Woo Hyung-June, Roux Benoît
Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA.
Proc Natl Acad Sci U S A. 2005 May 10;102(19):6825-30. doi: 10.1073/pnas.0409005102. Epub 2005 May 2.
A general methodology for calculating the equilibrium binding constant of a flexible ligand to a protein receptor is formulated on the basis of potentials of mean force. The overall process is decomposed into several stages that can be computed separately: the free ligand in the bulk is first restrained into the conformation it adopts in the bound state, position, and orientation by applying biasing potentials, then it is translated into the binding site, where it is released completely. The conformational restraining potential is based on the root-mean-square deviation of the peptide coordinates relative to its average conformation in the bound complex. Free energy contributions from each stage are calculated by means of free energy perturbation potential of mean force techniques by using appropriate order parameters. The present approach avoids the need to decouple the ligand from its surrounding (bulk solvent and receptor protein) as is traditionally performed in the double-decoupling scheme. It is believed that the present formulation will be particularly useful when the solvation free energy of the ligand is very large. As an application, the equilibrium binding constant of the phosphotyrosine peptide pYEEI to the Src homology 2 domain of human Lck has been calculated. The results are in good agreement with experimental values.
基于平均力势制定了一种计算柔性配体与蛋白质受体平衡结合常数的通用方法。整个过程被分解为几个可以单独计算的阶段：首先通过施加偏置势将本体中的游离配体限制为其在结合状态下所采用的构象、位置和取向，然后将其平移到结合位点，在那里完全释放。构象限制势基于肽坐标相对于其在结合复合物中的平均构象的均方根偏差。通过使用适当的序参量，借助平均力势的自由能微扰技术计算每个阶段的自由能贡献。本方法避免了传统双解耦方案中使配体与其周围环境（本体溶剂和受体蛋白）解耦的需求。据信，当配体的溶剂化自由能非常大时，本公式将特别有用。作为一个应用，计算了磷酸酪氨酸肽pYEEI与人Lck的Src同源2结构域的平衡结合常数。结果与实验值吻合良好。
