Volume 10(1) 014-016 (2017) - 14 J Comput Sci Syst Biol ISSN: 0974-7231 JCSB, an open access journal Research Article Kereselidze et al., J Comput Sci Syst Biol 2017, 10:1 DOI: 10.4172/jcsb.1000241 Research Article Open Access Journal of Computer Science & Systems Biology J o u r n a l o f C o m p u t e r S c i e n c e & S y s t e m s B i o l o g y ISSN: 0974-7230 *Corresponding author: Jumber Kereselidze, Department of Chemistry, Ivane Javkhishvili Tbilisi State University, Tbilisi 0179, Georgia, Tel: 995322225107; E-mail: jumber.kereselidze@tsu.ge Received January 16, 2017; Accepted January 30, 2017; Published January 31, 2017 Citation: Kereselidze J, Mikuchadze G, Bobokhidze L (2017) Quantum-Chemical Study of the Propensity of the Amino Acid Pairs for the Peptide Bond Formation. J Comput Sci Syst Biol 10: 014-016. doi:10.4172/jcsb.1000241 Copyright: © 2017 Kereselidze J, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Keywords: Amino acids; Peptide bonds; Parameter of propensity; DFT calculations Introduction Te theoretical description of biochemical processes is the main focus of modern natural science - Biophysical Chemistry. In recent years, for the quantitative description of complex biochemical processes are widely used modern quantum chemistry methods based on density functional theory (DFT). Including for research of peptide bond formation mechanism [1]. It is assumed that the inductive and feld efects of amino acid side chains have an essential efect on peptide bond formation [2]. Te quantum-mechanical study of diferent possible mechanisms of peptide synthesis in the ribosome has been carried out using density functional also [3]. Analysis of a database of protein sequences for all possible binary patterns of polar and non-polar amino acid residues revealed that alternating patterns occur signifcantly less ofen than others with similar composition [4]. To facilitate understanding of the information available for protein structures, has been constructed the structural classifcation of proteins (scop) database. Tis database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure [5]. Analysis of extant proteomes has the potential of revealing how amino acid frequencies within proteins have evolved over biological time. Evidence presented here indicates, that cysteine, tyrosine, and phenylalanine residues have substantially increased in frequency [6]. To understand 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. Te 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 refects historical events in the establishment of the genetic code [7]. Protein sequences contain many local regions of low compositional complexity. Tese include diferent types of residue clusters, some of which contain homopolymers, short period repeats or aperiodic mosaics of a few residue types. Several diferent formal defnitions 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 [8]. Te occurrence of all di- and tripeptide segments of proteins was counted in a large data base containing about 119 000 residues [9]. Systematic conformational analysis study of the tripeptide units (Gly-X-Pro) and (Gly-Pro-X), with X=Pro, Ala, Ser, Val, Leu, Ile, and Phe it has been reported. Te low- energy conformers obtained by quantum computations are discussed with respect to other theoretical investigations and experimental protein structures [10]. Pairing of Amino acids is only possible on a parallel β ribbon and involves both the polypeptide backbones and the side chains. Model building revealed that of the 210 possible amino acid pairs of the standard 20 amino acids, no more than 26 could be built to meet standard criteria for bonding. Of these 26, 14 were found to be genetically encoded when the codons are read as if they paired in a parallel manner [11]. Methods Density functional theory (DFT) is a computational quantum mechanical method used in physics, chemistry and biology for investigate the electronic structure in particular atoms, and molecules [12]. Te properties of a many-electron system can be determined by using functionals, which in this case is the spatially dependent electron density. Hence the name density functional theory comes from the use of functionals of the electron density. DFT is among the most popular and versatile methods available in computational biology. Unlike the wave function, which is not a physical reality, electron density is a physical characteristic of all molecules. Te electron density is a function with three variables - x − , y − , and z − position of the electrons. Hybrid methods, as the name suggests, attempt to incorporate some of the more useful features from ab initio methods (specifcally Hartree-Fock methods) with some of the improvements of DFT mathematics. Hybrid methods, such as B3LYP [13-15], tend to be the most commonly used methods Abstract The Modern method of quantum chemistry - the density functional theory (DFT) was used to quantitative describe the formation of the peptide bond between amino acid pairs. In particular the formula of parameter of propensity (K p ), which is a function of six variables: the length and order of the CO and NH bonds, (R CO , R NH , P CO P NH ), the activation energy for the formation of the peptide bond (ΔE # ), and difference between charges of the carbon atom of the carbonyl group and the amino nitrogen atom (Δq) was constructed. By means of the proposed formula the K p parameter for 400 amino acid pairs was calculated. Among them only 26 amino acid pairs are most likely to take part in the synthesis of proteins that have been selected based on the value of the parameter K p . This approach may have important meaning for quantitative description of the amino acid sequences in proteins. Quantum-Chemical Study of the Propensity of the Amino Acid Pairs for the Peptide Bond Formation Jumber Kereselidze 1* , George Mikuchadze 1 and Lia Bobokhidze 1 1 Department of Chemistry, Ivane Javkhishvili Tbilisi State University, Tbilisi 0179, Georgia