Mapping the transition state and pathway of protein folding by protein engineering

In the transition state for unfolding of barnase, the hydrophobic core between the major alpha-helix and beta-sheet is somewhat weakened, the C terminus of the major helix is largely intact but its N terminus is exposed and a major loop has been invaded by solvent.     

蛋白质折叠过程模型

蛋白质折叠过程模型研究一直是蛋白质折叠研究领域的热点课题．就这个问题,提出描述蛋白质折叠过程的拟蛇模型．并且提出一个新的概念,那就是所有蛋白质空间结构都可以通过2种类型函数构造出来,此外,还从理论方面来证明该模型是可行和正确的：通过与其他蛋白质折叠过程模型的对比实验,结果表明,拟蛇模型所构造的空间结构能量值最小、相似度最好．进而说明拟蛇模型在描述蛋白质折叠过程方面具有明显优势,开辟了研究蛋白质的一种新的途径．     

A surprising simplicity to protein folding

The polypeptide chains that make up proteins have thousands of atoms and hence millions of possible inter-atomic interactions. It might be supposed that the resulting complexity would make prediction of protein structure and protein-folding mechanisms nearly impossible. But the fundamental physics underlying folding may be much simpler than this complexity would lead us to expect folding rates and mechanisms appear to be largely determined by the topology of the native (folded) state, and new methods have shown great promise in predicting protein-folding mechanisms and the three-dimensional structures of proteins.     

A peptide model of a protein folding intermediate

It is difficult to determine the structures of protein folding intermediates because folding is a highly cooperative process. A disulphide-bonded peptide pair, designed to mimic the first crucial intermediate in the folding of bovine pancreatic trypsin inhibitor, contains secondary and tertiary structure similar to that found in the native protein. Peptide models like this circumvent the problem of cooperativity and permit characterization of structures of folding intermediates.     

从高分子构象与动力学到蛋白质折叠

针对作用在聚合物刷上的键拉力研究表明作用在接枝基面上的力随着聚合物刷接枝密度的增大反而减小,然而尾端单体上的拉伸张力并没有消失.高分子的构象和动力学转变决定了其物性和多种多样的应用,而生物大分子蛋白质作为由二十种不同属性的氨基酸构成的序列,更是具有由其序列所决定的特别的三维自然结构.本文就聚合物刷、聚合物纳米复合材料、聚合物网络等几种高分子体系的构象与动力学过程,及蛋白质构象和其折叠与去折叠的动力学过程做了介绍.特别是蛋白质的折叠与去折叠速率在单分子操纵实验中受到拉力的调控,通过测量这种拉力依赖的动力学过程、蛋白质的自由能曲面和折叠去折叠路径可以得到系统全面的研究.本文以肌肉蛋白titin的免疫球蛋白结构域I27为例对蛋白质折叠研究进行了阐述.     

一种基于双传输线的纳秒脉冲源的研制

采用双传输线发生纳秒级方波脉冲,设计了一种用来模拟核电磁脉冲在电路中激励的干扰信号的纳秒脉冲信号源,进行抗EMP试验。脉冲源由直流高压源、触发控制电路和脉冲形成电路三部分组成。试验中脉冲测量系统设计应注意阻抗匹配,电缆影响,抗干扰等问题。在负载不匹配情况下工作时信号具有较大波动且传送效率降低;负载匹配时,优化后的系统所获得的方波信号前沿1.4ns,脉冲宽度为50.6ns。     

Successive action of DnaK, DnaJ and GroEL along the pathway of chaperone-mediated protein folding.

The main stress proteins of Escherichia coli function in an ordered protein-folding reaction. DnaK (heat-shock protein 70) recognizes the folding polypeptide as an extended chain and cooperates with DnaJ in stabilizing an intermediate conformational state lacking ordered tertiary structure. Dependent on GrpE and ATP hydrolysis, the protein is then transferred to GroEL (heat-shock protein 60) which acts catalytically in the production of the native state. This sequential mechanism of chaperone action may represent an important pathway for the folding of newly synthesized polypeptides.     

Solution structure of a protein denatured state and folding intermediate

The most controversial area in protein folding concerns its earliest stages. Questions such as whether there are genuine folding intermediates, and whether the events at the earliest stages are just rearrangements of the denatured state or progress from populated transition states, remain unresolved. The problem is that there is a lack of experimental high-resolution structural information about early folding intermediates and denatured states under conditions that favour folding because competent states spontaneously fold rapidly. Here we have solved directly the solution structure of a true denatured state by nuclear magnetic resonance under conditions that would normally favour folding, and directly studied its equilibrium and kinetic behaviour. We engineered a mutant of Drosophila melanogaster Engrailed homeodomain that folds and unfolds reversibly just by changing ionic strength. At high ionic strength, the mutant L16A is an ultra-fast folding native protein, just like the wild-type protein; however, at physiological ionic strength it is denatured. The denatured state is a well-ordered folding intermediate, poised to fold by docking helices and breaking some non-native interactions. It unfolds relatively progressively with increasingly denaturing conditions, and so superficially resembles a denatured state with properties that vary with conditions. Such ill-defined unfolding is a common feature of early folding intermediate states and accounts for why there are so many controversies about intermediates versus compact denatured states in protein folding.     

