Gupta Parth Sarthi Sen, Banerjee Shyamashree, Islam Rifat Nawaz Ul, Sur Vishma Pratap, Bandyopadhyay Amal K
Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India.
Indian Institute of Chemical Biology, Animal House (IICB), Kolkata, West Bengal, India.
Bioinformation. 2017 Jan 19;13(1):1-7. doi: 10.6026/97320630013001. eCollection 2017.
Orthologous proteins, form due to divergence of parental sequence, perform similar function under different environmental and biological conditions. Amino acid changes at locus specific positions form hetero-pairs whose role in BLOCK evolution is yet to be understood. We involve eight protein BLOCKs of known divergence rate to gain insight into the role of hetero-pairs in evolution. Our procedure APBEST uses BLOCK-FASTA file to extract BLOCK specific evolutionary parameters such as dominantly used hetero-pair (D), usage of hetero-pairs (E), non-conservative to conservative substitution ratio (R), maximally-diverse residue (MDR), residue (RD) and class (CD) specific diversity. All these parameters show BLOCK specific variation. Conservative nature of D points towards restoration of function of BLOCK. While E sets the upper-limit of usage of hereto-pairs, strong correlation of R with divergence-rate indicates that the later is directly dependent on non-conservative substitutions. The observation that MDR, measure of positional diversity, occupy very limited positions in BLOCK indicates accommodation of diversity is positionally restricted. Overall, the study extract observed hetero-pair related quantitative and multi-parametric details of BLOCK, which finds application in evolutionary biology.
直系同源蛋白是由于亲本序列的分化而形成的，在不同的环境和生物学条件下执行相似的功能。基因座特定位置的氨基酸变化形成异源对，其在BLOCK进化中的作用尚待了解。我们研究了八个已知分化率的蛋白质BLOCK，以深入了解异源对在进化中的作用。我们的程序APBEST使用BLOCK-FASTA文件来提取BLOCK特定的进化参数，如主要使用的异源对（D）、异源对的使用情况（E）、非保守到保守的替换率（R）、最大多样性残基（MDR）、残基（RD）和类别（CD）特异性多样性。所有这些参数都显示出BLOCK特异性变化。D的保守性质表明BLOCK功能的恢复。虽然E设定了异源对使用的上限，但R与分化率的强相关性表明，分化率直接依赖于非保守替换。位置多样性的度量MDR在BLOCK中占据非常有限的位置，这一观察结果表明多样性的容纳在位置上受到限制。总体而言，该研究提取了观察到的与BLOCK相关的异源对定量和多参数细节，这些细节在进化生物学中有应用。
