Menéndez C A, Accordino S R, Gerbino D C, Appignanesi G A
INQUISUR-UNS-CONICET and Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000, Bahıa Blanca, Argentina.
Eur Phys J E Soft Matter. 2015 Oct;38(10):107. doi: 10.1140/epje/i2015-15107-3. Epub 2015 Oct 19.
We carry out a time-averaged contact matrix study to reveal the existence of protein backbone hydrogen bonds (BHBs) whose net persistence in time differs markedly form their corresponding PDB-reported state. We term such interactions as "chameleonic" BHBs, CBHBs, precisely to account for their tendency to change the structural prescription of the PDB for the opposite bonding propensity in solution. We also find a significant enrichment of protein binding sites in CBHBs, relate them to local water exposure and analyze their behavior as ligand/drug targets. Thus, the dynamic analysis of hydrogen bond propensity might lay the foundations for new tools of interest in protein binding-site prediction and in lead optimization for drug design.
我们进行了一项时间平均接触矩阵研究,以揭示蛋白质主链氢键(BHBs)的存在,其在时间上的净持续性与相应的PDB报告状态有显著差异。我们将这种相互作用称为“变色龙”BHBs,即CBHBs,正是为了解释它们在溶液中因相反的键合倾向而改变PDB结构规定的趋势。我们还发现CBHBs中蛋白质结合位点显著富集,将它们与局部水暴露相关联,并分析它们作为配体/药物靶点的行为。因此,氢键倾向的动态分析可能为蛋白质结合位点预测和药物设计的先导优化中感兴趣的新工具奠定基础。