Laser temperature jump study of the helix<==>coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model.
Laser temperature jump study of the helix<==>coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model.
复制标题
用“动力学拉链”模型解释丙氨酸肽的螺旋<==>线圈动力学的激光温度跳跃研究。
作者：
P. A. Thompson;W. Eaton;J. Hofrichter
通过 N 端探针 4-(甲基氨基)苯甲酸 (MABA) 的荧光监测激光诱导温度跳跃后基于丙氨酸的肽的螺旋 <==> 线圈转变的动力学。该探针与螺旋主链形成肽氢键，从而改变其荧光量子产率。 MABA 荧光强度在单次指数弛豫中降低，弛豫时间与温度的关系较弱，在熔化转变中点附近表现出约 20 ns 的最大值。我们开发了一个新模型，即螺旋<==>线圈转变的平衡“拉链”模型的动力学版本来解释这些结果。在这个“动力学拉链”模型中，由于假设每个分子不包含螺旋残基或包含单个连续的螺旋区域（单序列近似），因此可能的物种数量大幅减少。根据描述模型的动力学方程的数值解计算出的螺旋状 N 末端残基分数的衰减可以通过具有可比较幅度的两个指数弛豫来近似描述。较短的弛豫时间是由于响应温度跳跃而螺旋末端的快速拉开（和拉紧）造成的，而较长的弛豫时间是由于通过成核自由能垒而使含螺旋和不含螺旋的结构达到平衡。平均螺旋含量的衰减主要由较慢的过程决定。因此，该模型解释了实验观察结果，即 N 端荧光探针的弛豫速度比 Williams 等人的红外探针的弛豫速度大约快 8 倍。 [(1996) Biochemistry 35, 691-697]，它测量平均螺旋含量，但没有考虑荧光实验中缓慢弛豫的可观察振幅的缺失（<10% 慢相）。如果我们假设线圈-->螺旋速率的激活势垒是纯熵的，则该模型还可以解释荧光探针弛豫时间的温度依赖性最大值。最好地再现熔解曲线和弛豫时间比率的参数预测协同参数 sigma 的值，该值比先前报告的仅从拟合平衡数据获得的值大大约 3 倍。再现实验弛豫时间的螺旋生长速率约为 10(8) s-1，比分子动力学模拟中观察到的螺旋生长速率慢大约 100 倍。这些参数可用于模拟从全螺旋状态动力学协作形成螺旋。
The kinetics of the helix<==>coil transition of an alanine-based peptide following a laser-induced temperature jump were monitored by the fluorescence of an N-terminal probe, 4-(methylamino)benzoic acid (MABA). This probe forms a peptide hydrogen bond to the helix backbone, which changes its fluorescence quantum yield. The MABA fluorescence intensity decreases in a single exponential relaxation, with relaxation times that are weakly temperature dependent, exhibiting a maximum value of approximately 20 ns near the midpoint of the melting transition. We have developed a new model, the kinetic version of the equilibrium 'zipper' model for helix<==>coil transitions to explain these results. In this 'kinetic zipper' model, an enormous reduction in the number of possible species results from the assumption that each molecule contains either no helical residues or a single contiguous region of helix (the single-sequence approximation). The decay of the fraction of N-terminal residues that are helical, calculated from numerical solutions of the kinetic equations which describe the model, can be approximately described by two exponential relaxations having comparable amplitudes. The shorter relaxation time results from rapid unzipping (and zipping) of the helix ends in response to the temperature jump, while the longer relaxation time results from equilibration of helix-containing and non-helix-containing structures by passage over the nucleation free energy barrier. The decay of the average helix content is dominated by the slower process. The model therefore explains the experimental observation that relaxation for the N-terminal fluorescent probe is approximately 8-fold faster than that for the infrared probe of Williams et al. [(1996) Biochemistry 35, 691-697], which measures the average helix content, but does not account for the absence of observable amplitude for the slow relaxation in the fluorescence experiments (<10% slow phase). If we assume that the activation barrier for the coil-->helix rate is purely entropic, the model can also explain the maximum in the temperature dependence of the relaxation time for the fluorescent probe. Parameters that best reproduce the melting curves and the ratio of relaxation times predict a value of the cooperativity parameter sigma which is approximately 3-fold larger than previously reported values obtained from fitting equilibrium data only. The helix growth rate of approximately 10(8) s-1 that reproduces the experimental relaxation times is approximately 100-fold slower than those observed in molecular dynamics simulations. These parameters can be used to simulate the kinetically cooperative formation of a helix from the all-coil state.