Creamer T P, Srinivasan R, Rose G D
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
Biochemistry. 1995 Dec 19;34(50):16245-50. doi: 10.1021/bi00050a003.
The hydrophobic effect is the major factor that drives a protein molecule toward collapse and folding. In this process, residues with apolar side chains associate to form a solvent-shielded hydrophobic core. Often, this hydrophobic contribution to folding is quantified by measuring buried apolar surface area, reckoned as the difference in area between hydrophobic groups in the folded protein and in a standard state. Typically, the standard state area of a residue is obtained from tripeptide models, with the results taken to implicitly represent values appropriate for the unfolded state. Here, we show that a tripeptide is a poor descriptor of the unfolded state, and its widespread use has prompted erroneous conclusions about folding. As an alternative, we explore two limiting models, chosen to bracket the expected behavior of the unfolded chain between reliable extremes. One extreme is represented by simulated hard-sphere peptides and shown to behave like a homopolymer with excluded volume in a good solvent. The other extreme is represented by fragments excised from folded proteins and conjectured to approximate the time-average behavior of a thermally denatured protein at Tm, the midpoint of the unfolding transition. Using these models, it is shown that the area buried by apolar side chains upon folding is considerably less than earlier estimates. For example, upon transfer from the unfolded state to the middle of an alpha-helix, an alanine side chain buries negligible area and, surprisingly, a valine side chain actually gains area. Among other applications, an improved model of the unfolded state can be used to better evaluate the driving force for helix formation in peptides and proteins.
疏水作用是驱动蛋白质分子折叠和塌缩的主要因素。在此过程中，具有非极性侧链的残基相互结合，形成一个溶剂屏蔽的疏水核心。通常，这种对折叠的疏水贡献通过测量埋藏的非极性表面积来量化，该表面积被视为折叠蛋白中疏水基团与标准状态下疏水基团之间的面积差。通常，残基的标准状态面积是从三肽模型中获得的，其结果被认为隐含地代表了适合未折叠状态的值。在这里，我们表明三肽并不能很好地描述未折叠状态，其广泛使用导致了关于折叠的错误结论。作为替代方案，我们探索了两种极限模型，选择它们来界定未折叠链在可靠极端之间的预期行为。一种极端情况由模拟的硬球肽表示，在良溶剂中表现得像具有排除体积的均聚物。另一种极端情况由从折叠蛋白中切除的片段表示，推测其近似于在解折叠转变中点Tm时热变性蛋白的时间平均行为。使用这些模型表明，折叠时非极性侧链埋藏的面积比早期估计的要小得多。例如，从未折叠状态转移到α-螺旋中间时，丙氨酸侧链埋藏的面积可以忽略不计，令人惊讶的是，缬氨酸侧链实际上增加了面积。在其他应用中，改进的未折叠状态模型可用于更好地评估肽和蛋白质中螺旋形成的驱动力。
