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Biomedical subjects

J Tohá

Publications and source records attributed to J Tohá.

At least 19 recordsLinked to original sources
PubMed2003

A pentapeptide-based method for protein secondary structure prediction.

We present a new method for protein secondary structure prediction, based on the recognition of well-defined pentapeptides, in a large databank. Using a databank of 635 protein chains, we obtained a success rate of 68.6%. We show that progress is achieved when the databank is enlarged, when the 20 amino acids are adequately grouped in 10 sets and when more pentapeptides are attributed one of the defined conformations, alpha-helices or beta-strands. The analysis of the model indicates that the essential variable is the number of pentapeptides of well-defined structure in the database. Our model is simple, does not rely on arbitrary parameters and allows the analysis in detail of the results of each chosen hypothesis.

Databases, Protein↗
PubMed2000

Biocryptography.

A new cryptology that uses biomolecules as carriers of hidden information is described here. The huge dimension of biopolymers permits the insertion there of private messages and the rapidity and specificity of biomolecular interactions facilitate the identification of classified communications. Otherwise, this process can be implemented in a virtual context.

Base Sequence↗
PubMed2000

Fast DNA sequencing.

A method for fast nucleotide sequencing is described. It is based in the selection of well-known small oligomers able to be hybridized with the unknown target. The selected oligomers are afterwards ordered following a simple statistical approach. The use of capillary electrophoresis for the analysis is emphasized.

Base Sequence↗
PubMed1999

Secondary structure of proteins and three-dimensional pattern recognition.

We describe a new, parameter-free, method to predict the secondary structure of a protein. It is based on the recognition of well-defined pentapeptides, which allows the discrimination of alpha helices, beta sheets and random coils in proteins. Presently, a success rate of about 65% is achieved for a three-state model.

Algorithms↗
PubMed1996

Neural system states and networks.

A neural circuit at the human cerebellar cortex and nuclei is interpreted in terms of an optimized code and a reliable network.

Cell Communication↗
PubMed1995

On the nature of mutations in molecular evolution.

In this work it is proposed tht in evolution amino acid substitutions implying strong physico chemical and structural differences are more revelant and more frequent that substitutions between similar amino acids. This analysis is made over a group of protein families representing about 10000 substitutions and as examples the evolutionary trees of fibrinopeptides A and calcitonins were constructed and compared.

Amino Acid Sequence↗
PubMed1995

Neural network in the transcription-translation process in eukaryotic cells and viruses, a comparison.

The transcription-translation process in the virus-host cell system is analyzed in terms of a virtual neural network. In contrast to findings in the transcription-translation process in eukaryotic cells, an inverse correlation between the frequency of protein amino acids and code degeneracy and between code degeneracy and the rate of amino acid substitutions was not found. Misuse of the virtual host cell network by virus protein synthesis could be attributed to the different amino acid composition of the virus proteins (input unit) studied here.

Amino Acids↗
PubMed1994

Neural network in the transcription-translation process.

The transcription-translation process is represented by a virtual neural network. The input unit corresponds to the transcription process, the hidden unit to the mRNA-ribosome-tRNA interaction and the output unit to the final state of the protein. A correlation was found between the natural amino acid frequency and the degree of codon degeneracy and an inverse correlation between the code degeneracy and the number of amino acid substitutions in the protein.

Amino Acids↗
PubMed1985

Conservation of the secondary structure of protein during evolution and the role of the genetic code.

In this communication we demonstrate, in a group of modern proteins, following an algorithm described by Argyle (1980), that the ordination of the amino acids in terms of the most frequent substitutions agrees with the conservation of the alpha-helix, beta-sheet, and beta-turn formation tendencies during evolution. The same correspondence has been demonstrated for the conservation of the physico-chemical properties in the amino acid substitutions. Both parameters are similar in showing higher correlation with the most frequent amino acid substitutions than with the feasibility of changes at the level of the respective codons. Some kind of restrictions for the expression of the genomic changes, due to the conservation of the secondary structure of proteins and/or the physicochemical properties of the substituted amino acids, could account for the differences found between the distribution of the amino acid substitutions and the most probable codon changes.

Amino Acids↗
PubMed1984

Dissimilar rates in molecular evolution.

In this work we present an evolutionary tree based on the differences in the physico-chemical properties involved in amino acid substitutions, instead of considering, for its construction, only the number of changes between species. Phylogenetic trees were constructed from the differences in bulkiness, refractivity index, hydrophobicity, polarity and optical rotation of 9 vertebrate calcitonins. A correlation of the form y = a xb was found between the number of changes (x) and the differences in any given physico-chemical property (y). This correlation implies that the evolutionary time can not be evaluated directly from the number of changes between species.

Amino Acid Sequence↗
PubMed1983

Code dependent conservation of the physico-chemical properties in amino acid substitutions.

The frequency of amino acid replacements in families of typical proteins has been elegantly analyzed by Argyle (1980) showing that the most frequent replacements involve a conservation of the amino acid chemical properties. The cyclic arrangement of the twenty amino acids resulting from the most frequent replacements has been described as an amino acid chemical ring. In this work, a novel amino acid replacement frequency ring is proposed, for which a conservation of over 90% of the most general physico-chemical properties can be deduced. The amino acid chemical similarity ring is also analyzed in terms of the genetic code base probability changes, showing that the discrepancy that exists between the standard deviation value of the amino acid replacement frequency matrix and its respective ideal value is almost equal to that deduced from the corresponding base codon replacement probability matrices. These differences are finally evaluated and discussed in terms of the restrictions imposed by the structure of the genetic code and the physico-chemical dissimilarities between some codons of amino acids which are chemically similar.

Amino Acid Sequence↗
PubMed1983

Conservation of physico-chemical amino acid properties during the evolution of proteins.

Based on a similarity ring constructed from a substitution probability matrix, we have analyzed the conservation of some amino acid properties in the evolution of proteins. Refractive index and bulkiness are highly conserved, hydrophobicity and polarity are fairly well conserved while optical rotation appears to be a less relevant property. On the other hand, the analysis of the correspondence between phenotype and genotype shows that the most frequent amino acid substitutions in proteins do not always correspond to the most feasible codon changes. The apparent disagreement between amino acid substitutions in modern proteins and the primordial amino acid-codon assignment is discussed.

Amino Acids↗
PubMed1979

II. On the construction of a phylogenetic tree.

For the construction of a phylogenetic tree in algorithm is described. This, allows the correction of the original data and the proper selection, in each step of the process, of the nearest neighbours of a common ancestor.

Animals↗