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首页> 外文期刊>Journal of Molecular Biology >Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures.
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Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures.

机译：蛋白质的弹性特性：洞悉天然结构的折叠过程和进化选择。

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摘要

We carry out a theoretical study of the vibrational and relaxation properties of naturally occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model, we provide a full characterization of the spectrum and eigenmodes of vibration at various temperatures by merely exploiting the knowledge of the protein native structure. It is shown that the rate at which perturbations decay at the folding transition correlates well with experimental folding rates. This validation is carried out on a list of about 30 two-state folders. Furthermore, the qualitative analysis of residues mean square displacements (shown to reproduce crystallographic data accurately) provides a reliable and statistically accurate method to identify crucial folding sites/contacts. This novel strategy is validated against clinical data for human immunodeficiency virus type 1 (HIV-1) protease. Finally, we compare the spectra and eigenmodes of vibration of natural proteins against randomly generated compact structures and regular random graphs. The comparison reveals a distinctive enhanced flexibility of natural structures accompanied by slow relaxation times at the folding temperature. The fact that these properties are connected intimately to the presence and assembly of secondary motifs hints at the special criteria adopted by evolution in the selection of viable folds.
机译：我们对天然蛋白质的振动和弛豫特性进行了理论研究，目的是表征折叠和平衡热力学。通过合适的模型，我们仅利用蛋白质天然结构的知识即可提供各种温度下振动的频谱和本征模的完整表征。结果表明，扰动在折叠过渡处衰减的速率与实验折叠速率具有很好的相关性。该验证是在大约30个两个状态文件夹的列表上执行的。此外，对残留均方位移的定性分析（显示为准确再现晶体学数据）提供了一种可靠且统计准确的方法，可以识别关键的折叠位点/接触。针对人免疫缺陷病毒1型（HIV-1）蛋白酶的临床数据验证了这种新策略。最后，我们比较了天然蛋白质与随机生成的紧凑结构和规则随机图的振动谱和本征模。比较显示出天然结构的显着增强的柔韧性以及在折叠温度下缓慢的松弛时间。这些特性与次要基序的存在和组装紧密相关的事实提示了在选择可行折叠时进化所采用的特殊标准。

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