Spassov V Z, Karshikoff A D, Ladenstein R
Centre for Structural Biochemistry, Karolinska Institutet, NOVUM, Huddinge, Stockholm, Sweden.
Protein Sci. 1995 Aug;4(8):1516-27. doi: 10.1002/pro.5560040809.
Protein-solvent interactions were analyzed using an optimization parameter based on the ratio of the solvent-accessible area in the native and the unfolded protein structure. The calculations were performed for a set of 183 nonhomologous proteins with known three-dimensional structure available in the Protein Data Bank. The dependence of the total solvent-accessible surface area on the protein molecular mass was analyzed. It was shown that there is no difference between the monomeric and oligomeric proteins with respect to the solvent-accessible area. The results also suggested that for proteins with molecular mass above some critical mass, which is about 28 kDa, a formation of domain structure or subunit aggregation into oligomers is preferred rather than a further enlargement of a single domain structure. An analysis of the optimization of both protein-solvent and charge-charge interactions was performed for 14 proteins from thermophilic organisms. The comparison of the optimization parameters calculated for proteins from thermophiles and mesophiles showed that the former are generally characterized by a high degree of optimization of the hydrophobic interactions or, in cases where the optimization of the hydrophobic interactions is not sufficiently high, by highly optimized charge-charge interactions.
基于天然和未折叠蛋白质结构中溶剂可及面积的比率，使用一个优化参数来分析蛋白质与溶剂的相互作用。对蛋白质数据库中一组183个具有已知三维结构的非同源蛋白质进行了计算。分析了总溶剂可及表面积对蛋白质分子量的依赖性。结果表明，就溶剂可及面积而言，单体蛋白和寡聚蛋白之间没有差异。结果还表明，对于分子量高于约28 kDa的某些临界质量的蛋白质，形成结构域结构或亚基聚合成寡聚体比单个结构域结构的进一步扩大更可取。对14种嗜热生物的蛋白质进行了蛋白质与溶剂以及电荷 - 电荷相互作用的优化分析。对嗜热菌和嗜温菌蛋白质计算得到的优化参数的比较表明，前者通常具有高度优化的疏水相互作用，或者在疏水相互作用优化程度不够高的情况下，具有高度优化的电荷 - 电荷相互作用。
