Department of Physics and Astronomy, Oxford College of Emory University, Oxford, Georgia 30054, USA.
Open Learning, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
J Chem Phys. 2021 Feb 28;154(8):084903. doi: 10.1063/5.0038184.
We compare and contrast folding behavior in several coarse-grained protein models, both on- and off-lattice, in an attempt to uncover the effect of lattice constraints in these kinds of models. Using modern, extended ensemble Monte Carlo methods-Wang-Landau sampling, multicanonical sampling, replica-exchange Wang-Landau sampling, and replica-exchange multicanonical sampling, we investigate the thermodynamic and structural behavior of the protein Crambin within the context of the hydrophobic-polar, hydrophobic-"neutral"-polar (H0P), and semi-flexible H0P model frameworks. We uncover the folding process in all cases; all models undergo, at least, the two major structural transitions observed in nature-the coil-globule collapse and the folding transition. As the complexity of the model increases, these two major transitions begin to split into multi-step processes, wherein the lattice coarse-graining has a significant impact on the details of these processes. The results show that the level of structural coarse-graining is coupled to the level of interaction coarse-graining.
我们比较和对比了几种粗粒化蛋白质模型的折叠行为，包括晶格和非晶格模型，试图揭示晶格约束在这些模型中的影响。我们使用现代的扩展系综蒙特卡罗方法——Wang-Landau 采样、多正则抽样、复制交换 Wang-Landau 采样和复制交换多正则抽样，研究了疏水-极性、疏水-“中性”-极性（H0P）和半柔性 H0P 模型框架中蛋白 Crambin 的热力学和结构行为。我们揭示了所有情况下的折叠过程；所有模型都经历了至少两种在自然界中观察到的主要结构转变——螺旋-球蛋白坍塌和折叠转变。随着模型复杂性的增加，这两个主要转变开始分裂成多步过程，其中晶格粗粒化对这些过程的细节有重大影响。结果表明，结构粗粒化的程度与相互作用粗粒化的程度相关。
