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PubMed2006

Towards the creation of novel proteins by block shuffling.

We have been investigating the creation of novel proteins by means of block shuffling, where the term block refers to an amino acid sequence that corresponds to particular features of proteins, such as secondary structures, modules, functional motifs, and so on. Block shuffling makes it possible to explore the global sequence space, which is not feasible with conventional methods, such as DNA shuffling or family shuffling. To investigate what properties are required for the building blocks, we have analyzed the foldability and enzymatic activity of barnase mutants obtained by permutation of modules or secondary structure units. This reconstructive approach indicated that secondary structure units with mutual long-range interactions are more suitable than modules as building blocks, at least in the case of barnase. The results also suggested that proteins in evolutionarily intermediate states are created by block shuffling, and such proteins have the potential to be evolved into mature globular proteins. For the construction of combinatorial protein libraries, we have developed random multi-recombinant PCR (RM-PCR), which can combine different DNA fragments without homologous sequences. The libraries can be utilized for in vitro selection using in vitro virus (mRNA display) or stable (DNA display), which have also been developed in our laboratory. In this review article, we summarize our strategy to create novel proteins by block shuffling and review key literature in the field. Possible applications of the block shuffling strategy are also discussed.

Combinatorial Chemistry Techniques↗
PubMed1999

On the origin of metabolic pathways.

The heterotrophic theory of the origin of life is the only proposal available with experimental support. This comes from the ease of prebiotic synthesis under strongly reducing conditions. The prebiotic synthesis of organic compounds by reduction of CO(2) to monomers used by the first organisms would also be considered an heterotrophic origin. Autotrophy means that the first organisms biosynthesized their cell constituents as well as assembling them. Prebiotic synthetic pathways are all different from the biosynthetic pathways of the last common ancestor (LCA). The steps leading to the origin of the metabolic pathways are closer to prebiotic chemistry than to those in the LCA. There may have been different biosynthetic routes between the prebiotic and the LCAs that played an early role in metabolism but have disappeared from extant organisms. The semienzymatic theory of the origin of metabolism proposed here is similar to the Horowitz hypothesis but includes the use of compounds leaking from preexisting pathways as well as prebiotic compounds from the environment.

Amino Acids↗
PubMed1987

Metabolism of proteinoid microspheres.

The literature of metabolism in proteinoids and proteinoid microspheres is reviewed and criticized from a biochemical and experimental point of view. Closely related literature is also reviewed in order to understand the function of proteinoids and proteinoid microspheres. Proteinoids or proteinoid microspheres have many activities. Esterolyis, decarboxylation, amination, deamination, and oxidoreduction are catabolic enzyme activities. The formation of ATP, peptides or oligonucleotides is synthetic enzyme activities. Additional activities are hormonal and inhibitory. Selective formation of peptides is an activity of nucleoproteinoid microspheres; these are a model for ribosomes. Mechanisms of peptide and oligonucleotide syntheses from amino acids and nucleotide triphosphate by proteinoid microspheres are tentatively proposed as an integrative consequence of reviewing the literature.

Adenosine Triphosphate↗
PubMed2005

Reconstruction of phylogenetic relationships from metabolic pathways based on the enzyme hierarchy and the gene ontology.

There has been much interest in the structural comparison and alignment of metabolic pathways. Several techniques have been conceived to assess the similarity of metabolic pathways of different organisms. In this paper, we show that the combination of a new heuristic algorithm for the comparison of metabolic pathways together with any of three enzyme similarity measures (hierarchical, information content, and gene ontology) can be used to derive a metabolic pathway similarity measure that is suitable for reconstructing phylogenetic relationships from metabolic pathways. Experimental results on the Glycolysis pathway of 73 organisms representing the three domains of life show that our method outperforms previous techniques.

Enzymes↗
PubMed1990

Structural limits for evolutive capacities in complex molecular systems.

The possibilities of evolution for a system with and without a code of translation from nucleic acids into proteins are evaluated. Our interest is mainly centred on the enzymatic RNA case since this molecule has, at the same time, reproductive and functional properties. After scanning the evolutive capacities of the enzymatic RNAs, including the possibility to play the role of "synthetase" which would match nucleic acids with amino acids as a transition step towards a code, we will try to show that due to their own functional limitative factors, the matching system (code) is necessary. This would be the only way to transform the formal complexity--complexity which has not entered into action before the translation process--into functional information to drive the instructive self-reproductive process. Once this stage is reached, the system could evolve without a limit.

