Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 542/2 , 166 10 Praha 6 , Czech Republic.
J Chem Theory Comput. 2019 Jan 8;15(1):665-679. doi: 10.1021/acs.jctc.8b00715. Epub 2018 Dec 6.
Phosphorylation of serine, threonine, and tyrosine is one of the most frequently occurring and crucial post-translational modifications of proteins often associated with important structural and functional changes. We investigated the direct effect of phosphorylation on the intrinsic conformational preferences of amino acids as a potential trigger of larger structural events. We conducted a comparative study of force fields on terminally capped amino acids (dipeptides) as the simplest model for phosphorylation. Our bias-exchange metadynamics simulations revealed that all model dipeptides sampled a great heterogeneity of ensembles affected by introduction of mono- and dianionic phosphate groups. However, the detected changes in populations of backbone conformers and side-chain rotamers did not reveal a strong discriminatory shift in preferences, as could be anticipated for the bulky, charged phosphate group. Furthermore, the AMBER and CHARMM force fields provided inconsistent populations of individual conformers as well as net structural trends upon phosphorylation. Detailed analysis of ensembles revealed competition between hydration and formation of internal hydrogen bonds involving amide hydrogens and the phosphate group. The observed difference in hydration free energy and potential for hydrogen bonding in individual force fields could be attributed to the different partial atomic charges used in each force field and, hence, the different parametrization strategies. Nevertheless, conformational propensities and net structural changes upon phosphorylation are difficult to extract from experimental measurements, and existing experimental data provide limited guidance for force field assessment and further development.
丝氨酸、苏氨酸和酪氨酸的磷酸化是蛋白质最常见和最重要的翻译后修饰之一，通常与重要的结构和功能变化有关。我们研究了磷酸化对氨基酸固有构象偏好的直接影响，这可能是引发更大结构事件的一个潜在因素。我们对末端封端氨基酸（二肽）进行了力场的比较研究，作为磷酸化的最简单模型。我们的偏置交换元动力学模拟表明，所有模型二肽都采样了很大的多样性的构象，这些构象受到单和二阴离子磷酸盐基团的影响。然而，在主链构象和侧链旋转异构体的种群中检测到的变化并没有显示出对大体积、带电荷的磷酸盐基团的偏好的强烈区分性转变。此外，AMBER 和 CHARMM 力场提供了不一致的单个构象的种群以及磷酸化后的净结构趋势。对构象的详细分析揭示了水合作用与涉及酰胺氢和磷酸盐基团的内部氢键形成之间的竞争。在各个力场中使用的不同部分原子电荷，以及由此产生的不同参数化策略，可以归因于各个力场中观察到的水合自由能和氢键形成潜力的差异。然而，磷酸化后的构象倾向和净结构变化很难从实验测量中提取，并且现有的实验数据为力场评估和进一步发展提供了有限的指导。
