结构水分子对结合自由能贡献的影响

结晶水分子存在于大多数蛋白质-配体复合物中,研究其对维持复合物的结构及在蛋白质-配体的结合过程中所发挥的作用有重要的意义。先前的分子对接、药物设计等均未考虑水分子的参与,近几年考虑到水分子后获得了更加精确的结果,表明结晶水分子在理论研究上的重要性。本文引用文献39篇,以HIV-1PR与抑制剂形成的复合物为例,综述了结合部位的结晶水分子在维持复合物结构及增强蛋白质-配体的亲和力等方面所起的作用。     

小分子物质与蛋白质相互作用研究方法的现状与进展

小分子与蛋白质相互作用的研究是化学生物学的重要研究内容.蛋白质能与许多内源性和外源性小分子物质结合形成超分子复合物.通过实验方法可以获得蛋白质与小分子配体作用的结合常数、结合位点数、结合位置、作用力类型以及在客体小分子作用下蛋白质结构与功能的变化等信息.简述紫外可见光谱、荧光光谱法、傅立叶变换红外光谱和分子模拟法及其他分析方法在小分子与蛋白质相互作用方面的应用和研究进展.     

Ⅱ型抗癌晶体蛋白的芳香族氨基酸及其与抗肝癌活性间的关系

利用氨基酸序列比对,蛋白质间相互作用位点预测和蛋白质与蛋白质对接,研究Ⅱ型抗癌晶体蛋白的氨基酸组成与其抗肝癌活性之间关系.结果表明:Ⅱ型抗癌晶体蛋白分子上位点49,51,52,55～60,194和205～212的氨基酸残基,特别是芳香族氨基酸在配体和受体蛋白质间的相互作用中起着重要作用;在Hex的蛋白质与蛋白质对接中,配体P11和P32与受体甘油醛-3-磷酸脱氢酶(GAPDH)的结合能量最低,表明P11和P32更容易与GAPDH结合.     

局部碱基对梯阶参量对蛋白质折叠速率的影响

相关研究表明mRNA序列中GC含量、回文密度和二级结构对蛋白质折叠速率都有重要影响,为了研究mRNA三级结构是否对蛋白质折叠速率也存在重要影响,收集了具有实验折叠速率的蛋白质作为研究对象,对其中的每一个蛋白质,计算其相应mRNA三级结构中各种局部碱基对梯阶参量值,并分析了这些参量值与相应蛋白质折叠速率的相关性.将蛋白质...     

蛋白质力学及其力-化关系研究

基于分子生物力学方法详细介绍了蛋白质结构功能域的力学理论分析。首先,从力学、物理学和医学角度阐述了蛋白质中铰运动、蛋白质功能域的铺展变形和受体-配体的接合,最后详细讨论了蛋白质在机械力作用下发生的运动和变形与生物学及生物化学之间相耦合的基本原理,旨在探索力学和生物化学之间的联系及其生理学意义。     

基于蛋白质药效团匹配的化合物功能预测

采用了基于蛋白质药效团匹配的化合物评价策略.以配体分子为提问结构对相应数据库进行反向筛选,根据筛选结果可以得到提问分子在人体内可能的作用受体,并以此为依据进行分子结构改造,以加强配体分子的结合专一性.选取环氧合酶2的专一性抑制剂Rofecoxib按照药效团匹配方法进行反向筛选评价,结果与实验事实吻合,并且提出了一个Rofecoxib的潜在靶标.此方法为未知化合物的功能预测和"老药新用"提供了一种新方法、新思路.     

