Quantum-Chemical Description of the Propensity of Amino Acids of Formation of the Peptide Bond

                    http://austinpublishinggroup.com/computational-biology-bioinformatics/

Thetheoretical description of biochemical processes for the development of the main direction of natural science - biophysical chemistry is very actual. In recent years, for a quantitative description of complex biochemical processes the modern method of quantum chemistry - Density Functional Theory (DFT) is widely used. Including and for investigation of the mechanism of peptide bond formation too. It is assumed that the inductive and steric effects of the R-groups of amino acids have an effect on propensity of peptide bond formation. A quantum-mechanical study of different possible mechanisms of peptide synthesis in the ribosome has been carried out using density functional also. Analysis of database of protein sequences for all possible binary patterns of polar and non-polar amino acid residues revealed that alternating patterns occur significantly less often than others with similar composition. To facilitate understanding of the information available for protein structures, has been constructed the structural classification of proteins (scop) database. This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of the known structure. Analysis of extant proteomes has the potential of revealing how the frequencies of amino acids within proteins have evolved over biological time. It was shown that presented here residues of cysteine, tyrosine and phenylalanine have substantially increased in frequency.

Tounderstand more fully how amino acid composition of proteins has changed over the course of evolution, a method has been developed for estimating the composition of proteins in an ancestral genome. This method was used to infer the amino acid composition of a large protein set in the Last Universal Ancestor (LUA) of all extant species. It is proposed that the inferred amino acid composition of proteins in the LUA probably reflects historical events in the establishment of the genetic code. Several different formal definitions of local complexity and probability are presented and are compared for their utility in algorithms for localization of such regions in amino acid sequences and sequence databases. The occurrence of all di- and tripeptide segments of proteins was counted in a large data base containing about 119 000 residues.