Urea-Mediated Protein Denaturation: A Consensus View
Urea-Mediated Protein Denaturation: A Consensus View
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DOI：
10.1021/jp906350s
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发表时间：
2009-09-24
影响因子：
3.3
通讯作者：
Mukhopadhyay, Chaitali
中科院分区：
文献类型：
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作者：
Das, Atanu;Mukhopadhyay, Chaitali
我们对 8 M 尿素中三种结构相似的小球状蛋白质进行了全原子分子动力学模拟，并将结果与纯水模拟进行了比较。在蛋白质变性之前，首先从第一个溶剂化壳中失去水，随后尿素流入蛋白质。尿素到达蛋白质的第一个溶剂化壳主要是由于静电相互作用，其中相当大的贡献来自分散相互作用。尿素通过使蛋白质-蛋白质接触不如蛋白质-尿素接触稳定，将平衡从天然整体转变为变性整体，这与纯水中的情况正好相反，其中蛋白质-蛋白质接触比蛋白质-水接触更稳定。我们还看到，水跟随尿素并在变性的后期到达蛋白质内部，而尿素优先且有效地溶剂化蛋白质的不同部分。通过氢键溶解蛋白质骨架、与亲水残基的有利静电相互作用以及与疏水残基的分散相互作用是尿素侵入蛋白质核心并使其变性的关键步骤。为什么尿素比水更适合与蛋白质骨架结合，以及尿素如何将自身定向到蛋白质骨架上，这些都已得到全面的鉴定。研究发现分子间力的所有关键组成部分在尿素诱导的蛋白质变性以及变性状态整体的稳定性中发挥着重要作用。水网络/结构和动力学性质的变化以及疏水残基更高程度的溶剂化验证了“间接机制”和“直接机制”的存在，并加强了尿素对蛋白质的影响。
We have performed all-atom molecular dynamics simulations of three structurally similar small globular proteins in 8 M urea and compared the results with pure aqueous simulations. Protein denaturation is preceded by an initial loss of water from the first solvation shell and consequent in-flow of urea toward the protein. Urea reaches the first solvation shell of the protein mainly due to electrostatic interaction with a considerable contribution coming from the dispersion interaction. Urea shifts the equilibrium from the native to denatured ensemble by making the protein-protein contact less stable than protein-urea contact, which is just the reverse of the condition in pure water, where protein-protein contact is more stable than protein-water contact. We have also seen that water follows urea and reaches the protein interior at later stages of denaturation, while urea preferentially and efficiently solvates different parts of the protein. Solvation of the protein backbone via hydrogen bonding, favorable electrostatic interaction with hydrophilic residues, and dispersion interaction with hydrophobic residues are the key steps through which urea intrudes the core of the protein and denatures it. Why urea is preferred over water for binding to the protein backbone and how urea orients itself toward the protein backbone have been identified comprehensively. All the key components of intermolecular forces are found to play a significant part in urea-induced protein denaturation and also toward the stability of the denatured state ensemble. Changes in water network/structure and dynamical properties and higher degree of solvation of the hydrophobic residues validate the presence of "indirect mechanism" along with the "direct mechanism" and reinforce the effect of urea on protein.