Munich Center for Integrated Protein Science and Department of Chemistry, Technische Universität München, D-85747 Garching, Germany.
Proc Natl Acad Sci U S A. 2013 Aug 6;110(32):12905-10. doi: 10.1073/pnas.1303515110. Epub 2013 Jul 22.
The dynamics of peptide α-helices have been studied extensively for many years, and the kinetic mechanism of the helix-coil dynamics has been discussed controversially. Recent experimental results have suggested that equilibrium helix-coil dynamics are governed by movement of the helix/coil boundary along the peptide chain, which leads to slower unfolding kinetics in the helix center compared with the helix ends and position-independent helix formation kinetics. We tested this diffusion of boundary model in helical peptides of different lengths by triplet-triplet energy transfer measurements and compared the data with simulations based on a kinetic linear Ising model. The results show that boundary diffusion in helical peptides can be described by a classical, Einstein-type, 1D diffusion process with a diffusion coefficient of 2.7⋅10(7) (amino acids)(2)/s or 6.1⋅10(-9) cm(2)/s. In helices with a length longer than about 40 aa, helix unfolding by coil nucleation in a helical region occurs frequently in addition to boundary diffusion. Boundary diffusion is slowed down by helix-stabilizing capping motifs at the helix ends in agreement with predictions from the kinetic linear Ising model. We further tested local and nonlocal effects of amino acid replacements on helix-coil dynamics. Single amino acid replacements locally affect folding and unfolding dynamics with a ϕf-value of 0.35, which shows that interactions leading to different helix propensities for different amino acids are already partially present in the transition state for helix formation. Nonlocal effects of amino acid replacements only influence helix unfolding (ϕf = 0) in agreement with a diffusing boundary mechanism.
多年来，人们对肽α-螺旋的动力学进行了广泛的研究，并且螺旋-线团动力学的动力学机制存在争议。最近的实验结果表明，平衡态螺旋-线团动力学受螺旋/线团边界沿肽链移动的控制，这导致与螺旋两端相比，螺旋中心的解折叠动力学较慢，并且形成螺旋的动力学与位置无关。我们通过三态-三态能量转移测量检验了不同长度的螺旋肽中的这种边界扩散模型，并将数据与基于动力学线性伊辛模型的模拟进行了比较。结果表明，螺旋肽中的边界扩散可以用经典的爱因斯坦型 1D 扩散过程来描述，扩散系数为 2.7⋅10(7)（氨基酸）(2)/s 或 6.1⋅10(-9) cm(2)/s。在长度长于约 40 个氨基酸的螺旋中，除了边界扩散之外，螺旋区域中的线团成核也经常导致螺旋展开。与动力学线性伊辛模型的预测一致，螺旋末端的螺旋稳定封端基序使边界扩散减慢。我们进一步测试了氨基酸取代对螺旋-线团动力学的局部和非局部影响。单个氨基酸取代会局部影响折叠和展开动力学，其 ϕf 值为 0.35，这表明导致不同氨基酸具有不同螺旋倾向的相互作用已经部分存在于螺旋形成的过渡态中。与扩散边界机制一致，氨基酸取代的非局部影响仅影响螺旋展开（ϕf = 0）。
