Abstract
Periplasmic c7 type cytochrome A (PpcA) protein is determined in Geobacter sulfurreducens along with its other four homologs (PpcB-E). From the crystal structure viewpoint the observation emerges that PpcA protein can bind with Deoxycholate (DXCA), while its other homologs do not. But it is yet to be established with certainty the reason behind this from primary protein sequence information. This study is primarily based on primary protein sequence analysis through the chemical basis of embedded amino acids. Firstly, we look for the chemical group specific score of amino acids. Along with this, we have developed a new methodology for the phylogenetic analysis based on chemical group dissimilarities of amino acids. This new methodology is applied to the cytochrome c7 family members and pinpoint how a particular sequence is differing with others. Secondly, we build a graph theoretic model on using amino acid sequences which is also applied to the cytochrome c7 family members and some unique characteristics and their domains are highlighted. Thirdly, we search for unique patterns as subsequences which are common among the group or specific individual member. In all the cases, we are able to show some distinct features of PpcA that emerges PpcA as an outstanding protein compared to its other homologs, resulting towards its binding with deoxycholate. Similarly, some notable features for the structurally dissimilar protein PpcD compared to the other homologs are also brought out. Further, the five members of cytochrome family being homolog proteins, they must have some common significant features which are also enumerated in this study.
Highlights
Amino acids play the vital role for determining the protein structure and functions
We introduced a new method of phylogenetic analysis based on chemical group dissimilarity of amino acids
Based on the phylogenetic tree of five members, we find that the Periplasmic c7 type cytochrome A (PpcA) and PpcD, PpcB and PpcE are mostly closed with regards to the frequency of amino acids of respective eight chemical groups
Summary
Amino acids play the vital role for determining the protein structure and functions. But it is informative to know how the functionality of the group of proteins is changed while amino acid patterns are getting changed from one protein to another. Finding the functional/structural similarity from homolog sequences with low sequence similarity is a big challenging task in bioinformatics To tackle this problem, several methods have been introduced that can identify homolog proteins which are distantly distributed in their evolutionary relationships [22,23,24,25]. Methods have been introduced for the 2D graphical representation of DNA/RNA or protein sequences [34,35,36,37,38,39,40] where methods are based on individual score and position wise graphical representation In this field establishment of a new methodology is always welcome with distinct findings. 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]. Working with reduced alphabets and designing the graph require less complexity and easy visualization even if working with the larger sequences
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