蛋白质工程和蛋白质折叠

蛋白质一级结构决定着高级结构。蛋白质肽链在适宜条件下会自动卷曲形成其相应的高级结构,即自动发生蛋白质折叠,其自动发生的原因和过程仍不十分清楚,但是随着蛋白质工程的日益兴起,这些与折叠有关的问题也愈显重要,就此已有文章进行过讨论[1,2]。反之,如把新兴的蛋白质工程手段(尤其是基因定点诱变技术)应用来研究这些折叠问题,必将推动蛋白质折叠的研究。本文将就蛋白质折叠与蛋白质工程相互影响的一些例子进行讨论。     

蛋白质折叠速率预测研究进展

蛋白质折叠速率预测是当今生物物理学最具挑战性的课题之一。近年来,该领域的研究取得了很大的进展,提出了许多经验参数,例如:接触序、长程序、总接触距离、链拓扑参数、二级结构含量、有效长度、螺旋参数、n-阶接触距离等。这些参数都和蛋白质的折叠速率有很好的相关性,基于这些参数的各种预测方法所得到的预测结果也与实验数据较好地吻合。     

基于HP模型的蛋白质折叠问题的研究

基于蛋白质二维HP模型提出改进的遗传算法对真实蛋白质进行计算机折叠模拟。结果显示疏水能量函数最小值的蛋白质构象对应含疏水核心的稳定结构,疏水作用在蛋白质折叠中起主要作用。研究表明二维HP模型在蛋白质折叠研究中是可行的和有效的并为进一步揭示蛋白质折叠机理提供重要参考信息。     

蛋白质折叠和分子伴侣

一个有活性的蛋白质分子不但有特定的氨基酸序列,还处于特定的由氨基酸序列决定的三维空间结构。三维结构的完整性受到干扰,生物活性也会发生变化：有时即使只是轻微的破坏,都可能导致其生物活性全部丧失。所以蛋白质的生物功能是与其三维空间结构密切联系在一起的。     

天然无折叠蛋白质

天然无折叠蛋白质是一类与传统蛋白质结构完全不同的蛋白质,这类蛋白质的数目在不断地增加。它们的出现是对蛋白质学科基本信条的挑战。     

未折叠蛋白质应答

内质网是真核细胞中蛋白质合成、折叠与分泌的重要细胞器.细胞进化出一套完整的机制来监督和帮助内质网内蛋白质的折叠与修饰.而当错误折叠的蛋白质累积时,细胞通过一系列信号转导途径,对其进行应答,包括增强蛋白质折叠能力、停滞大多数蛋白质的翻译、加速蛋白质的降解等.如果内质网功能素乱持续,细胞将最终启动凋亡程序.这些反应被统称为未折叠蛋白质应答(unfolded protein response,UPR).UPR是多个信号转导通路的总称,包括IRE1-XBP1、PERK-ATF4以及ATF6等信号途径.除了应激条件外,UPR还被用于正常生理条件下的调节,例如胆固醇合成代谢的负反馈调控.     

蛋白质折叠机理的理论研究

简要综述了近年来蛋白质折叠机理的理论研究。首先回顾了蛋白质折叠理论的发展历程,然后对折叠中间体的研究现状作了较详细的介绍。同时,对折叠机理理论研究中的几种理论模型和模拟算法作了细致评述,分析了其现状和存在的问题。最后,总结和讨论了折叠机理理论研究的现存问题及研究热点,并展望了该领域研究的发展趋势。     

分子伴侣在蛋白质折叠中的作用

分子伴侣主要由三个高度保守的蛋白质家族组成,这三个家族的成员广泛分布于原核和真核细胞中。TCP1复合物是真核细胞细胞溶质内的伴侣蛋白。分子伴侣在蛋白质折叠过程中防止多肽链形成聚集物或无活性结构,提高正确折叠率。本文重点讨论Stress-70家族蛋白质和伴侣蛋白协助蛋白质折叠过程中的协同性以及伴侣蛋白GroEL和GroES的作用机理。     

蛋白质折叠与装配研究新进展

蛋白质折叠与装配成天然状态的机制,过去根据离体复性实验观察认为是自组装,而近几年来的研究表明体内蛋白质的折叠 与装配并非如此,而是常常依赖于其它辅助因子和ＡＴＰ水解供能,为辅助性组装。这些辅助因子基本可概括为分子内伴侣、酶类和分子伴侣三大类。     

First-Principles Protein Folding Simulations

Abstract

It is widely believed that the prediction of the three-dimensional structures of proteins from the first principles is impossible. This view is based on the fact that the number of possible structures for each protein is astronomically large. The question is then why a protein folds into its native structure with the proper biological functions in the time scale of milliseconds to minutes, and this is called Levinthal's paradox. In this article I will discuss our strategy for attacking the protein folding problem. Our approach consists of two elements: the inclusion of accurate solvent effects and the development of powerful simulation algorithms that can avoid getting trapped in states of energy local minima. For the former, we discuss several models varying in nature from crude (distance-dependent dielectric function) to rigorous (reference interaction site model). For the latter, we show the effectiveness of Monte Carlo simulated annealing and generalized-ensemble algorithms.     

