Rational modification of enzyme catalysis by engineering surface charge

Changing the surface charge of subtilisin by site-directed mutagenesis produces enzymes with significantly shifted pH-activity profiles, higher catalytic activities and altered specificities. Insight into water as a dielectric, the role of ions in electrostatic shielding and the field effects on catalysis is obtained and suggests rules for tailoring pH-activity profiles.     

Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin

Small molecules such as NO, O2, CO or H2 are important biological ligands that bind to metalloproteins to function crucially in processes such as signal transduction, respiration and catalysis. A key issue for understanding the regulation of reaction mechanisms in these systems is whether ligands gain access to the binding sites through specific channels and docking sites, or by random diffusion through the protein matrix. A model system for studying this issue is myoglobin, a simple haem protein. Myoglobin has been studied extensively by spectroscopy, crystallography, computation and theory. It serves as an aid to oxygen diffusion but also binds carbon monoxide, a byproduct of endogenous haem catabolism. Molecular dynamics simulations, random mutagenesis and flash photolysis studies indicate that ligand migration occurs through a limited number of pathways involving docking sites. Here we report the 1.4 A resolution crystal structure of a ligand-binding intermediate in carbonmonoxy myoglobin that may have far-reaching implications for understanding the dynamics of ligand binding and catalysis.     

燕麦多肽数据库及降血糖活性的虚拟筛选

为了深入研究燕麦多肽中可能发挥降血糖功能的活性多肽分子，本文首先从文献中调研了从燕麦中提取鉴定得到的多肽，构建了对应的燕麦多肽数据库，并基于DPP4蛋白对多肽数据库进行了虚拟筛选.随后，针对筛选获得的6个多肽分别进行了100 ns的分子动力学模拟.从模拟之后稳定结合的构象分析了不同多肽分子与DPP4的相互作用信息，并分别计算了不同多肽分子与DPP4的结合自由能.结果表明，从燕麦多肽数据库中筛选得到的多肽可以与DPP4蛋白稳定结合，其中2个多肽分子与DPP4的亲和力相对较强.本文得到的多肽分子可以作为后续DPP4抑制剂设计和改造的先导分子，燕麦多肽数据库也可用于研究燕麦的其他生物学功能.     

The role of protein surface charges in ion binding

Protein engineering is a means of probing the role of electrostatic interactions in protein functions; this elegant technique has been applied to the elucidation of electrostatic effects in enzyme catalysis. Here we show how the use of mutant proteins allows the determination of the contributions of individual charges to the free energy of ion binding to proteins. We have investigated the importance of three negatively charged side chains in the binding of Ca2+ to bovine calbindin D9K (ref.2): these are clustered around the calcium sites but are not directly involved as ligands. Each of these charges is found to contribute approximately 7 kJ mol-1 to the free energy of binding of two Ca2+ ions and to affect the cooperativity of Ca2+ binding. The influence of surface charges on ion binding to proteins may be more common than generally supposed and could have important consequences for protein function.     

基于氨基作为质子转移桥梁的赖氨酸分子手性转变机理

采用密度泛函理论的B3LYP方法和微扰理论的MP2方法, 考察赖氨酸分子基于氨基作为质子转移桥梁的手性转变机理以及水分子和羟基自由基对氢迁移反应的催化作用. 结果表明, 赖氨酸分子手性转变有2个通道a和b, 通道a为主反应通道, 决速步骤裸反应Gibbs自由能垒为252.6 kJ/mol, 2个水分子构成的链以及羟基自由基和水分子构成的链使通道a决速步骤的自由能垒分别降为119.5,98.5 kJ/mol. 表明水分子和羟自由基对H迁移反应有较好的催化作用, 生命体内的羟基自由基是导致左旋赖氨酸旋光异构的主要原因.     

Intrinsic motions along an enzymatic reaction trajectory

The mechanisms by which enzymes achieve extraordinary rate acceleration and specificity have long been of key interest in biochemistry. It is generally recognized that substrate binding coupled to conformational changes of the substrate-enzyme complex aligns the reactive groups in an optimal environment for efficient chemistry. Although chemical mechanisms have been elucidated for many enzymes, the question of how enzymes achieve the catalytically competent state has only recently become approachable by experiment and computation. Here we show crystallographic evidence for conformational substates along the trajectory towards the catalytically competent 'closed' state in the ligand-free form of the enzyme adenylate kinase. Molecular dynamics simulations indicate that these partially closed conformations are sampled in nanoseconds, whereas nuclear magnetic resonance and single-molecule fluorescence resonance energy transfer reveal rare sampling of a fully closed conformation occurring on the microsecond-to-millisecond timescale. Thus, the larger-scale motions in substrate-free adenylate kinase are not random, but preferentially follow the pathways that create the configuration capable of proficient chemistry. Such preferred directionality, encoded in the fold, may contribute to catalysis in many enzymes.     