Computer simulation of protein folding.

A new and very simple representation of protein conformations has been used together with energy minimisation and thermalisation to simulate protein folding. Under certain conditions, the method succeeds in "renaturing" bovine pancreatic trypsin inhibitor from an open-chain conformation into a folded conformation close to that of the native molecule.     

Catalysis of protein folding by prolyl isomerase

Rates of protein folding reactions vary considerably. Some denatured proteins regain the native conformation within milliseconds or seconds, whereas others refold very slowly in the time range of minutes or hours. Varying folding rates are observed not only for different proteins, but can also be detected for single polypeptide species. This originates from the co-existence of fast- and slow-folding forms of the unfolded protein, which regain the native state with different rates. The proline hypothesis provides a plausible explanation for this heterogeneity. It assumes that the slow-folding molecules possess non-native isomers of peptide bonds between proline and another residue, and that crucial steps in the refolding of the slow-folding molecules are limited in rate by the slow reisomerization of such incorrect proline peptide bonds. Recently the enzyme peptidyl-prolyl cis-trans isomerase (PPIase) was discovered and purified from pig kidney. It catalyses efficiently the cis in equilibrium trans isomerization of proline imidic peptide bonds in oligopeptides. Here we show that it also catalyses slow steps in the refolding of a number of proteins of which fast- and slow-folding species have been observed and where it was suggested that proline isomerization was involved in slow refolding. The efficiency of catalysis depends on the accessibility for the isomerase of the particular proline peptide bonds in the refolding protein chain.     

Atom-by-atom analysis of global downhill protein folding

Protein folding is an inherently complex process involving coordination of the intricate networks of weak interactions that stabilize native three-dimensional structures. In the conventional paradigm, simple protein structures are assumed to fold in an all-or-none process that is inaccessible to experiment. Existing experimental methods therefore probe folding mechanisms indirectly. A widely used approach interprets changes in protein stability and/or folding kinetics, induced by engineered mutations, in terms of the structure of the native protein. In addition to limitations in connecting energetics with structure, mutational methods have significant experimental uncertainties and are unable to map complex networks of interactions. In contrast, analytical theory predicts small barriers to folding and the possibility of downhill folding. These theoretical predictions have been confirmed experimentally in recent years, including the observation of global downhill folding. However, a key remaining question is whether downhill folding can indeed lead to the high-resolution analysis of protein folding processes. Here we show, with the use of nuclear magnetic resonance (NMR), that the downhill protein BBL from Escherichia coli unfolds atom by atom starting from a defined three-dimensional structure. Thermal unfolding data on 158 backbone and side-chain protons out of a total of 204 provide a detailed view of the structural events during folding. This view confirms the statistical nature of folding, and exposes the interplay between hydrogen bonding, hydrophobic forces, backbone conformation and side-chain entropy. From the data we also obtain a map of the interaction network in this protein, which reveals the source of folding cooperativity. Our approach can be extended to other proteins with marginal barriers (less than 3RT), providing a new tool for the study of protein folding.     

Structural biology: analysis of 'downhill' protein folding

There is controversy as to whether homologues from the peripheral subunit binding domain family of small proteins fold 'downhill' (that is, non-cooperatively, in the absence of free-energy barriers between conformations) and whether they modulate their size for biological function. Sadqi et al. claim that Naf-BBL--a naphthylalanine-labelled, truncated version of this domain--folds in this way, on the grounds that they recorded a wide spread of melting temperatures of individual atoms measured by proton nuclear magnetic resonance (NMR) during their thermal denaturation. But their data are not of adequate quality to distinguish, within experimental error, between downhill folding and folding with a cooperative transition. Accordingly, their results offer no compelling evidence that Naf-BBL folds downhill, particularly as non-truncated, unmodified peripheral subunit binding domains seem to fold cooperatively.     

蛋白质构象与折叠行为的研究

蛋白质结构预测与蛋白质折叠是生命科学研究的核心问题之一,也是后基因时代推动生物学朝着定量化发展的重要方向之一,它是分子生物学中心法则还没有解决的一个重大生物学问题.简单介绍了蛋白质分子的结构特点,讨论了蛋白质分子构象研究的重点,即蛋白质结构预测与蛋白质折叠.重点介绍了拥挤环境对蛋白质构象的影响和蛋白质分子的力学性质,这是蛋白质分子构象研究的深入.这些介绍可以帮助我们更清楚地认识蛋白质分子.     

