Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700 054, India.
Protein Sci. 2013 Oct;22(10):1453-7. doi: 10.1002/pro.2330. Epub 2013 Sep 4.
The buried surface area (BSA), which measures the size of the interface in a protein-protein complex may differ from the accessible surface area (ASA) lost upon association (which we call DSA), if conformation changes take place. To evaluate the DSA, we measure the ASA of the interface atoms in the bound and unbound states of the components of 144 protein-protein complexes taken from the Protein-Protein Interaction Affinity Database of Kastritis et al. (2011). We observe differences exceeding 20%, and a systematic bias in the distribution. On average, the ASA calculated in the bound state of the components is 3.3% greater than in their unbound state, and the BSA, 7% greater than the DSA. The bias is observed even in complexes where the conformation changes are small. An examination of the bound and unbound structures points to a possible origin: local movements optimize contacts with the other component at the cost of internal contacts, and presumably also the binding free energy.
埋置表面积（BSA）衡量的是蛋白质-蛋白质复合物界面的大小，如果构象发生变化，可能与结合后丧失的可及表面积（我们称之为 DSA）不同。为了评估 DSA，我们测量了 Kastritis 等人从蛋白质-蛋白质相互作用亲和力数据库（2011）中获得的 144 个蛋白质-蛋白质复合物的组成部分在结合和非结合状态下的界面原子的可及表面积。我们观察到差异超过 20%，并且分布存在系统偏差。平均而言，在组件的结合状态下计算的 ASA 比在非结合状态下大 3.3%，BSA 比 DSA 大 7%。即使在构象变化较小的复合物中也观察到这种偏差。对结合和非结合结构的检查指出了可能的原因：局部运动以牺牲内部接触为代价优化了与另一个组件的接触，可能还有结合自由能。