基于序列剖面和可及表面积的蛋白质相互作用位点的预测

蛋白质相互作用位点的预测对于突变设计和蛋白质相互作用网络的重构都是至关重要的.由于实验确定的蛋白质复合物和蛋白质配体复合物的结构依然相当少,预测蛋白质相互作用位点的计算方法就显得十分重要.该文提出了一种以支持向量机为分类器,以邻近残基的序列剖面和可及表面积为输入数据来预测蛋白质相互作用位点的方法.计算结果显示,界面残基和非界面残基被识别的准确率为75.12%,假阳性率为28.04%.与输入数据仅有序列剖面的方法相比,界面残基和非界面残基被识别的准确率提高了4.34%,假阳性率降低了4.63%.     

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.     

金刚乙胺邻香草醛Schiff碱铟配合物的合成与表征

利用四水合三氯化铟与金刚乙胺缩邻香草醛Schiff碱(即配体L)进行反应,合成了新的配合物.用核磁共振、红外光谱、元素分析及热重分析等测试手段,对新的配合物进行了结构表征.结果表明,配合物的组成为InCl3L.C2H5OH,即每个配合物分子由1个三价In离子、1个配体L、3个氯离子,以及1个乙醇分子以类似结晶水的形式共同组成.配体中酚羟基上的H原子与N原子相吸形成了分子内氢键,并以氢键连接构成了一个新六元环.由配体形成配合物时,配体上原来成键模式完全保留了下来.配体分子内亚胺基中的氮未参与配位,而配体上酚羟基的氧及甲氧基的氧同时与中心原子In配位,形成双齿螯合配位构型.配合物中In原子为五配位的.     

FT-IR在研究蛋白质二级结构中的应用

目的 研究蛋白质的二级结构.方法 介绍蛋白质二级结构定量分析方法,综述FT-IR在蛋白质二级结构研究中的应用进展情况,并对其应用前景进行了展望.结果 FT-IR分析技术是一种高效、快速研究蛋白质结构的现代分析技术.结论 为了获得更精确的信息,须将FT-IR技术与生物样品的处理与实验设计相结合.     

Distal residues in the oxygen binding site of haemoglobin studied by protein engineering

The geometries of the Fe-O2 and Fe-CO bonds in myoglobin and haemoglobin differ significantly from those in free porphyrin model compounds. It has been suggested that steric hindrance by Val-E11 and His-E7 and a hydrogen bond between His-E7 and oxygen affect the geometry and electronic state of the Fe-ligand bond, and that these interactions may be important in controlling oxygen affinity. We have produced mutant haemoglobins in E. coli having Val(67 beta)E11 replaced by Ala, Met, Leu or Ile and His(58 beta)E7 by Gln, Val or Gly. We have studied the effect of these mutations on the equilibrium and kinetics of ligand binding. The conformation of the new side chains and their effect on the protein structure have been examined by X-ray crystallography, and the vibrational properties of the Fe-CO bond observed by resonance Raman spectroscopy. We found that the steric hindrance of ligand binding by the E11 residue and the polarity of the E7 residue in the beta subunit are critical for fine-tuning ligand affinity.     

Grafting of protein-protein binding sites

A strategy for grafting protein-protein binding sites is described. Firstly, key interaction residues at the interface of ligand protein to be grafted are identified and suitable positions in scaffold protein for grafting these key residues are sought. Secondly, the scaffold proteins are superposed onto the ligand protein based on the corresponding C_α and C_β atoms. The complementarity between the scaffold protein and the receptor protein is evaluated and only matches with high score are accepted. The relative position between scaffold and receptor proteins is adjusted so that the interface has a reasonable packing density. Then the scaffold protein is mutated to corresponding residues in ligand protein at each candidate position. And the residues having bad steric contacts with the receptor proteins, or buried charged residues not involved in the formation of any salt bridge are mutated. Finally, the mutated scaffold protein in complex with receptor protein is co-minimized by Charmm. In addition, we deduce a scoring function to evaluate the affinity between mutated scaffold protein and receptor protein by statistical analysis of rigid binding data sets.     

