Dynamics of a type VI reverse turn in a linear peptide in aqueous solution.
Dynamics of a type VI reverse turn in a linear peptide in aqueous solution.
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水溶液中线性肽 VI 型反转的动力学。
DOI：
10.1016/s1359-0278(97)00004-7
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发表时间：
1997
期刊：
影响因子：
--
通讯作者：
Case,DA
中科院分区：
文献类型：
--
作者：
Demchuk,E;Bashford,D;Case,DA
背景技术已知具有侧接于酸-脯氨酸残基的芳族基团的肽序列具有采用紧密结构的高倾向性，其中芳族侧链与脯氨酸环相堆积。特别地，通过NMR已知序列Ser-Tyr-Pro-Phe-Asp-Val（及其变体）在水溶液中形成高比例的VI型转角。我们着手探索这些序列的能量和动力学特征，使用分子动力学模拟techniques.ResultsThe构象特性的线性五肽NH3+-Ala-Tyr-cisPro-Tyr-Asp-NMA（顺式-AYPYD）已被探索在三个溶剂化的分子动力学模拟。第一个开始从NMR衍生的模型结构包含一个类型VIa转向和酪氨酸和脯氨酸侧链之间的紧密堆积的相互作用。在20 ns的模拟，肽之间的转换类型VIa和VIb的转折，但没有“展开”到更多的扩展构象，与不寻常的稳定性，通过NMR观察到的折叠形式，该序列一致。由核Overhauser峰和侧链旋转异构体群体在轨迹中监测的距离与NMR数据良好一致。两个额外的5 ns轨迹开始从更广泛的构象。第一个折叠成构象非常像NMR衍生的结构在3 ns内，并保持折叠的轨迹的其余部分。第二个是开始从一个结构中，侧链的方向是故意错误折叠相对于所需的转向formation.ConclusionThe折叠形式的AYPYD的动力学稳定性，沿着观察自发折叠从一个扩展的构象，表明实验中看到的特殊稳定性反映在计算机模拟。结果提供了新的信息，特别是通过芳香族脯氨酸相互作用的稳定的二级结构的短肽，并提供了描述的途径的相互转换的VIa和VIb型的转折。
BackgroundPeptide sequences with aromatic groups flanking acis-proline residue are known to have a high propensity for adopting compact structures in which the aromatic sidechains pack against the proline ring. In particular, the sequence Ser-Tyr-Pro-Phe-Asp-Val (and variants of this) is known by NMR to form a high proportion of type VI turns in aqueous solution. We set out to explore the energetic and dynamic features of such sequences using molecular dynamics simulation techniques.ResultsThe conformation properties of the linear pentapeptide NH3+-Ala-Tyr-cisPro-Tyr-Asp-NMA (cis-AYPYD) have been explored in three solvated molecular dynamics simulations. The first began from an NMR-derived model structure containing a type VIa turn and close-stacking interactions between the tyrosine and proline sidechains. During 20 ns of simulation, the peptide made transitions between type VIa and VIb turns, but did not ‘unfold' to more extended conformers, consistent with the unusual stability for folded forms observed by NMR for this sequence. Distances monitored by nuclear Overhauser peaks and sidechain rotamer populations in the trajectory are in good agreement with NMR data. Two additional 5 ns trajectories were begun from more extended conformers. The first folded into a conformer much like the NMR-derived structure within 3 ns and remained folded for the remainder of the trajectory. The second was begun from a structure in which the sidechain orientations were deliberately misfolded relative to that required for turn formation; this structure did not make a transition to a turn-like state.ConclusionThe kinetic stability of folded forms of AYPYD, along with the observation of spontaneous folding from an extended conformation, indicates that the special stability seen experimentally is reflected in computer simulations. The results provide new information about the stabilization of secondary structure in short peptides, particularly by aromatic–proline interactions, and offer a description of pathways of interconversion of type VIa and VIb turns.
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DOI：
10.1146/annurev.bb.20.060191.002511
发表时间：
1991
期刊：
Annual review of biophysics and biophysical chemistry
影响因子：
--
作者：
Dyson Hj;P. Wright
通讯作者：
Dyson Hj;P. Wright
蛋白质弯曲中的局部相互作用。
DOI：
--
发表时间：
1977
影响因子：
11.1
作者：
S. Zimmerman;H. Scheraga
通讯作者：
H. Scheraga
DOI：
10.3109/10409238009105470
发表时间：
1980
期刊：
--
影响因子：
--
作者：
John A. Smith;L. G. Pease;K. Kopple
通讯作者：
John A. Smith;L. G. Pease;K. Kopple
影响因子：
5.6
作者：
DYSON, HJ;RANCE, M;WRIGHT, PE
通讯作者：
WRIGHT, PE
影响因子：
--
作者：
S. Burley;G. Petsko
通讯作者：
S. Burley;G. Petsko