蛋白质折叠及二级结构预测

蛋白质二级结构预测是研究蛋白质折叠的主要内容之一,也是获得新氨基酸序列结构信息的一般方法。从热力学和动力学两方面对蛋白质折叠机理进行分析,对蛋白质二级结构预测的常用方法进行分析和评价,并提出蛋白质空间结构预测的途径。     

蛋白质体外折叠技术研究现状与展望

蛋白质折叠技术是生物工程的新“单元操作”。本文阐述了蛋白质体外折叠研究的重要理论意义和应用价值，综述了目前蛋白质体外折叠技术研究进展，最后对蛋白质折叠技术的研究进行了展望。     

利用体积排阻色谱法进行蛋白质折叠

以溶菌酶为模拟体系对体积排阻色谱法进行蛋白质折叠过程实验研究 .圆二色性光谱法分析结果证实了复性溶菌酶与天然溶菌酶的二级结构一致性 ;复性溶菌酶与天然溶菌酶色谱保留体积的差异揭示出折叠过程中无活性蛋白质聚集体的存在及其向复性蛋白质转化的机制 ;不同初始浓度的复性实验证实了蛋白质聚集体的存在及其与变性蛋白质初始浓度的关系 ;采用短色谱柱的折叠分离实验结果表明蛋白质折叠是一个快速过程 ;不同尿素浓度下的折叠分离实验结果表明尿素在SEC法中具有非常重要的作用 .与稀释复性法的对比实验表明 :体积排阻色谱法具有稀释倍数小、复性产品活性收率高、复性蛋白质浓度高等优点 .     

分子动力学模拟研究多肽Trp-cage的折叠机制

蛋白质折叠是当前生物和化学领域研究的热点问题,是未来几十年物理、化学以及生物领域亟待解决的难题之一。简述了蛋白质折叠所面临的问题,以及传统分子力场缺陷及其改进方法,并以Trp-cage蛋白质为例介绍了国内外最近的研究进展。     

表面活性剂辅助蛋白质体外折叠：分子模拟

采用分子模拟方法考察表面活性剂与蛋白质分子之间的相互作用及其对蛋白质折叠过程热力学特性的影响，蛋白质分子构建采用HP模型并引入了方阱类势函数.模拟结果显示：模型蛋白分子的某些折叠中间态会陷入局部能量最低状态而无法完成折叠;弱疏水性表面活性剂对模型蛋白的稳定性影响小，但可有效地帮助处于局部能量最低状态的蛋白折叠中间态通过能量壁垒而实现折叠;强疏水性表面活性剂则可与蛋白质形成高稳定性的复合物而阻止折叠的进行，需将其脱除才能使折叠过程重新开始.模拟结果还显示：表面活性剂的加入会使蛋白质折叠中间态更加丰富，从而能够光滑折叠过程中的能量阱;表面活性剂与变性环境对于蛋白质的折叠具有协同效应.模拟结果与文献报道的实验结果具有一致性，显示分子模拟的方法在揭示蛋白质折叠过程的微观机理以及表面活性剂类折叠助剂的分子设计方面有很好的应用前景.     

液固层析辅助蛋白质从变性态恢复到活性态

层析是化工中分离纯化一些价格昂贵的精细化工产品的常用手段,而液固层析因其温和、快捷、高效等优点已经成为蛋白质纯化过程中必不可少的工具.近年来层析技术的一个拓展是用于辅助蛋白质从变性态恢复到活性态,即所谓的复性,取得了令人瞩目的进展.液固层析辅助蛋白质复性可在高蛋白浓度下操作,适用于大规模生产,同时还能使目标蛋白得到部分纯化.对近年来发展的利用液固层析辅助蛋白质复性的方法做了归纳,包括凝胶过滤层析、离子交换层析、疏水相互作用层析、亲和层析和固定化的折叠催化剂及人工分子伴侣辅助蛋白质复性的方法,并对各自的优缺点和适用范围进行了比较分析.     

