Modeling unfolded states of proteins and peptides .2. Backbone solvent accessibility
Modeling unfolded states of proteins and peptides .2. Backbone solvent accessibility
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DOI：
10.1021/bi962819o
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发表时间：
1997-03-11
期刊：
影响因子：
2.9
通讯作者：
Rose, GD
中科院分区：
文献类型：
--
作者：
Creamer, TP;Srinivasan, R;Rose, GD
掩埋表面积通常被用作疏水效应对蛋白质折叠的贡献的量度。在数量上，折叠时掩埋的表面被认为是天然状态和未折叠状态之间的面积差。该计算对于已知结构是很好定义的，但是对于展开状态是依赖于模型的。在先前的论文[Creamer，T. P.，斯里尼瓦桑河，巴西-地& Rose，G. D.（1995）Biochemistry 34，16245-16250]，我们开发了两个模型，其将未折叠状态的表面积括在极限值之间。使用这些极值，它表明，早期的模型，如一个扩展的三肽，高估了侧链在未折叠状态的表面积。在我们之前的论文的续集中，我们专注于展开状态下的骨干表面，再次采用捕获极限极值之间的区域的策略。本研究的一个主要结论是，大多数蛋白质的骨架表面埋在局部结构。
Buried surface area is often used as a measure of the contribution to protein folding from the hydrophobic effect. Quantitatively, the surface buried upon folding is reckoned as the difference in area between the native and unfolded states. This calculation is well defined for a known structure but model-dependent for the unfolded state. In a previous paper [Creamer, T. P., Srinivasan, R., & Rose, G. D. (1995) Biochemistry 34, 16245-16250], we developed two models that bracket the surface area of the unfolded state between Limiting extremes. Using these extrema, it was shown that earlier models, such as an extended tripeptide, overestimate the surface area of side chains in the unfolded state. In this sequel to our previous paper, we focus on backbone surface in the unfolded state, again adopting the strategy of trapping the area between limiting extrema. A principal conclusion of this present study is that most backbone surface in proteins is buried within local structure.