Hao M H, Pincus M R, Rackovsky S, Scheraga H A
Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301.
Biochemistry. 1993 Sep 21;32(37):9614-31. doi: 10.1021/bi00088a014.
A new procedure for studying the folding and unfolding of proteins, with an application to bovine pancreatic trypsin inhibitor (BPTI), is reported. The unfolding and refolding of the native structure of the protein are characterized by the dimensions of the protein, expressed in terms of the three principal radii of the structure considered as an ellipsoid. A dynamic equation, describing the variations of the principal radii on the unfolding path, and a numerical procedure to solve this equation are proposed. Expanded and distorted conformations are refolded to the native structure by a dimensional-constraint energy minimization procedure. A unique and reproducible unfolding pathway for an intermediate of BPTI lacking the [30,51] disulfide bond is obtained. The resulting unfolded conformations are extended; they contain near-native local structure, but their longest principal radii are more than 2.5 times greater than that of the native structure. The most interesting finding is that the majority of expanded conformations, generated under various conditions, can be refolded closely to the native structure, as measured by the correct overall chain fold, by the rms deviations from the native structure of only 1.9-3.1 A, and by the energy differences of about 10 kcal/mol from the native structure. Introduction of the [30,51] disulfide bond at this stage, followed by minimization, improves the closeness of the refolded structures to the native structure, reducing the rms deviations to 0.9-2.0 A. The unique refolding of these expanded structures over such a large conformational space implies that the folding is strongly dictated by the interactions in the amino acid sequence of BPTI. The simulations indicate that, under conditions that favor a compact structure as mimicked by the volume constraints in our algorithm, the expanded conformations have a strong tendency to move toward the native structure; therefore, they probably would be favorable folding intermediates. The results presented here support a general model for protein folding, i.e., progressive formation of partially folded structural units, followed by collapse to the compact native structure. The general applicability of the procedure is also discussed.
报道了一种研究蛋白质折叠与去折叠的新方法，并将其应用于牛胰蛋白酶抑制剂（BPTI）。蛋白质天然结构的去折叠和再折叠通过蛋白质的尺寸来表征，该尺寸以被视为椭球体的结构的三个主半径表示。提出了一个描述去折叠路径上主半径变化的动力学方程以及求解该方程的数值方法。通过尺寸约束能量最小化程序，将扩展和扭曲的构象重新折叠为天然结构。获得了缺少[30,51]二硫键的BPTI中间体的独特且可重复的去折叠途径。得到的去折叠构象是伸展的；它们包含接近天然的局部结构，但其最长主半径比天然结构的长2.5倍以上。最有趣的发现是，在各种条件下产生的大多数扩展构象，可以通过正确的整体链折叠、与天然结构的均方根偏差仅为1.9 - 3.1 Å以及与天然结构的能量差约为10 kcal/mol来衡量，被紧密地重新折叠为天然结构。在此阶段引入[30,51]二硫键，然后进行最小化，可提高重新折叠结构与天然结构的接近程度，将均方根偏差降低至0.9 - 2.0 Å。这些扩展结构在如此大的构象空间中的独特重新折叠意味着折叠过程强烈地由BPTI氨基酸序列中的相互作用决定。模拟表明，在我们算法中体积约束所模拟的有利于紧凑结构的条件下，扩展构象有强烈的向天然结构移动的趋势；因此，它们可能是有利的折叠中间体。这里给出的结果支持了蛋白质折叠的一般模型，即部分折叠的结构单元逐步形成，随后折叠成紧凑的天然结构。还讨论了该方法的普遍适用性。
