Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids

Abstract

Comparison of amino acid sequence similarity is the fundamental concept behind the protein phylogenetic tree formation. By virtue of this method, we can explain the evolutionary relationships, but further explanations are not possible unless sequences are studied through the chemical nature of individual amino acids. Here we develop a new methodology to characterize the protein sequences on the basis of the chemical nature of the amino acids. We design various algorithms for studying the variation of chemical group transitions and various chemical group combinations as patterns in the protein sequences. The amino acid sequence of conventional myosin II head domain of 14 family members are taken to illustrate this new approach. We find two blocks of maximum length 6 aa as ‘FPKATD’ and ‘Y/FTNEKL’ without repeating the same chemical nature and one block of maximum length 20 aa with the repetition of chemical nature which are common among all 14 members. We also check commonality with another motor protein sub-family kinesin, KIF1A. Based on our analysis we find a common block of length 8 aa both in myosin II and KIF1A. This motif is located in the neck linker region which could be responsible for the generation of mechanical force, enabling us to find the unique blocks which remain chemically conserved across the family. We also validate our methodology with different protein families such as MYOI, Myosin light chain kinase (MLCK) and Rho-associated protein kinase (ROCK), Na+/K+-ATPase and Ca2+-ATPase. Altogether, our studies provide a new methodology for investigating the conserved amino acids’ pattern in different proteins.

Effective Variations of related Physicochemical Properties of Nucleotides Leading to Amino Acids for Characterizing Genes and Proteins

“…The chemical features of 20 amino acids have basically depended on eight chemical properties [7], [16], [17] All…”

“…http://dx.doi.org/10.1101/332171 doi: bioRxiv preprint first posted online May. 28, 2018; Previously many researchers [4][5][6][7][8][9][10][11][12][13][14] contributed with one or other encodings. For example, the Louises [3] paper the encoding used is shown in the above table demonstrating the inconsistencies of our perceptions of the said chemical properties of the nucleotides as explained above.…”

Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach

“…There are twenty standard naturally occurring amino acids which are diverse, arises complexity in the sequences, and have some group specific susceptibility. Various reduced alphabet methods are established which can perform much better in certain conditions [14][15][16][17]. Sequence similarity is the most widely reliable strategy that has been used for characterizing the newly determined sequences [18][19][20][21].…”

“…Combining with various features for DNA, RNA and protein sequence a web server called Pse-in-One (http:// bioinformatics.hitsz.edu.cn/Pse-in-One/home/) is developed [41] which is user friendly and can be modified by users themselves. Recently, the authors have classified the twenty standard amino acids into the eight chemical groups and have found some group and/or family specific conserved patterns which are involved in some functional role specially in motor protein family members [17].…”

“…In this study, the previously defined method [17] of reduced alphabets are used as an application into the cytochrome c7 family protein members. We introduced a new method of phylogenetic analysis based on chemical group dissimilarity of amino acids.…”