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快速蛋白质折叠动力学

Fast protein folding kinetics.

作者信息

Gelman Hannah, Gruebele Martin

机构信息

Departments of Physics, Chemistry, and Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA.

出版信息

Q Rev Biophys. 2014 May;47(2):95-142. doi: 10.1017/S003358351400002X. Epub 2014 Mar 18.

Abstract

Fast-folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast-folding proteins has provided insight into the mechanisms, which allow some proteins to find their native conformation well <1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even 'slow' folding processes: fast folders are small; relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast-folding proteins and provides an overview of the major findings of fast-folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general, as well as some work that is left to do.

摘要

快速折叠蛋白一直是计算研究和实验研究的主要焦点,因为这两种技术都适用于它们:它们体积小且折叠速度快,凭借当前的计算能力能够进行合理模拟,但动力学速度又足够慢,可用专门开发的实验技术进行观测。对快速折叠蛋白的这种联合研究深入了解了其机制,这些机制使一些蛋白能在不到1毫秒的时间内找到其天然构象,还发现了诸如下坡折叠等理论预测现象的实例。对快速折叠蛋白的研究也增进了我们对甚至“缓慢”折叠过程的理解:快速折叠蛋白体积小,是相对简单的蛋白质结构域,支配其折叠的原理同样也支配更复杂系统的折叠。本综述总结了用于研究快速折叠蛋白的主要理论和实验技术,并概述了快速折叠研究的主要发现。最后,我们审视了研究快速折叠蛋白过程中出现的主题,并简要总结它们在一般蛋白质折叠中的应用,以及一些有待开展的工作。

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本文引用的文献

1
Atomistic description of the folding of a dimeric protein.
J Phys Chem B. 2013 Oct 24;117(42):12935-42. doi: 10.1021/jp4020993. Epub 2013 Aug 15.
2
NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers.
Proc Natl Acad Sci U S A. 2013 Aug 6;110(32):12867-74. doi: 10.1073/pnas.1305688110. Epub 2013 Jul 18.
3
Using VIPT-jump to distinguish between different folding mechanisms: application to BBL and a Trpzip.
J Am Chem Soc. 2013 May 22;135(20):7668-73. doi: 10.1021/ja401473m. Epub 2013 May 14.
4
Misplaced helix slows down ultrafast pressure-jump protein folding.
Proc Natl Acad Sci U S A. 2013 May 14;110(20):8087-92. doi: 10.1073/pnas.1219163110. Epub 2013 Apr 25.
5
Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry.
Proc Natl Acad Sci U S A. 2013 May 7;110(19):7684-9. doi: 10.1073/pnas.1305887110. Epub 2013 Apr 19.
6
Raising the speed limit for β-hairpin formation.
J Am Chem Soc. 2012 Sep 5;134(35):14476-82. doi: 10.1021/ja3046734. Epub 2012 Aug 21.
7
Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.
PLoS One. 2012;7(6):e39918. doi: 10.1371/journal.pone.0039918. Epub 2012 Jun 29.
8
Downhill protein folding modules as scaffolds for broad-range ultrafast biosensors.
J Am Chem Soc. 2012 May 16;134(19):8010-3. doi: 10.1021/ja301092z. Epub 2012 May 7.
9
Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.
Proteins. 2012 Aug;80(8):2071-9. doi: 10.1002/prot.24098. Epub 2012 May 15.
10
Order out of disorder: working cycle of an intrinsically unfolded chaperone.
Cell. 2012 Mar 2;148(5):947-57. doi: 10.1016/j.cell.2012.01.045.

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