Measurement of energy landscape roughness of folded and unfolded proteins
Measurement of energy landscape roughness of folded and unfolded proteins
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DOI：
10.1073/pnas.1211764109
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发表时间：
2012-11-27
影响因子：
11.1
通讯作者：
Volk, Martin
中科院分区：
文献类型：
--
作者：
Milanesi, Lilia;Waltho, Jonathan P.;Volk, Martin
蛋白质构象变化的动力学，从蛋白质折叠到较小的变化，如参与配基结合的变化，由构象能量格局的性质决定。不同的技术已经被用来跟踪蛋白质在这片土地上的运动，从而量化其性质。然而，这些技术通常局限于短时间尺度和低能量构象。在这里，我们描述一种克服这些限制的一般方法。从芳香族二硫键的非固有构象出发，我们使用时间分辨光谱观察了二硫键光解后九个数量级的非平衡主链动力学，从皮秒到毫秒。我们发现，最初密切接触的残基的重遇概率随着时间的推移而下降，遵循一个不寻常的幂定律，该定律在整个时间范围内持续存在，并且与初级序列无关。模型模拟表明，这一幂定律源于次扩散运动，表明捕获时间在能量景观的局部极小值中广泛分布，并使我们能够量化能量景观的粗糙度(4-5k(B)T)。令人惊讶的是，即使在变性条件下，能量格局仍然高度崎岖，深陷阱(>；20k(B)T)是由多个非自然相互作用产生的，足以在毫秒级的时间尺度上捕获。最后，我们认为，这里发现的蛋白质骨架的亚扩散运动可能通过促进附近残基之间的接触形成来促进低接触顺序的蛋白质的快速折叠。
The dynamics of protein conformational changes, from protein folding to smaller changes, such as those involved in ligand binding, are governed by the properties of the conformational energy landscape. Different techniques have been used to follow the motion of a protein over this landscape and thus quantify its properties. However, these techniques often are limited to short timescales and low-energy conformations. Here, we describe a general approach that overcomes these limitations. Starting from a nonnative conformation held by an aromatic disulfide bond, we use time-resolved spectroscopy to observe nonequilibrium backbone dynamics over nine orders of magnitude in time, from picoseconds to milliseconds, after photolysis of the disulfide bond. We find that the reencounter probability of residues that initially are in close contact decreases with time following an unusual power law that persists over the full time range and is independent of the primary sequence. Model simulations show that this power law arises from subdiffusional motion, indicating a wide distribution of trapping times in local minima of the energy landscape, and enable us to quantify the roughness of the energy landscape (4-5 k(B)T). Surprisingly, even under denaturing conditions, the energy landscape remains highly rugged with deep traps (>20 k(B)T) that result from multiple nonnative interactions and are sufficient for trapping on the millisecond timescale. Finally, we suggest that the subdiffusional motion of the protein backbone found here may promote rapid folding of proteins with low contact order by enhancing contact formation between nearby residues.