Transforming binding affinities from three dimensions to two with application to cadherin clustering

Membrane-bound receptors often form large assemblies resulting from binding to soluble ligands, cell-surface molecules on other cells and extracellular matrix proteins. For example, the association of membrane proteins with proteins on different cells (trans-interactions) can drive the oligomerization of proteins on the same cell (cis-interactions). A central problem in understanding the molecular basis of such phenomena is that equilibrium constants are generally measured in three-dimensional solution and are thus difficult to relate to the two-dimensional environment of a membrane surface. Here we present a theoretical treatment that converts three-dimensional affinities to two dimensions, accounting directly for the structure and dynamics of the membrane-bound molecules. Using a multiscale simulation approach, we apply the theory to explain the formation of ordered, junction-like clusters by classical cadherin adhesion proteins. The approach features atomic-scale molecular dynamics simulations to determine interdomain flexibility, Monte Carlo simulations of multidomain motion and lattice simulations of junction formation. A finding of general relevance is that changes in interdomain motion on trans-binding have a crucial role in driving the lateral, cis-, clustering of adhesion receptors.     

杯芳烃内相中3-环丁烯砜的分解反应研究

采用分子动态模拟及量子化学方法对杯芳烃内相中3环丁烯砜的取向及分解为二氧化硫和丁二烯的反应进行了研究。结果表明,3-环丁烯砜在杯芳烃分子反应器中发生分解反应的活化能比在自由状态下反应的活化能略高,这与3-环丁烯砜在杯芳烃中的表观分解温度提高的实验现象吻合。分析分子反应器与小分子的相互作用能以及分子反应器的变形能随反应进程的变化趋势,发现活化能的变化主要源自分子反应器与小分子的相互排斥作用。     

Intrinsic dynamics of an enzyme underlies catalysis

A unique feature of chemical catalysis mediated by enzymes is that the catalytically reactive atoms are embedded within a folded protein. Although current understanding of enzyme function has been focused on the chemical reactions and static three-dimensional structures, the dynamic nature of proteins has been proposed to have a function in catalysis. The concept of conformational substates has been described; however, the challenge is to unravel the intimate linkage between protein flexibility and enzymatic function. Here we show that the intrinsic plasticity of the protein is a key characteristic of catalysis. The dynamics of the prolyl cis-trans isomerase cyclophilin A (CypA) in its substrate-free state and during catalysis were characterized with NMR relaxation experiments. The characteristic enzyme motions detected during catalysis are already present in the free enzyme with frequencies corresponding to the catalytic turnover rates. This correlation suggests that the protein motions necessary for catalysis are an intrinsic property of the enzyme and may even limit the overall turnover rate. Motion is localized not only to the active site but also to a wider dynamic network. Whereas coupled networks in proteins have been proposed previously, we experimentally measured the collective nature of motions with the use of mutant forms of CypA. We propose that the pre-existence of collective dynamics in enzymes before catalysis is a common feature of biocatalysts and that proteins have evolved under synergistic pressure between structure and dynamics.     

氮化铝分子及氯化锂分子结合能的量子蒙特卡罗研究

通过量子蒙特卡罗方法(QMC)利用不同的密度泛函轨道对氮化铝分子及氯化锂分子的结合能进行研究.采用扩散蒙特卡罗方法(DMC)得到氮化铝分子的结合能为2.993 eV,氯化锂分子的结合能为6.694 eV.与其他理论计算相比较,更接近实验得到氮化铝和氯化锂分子的结合能(2.862±0.391 eV和6.646 eV).同时,利用密度泛函理论对氮化铝分子及氯化锂分子的结合能进行研究时发现,利用密度泛函理论计算得到的结合能范围跨度很大且非常不准确.另外,在利用量子蒙特卡罗方法的计算中发现,不同类型的密度泛函轨道对结合能的计算产生一定的影响,这就需要在利用量子蒙特卡罗方法进行计算时考虑轨道的选择.     

