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.
Highlights
All living organisms are made up of proteins
XIE et al [14] proposed a new method by using hydropathy group of amino acids to analyze the similarity/ dissimilarity of protein sequence based on the conditional probability of the protein sequence [14]
To find a correct position of two newly sequenced myosin II (MYH15 and MYH7B) in the existing phylogenetic tree, we deploy pair wise percent identity matrix shown in Table 10 of the myosin head domain (839-860 aa) for every pair of sequences of the myosin II fourteen members
Summary
All living organisms are made up of proteins. The biochemical information that resides in the protein primary sequence maintain their structure, function, and even its own stability. Mathematical Characterization and Protein Sequences biochemical information is instructed/governed by the amino acid sequences. Phylogenetic tree can find only similarity analysis of amino acid sequences but not the chemical nature of amino acids in a protein. XIE et al [14] proposed a new method by using hydropathy group of amino acids to analyze the similarity/ dissimilarity of protein sequence based on the conditional probability of the protein sequence [14]. Studying only the amino acid sequences of proteins limits our scope of understanding of the similarities and differences among proteins with regard to their biochemical nature. Further analyses of the sequences considering chemical nature are required and it can be done if the sequences can be studied through the chemical nature of individual amino acid
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