蛋白质在层析过程中的失活与复性

在层析分离过程中,层析的固相介质和溶液环境会引起蛋白质的结构变化：天然的蛋白质可能会降低活性甚至完全失去活性,而结构变化了的蛋白质也可能重新折叠恢复活性.此类现象已经引起研究者特别是生化工程学家的关注,层析介质的种类和操作手段是影响此两个过程的关键因素.利用不同的层析方法,对不同的蛋白质采取相应的措施有利于提高活性蛋白质的回收率,具有重要的理论和应用价值.     

毒素肽αB-VxXXIVA片段化学合成及质谱分析

芋螺毒素能够选择性作用一系列离子通道和受体,使其作为一类重要工具广泛应用于神经系统研究。发现于旗帜芋螺的芋螺毒素αB-VxXXIVA能够作用于α9α10乙酰胆碱受体,具有重要的药用潜能。本研究通过化学手段合成αB-VxXXIVA重要序列片段,优化其线性肽合成后氧化折叠方法。同时通过电喷雾离子阱飞行时间串联质谱诱导碰撞解离分析线性肽和折叠肽的二级质谱碎片离子峰,根据y和b系列离子分布分析其二级质谱解离规律。实验结果显示铁氰化钾氧化体系能够显著提高氧化折叠产率。二级质谱离子峰显示线性肽中y离子占主要部分,同时线性肽产生y碎片离子明显多于氧化态,长链多肽也不适用串联质谱从头测序。     

融合标签在蛋白质可溶性表达中的应用进展

融合标签是大规模生产可溶性蛋白质的有效工具,因此融合标签在蛋白质可溶性表达中的应用已成为外源蛋白表达的研究热点。本文重点介绍了常用融合标签及其提高重组蛋白质可溶性表达的机理,主要用5种模型从不同的角度阐述融合标签在蛋白折叠中的作用,其中大多数功能较强的融合标签（如MBP和NusA）作为分子伴侣帮助重组蛋白正确折叠从而提高蛋白质可溶性。此外,阐述了实际应用中常用的组合标签和标签的去除。最后提出了融合标签在大规模生产可溶性蛋白质中的应用前景、面临的挑战,以及今后研究的方向。     

依次折叠静脉输液管巧排管内空气在临床工作中的体会

目的探讨依次折叠输液管巧排管内空气在临床护理工作中的应用。方法针对未能及时加药的输液患者,液面下滑至莫菲氏滴管以下时,采用依次折叠输液管,将下滑液面向上挤至莫菲氏管内,达到排除输液管内空气,使输液继续进行。结果依次折叠输液管巧排管内空气能够快速有效排除输液管内空气。结论依次折叠输液管排除管内空气的方法优于其他排气方法。     

Normal and aberrant biological self-assembly: Insights from studies of human lysozyme and its amyloidogenic variants

Studies of lysozyme have played a major role over several decades in defining the general principles underlying protein structure, folding, and stability. Following the discovery some 10 years ago that two mutational variants of lysozyme are associated with systemic amyloidosis, these studies have been extended to investigate the mechanism of amyloid fibril formation. This Account describes our present knowledge of lysozyme folding and misfolding, and how the latter can give rise to amyloid disease. It also discusses the significance of these studies for our general understanding of normal and aberrant protein folding in the context of human health and disease.     

GroEL-Assisted Protein Folding: Does It Occur Within the Chaperonin Inner Cavity?

The folding of protein molecules in the GroEL inner cavity under the co-chaperonin GroES lid is widely accepted as a crucial event of GroEL-assisted protein folding. This review is focused on the data showing that GroEL-assisted protein folding may proceed out of the complex with the chaperonin. The models of GroEL-assisted protein folding assuming ligand-controlled dissociation of nonnative proteins from the GroEL surface and their folding in the bulk solution are also discussed.     

Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding

Despite recent developments in protein structure prediction, the process of the structure formation, folding, remains poorly understood. Notably, folding of multidomain proteins, which involves multiple steps of segmental folding, is one of the biggest questions in protein science. Multidomain protein folding often requires the assistance of molecular chaperones. Molecular chaperones promote or delay the folding of the client protein, but the detailed mechanisms are still unclear. This review summarizes the findings of biophysical and structural studies on the mechanism of multidomain protein folding mediated by molecular chaperones and explains how molecular chaperones recognize the client proteins and alter their folding properties. Furthermore, we introduce several recent studies that describe the concept of kinetics–activity relationships to explain the mechanism of functional diversity of molecular chaperones.     