Biological Evolution↗
PubMed1986

[Biological order].

Explore the source record for details and available documents.

Adaptation, Biological↗
PubMed1978

Applied and theoretical significance of electrohoretic studies in mosquitoes (Diptera: Culicidae).

The more relevant results obtained in the past decade with the use of electrophoretic techniques in studying mosquitoes are reviewed and discussed. These results mainly concern the evaluation of genetic variability of natural and laboratory populations; the study of the role of natural selection and genetic drift in the maintenance and evolution of enzyme polymorphisms; the estimate of genetic differentiation between populations, subspecies and species; the identification of sibling species and of their possible hybrids; the field study of precopulatory isolating mechanisms by the release of electrophoretically recognizable population samples; the elaboration of genetic maps; the study of the phenomenon of multiple insemination; and the evaluation of sexual competitiveness, particularly in connection with the planning of genetic control measures. The importance of this approach in the study of mosquito biology from the applied and theoretical points of view is stressed.

Aedes↗
PubMed1981

Pyridine nucleotide-dependent generation of hydrogen peroxide by a particulate fraction from human neutrophils.

The catalytic oxidation of [14C]-formate to 14CO2 was adapted to measure H2O2 formation in cellfree system. Standard curves employing glucose-glucose oxidase and xanthine-xanthine oxidase demonstrated linearity between 14CO2 evolution and enzyme concentration. A particulate fraction from human neutrophils was capable of oxidizing [14C]-formate; this reaction was dependent upon the presence of catalase, reduced pyridine nucleotide, and cellular material. Reaction increased with time of incubation and protein concentration, although not in a strictly linear fashion. The pH optimum was approximately 5.5 NADPH was a significantly better substrate than NADH, although both were capable of generating H2O2. The particulate fraction derived from phagocytizing cells was more active than a corresponding fraction from resting cells with either substrate. H2O2 production was abnormal in particulate fractions derived from 2 patients with chronic granulomatous disease. H2O2 production was markedly inhibited by superoxide dismutase or cytochrome c (scavengers of superoxide anion) but not by scavengers of singlet oxygen or hydroxyl radical. Reaction was greatly stimulated by the addition of manganous ion. These results are consistent with the hypothesis that the respiratory burst in human neutrophils is initiated by an oxidase that can utilize either NADPH or NADH but exhibits a marked preference for the former. Further, the inhibitor studies strongly support a mechanism involving an initial enzymatic reaction followed by a self-sustaining free radical reaction involving superoxide anion.

Cell-Free System↗
PubMed1993

[Coexistence of WPW syndrome, coronary disease and segmental disorders of myocardial contraction. Diagnostic difficulties. Description of a case].

A 61 years old patient with Wolff-Parkinson-White's syndrome, and hypertension was admitted to the CCU, because of the first episode of substernal chest pain. ECG was deformed by Wolff-Parkinson-White's syndrome, type B, with accessory pathway located on the right side, without evolution. Serum enzymes remained low. Echocardiography showed akinesis of the posterior wall and hypokinesis of the lateral wall (the same contraction disorders were described in previous echocardiographical examination 5 years ago), it was observed that the first portion of myocardium to contract was the base of the right ventricle. To elucidate the etiology of the contraction disorders, scintigraphy of the heart, using Thallium 201, was performed, showing normal perfusion of the myocardium. To illustrate the dependence of the contraction disorders and abnormal depolarization pattern of the heart, echocardiographical examination was repeated, confirming the previous results, then 100 mg of Ajmaline was given to the patient intravenously, and echocardiographical examination was continued. Administration of the drug caused antidromic atrioventricular re-entrant tachycardia during which the lateral wall of the heart had been contracting properly. This case shows contraction disorders of the heart caused by the abnormal depolarization pattern, resulting from the presence of accessory pathway. It also illustrates the diagnostic difficulties in patients with Wolff-Parkinson-White's syndrome and suspected myocardial infarction, at the same time showing that scintigraphy of the heart might be very helpful in such patients. This case confirms the usefulness of echocardiography for localization of the accessory pathway.

Coronary Disease↗