Davis Caitlin M, Zanetti-Polzi Laura, Gruebele Martin, Amadei Andrea, Dyer R Brian, Daidone Isabella
Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.
Department of Chemistry , Emory University , Atlanta , GA 30322 , USA . Email:
Chem Sci. 2018 Oct 3;9(48):9002-9011. doi: 10.1039/c8sc03786h. eCollection 2018 Dec 28.
For small molecule reaction kinetics, computed reaction coordinates often mimic experimentally measured observables quite accurately. Although nowadays simulated and measured biomolecule kinetics can be compared on the same time scale, a gap between computed and experimental observables remains. Here we directly compared temperature-jump experiments and molecular dynamics simulations of protein folding dynamics using the same observable: the time-dependent infrared spectrum. We first measured the stability and folding kinetics of the fastest-folding β-protein, the GTT35 WW domain, using its structurally specific infrared spectrum. The relaxation dynamics of the peptide backbone, β-sheets, turn, and random coil were measured independently by probing the amide I' region at different frequencies. Next, the amide I' spectra along folding/unfolding molecular dynamics trajectories were simulated by accurate mixed quantum/classical calculations. The simulated time dependence and spectral amplitudes at the exact experimental probe frequencies provided relaxation and folding rates in agreement with experimental observations. The calculations validated by experiment yield direct structural evidence for a rate-limiting reaction step where an intermediate state with either the first or second hairpin is formed. We show how folding switches from a more homogeneous (apparent two-state) process at high temperature to a more heterogeneous process at low temperature, where different parts of the WW domain fold at different rates.
对于小分子反应动力学，计算得到的反应坐标通常能非常准确地模拟实验测量的可观测量。尽管如今模拟和测量的生物分子动力学可以在相同的时间尺度上进行比较，但计算得到的可观测量与实验可观测量之间仍然存在差距。在这里，我们使用相同的可观测量——随时间变化的红外光谱，直接比较了蛋白质折叠动力学的温度跳跃实验和分子动力学模拟。我们首先利用其结构特异性红外光谱测量了折叠速度最快的β蛋白GTT35 WW结构域的稳定性和折叠动力学。通过探测不同频率下的酰胺I'区域，独立测量了肽主链、β折叠、转角和无规卷曲的弛豫动力学。接下来，通过精确的混合量子/经典计算模拟了折叠/去折叠分子动力学轨迹上的酰胺I'光谱。在精确的实验探测频率下模拟的时间依赖性和光谱幅度提供了与实验观测结果一致的弛豫和折叠速率。经实验验证的计算结果为限速反应步骤提供了直接的结构证据，在该步骤中形成了具有第一个或第二个发夹结构的中间态。我们展示了折叠如何从高温下更均匀（表观二态）的过程转变为低温下更不均匀的过程，其中WW结构域的不同部分以不同的速率折叠。
