Favrin Giorgio, Irbäck Anders, Samuelsson Björn, Wallin Stefan
Complex Systems Division, Department of Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden.
Biophys J. 2003 Sep;85(3):1457-65. doi: 10.1016/S0006-3495(03)74578-0.
We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded states of this protein is found to be weak, even at the folding temperature. Nevertheless, we find that melting curves to a good approximation can be described in terms of a simple two-state system, and that the relaxation behavior is close to single exponential. The motion along individual reaction coordinates is roughly diffusive on timescales beyond the reconfiguration time for a single helix. A simple estimate based on diffusion in a square-well potential predicts the relaxation time within a factor of two.
我们对一种含有54个氨基酸的模型蛋白进行了蒙特卡罗研究，该蛋白直接折叠成其天然的三螺旋束状态，不形成任何明确的中间状态。即使在折叠温度下，发现该蛋白天然态和未折叠态之间的自由能垒也很弱。然而，我们发现，熔解曲线可以很好地用一个简单的两态系统来描述，并且弛豫行为接近单指数形式。在单个螺旋的重新配置时间之后的时间尺度上，沿着各个反应坐标的运动大致是扩散性的。基于方阱势中的扩散的简单估计预测的弛豫时间误差在两倍以内。
