Petukhov M, Cregut D, Soares C M, Serrano L
European Molecular Biology Laboratory, Heidelberg, Germany.
Protein Sci. 1999 Oct;8(10):1982-9. doi: 10.1110/ps.8.10.1982.
Recent studies have pointed out the important role of local water structures in protein conformational stability. Here, we present an accurate and computationally effective way to estimate the free energy contribution of the simplest water structure motif--the water bridge. Based on the combination of empirical parameters for accessible protein surface area and the explicit consideration of all possible water bridges with the protein, we introduce an improved protein solvation model. We find that accounting for water bridge formation in our model is essential to understand the conformational behavior of polypeptides in water. The model formulation, in fact, does not depend on the polypeptide nature of the solute and is therefore applicable to other flexible biomolecules (i.e., DNAs, RNAs, polysaccharides, etc.).
最近的研究指出了局部水结构在蛋白质构象稳定性中的重要作用。在此，我们提出了一种准确且计算高效的方法来估算最简单的水结构基序——水桥的自由能贡献。基于可及蛋白质表面积的经验参数组合以及对蛋白质所有可能水桥的明确考虑，我们引入了一种改进的蛋白质溶剂化模型。我们发现，在我们的模型中考虑水桥的形成对于理解多肽在水中的构象行为至关重要。实际上，该模型公式并不依赖于溶质的多肽性质，因此适用于其他柔性生物分子（即DNA、RNA、多糖等）。
