Hagmann Johannes-Geert, Nakagawa Naoko, Peyrard Michel
Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS, 46 Allée d'Italie, 69364 Lyon, France.
Department of Mathematical Sciences, Ibaraki University, Mito, Ibaraki 310-8512, Japan.
Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Jan;89(1):012705. doi: 10.1103/PhysRevE.89.012705. Epub 2014 Jan 8.
Prompted by results that showed that a simple protein model, the frustrated Gō model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature properties of proteins. First, we examine equilibrium fluctuations. We calculate its incoherent neutron-scattering structure factor and show that it can be well described by a theory using the one-phonon approximation. By performing an inherent structure analysis, we assess the transitions among energy states at low temperatures. Then, we examine nonequilibrium fluctuations after a sudden cooling of the protein. We investigate the violation of the fluctuation-dissipation theorem in order to analyze the protein glass transition. We find that the effective temperature of the quenched protein deviates from the temperature of the thermostat, however it relaxes towards the actual temperature with an Arrhenius behavior as the waiting time increases. These results of the equilibrium and nonequilibrium studies converge to the conclusion that the apparent dynamical transition of this coarse-grained model cannot be attributed to a glassy behavior.
受结果的启发，即一个简单的蛋白质模型——受挫的Gō模型，似乎表现出一种让人联想到蛋白质动力学转变的转变，我们研究了该模型描述蛋白质低温特性的有效性。首先，我们研究平衡涨落。我们计算了它的非相干中子散射结构因子，并表明它可以用一个使用单声子近似的理论很好地描述。通过进行固有结构分析，我们评估了低温下能量状态之间的转变。然后，我们研究了蛋白质突然冷却后的非平衡涨落。我们研究涨落耗散定理的违反情况，以分析蛋白质玻璃化转变。我们发现，猝灭蛋白质的有效温度偏离恒温器的温度，然而随着等待时间的增加，它以阿仑尼乌斯行为向实际温度弛豫。平衡和非平衡研究的这些结果都得出这样的结论：这个粗粒化模型明显的动力学转变不能归因于玻璃态行为。
