Solution study of engineered quartz binding peptides using replica exchange molecular dynamics.
Solution study of engineered quartz binding peptides using replica exchange molecular dynamics.
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DOI：
10.1021/bm100646z
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发表时间：
2010-10
影响因子：
6.2
通讯作者：
R. Notman;E. Oren;C. Tamerler;M. Sarikaya;R. Samudrala;T. Walsh
中科院分区：
文献类型：
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作者：
R. Notman;E. Oren;C. Tamerler;M. Sarikaya;R. Samudrala;T. Walsh
我们使用复制交换分子动力学 (REMD) 来研究四种工程十二肽（在溶液中，在没有表面的情况下）的分子结构和性质，这些十二肽已被证明能够以不同的倾向与石英结合。我们发现，与弱结合剂相比，所有强结合肽都具有一些聚脯氨酸 II 型二级结构，具有较少的构象自由度，并且具有较少的肽内氢键。给定序列中连续脯氨酸含量的区域似乎在促进强结合物的一些特性中发挥作用。为了初步了解石英结合，我们在与石英 (100) 表面相对应的网格和强结合肽 REMD 结构之间进行了晶格匹配研究。我们的研究结果表明，即使对于具有非常不同主链构象的肽结构，假定的接触残基之间也存在共性。此外，还研究了溶液中肽间相互作用。我们的初步研究结果表明，强结合肽间接触主要是弱的、非特异性的疏水相互作用，而弱结合肽由于带电残基的分布而表现出更多的可变行为。总之，肽的溶液结构似乎很重要。我们认为，肽内和肽间相互作用的这些差异可能会影响它们与固体基质结合的倾向。
We use replica-exchange molecular dynamics (REMD) to interrogate molecular structures and properties of four engineered dodecapeptides (in solution, in the absence of a surface) that have been shown to bind to quartz with different propensities. We find that all of the strong-binding peptides feature some polyproline type II secondary structure, have less conformational freedom, and feature fewer intrapeptide hydrogen bonds compared with the weak binder. The regions of contiguous proline content in a given sequence appear to play a role in fostering some of these properties of the strong binders. For preliminary insights into quartz binding, we perform lattice-matching studies between a grid corresponding with the quartz (100) surface and the strong-binding peptide REMD structures. Our findings indicate a commonality among the putative contact residues, even for peptide structures with very different backbone conformations. Furthermore, interpeptide interactions in solution are studied. Our preliminary findings indicate that the strong-binder interpeptide contacts are dominated by weak, nonspecific hydrophobic interactions, while the weak-binding peptide shows more variable behavior due to the distribution of charged residues. In summary, the solution structures of peptides appear to be significant. We propose that these differences in their intra- and interpeptide interactions can influence their propensity to bind onto a solid substrate.