Using Cooperatively Folded Peptides To Measure Interaction Energies and Conformational Propensities.
Using Cooperatively Folded Peptides To Measure Interaction Energies and Conformational Propensities.
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DOI：
10.1021/acs.accounts.7b00195
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发表时间：
2017-08-15
影响因子：
18.3
通讯作者：
Kelly JW
中科院分区：
文献类型：
--
作者：
Ardejani MS;Powers ET;Kelly JW
生物聚合物折叠的速率和平衡由构成生物聚合物序列的亚基的构象偏好以及折叠状态下形成的相互作用决定。由于这些过程对生命至关重要，量化构象倾向和相互作用强度对于理解生物学至关重要。在这篇文章中，我们描述了我们对肽模型系统的使用，这些系统可以协同折叠，但又足够小，可以通过化学合成来测量这样的数量。通过突变干扰感兴趣的相互作用或构象并测量野生型（其中相互作用或构象未受干扰）和突变模型肽（其中相互作用已被消除或构象倾向已改变）的折叠自由能之间的差异来进行必要的测量。通过适当的控制，并且假设所讨论的肽模型系统通过二态过程折叠，这些折叠自由能差异可以准确测量相互作用强度或构象倾向。该方法具有高灵敏度和高动态范围的优点，因为感兴趣的能量与折叠自由能耦合，可以通过成熟的生物物理方法（例如通过荧光或圆二色性监测的离液剂或热变性研究）以千卡量级的精度测量折叠自由能。此外，由于模型肽可以化学合成，因此可以使用天然和非天然氨基酸的完整库来将扰动调整为所需的剧烈或微妙。这一功能特别值得注意，因为它使得能够使用为物理有机化学开发的分析工具，特别是线性自由能关系，将相互作用能分解为其组成部分，从而更深入地了解驱动生物聚合物中相互作用的力。我们使用这种方法，主要使用源自人类 Pin1 蛋白的 WW 结构域作为我们的模型系统，来评估氢键强度（尤其是由主链酰胺形成的氢键强度）；氢键强度对其形成环境的依赖性；天然序列和小分子β-转角模拟物的β-转角倾向；以及碳水化合物-蛋白质相互作用的能量学。在每种情况下，合成可及性、测量折叠能的简便性以及 Pin1 WW 结构域结构对突变的鲁棒性相结合，使我们能够获得对其他方法难以测量的量的深入测量。
The rates and equilibria of the folding of biopolymers are determined by the conformational preferences of the subunits that make up the sequence of the biopolymer and by the interactions that are formed in the folded state. Because of the centrality of these processes to life, quantifying conformational propensities and interaction strengths is vitally important to understanding biology. In this Account, we describe our use of peptide model systems that fold cooperatively, yet are small enough to be chemically synthesized to measure such quantities. The necessary measurements are made by perturbing an interaction or conformation of interest by mutation and measuring the difference between the folding free energies of the wild type (in which the interaction or conformation is undisturbed) and the mutant model peptides (in which the interaction has been eliminated or the conformational propensities modified). With the proper controls, and provided that the peptide model system in question folds via a two-state process, these folding free energy differences can be accurate measures of interaction strengths or conformational propensities. This method has the advantage of having high sensitivity and high dynamic range because the energies of interest are coupled to folding free energies, which can be measured with precisions on the order of a few tenths of a kilocalorie by well-established biophysical methods, like chaotrope or thermal denaturation studies monitored by fluorescence or circular dichroism. In addition, because the model peptides can be chemically synthesized, the full arsenal of natural and unnatural amino acids can be used to tune perturbations to be as drastic or subtle as desired. This feature is particularly noteworthy because it enables the use of analytical tools developed for physical organic chemistry, especially linear free energy relationships, to decompose interaction energies into their component parts to obtain a deeper understanding of the forces that drive interactions in biopolymers. We have used this approach, primarily with the WW domain derived from the human Pin1 protein as our model system, to assess hydrogen bond strengths (especially those formed by backbone amides); the dependence of hydrogen bond strengths on the environment in which they form; β-turn propensities of both natural sequences and small molecule β-turn mimics; and the energetics of carbohydrate–protein interactions. In each case, the combination of synthetic accessibility, the ease of measuring folding energies, and the robustness of the structure of the Pin1 WW domain to mutation enabled us to obtain incisive measurements of quantities that have been challenging to measure by other methods.
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DOI：
10.1126/science.1198461
发表时间：
2011-02-04
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Culyba EK;Price JL;Hanson SR;Dhar A;Wong CH;Gruebele M;Powers ET;Kelly JW
通讯作者：
Kelly JW
碳水化合物 - 芳族相互作用强度对碳水化合物结构的依赖性。
影响因子：
15
作者：
Hsu CH;Park S;Mortenson DE;Foley BL;Wang X;Woods RJ;Case DA;Powers ET;Wong CH;Dyson HJ;Kelly JW
通讯作者：
Kelly JW
影响因子：
15
作者：
Hudson KL;Bartlett GJ;Diehl RC;Agirre J;Gallagher T;Kiessling LL;Woolfson DN
通讯作者：
Woolfson DN
影响因子：
64.5
作者：
CARTER, PJ;WINTER, G;FERSHT, AR
通讯作者：
FERSHT, AR
影响因子：
5.2
作者：
Carroll, William R.;Zhao, Chen;Shimizu, Ken D.
通讯作者：
Shimizu, Ken D.