous media to a dominance of the keto form in spite of nearly equal intrinsic stability of keto and enol tautomers. The results of guanine hydration computations are discussed in relation to mechanisms of base mispairing errors in nucleic acid biosynthesis. The data presented in this paper along with previous results on simulation of hydration shell structures in DNA duplex grooves provide ample evidence for the advantages of PM PF in studies of nucleic-acid hydration.


Assuntos
Simulação por Computador , DNA/química , Computação Matemática , Modelos Moleculares , Água/metabolismo , Composição de Bases , DNA/metabolismo , Método de Monte Carlo
10.
J Biomol Struct Dyn ; 13(3): 515-22, 1995 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-8825731

RESUMO

Here we describe a possible model of the cleavage mechanism in the hammerhead ribozyme. In this model, the 2' hydroxyl of C17 is moved into an appropriate orientation for an in-line attack on the G1.1 phosphate through a change in its sugar pucker from C3' endo to C2' endo. This conformational change in the active site is caused by a change in the uridine turn placing the N2 and N3 atoms of G5 of the conserved core in hydrogen bonding geometry with the N3 and N2 atoms on the conserved G16.2 residue. The observed conformational change in the uridine turn suggests an explanation for the conservation of G5. In the crystal structure of H.M. Pley et al., Nature 372, 68-74 (1994), G5 is situated 5.3A away from G16.2. However, the uridine turn is sufficiently flexible to allow this conformational change with relatively modest changes in the backbone torsion angles (average change of 14.2 degrees). Two magnesium ions were modeled into the active site with positions analogous to those described in the functionally similar Klenow fragment 3'-5' exonuclease (L.S. Beese and T.A. Steitz, EMBO J. 10, 25-33 (1991)), the Group I intron (T.A. Steitz and J.A. Steitz, P.N.A.S. U.S.A. 90, 6498-6502 (1993); R.F. Setlik et al., J. Biomol. Str. Dyn. 10, 945-972 (1993)) and other phosphotransferases. Comparison of this model with one in which the uridine turn conformation was not changed showed that although the changes in the C17 sugar pucker could be modeled, insufficient space existed for the magnesium ions in the active site.


Assuntos
Modelos Moleculares , RNA Catalítico/química , Sequência de Bases , Sítios de Ligação , Catálise , Ativação Enzimática , Dados de Sequência Molecular , Conformação de Ácido Nucleico , Relação Estrutura-Atividade
11.
Cell Mol Biol (Noisy-le-grand) ; 41(7): 883-905, 1995 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-8595368

RESUMO

The use of non-radioactive nucleic acid probes has increased dramatically over the last years. The convenience of not having to deal with radioactive isotopes combined with the stability and economy of the non-radioactive systems has led to applications in various techniques. One of the most successful labelling and detection systems is based on the hapten digoxigenin. Here, the different methods for labelling nucleic acids with digoxigenin as well as the various possibilities for detection are described. Some typical applications illustrate the utility of the DIG system.


Assuntos
Digoxigenina , Técnicas de Sonda Molecular , Ácidos Nucleicos/análise , Animais , DNA/análise , DNA/química , DNA/genética , Sondas de DNA , Humanos , Hibridização In Situ/métodos , Hibridização in Situ Fluorescente/métodos , Hibridização de Ácido Nucleico , Ácidos Nucleicos/química , Ácidos Nucleicos/genética , Nucleotídeos/química , Fotoquímica , Reação em Cadeia da Polimerase , Biossíntese de Proteínas , RNA/análise , RNA/química , RNA/genética , Sondas RNA , Radioisótopos , Análise de Sequência/métodos
12.
Protein Eng ; 8(9): 893-904, 1995 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-8746727