蛋白质微秒级折叠过程的快速模拟

使用ff12SB力场和广义玻恩(GB Neck2)隐性水模型在GTX670 GPU上对4个蛋白质CLN025 (2ZEI)、MHA6(2I9M)、Trp Cage (1L2Y)、Villin (3TRW)的微秒级折叠过程进行了分子动力学模拟,2ZEI的折叠时间和均方根偏差为5.94 μs和0.897 ,2I9M的折叠时间和均方根偏差为0.191 μs和1.142 ,Villin的折叠时间和均方根偏差为4.23 μs和1.37 ,Trp Cage的折叠时间和均方根偏差为2.48 μs和0.63 。结果表明,蛋白质折叠模拟已经能够通过GPU计算在桌面计算机上实现。     

Three key residues form a critical contact network in a protein folding transition state

Determining how a protein folds is a central problem in structural biology. The rate of folding of many proteins is determined by the transition state, so that a knowledge of its structure is essential for understanding the protein folding reaction. Here we use mutation measurements--which determine the role of individual residues in stabilizing the transition state--as restraints in a Monte Carlo sampling procedure to determine the ensemble of structures that make up the transition state. We apply this approach to the experimental data for the 98-residue protein acylphosphatase, and obtain a transition-state ensemble with the native-state topology and an average root-mean-square deviation of 6 A from the native structure. Although about 20 residues with small positional fluctuations form the structural core of this transition state, the native-like contact network of only three of these residues is sufficient to determine the overall fold of the protein. This result reveals how a nucleation mechanism involving a small number of key residues can lead to folding of a polypeptide chain to its unique native-state structure.     

Respective roles of short-and long-range interactions in protein folding

A new method was presented to discuss the respective roles of short- and long-range interactions in protein folding. It‘s based on an off-lattice model, which is also being called as toy model. Simulated annealing algorithm was used to search its native conformation. When it is applied to analysis proteins lagt and laho, we find that helical segment catmot fold into native conformation without the influence of long-range interactions. That‘s to say that long-range interactions are the main determinants in protein folding.     

完备黎曼流形的几何性质

利用Ｊａｃｏｂｉ场，Ｒａｕｃｈ比较定理，核心等概念和定理讨论了完备黎曼流形的若干几何性质。     

Chaperonin-mediated protein folding at the surface of groEL through a 'molten globule'-like intermediate.

Folding of two monomeric enzymes mediated by groE has been reconstituted in vitro. The groEL protein stabilizes the polypeptides in a conformation resembling the 'molten globule' state. Mg-ATP and groES then promote the acquisition of ordered tertiary structure at the surface of groEL. Folding requires the hydrolysis of about 100 ATP molecules per protein monomer. This active process of surface-mediated chain folding might represent a general mechanism for the formation of protein structure in vivo.     

关于可测集用疏朗完备集逼近问题

勒贝格可测集和疏朗完备集是两类重要集合,是实变函数中的重要内容.而康托尔集又是一种特殊的疏朗完备集,先从直线上的康托尔集谈起,说明了它与勒贝格可测集之间的几个关系,然后将有关结论推广到高维空间里的一般疏朗完备集的情形,讨论了可测集用疏朗完备集来逼近的问题.     

Transformation from temporal to rate coding in a somatosensory thalamocortical pathway

The anatomical connections from the whiskers to the rodent somatosensory (barrel) cortex form two parallel (lemniscal and paralemniscal) pathways. It is unclear whether the paralemniscal pathway is directly involved in tactile processing, because paralemniscal neuronal responses show poor spatial resolution, labile latencies and strong dependence on cortical feedback. Here we show that the paralemniscal system can transform temporally encoded vibrissal information into a rate code. We recorded the representations of the frequency of whisker movement along the two pathways in anaesthetized rats. In response to varying stimulus frequencies, the lemniscal neurons exhibited amplitude modulations and constant latencies. In contrast, paralemniscal neurons in both thalamus and cortex coded the input frequency as changes in latency. Because the onset latencies increased and the offset latencies remained constant, the latency increments were translated into a rate code: increasing onset latencies led to lower spike counts. A thalamocortical loop that includes cortical oscillations and thalamic gating can account for these results. Thus, variable latencies and effective cortical feedback in the paralemniscal system can serve the processing of temporal sensory cues, such as those that encode object location during whisking. In contrast, fixed time locking in the lemniscal system is crucial for reliable spatial processing.