Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
J Phys Chem B. 2010 Apr 8;114(13):4389-99. doi: 10.1021/jp905411n.
The stability of peptide bonds is a critical aspect of biological chemistry and therapeutic protein applications. Recent studies found elevated nonenzymatic hydrolysis in the hinge region of antibody molecules, but no mechanism was identified. As a first step in providing a mechanistic interpretation, this computational study examines the rate-determining step of the hydrolytic reaction of a peptide bond under acidic pH by a path sampling technique using a model compound N-MAA. Most previous computational studies did not include explicit water molecules, whose effects are significant in solution chemistry, nor did they provide a dynamic picture for the reaction process in aqueous conditions. Because no single trajectory can be used to describe the reaction dynamics due to fluctuations at finite temperatures, a variant version of the transition path sampling technique, the aimless shooting algorithm, was used to sample dynamic trajectories and to generate an ensemble of transition trajectories according to their statistical weights in the trajectory space. Each trajectory was computed as the time evolution of the molecular system using the Car-Parrinello molecular dynamics technique. The likelihood maximization procedure and its modification were used in extracting dynamically relevant degrees of freedom in the system, and approximations of the reaction coordinate were compared. Its low log-likelihood score and poor p(B) histogram indicate that the C-O distance previously assumed as the reaction coordinate for the rate-determining step is inadequate in describing the dynamics of the reaction. More than one order parameter in a candidate set including millions of geometric quantities was required to produce a convergent reaction coordinate model; its involvement of many degrees of freedom suggests that this hydrolytic reaction step is very complex. In addition to affecting atoms directly involved in bond-making and -breaking processes, the water network also has determining effects on the hydrolytic reaction, a fact that is manifest in the expression of the one-dimensional best-ranked reaction coordinate, which includes three geometric quantities. The p(B) histograms were computed to verify the results of the likelihood maximization and to verify the accuracy of approximation to the "true" reaction coordinate.
肽键的稳定性是生物化学和治疗性蛋白质应用的一个关键方面。最近的研究发现，抗体分子铰链区域的非酶促水解增加，但没有确定其机制。作为提供机制解释的第一步，这项计算研究使用模型化合物 N-MAA 通过路径采样技术检查了在酸性 pH 下肽键水解反应的速率决定步骤。大多数先前的计算研究没有包括显式水分子，而水分子在溶液化学中具有重要作用，也没有提供水相条件下反应过程的动态图像。由于在有限温度下波动，单个轨迹不能用于描述反应动力学，因此使用过渡路径采样技术的变体——无目的射击算法来采样动态轨迹，并根据其在轨迹空间中的统计权重生成一组过渡轨迹。每个轨迹都是使用 Car-Parrinello 分子动力学技术计算分子系统的时间演化。似然最大化程序及其修改用于提取系统中动态相关自由度，并比较了反应坐标的近似值。其低对数似然评分和较差的 p(B)直方图表明，以前假设为速率决定步骤的反应坐标的 C-O 距离在描述反应动力学方面是不够的。在包括数百万个几何量的候选集中，需要一个以上的参数来产生收敛的反应坐标模型；它涉及到许多自由度，这表明该水解反应步骤非常复杂。除了直接影响参与键形成和断裂过程的原子外，水分子网络也对水解反应有决定性的影响，这一事实体现在一维最佳排序反应坐标的表达式中，其中包括三个几何量。计算 p(B)直方图以验证似然最大化的结果，并验证对“真实”反应坐标的近似的准确性。