The molten globule protein conformation probed by disulphide bonds

The molten globule is a compact protein conformation that has a secondary structure content like that of the native protein, but poorly defined tertiary structure. It is a stable state for a few proteins under particular conditions and could be a ubiquitous kinetic intermediate in protein folding. The extent to which native interactions, above the level of the secondary structure, are preserved in this conformation is not so far known. Here we report that alpha-lactalbumin can adopt a molten globule conformation when one of its four disulphide bonds is reduced. In this state, the three other disulphide bonds rearrange spontaneously, at the same rate as when the protein is fully unfolded, to a number of different disulphide bond isomers that tend to maintain the molten globule conformation. That the molten globule state is compatible with a variety of disulphide bond pairings suggests that it is unlikely to be stabilized by many specific tertiary interactions.     

基于分子对接探究熊果酸衍生物H21对引起炎症的关键蛋白的作用

利用分子对接方法,探究 H21 对分泌炎症因子的关键蛋白的影响. 从引起炎症的经典通路中选取关键靶蛋白,通过Glide分子对接,将 H21 和原配体、靶蛋白对接. 通过二者对接得到分值,筛选与 H21 结合较好的靶蛋白及关键氨基酸,并分析其二者的相互作用. 结果显示: H21 与Toll-like通路中关键蛋白IRAK1蛋白结合较好,Glide-gscore为-9.873, 优于原配体, H21 与IRAK1结合的关键氨基酸为Ile218;理论数据表明:抗炎药物 H21 可能作用于IRAK1蛋白,通过影响IRAK1蛋白的表达,从而发挥抗炎作用,为揭示 H21 的抗炎机制和作用靶点提供了理论依据.     

Sequence of protein disulphide isomerase and implications of its relationship to thioredoxin

The formation of disulphide bonds is essential to the structure and function of proteins. These bonds rapidly form either cotranslationally or immediately post-translationally in the lumen of the endoplasmic reticulum. Native disulphide pairing for such proteins has been achieved in vitro; however, the rates of reassembly are slow and the conditions non-physiological. To account for these observations, Anfinsen et al. proposed that a 'disulphide interchange protein' was the in vivo catalyst of disulphide bond rearrangement. Other groups discovered an activity with similar characteristics that catalysed the reductive cleavage of insulin and may be associated with insulin degradation, although this result has been disputed. The enzyme involved, protein disulphide isomerase (PDI; EC 5.3.4.1), may be the in vivo catalyst of disulphide bond formation. Here we describe the sequence of cloned rat liver PDI complementary DNA which predicts a protein with two distinct regions homologous with Escherichia coli thioredoxin, a known cofactor in oxidation-reduction reactions. Each of these regions contains the presumed active site sequence Trp-Cys-Gly-His-Cys-Lys, suggesting that PDI, similar in action to thioredoxin, catalyses disulphide bond interchange via an internal disulphide-sulphydryl interchange. The cDNA predicts a signal peptide consistent with the view that PDI is a luminal endoplasmic reticulum protein. PDI messenger RNA, although ubiquitous, is more highly concentrated in secretory cells.     

Progress in measuring biophysical properties of membrane proteins with AFM single-molecule force spectroscopy

Membrane proteins are crucial in cell physiological activities and are the targets for most drugs.Thus,investigating the behaviors of membrane proteins not only provide deeper insights into cell function,but also help disease treatment and drug development.Atomic force microscopy is a unique tool for investigating the structure of membrane proteins.It can both image the morphology of single native membrane proteins with high resolution and,via single-molecule force spectroscopy(SMFS),directly measure their biophysical properties during molecular physiological activities such as ligand binding and protein unfolding.In the context of molecular biomechanics,SMFS has been successfully used to understand the structure and function of membrane proteins,complementing the static three-dimensional structures of proteins obtained by X-ray crystallography.Here,based on the authors’antigen-antibody binding force measurements in clinical tumor cells,the principle and method of SMFS is discussed,the progress in using SMFS to characterize membrane proteins is summarized,and challenges for SMFS are presented.     

