Creamer T P, Srinivasan R, Rose G D
Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
Biochemistry. 1997 Mar 11;36(10):2832-5. doi: 10.1021/bi962819o.
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.
埋藏表面积常被用作衡量疏水作用对蛋白质折叠贡献的指标。从定量角度来看，折叠时埋藏的表面积被视为天然态与未折叠态之间的面积差。对于已知结构，这种计算定义明确，但对于未折叠态则依赖于模型。在之前的一篇论文中[Creamer, T. P., Srinivasan, R., & Rose, G. D. (1995) Biochemistry 34, 16245 - 16250]，我们开发了两个模型，这两个模型界定了未折叠态表面积的极限范围。利用这些极值表明，早期的模型，如延伸三肽模型，高估了未折叠态侧链的表面积。在本文作为我们之前论文的续篇中，我们聚焦于未折叠态的主链表面，同样采用界定极限范围之间面积的策略。本研究的一个主要结论是，蛋白质中的大多数主链表面埋藏于局部结构之中。