Directed evolution of new catalytic activity using the alpha/beta-barrel scaffold

In biological systems, enzymes catalyse the efficient synthesis of complex molecules under benign conditions, but widespread industrial use of these biocatalysts depends crucially on the development of new enzymes with useful catalytic functions. The evolution of enzymes in biological systems often involves the acquisition of new catalytic or binding properties by an existing protein scaffold. Here we mimic this strategy using the most common fold in enzymes, the alpha/beta-barrel, as the scaffold. By combining an existing binding site for structural elements of phosphoribosylanthranilate with a catalytic template required for isomerase activity, we are able to evolve phosphoribosylanthranilate isomerase activity from the scaffold of indole-3-glycerol-phosphate synthase. We find that targeting the catalytic template for in vitro mutagenesis and recombination, followed by in vivo selection, results in a new phosphoribosylanthranilate isomerase that has catalytic properties similar to those of the natural enzyme, with an even higher specificity constant. Our demonstration of divergent evolution and the widespread occurrence of the alpha/beta-barrel suggest that this scaffold may be a fold of choice for the directed evolution of new biocatalysts.     

Prediction of electrostatic effects of engineering of protein charges

Accurate prediction of electrostatic effects on catalytic activity is an essential component of protein design. Site-directed mutagenesis of charged groups in subtilisin of Bacillus amyloliquefaciens has provided experimental measurements of electrostatic interactions which may be used to test such theoretical methods. The pKa of the histidine of the active site has been perturbed by +0.08 to -1.0 units by modifying one or two residues. Electrostatic effects in proteins can be modelled by the algorithm of Warwicker and Watson, which uses classical electrostatics and considers both the charge position and the shape of the molecule. Here we report that the algorithm can model several pKa shifts in subtilisin to fair accuracy.     

Proline-catalysed Mannich reactions of acetaldehyde

Small organic molecules recently emerged as a third class of broadly useful asymmetric catalysts that direct reactions to yield predominantly one chiral product, complementing enzymes and metal complexes. For instance, the amino acid proline and its derivatives are useful for the catalytic activation of carbonyl compounds via nucleophilic enamine intermediates. Several important carbon-carbon bond-forming reactions, including the Mannich reaction, have been developed using this approach, all of which are useful for making chiral, biologically relevant compounds. Remarkably, despite attempts, the simplest of all nucleophiles, acetaldehyde, could not be used in this way. Here we show that acetaldehyde is a powerful nucleophile in asymmetric, proline-catalysed Mannich reactions with N-tert-butoxycarbonyl (N-Boc)-imines, yielding beta-amino aldehydes with extremely high enantioselectivities-desirable products as drug intermediates and in the synthesis of other biologically active molecules. Although acetaldehyde has been used as a nucleophile in reactions with biological catalysts such as aldolases and thiamine-dependent enzymes, and has also been employed indirectly, its use as an inexpensive and versatile two-carbon nucleophile in asymmetric, small-molecule catalysis will find many practical applications.     

Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation

Both prokaryotic and eukaryotic organisms contain DNA bridging proteins, which can have regulatory or architectural functions. The molecular and mechanical details of such proteins are hard to obtain, in particular if they involve non-specific interactions. The bacterial nucleoid consists of hundreds of DNA loops, shaped in part by non-specific DNA bridging proteins such as histone-like nucleoid structuring protein (H-NS), leucine-responsive regulatory protein (Lrp) and SMC (structural maintenance of chromosomes) proteins. We have developed an optical tweezers instrument that can independently handle two DNA molecules, which allows the systematic investigation of protein-mediated DNA-DNA interactions. Here we use this technique to investigate the abundant non-specific nucleoid-associated protein H-NS, and show that H-NS is dynamically organized between two DNA molecules in register with their helical pitch. Our optical tweezers also allow us to carry out dynamic force spectroscopy on non-specific DNA binding proteins and thereby to determine an energy landscape for the H-NS-DNA interaction. Our results explain how the bacterial nucleoid can be effectively compacted and organized, but be dynamic in nature and accessible to DNA-tracking motor enzymes. Finally, our experimental approach is widely applicable to other DNA bridging proteins, as well as to complex DNA interactions involving multiple DNA molecules.     

