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通过分子动力学模拟预测的肽的多种环构象与核磁共振结果相符。

Multiple loop conformations of peptides predicted by molecular dynamics simulations are compatible with nuclear magnetic resonance.

作者信息

Carstens Heiko, Renner Christian, Milbradt Alexander G, Moroder Luis, Tavan Paul

机构信息

Lehrstuhl für BioMolekulare Optik, Oettingenstrasse 67, Ludwig-Maximilians-Universität München, 80538 München, Germany.

出版信息

Biochemistry. 2005 Mar 29;44(12):4829-40. doi: 10.1021/bi047453r.

Abstract

The affinity and selectivity of protein-protein interactions can be fine-tuned by varying the size, flexibility, and amino acid composition of involved surface loops. As a model for such surface loops, we study the conformational landscape of an octapeptide, whose flexibility is chemically steered by a covalent ring closure integrating an azobenzene dye into and by a disulfide bridge additionally constraining the peptide backbone. Because the covalently integrated azobenzene dyes can be switched by light between a bent cis state and an elongated trans state, six cyclic peptide models of strongly different flexibilities are obtained. The conformational states of these peptide models are sampled by NMR and by unconstrained molecular dynamics (MD) simulations. Prototypical conformations and the free-energy landscapes in the high-dimensional space spanned by the phi/psi angles at the peptide backbone are obtained by clustering techniques from the MD trajectories. Multiple open-loop conformations are shown to be predicted by MD particularly in the very flexible cases and are shown to comply with the NMR data despite the fact that such open-loop conformations are missing in the refined NMR structures.

摘要

蛋白质-蛋白质相互作用的亲和力和选择性可通过改变参与的表面环的大小、柔韧性和氨基酸组成来进行微调。作为此类表面环的一个模型,我们研究了一种八肽的构象态势,其柔韧性通过将偶氮苯染料共价整合到其中以及通过一个额外限制肽主链的二硫键进行化学调控。由于共价整合的偶氮苯染料可通过光在弯曲的顺式状态和伸长的反式状态之间切换,因此获得了六种柔韧性差异极大的环状肽模型。这些肽模型的构象状态通过核磁共振(NMR)和无约束分子动力学(MD)模拟进行采样。通过聚类技术从MD轨迹中获得了肽主链上由φ/ψ角所跨越的高维空间中的典型构象和自由能态势。MD显示,尤其是在非常灵活的情况下,会预测出多种开环构象,并且尽管在精制的NMR结构中缺少此类开环构象,但这些构象与NMR数据相符。

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