模拟蛋白质折叠过程的新算法研究

蛋白质折叠过程模拟是当前蛋白质研究领域的一个难点问题。针对这一问题,提出了一个描述蛋白质折叠过程的算法-拟蛇算法,并且从分子振荡和分子动力学理论两个方面来证明该算法的核心函数是可行和正确的。经过实验总结出所有蛋白质空间结构都可以通过两种类型函数构造出来,提出了描述蛋白质折叠过程模型。与其它蛋白质折叠过程模拟算法的实验结果比较表明,拟蛇算法所构造的空间结构能量值最小、相似度最好。进而说明拟蛇算法和蛋白质折叠过程模型在描述蛋白质折叠过程方面具有明显优势。     

Cystic Fibrosis: A Disease of Altered Protein Folding

Cystic fibrosis (CF) is caused by mutations in the gene that encodes the cystic fibrosis transmembrane conductance regulator, CFTR. Previously we demonstrated that the common F508 mutation in the first nucleotide binding domain (NBD1) alters the ability of the domain to fold into a functional three-dimensional structure, providing a molecular explanation for the observation that the mutant CFTR is retained in the endoplasmic reticulum and does not traffic to the apical membrane of affected epithelial cells. Notably, when conditions are altered to promote folding of the mutant protein, it can assume a functional conformation. Correcting the folding defect may have therapeutic benefit for the treatment of cystic fibrosis. Here we summarize these results and discuss the implications in vitro folding studies have for understanding the pathobiology of CF.     

Single-Molecule Force Spectroscopy of Protein Folding

The use of force probes to induce unfolding and refolding of single molecules through the application of mechanical tension, known as single-molecule force spectroscopy (SMFS), has proven to be a powerful tool for studying the dynamics of protein folding. Here we provide an overview of what has been learned about protein folding using SMFS, from small, single-domain proteins to large, multi-domain proteins. We highlight the ability of SMFS to measure the energy landscapes underlying folding, to map complex pathways for native and non-native folding, to probe the mechanisms of chaperones that assist with native folding, to elucidate the effects of the ribosome on co-translational folding, and to monitor the folding of membrane proteins.     

Back to Units of Protein Folding

Abstract

In response to the criticism by A. Finkelstein (J. Biomol. Struct. Dyn. 20, 311–314, 2002) of our Communication (J. Biomol. Struct. Dyn. 20, 5–6, 2002) several issues are dealt with. Importance of the notion of elementary folding unit, its size and structure, and the necessity of further characterization of the units for the elucidation of the protein folding in vivo are discussed. The criticism (J. Biomol. Struct. Dyn. 20, 311–314, 2002) on the hierarchical protein folding is also briefly addressed.     

Chaperonin-mediated Protein Folding

We have been studying chaperonins these past twenty years through an initial discovery of an action in protein folding, analysis of structure, and elucidation of mechanism. Some of the highlights of these studies were presented recently upon sharing the honor of the 2013 Herbert Tabor Award with my early collaborator, Ulrich Hartl, at the annual meeting of the American Society for Biochemistry and Molecular Biology in Boston. Here, some of the major findings are recounted, particularly recognizing my collaborators, describing how I met them and how our great times together propelled our thinking and experiments.     

Evolutionary Aspects of Protein Structure and Folding

Four basic stages of evolution of protein structure are described, basing on recent work of the authors aimed specifically to reconstruct the earliest events in the protein evolution. According to this reconstruction, the initial stage of short peptides comprising, probably, only a few amino acid residues had been followed by formation of closed loops of 25–30 residues, which corresponds to the polymer-statistically optimal ring closure size for mixed polypeptide chains. The next stage involved fusion of relatively small linear genes and formation of protein structures consisting of several closed loops of a nearly standard size, with 4–6 loops (100–200 amino acid residues) in a typical protein fold. The last, modern stage began with combinatorial fusion of the presumably circular 300–600 bp DNA units and, accordingly, formation of multidomain proteins.     

二级结构形成：蛋白质折叠起始过程的框架模型

框架模型认为二级结构形成是蛋白质起始过程的结构基础.文章介绍蛋白质同源片段的溶液构象及其构象研究法和多肽二级结构的从头设计,并综述这些研究成果应用于折叠起始过程的理论模型和蛋白质折叠起始过程的最新研究进展.     

Toward Correct Protein Folding Potentials

Empirical protein folding potentialfunctions should have a global minimum nearthe native conformationof globular proteins that fold stably, andthey should give the correct free energy offolding. We demonstrate that otherwise verysuccessful potentials fail to have even alocal minimumanywhere near the native conformation, anda seemingly well validated method ofestimatingthe thermodynamic stability of the nativestate is extremely sensitive to smallperturbations inatomic coordinates. These are bothindicative of fitting a great deal ofirrelevant detail. Here weshow how to devise a robust potentialfunction that succeeds very well at bothtasks, at least for alimited set of proteins, and this involvesdeveloping a novel representation of thedenatured state.Predicted free energies of unfolding for 25mutants of barnase are in close agreementwith theexperimental values, while for 17 mutantsthere are substantial discrepancies.