RESUMO

The 'fuzzy end elimination theorem' (FEE) is a mathematically proven theorem that identifies rotameric states in proteins which are incompatible with the global minimum energy conformation. While implementing the FEE we noticed two different aspects that directly affected the final results at convergence. First, the identification of a single dead-ending rotameric state can trigger a 'domino effect' that initiates the identification of additional rotameric states which become dead-ending. A recursive check for dead-ending rotameric states is therefore necessary every time a dead-ending rotameric state is identified. It is shown that, if the recursive check is omitted, it is possible to miss the identification of some dead-ending rotameric states causing a premature termination of the elimination process. Second, we examined the effects of removing dead-ending rotameric states from further considerations at different moments of time. Two different methods of rotameric state removal were examined for an order dependence. In one case, each rotamer found to be incompatible with the global minimum energy conformation was removed immediately following its identification. In the other, dead-ending rotamers were marked for deletion but retained during the search, so that they influenced the evaluation of other rotameric states. When the search was completed, all marked rotamers were removed simultaneously. In addition, to expand further the usefulness of the FEE, a novel method is presented that allows for further reduction in the remaining set of conformations at the FEE convergence. In this method, called a tree-based search, each dead-ending pair of rotamers which does not lead to the direct removal of either rotameric state is used to reduce significantly the number of remaining conformations. In the future this method can also be expanded to triplet and quadruplet sets of rotameric states. We tested our implementation of the FEE by exhaustively searching ten protein segments and found that the FEE identified the global minimum every time. For each segment, the global minimum was exhaustively searched in two different environments: (i) the segments were extracted from the protein and exhaustively searched in the absence of the surrounding residues; (ii) the segments were exhaustively searched in the presence of the remaining residues fixed at crystal structure conformations. We also evaluated the performance of the method for accurately predicting side chain conformations. We examined the influence of factors such as type and accuracy of backbone template used, and the restrictions imposed by the choice of potential function, parameterization and rotamer database. Conclusions are drawn on these results and future prospects are given.


Assuntos
Algoritmos , Conformação Proteica , Proteínas/química , Sequência de Aminoácidos , Cristalografia por Raios X , Bases de Dados Factuais , Ligação de Hidrogênio , Espectroscopia de Ressonância Magnética , Muramidase/química , Proteínas de Plantas/química , Dobramento de Proteína , Estrutura Secundária de Proteína
13.
FEBS Lett ; 357(3): 317-23, 1995 Jan 09.
Artigo em Inglês | MEDLINE | ID: mdl-7835436

RESUMO

Two hammerhead chimeric RNA/DNA ribozymes (HRz) were synthesized in pure form. Both were 30 nucleotides long, and the sequences were such that they could be targeted to cleave the HIV-1 gag RNA. Named HRz-W and HRz-M, the former had its invariable core region conserved, the latter had a uridine in the invariable region replaced by a guanine. Their secodary structures were determined by 2D NOESY 1H 500 MHz NMR spectroscopy in 90% water and 10% D2(0), following the imino protons. The data show that both HRz-M and HRz-W form identical secondary structures with stem regions consisting of continuous stacks of AT and GT pairs. An energy minimized computer model of this stem region is provided. The results suggest that the loss of catalytic activity that is known to result when an invariant core residue is replaced is not related to the secondary structure of the ribozymes in the absence of substrate.


Assuntos
HIV-1/efeitos dos fármacos , Espectroscopia de Ressonância Magnética/métodos , Estrutura Secundária de Proteína , RNA Catalítico/química , Sequência de Bases , Dados de Sequência Molecular , RNA Catalítico/farmacologia , Soluções
14.
J Biomol Struct Dyn ; 12(1): 037-60, 1994 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-7531452

RESUMO

We present a full-coordinate model of residues 1-319 of the polymerase domain of HIV-I reverse transcriptase. This model was constructed from the x-ray crystallographic structure of Jacobo-Molina et al. (Jacobo-Molina et al., P.N.A.S. USA 90, 6320-6324 (1993)) which is currently available to the degree of C-coordinates. The backbone and side-chain atoms were constructed using the MAXSPROUT suite of programs (L. Holm and C. Sander, J. Mol. Biol. 218, 183-194 (1991)) and refined through molecular modeling. A seven base pair A-form dsDNA was positioned in the nucleic acid binding cleft to represent the template-primer complex. The orientation of the template-primer complex in the nucleic acid binding cleft was guided by the positions of phosphorus atoms in the crystal structure.


Assuntos
DNA Polimerase Dirigida por DNA/química , HIV-1/química , Modelos Moleculares , Ácidos Nucleicos/química , DNA Polimerase Dirigida por RNA/química , Sequência de Aminoácidos , Transcriptase Reversa do HIV , HIV-1/enzimologia , Magnésio/fisiologia , Dados de Sequência Molecular , Estrutura Terciária de Proteína , Alinhamento de Sequência , Especificidade por Substrato
15.
Orig Life Evol Biosph ; 23(5-6): 419-27, 1993 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-8115165

RESUMO

A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on the system under investigation. In the present study we assess the validity of the MNDO/PM3 method on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.


