Wilson Carter J, de Groot Bert L, Gapsys Vytautas
Department of Mathematics, The University of Western Ontario, London, Ontario, Canada.
Centre for Advanced Materials and Biomaterials Research (CAMBR), The University of Western Ontario, London, Ontario, Canada.
J Comput Chem. 2024 Jun 30;45(17):1444-1455. doi: 10.1002/jcc.27318. Epub 2024 Mar 12.
In a protein, nearby titratable sites can be coupled: the (de)protonation of one may affect the other. The degree of this interaction depends on several factors and can influence the measured . Here, we derive a formalism based on double free energy differences ( ) for quantifying the individual site values of coupled residues. As values can be obtained by means of alchemical free energy calculations, the presented approach allows for a convenient estimation of coupled residue s in practice. We demonstrate that our approach and a previously proposed microscopic formalism, can be combined with alchemical free energy calculations to resolve pH-dependent protein values. Toy models and both, regular and constant-pH molecular dynamics simulations, alongside experimental data, are used to validate this approach. Our results highlight the insights gleaned when coupling and microstate probabilities are analyzed and suggest extensions to more complex enzymatic contexts. Furthermore, we find that naïvely computed values that ignore coupling, can be significantly improved when coupling is accounted for, in some cases reducing the error by half. In short, alchemical free energy methods can resolve the values of both uncoupled and coupled residues.
在蛋白质中，附近的可滴定位点可能会相互耦合：一个位点的（去）质子化可能会影响另一个位点。这种相互作用的程度取决于几个因素，并且会影响测量的 。在这里，我们基于双自由能差（ ）推导出一种形式体系，用于量化耦合残基的各个位点 值。由于 值可以通过炼金术自由能计算获得，因此本文提出的方法在实践中可以方便地估计耦合残基的 值。我们证明，我们的方法和先前提出的微观 形式体系，可以与炼金术自由能计算相结合，以解析pH依赖的蛋白质 值。使用玩具模型以及常规和恒定pH分子动力学模拟， alongside实验数据，来验证这种方法。我们的结果突出了在分析耦合和微观状态概率时获得的见解，并建议将其扩展到更复杂的酶环境中。此外，我们发现，在考虑耦合时，忽略耦合的简单计算的 值可以得到显著改善，在某些情况下误差可减少一半。简而言之，炼金术自由能方法可以解析未耦合和耦合残基的 值。
