Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility.
Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility.
复制标题
对蛋白质和肽的未折叠状态进行建模。
作者：
Trevor P. Creamer;Rajgopal Srinivasan;George D. Rose
掩埋表面积通常被用来衡量疏水效应对蛋白质折叠的贡献。在定量上，褶皱时埋藏的表面被认为是自然状态和未褶皱状态之间的面积差异。对于已知结构，该计算被很好地定义，但是对于展开状态，该计算取决于模型。在之前的一篇论文[Creamer，T.P.，Srinivesan，R.，&Rose，G.D.(1995年)生物化学34,16245-16250]中，我们开发了两个模型，将展开状态的表面积限定在两个极限之间。利用这些极值，研究表明，早期的模型，如扩展的三肽，高估了侧链在未折叠状态下的表面积。在上一篇文章的续篇中，我们将重点放在展开状态下的主干表面上，同样采用了限制极值之间区域的捕获策略。这项研究的一个主要结论是，蛋白质中的大部分主干表面埋藏在局部结构中。
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.