Department of Physics and Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, British Columbia V6T 1Z1, Canada.
J Chem Phys. 2013 Sep 28;139(12):121925. doi: 10.1063/1.4817215.
Computer simulations can provide critical information on the unfolded ensemble of proteins under physiological conditions, by explicitly characterizing the geometrical properties of the diverse conformations that are sampled in the unfolded state. A general computational analysis across many proteins has not been implemented however. Here, we develop a method for generating a diverse conformational ensemble, to characterize properties of the unfolded states of intrinsically disordered or intrinsically folded proteins. The method allows unfolded proteins to retain disulfide bonds. We examined physical properties of the unfolded ensembles of several proteins, including chemical shifts, clustering properties, and scaling exponents for the radius of gyration with polymer length. A problem relating simulated and experimental residual dipolar couplings is discussed. We apply our generated ensembles to the problem of folding kinetics, by examining whether the ensembles of some proteins are closer geometrically to their folded structures than others. We find that for a randomly selected dataset of 15 non-homologous 2- and 3-state proteins, quantities such as the average root mean squared deviation between the folded structure and unfolded ensemble correlate with folding rates as strongly as absolute contact order. We introduce a new order parameter that measures the distance travelled per residue, which naturally partitions into a smooth "laminar" and subsequent "turbulent" part of the trajectory. This latter conceptually simple measure with no fitting parameters predicts folding rates in 0 M denaturant with remarkable accuracy (r = -0.95, p = 1 × 10(-7)). The high correlation between folding times and sterically modulated, reconfigurational motion supports the rapid collapse of proteins prior to the transition state as a generic feature in the folding of both two-state and multi-state proteins. This method for generating unfolded ensembles provides a powerful approach to address various questions in protein evolution, misfolding and aggregation, transient structures, and molten globule and disordered protein phases.
计算机模拟可以提供在生理条件下蛋白质未折叠整体的关键信息，通过明确描述在未折叠状态下采样的不同构象的几何性质。然而，尚未实现针对许多蛋白质的一般计算分析。在这里，我们开发了一种生成多样化构象整体的方法，以表征无规卷曲或固有折叠蛋白质的未折叠状态的性质。该方法允许未折叠的蛋白质保留二硫键。我们检查了包括化学位移、聚类性质以及旋转半径与聚合物长度的标度指数在内的几种蛋白质的未折叠整体的物理性质。讨论了与模拟和实验残基偶极耦合相关的问题。我们通过检查某些蛋白质的整体是否在几何上比其他蛋白质更接近其折叠结构，将我们生成的整体应用于折叠动力学问题。我们发现，对于 15 个非同源的 2 态和 3 态蛋白质的随机选择数据集，折叠结构和未折叠整体之间的平均均方根偏差等数量与折叠速率的相关性与绝对接触顺序一样强。我们引入了一个新的序参数，该参数测量每个残基的移动距离，它自然地分为轨迹的平滑“层流”和随后的“湍流”部分。这个概念简单、无需拟合参数的度量标准，以惊人的准确性（r = -0.95，p = 1×10(-7)）预测了在 0 M 变性剂中的折叠速率。折叠时间与受空间位阻调制的、重新配置运动之间的高度相关性支持在过渡态之前蛋白质快速折叠作为 2 态和多态蛋白质折叠的普遍特征。这种生成未折叠整体的方法为解决蛋白质进化、错误折叠和聚集、瞬态结构以及无规卷曲和无序蛋白质相中的各种问题提供了一种强大的方法。