Assuntos
RNA Catalítico/metabolismo , Modelos Biológicos , Modelos Químicos , Estrutura Molecular , Fosforilação , RNA Catalítico/química , RNA Catalítico/genética , Termodinâmica
16.
Mol Biol (Mosk) ; 27(4): 734-57, 1993.
Artigo em Russo | MEDLINE | ID: mdl-8361483

RESUMO

The review is presented of experimental and computational data on the influence of genotoxic modification of bases (deamination, alkylation, oxidation) on the structure and biological functioning of nucleic acids. Pathways are discussed for the influence of modification on coding properties of bases, on possible errors of nucleic acid biosynthesis, and on configurations of nucleotide mispairs. The atomic structure of nucleic acid fragments with modified bases and the role of base damages in mutagenesis and carcinogenesis are considered.


Assuntos
Mutagênicos/química , Ácidos Nucleicos/química , Alquilação , Aminação , Sequência de Bases , Dano ao DNA , Dados de Sequência Molecular , Ácidos Nucleicos/biossíntese , Espécies Reativas de Oxigênio
17.
J Biomol Struct Dyn ; 10(6): 945-72, 1993 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-8357544

RESUMO

A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.


Assuntos
DNA de Protozoário/química , Íntrons , Conformação de Ácido Nucleico , Tetrahymena thermophila/metabolismo , Animais , Sequência de Bases , Sítios de Ligação , DNA de Protozoário/metabolismo , Éxons , Ligação de Hidrogênio , Magnésio/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Tetrahymena thermophila/genética
18.
Eur J Clin Microbiol Infect Dis ; 12(2): 98-104, 1993 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-8500489

RESUMO

Helicobacter pylori cells cultured on solid medium were quantitatively tested for haemolytic activity against erythrocytes of man, sheep, the guinea pig and rabbit. Using 4-day and 8-day cultures of two standard strains (ATCC 43504, IMMi 676), human erythrocytes were not lysed by 10% bacterial suspensions. Rabbit erythrocytes were the most sensitive to 8-day cultures. Hot-cold incubation yielded the highest haemolysis titres. The extent of haemolysis strongly correlated with the number of bacterial cells. Supplementation of the test medium (PBS, pH 7.4) with L-cysteine, dithiothreitol, MgCl2, EDTA, cholesterol, lecithin or sphingomyelin did not influence the haemolysis titres. They were significantly reduced in the presence of pronase E, human serum, bovine serum albumin or CaCl2, and by heat treatment of the bacteria. Supplementation of the test medium with cardiolipin strongly increased the haemolysis titres. Comparing the cell-associated haemolytic activity of 18 strains, the titres ranged from < 2 to 64, with a median titre of 16. No correlation was found between the haemolytic activity and phospholipase C activity of the cell suspensions. It was concluded that the formation of lysophosphatides and non-enzymatic factors rather than a sulphydryl-activated cytolysin or phospholipase C are responsible for the cell-associated haemolytic activity. This property may be involved in the pathogenicity and virulence of Helicobacter pylori.


Assuntos
Helicobacter pylori/patogenicidade , Hemólise , Animais , Antiestreptolisina/farmacologia , Cloreto de Cálcio/farmacologia , Cardiolipinas/farmacologia , Contagem de Colônia Microbiana , Meios de Cultura , Cobaias , Helicobacter pylori/enzimologia , Helicobacter pylori/crescimento & desenvolvimento , Hemólise/efeitos dos fármacos , Humanos , Concentração de Íons de Hidrogênio , Técnicas In Vitro , Pronase/farmacologia , Coelhos , Soroalbumina Bovina/farmacologia , Ovinos , Temperatura , Fosfolipases Tipo C/biossíntese , Virulência
19.
J Comput Chem ; 14(8): 970-6, 1993.
Artigo em Inglês | MEDLINE | ID: mdl-11539835

RESUMO

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.


Assuntos
Elétrons , Modelos Moleculares , Peptídeos/química , Software , Físico-Química/métodos , Ligação de Hidrogênio , Conformação Proteica , Eletricidade Estática
20.
Theor Chim Acta ; 85: 209-16, 1993.
Artigo em Inglês | MEDLINE | ID: mdl-11539836

RESUMO

Distributed Point Charge Models (PCM) for CO, (H2O)2, and HS-SH molecules have been computed from analytical expressions using multi-center multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.


Assuntos
Monóxido de Carbono/química , Modelos Moleculares , Compostos de Sulfidrila/química , Enxofre/química , Água/química , Dimerização , Ligação de Hidrogênio , Eletricidade Estática
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