Water-Centered Interpretation of Intrinsic pPII Propensities of Amino Acid Residues: In Vitro-Driven Molecular Dynamics Study.
Water-Centered Interpretation of Intrinsic pPII Propensities of Amino Acid Residues: In Vitro-Driven Molecular Dynamics Study.
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以水为中心的氨基酸残基内在 pPII 倾向的解释：体外驱动的分子动力学研究。
DOI：
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发表时间：
2015
影响因子：
3.3
通讯作者：
B. Urbanc
中科院分区：
文献类型：
--
作者：
Derya Meral;Siobhan E Toal;R. Schweitzer‐Stenner;B. Urbanc
水样品中未折叠肽的氨基酸残基在Ramachandran图中只有几个盆地，包括突出的聚脯氨酸II样（pPII）构象。GXG肽中客体残基X在水中的动力学最近被报道由pPII和β-链样（β）构象主导，导致在300 K下的熵补偿。本文利用分子动力学（MD）方法研究了GXG肽中15个客体残基的pPII和β构象集合，通过新颖的水取向图定量了其侧链周围水的局部取向，并研究了它们的水化和氢键性质。我们表明，pPII和β系综具有不同的水取向特征：pPII系综与平行于侧链表面取向的水数量增加有关，而β系综则表现出更不均匀的水取向。pPII中的主链水合作用显著高于β系综。重要的是，pPII与β水合作用的差异和Cβ氢的溶剂可及表面积都与实验pPII倾向相关。我们建议，pPII构象稳定的本地，氢键笼形水结构和残留物特定的内在pPII倾向反映不同的能力，侧链模板这种水结构。
Amino acid residues of unfolded peptides in water sample only a few basins in the Ramachandran plot, including prominent polyproline II-like (pPII) conformations. Dynamics of guest residues, X, in GXG peptides in water were recently reported to be dominated by pPII and β-strand-like (β) conformations, resulting in an enthalpy-entropy compensation at ∼300 K. Using molecular dynamics (MD) in explicit solvent, we here examine pPII and β conformational ensembles of 15 guest residues in GXG peptides, quantify local orientation of water around their side chains through novel water orientation plots, and study their hydration and hydrogen bonding properties. We show that pPII and β ensembles are characterized by distinct water orientations: pPII ensembles are associated with an increased population of water oriented in parallel to the side chain surface whereas β ensembles exhibit more heterogeneous water orientations. The backbone hydration is significantly higher in pPII than in β ensembles. Importantly, pPII to β hydration differences and the solvent accessible surface area of Cβ hydrogens both correlate with experimental pPII propensities. We propose that pPII conformations are stabilized by a local, hydrogen-bonded clathrate-like water structure and that residue-specific intrinsic pPII propensities reflect distinct abilities of side chains to template this water structure.
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影响因子：
56.9
作者：
ROSE, GD;GESELOWITZ, AR;ZEHFUS, MH
通讯作者：
ZEHFUS, MH
影响因子：
2.9
作者：
WOLFENDEN, R;ANDERSSON, L;SOUTHGATE, CCB
通讯作者：
SOUTHGATE, CCB
影响因子：
3.3
作者：
Toal, Siobhan;Meral, Derya;Verbaro, Daniel;Urbanc, Brigita;Schweitzer-Stenner, Reinhard
通讯作者：
Schweitzer-Stenner, Reinhard
影响因子：
2.9
作者：
Jha, AK;Colubri, A;Freed, KF
通讯作者：
Freed, KF
影响因子：
3.4
作者：
Wickstrom, Lauren;Okur, Asim;Simmerling, Carlos
通讯作者：
Simmerling, Carlos