Morton A, Baase W A, Matthews B W
Institute of Molecular Biology, Howard Hughes Medical Institute, Eugene, Oregon, USA.
Biochemistry. 1995 Jul 11;34(27):8564-75. doi: 10.1021/bi00027a006.
To determine the constraints on interactions within the core of a folded protein, we have analyzed the binding of 91 different compounds to an internal cavity created in the interior of phage T4 lysozyme by site-directed mutagenesis [Eriksson et al. (1992a) Nature 355, 371-373]. The cavity is able to accommodate a variety of small, mainly nonpolar, ligands. Molecules which do not appear to bind include those that are very polar, those that are too large, and those that have appropriate volume and polarity but inappropriate shape. Calorimetric analysis of 16 of these ligands reveals that their free energies of binding are poorly correlated with their solvent-transfer free energies. In addition, their enthalpies of binding are much larger than expected on the basis of transfer of the ligands from an aqueous to a nonpolar liquid phase. The binding energetics were analyzed by dividing the reaction into three processes: desolvation, immobilization, and packing. This analysis indicates that all three processes contribute to binding specificity. For a subset of these ligands that are structurally related, however, packing interactions in the protein interior are well modeled by the interactions of the ligands with octanol.
为了确定折叠蛋白质核心区域内相互作用的限制因素，我们分析了91种不同化合物与通过定点诱变在噬菌体T4溶菌酶内部产生的内部空腔的结合情况[埃里克森等人（1992a）《自然》355, 371 - 373]。该空腔能够容纳多种主要为非极性的小分子配体。似乎不结合的分子包括那些极性很强的分子、那些太大的分子以及那些具有合适体积和极性但形状不合适的分子。对其中16种配体的量热分析表明，它们的结合自由能与其溶剂转移自由能相关性很差。此外，它们的结合焓比基于配体从水相转移到非极性液相所预期的要大得多。通过将反应分为三个过程来分析结合能：去溶剂化、固定化和堆积。该分析表明所有这三个过程都对结合特异性有贡献。然而，对于这些结构相关的配体子集，蛋白质内部的堆积相互作用可以通过配体与辛醇的相互作用很好地模拟。
