Center of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Allahabad 211002, India.
J Biomol Struct Dyn. 2012;30(5):532-41. doi: 10.1080/07391102.2012.687519. Epub 2012 Jun 26.
The cold shock proteins are evolutionarily conserved nucleic acid-binding proteins. Their eukaryotic homologs are present as cold shock domain (CSD) in Y-box proteins. CSDs too share striking similarity among different organisms and show nucleic acid binding properties. The purpose of the study was to investigate the preferential binding affinity of CSD protein for nucleic acids in Philosamia ricini. We have cloned and sequenced the first cDNA coding for Y-box protein in P. ricini; the sequence has been deposited in GenBank. Comparative genomics and phylogenetic analytics further confirmed that the deduced amino acid sequence belongs to the CSD protein family. A comparative study employing molecular docking was performed with P. ricini CSD, human CSD, and bacterial cold shock protein with a range of nucleic acid entities. The results indicate that CSD per se exhibits preferential binding affinity for single-stranded RNA and DNA. Possibly, the flanking N- and C-terminal domains are additionally involved in interactions with dsDNA or in conferring extra stability to CSD for improved binding.
冷休克蛋白是进化上保守的核酸结合蛋白。其真核同源物以 Y 盒蛋白中的冷休克结构域（CSD）的形式存在。CSD 在不同生物之间也具有惊人的相似性，并表现出核酸结合特性。本研究旨在探讨 CSD 蛋白在蓖麻蚕中对核酸的优先结合亲和力。我们已经克隆并测序了 P. ricini 中第一个编码 Y 盒蛋白的 cDNA；该序列已在 GenBank 中提交。比较基因组学和系统发育分析进一步证实，推导的氨基酸序列属于 CSD 蛋白家族。采用分子对接的比较研究，研究了 P. ricini CSD、人 CSD 和细菌冷休克蛋白与一系列核酸实体的优先结合亲和力。结果表明，CSD 本身对单链 RNA 和 DNA 表现出优先的结合亲和力。可能是侧翼的 N 端和 C 端结构域还参与与 dsDNA 的相互作用，或者赋予 CSD 额外的稳定性，以提高结合能力。