Regulation by Different Types of Chaperones of Amyloid Transformation of Proteins Involved in the Development of Neurodegenerative Diseases

The review highlights various aspects of the influence of chaperones on amyloid proteins associated with the development of neurodegenerative diseases and includes studies conducted in our laboratory. Different sections of the article are devoted to the role of chaperones in the pathological transformation of alpha-synuclein and the prion protein. Information about the interaction of the chaperonins GroE and TRiC as well as polymer-based artificial chaperones with amyloidogenic proteins is summarized. Particular attention is paid to the effect of blocking chaperones by misfolded and amyloidogenic proteins. It was noted that the accumulation of functionally inactive chaperones blocked by misfolded proteins might cause the formation of amyloid aggregates and prevent the disassembly of fibrillar structures. Moreover, the blocking of chaperones by various forms of amyloid proteins might lead to pathological changes in the vital activity of cells due to the impaired folding of newly synthesized proteins and their subsequent processing. The final section of the article discusses both the little data on the role of gut microbiota in the propagation of synucleinopathies and prion diseases and the possible involvement of the bacterial chaperone GroE in these processes.     

A Hamiltonian Replica Exchange Molecular Dynamics (MD) Method for the Study of Folding,Based on the Analysis of the Stabilization Determinants of Proteins

Herein, we present a novel Hamiltonian replica exchange protocol for classical molecular dynamics simulations of protein folding/unfolding. The scheme starts from the analysis of the energy-networks responsible for the stabilization of the folded conformation, by means of the energy-decomposition approach. In this framework, the compact energetic map of the native state is generated by a preliminary short molecular dynamics (MD) simulation of the protein in explicit solvent. This map is simplified by means of an eigenvalue decomposition. The highest components of the eigenvector associated with the lowest eigenvalue indicate which sites, named “hot spots”, are likely to be responsible for the stability and correct folding of the protein. In the Hamiltonian replica exchange protocol, we use modified force-field parameters to treat the interparticle non-bonded potentials of the hot spots within the protein and between protein and solvent atoms, leaving unperturbed those relative to all other residues, as well as solvent-solvent interactions. We show that it is possible to reversibly simulate the folding/unfolding behavior of two test proteins, namely Villin HeadPiece HP35 (35 residues) and Protein A (62 residues), using a limited number of replicas. We next discuss possible implications for the study of folding mechanisms via all atom simulations.     

Is Protein Folding a Thermodynamically Unfavorable,Active, Energy-Dependent Process?

The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.     

Amyloid assemblies: protein legos at a crossroads in bottom-up synthetic biology

One of the major objectives that bottom-up synthetic biology shares with chemical biology is to engineer extant biological molecules to implement novel functionalities in living systems. Proteins, due to their astonishing structural and functional versatility and to their central roles in the biology of cells, should be cornerstones of synthetic biology. In particular, protein amyloid cross-β assemblies constitute one of the most stable, conceptually simple and universal macromolecular architectures ever found in Nature and thus have enormous potential to be explored. This article focuses on the concepts behind the use of the amyloid cross-β-structural framework as a synthetic biology part, underlining recent basic findings and ideas. The pros and the cons associated with the polymorphism and the cellular toxicity of protein amyloids are also discussed, keeping in mind the possible suitability of these protein assemblies for scaffolding novel orthogonal macromolecular devices in vivo.     

Misfolding and Amyloid Aggregation of Apomyoglobin

Apomyoglobin is an excellent example of a monomeric all α-helical globular protein whose folding pathway has been extensively studied and well characterized. Structural perturbation induced by denaturants or high temperature as well as amino acid substitution have been described to induce misfolding and, in some cases, aggregation. In this article, we review the molecular mechanism of the aggregation process through which a misfolded form of a mutated apomyoglobin aggregates at physiological pH and room temperature forming an amyloid fibril. The results are compared with data showing that either amyloid or aggregate formation occurs under particular denaturing conditions or upon cleavage of the residues corresponding to the C-terminal helix of apomyoglobin. The results are discussed in terms of the sequence regions that are more important than others in determining the amyloid aggregation process.