Conformational entropy in molecular recognition by proteins

Molecular recognition by proteins is fundamental to almost every biological process, particularly the protein associations underlying cellular signal transduction. Understanding the basis for protein-protein interactions requires the full characterization of the thermodynamics of their association. Historically it has been virtually impossible to experimentally estimate changes in protein conformational entropy, a potentially important component of the free energy of protein association. However, nuclear magnetic resonance spectroscopy has emerged as a powerful tool for characterizing the dynamics of proteins. Here we employ changes in conformational dynamics as a proxy for corresponding changes in conformational entropy. We find that the change in internal dynamics of the protein calmodulin varies significantly on binding a variety of target domains. Surprisingly, the apparent change in the corresponding conformational entropy is linearly related to the change in the overall binding entropy. This indicates that changes in protein conformational entropy can contribute significantly to the free energy of protein-ligand association.     

多巴胺D3R蛋白同源模建及其应用

以分辨率为2.2的牛视紫红质蛋白的晶体结构为模板,采用同源模建方法,建立D3R模蛋白。对接D3R模蛋白与刺桐属配体分子,在对接的D3R蛋白的结合腔中选定一个以药物分子为质心,以半径为6的空间范围,计算此空间范围内的所有氨基酸残基与配体分子的作用能量,即残基/配体的结合能或排斥能,据此得到配体分子与受体蛋白的活性结合位点。     

细胞色素P450酶生物转化及新催化反应的最新进展

细胞色素P450酶(P450s或CYPs)是一类广泛存在于生命体中,依赖于亚铁血红素催化多种底物的单加氧酶。一方面,它涉及许多高活性天然产物生物合成的关键步骤,对其生物转化研究有助于提高活性分子的产率和活性;另一方面,其催化涉及金属元素以及辅助因子,其蛋白质改造和新催化反应的研发也不断取得新突破。本文就细胞色素P450酶这两方面的最近研究进展进行了总结与论述。     

Dissecting the catalytic triad of a serine protease

Serine proteases are present in virtually all organisms and function both inside and outside the cell; they exist as two families, the 'trypsin-like' and the 'subtilisin-like', that have independently evolved a similar catalytic device characterized by the Ser, His, Asp triad, an oxyanion binding site, and possibly other determinants that stabilize the transition state (Fig. 1). For Bacillus amyloliquefaciens subtilisin, these functional elements impart a total rate enhancement of at least 10(9) to 10(10) times the non-enzymatic hydrolysis of amide bonds. We have examined the catalytic importance and interplay between residues within the catalytic triad by individual or multiple replacement with alanine(s), using site-directed mutagenesis of the cloned B. amyloliquefaciens subtilisin gene. Alanine substitutions were chosen to minimize unfavourable steric contacts and to avoid imposing new charge interactions or hydrogen bonds from the substituted side chains. In contrast to the effect of mutations in residues involved in substrate binding, the mutations in the catalytic triad greatly reduce the turnover number and cause only minor effects on the Michaelis constant. Kinetic analyses of the multiple mutants demonstrate that the residues within the triad interact synergistically to accelerate amide bond hydrolysis by a factor of approximately 2 X 10(6).     

Modular enzymes

Although modular macromolecular devices are encountered frequently in a variety of biological situations, their occurrence in biocatalysis has not been widely appreciated. Three general classes of modular biocatalysts can be identified: enzymes in which catalysis and substrate specificity are separable, multisubstrate enzymes in which binding sites for individual substrates are modular, and multienzyme systems that can catalyse programmable metabolic pathways. In the postgenomic era, the discovery of such systems can be expected to have a significant impact on the role of enzymes in synthetic and process chemistry.     

体外定向分子进化的新策略及新应用

体外定向分子进化是发现和改造生物活性分子的重要方法,提供了一种高效的获得多样性的方法。DNA改组(DNA shuffling)是重要的体外分子进化技术,结合高通量筛选能够改造许多重要的医药、工业、环境保护等方面的商业酶。近年来,许多体外分子进化的新策略和新方法层出不穷,得到了良好的发展和应用,其中有代表性的11种是DNA家族改组(DNA family shuffling),部分基因片段改组、单链DNA家族改组(SSDNAs)、简并引物基因改组(DOGS)、基因组改组(Genome Shuffling)、瞬时模板的随机嵌合(RACHITT)、单向引物的随机重组(MURA)、自我复制(CSR)改组、易错环行扩增(error-prone RCA)、基于遗传密码随机切除(COBARDE)、核酸内切酶V(endonuclease V)替代核酸内切酶DNaseI等。