麻疯树核糖体失活蛋白Curcin和Curcin C与腺苷及腺嘌呤的互作方式分析

麻疯树核糖体失活蛋白Curcin和Curcin C均具N-糖苷酶活性，然而两者的体外翻译抑制能力却具有明显差异，这暗示着两者的N-糖苷酶活性也存在差异.为了探究造成这一差异的结构基础，本研究使用trRosetta对两种蛋白进行了三级结构的预测，通过PROCHECK和Qmean对预测得到的三级结构模型进行了质量评估，利用Chem3D对小分子配体腺嘌呤和腺苷进行了结构优化，借助UCSF Chimera对Curcin及Curcin C活性位点的氨基酸组成进行了预测.最终使用分子对接软件AutoDock将预测得到的模型与小分子腺嘌呤及腺苷进行分子对接.对接结果显示，两种蛋白与腺嘌呤的相互作用模式具有较高的相似性，但Curcin的关键氨基酸Arg并未参与到与配体的相互作用.此外Curcin C与腺嘌呤和腺苷之间的结合能都低于Curcin,且其和腺苷与腺嘌呤之间结合能的差值也要高于Curcin.这一结果暗示着Curcin和Curcin C之间的活性差异与其活性位点处的结构特征有关，Curcin C中的关键氨基酸Arg与腺嘌呤及腺苷的结合位点更为靠近，从而导致Curcin C与底物之间的结合能更低，...     

Crystal structure of squid rhodopsin

Invertebrate phototransduction uses an inositol-1,4,5-trisphosphate signalling cascade in which photoactivated rhodopsin stimulates a G(q)-type G protein, that is, a class of G protein that stimulates membrane-bound phospholipase Cbeta. The same cascade is used by many G-protein-coupled receptors, indicating that invertebrate rhodopsin is a prototypical member. Here we report the crystal structure of squid (Todarodes pacificus) rhodopsin at 2.5 A resolution. Among seven transmembrane alpha-helices, helices V and VI extend into the cytoplasmic medium and, together with two cytoplasmic helices, they form a rigid protrusion from the membrane surface. This peculiar structure, which is not seen in bovine rhodopsin, seems to be crucial for the recognition of G(q)-type G proteins. The retinal Schiff base forms a hydrogen bond to Asn 87 or Tyr 111; it is far from the putative counterion Glu 180. In the crystal, a tight association is formed between the amino-terminal polypeptides of neighbouring monomers; this intermembrane dimerization may be responsible for the organization of hexagonally packed microvillar membranes in the photoreceptor rhabdom.     

Structure of a C-type mannose-binding protein complexed with an oligosaccharide.

C-type (Ca(2+)-dependent) animal lectins such as mannose-binding proteins mediate many cell-surface carbohydrate-recognition events. The crystal structure at 1.7 A resolution of the carbohydrate-recognition domain of rat mannose-binding protein complexed with an oligomannose asparaginyl-oligosaccharide reveals that Ca2+ forms coordination bonds with the carbohydrate ligand. Carbohydrate specificity is determined by a network of coordination and hydrogen bonds that stabilizes the ternary complex of protein, Ca2+ and sugar. Two branches of the oligosaccharide crosslink neighbouring carbohydrate-recognition domains in the crystal, enabling multivalent binding to a single oligosaccharide chain to be visualized directly.     

Stabilization of charges on isolated ionic groups sequestered in proteins by polarized peptide units

Electrostatic interactions are of considerable importance in protein structure and function, and in a variety of cellular and biochemical processes. Here we report three similar findings from highly refined atomic structures of periplasmic binding proteins. Hydrogen bonds, acting primarily through backbone peptide units, are mainly responsible for the involvement of the positively charged arginine 151 residue in the ligand site of the arabinose-binding protein, for the association between teh sulphate-binding protein and the completely buried sulphate dianion, and for the formation of the complex of the leucine/isoleucine/valine-binding protein with the leucine zwitterion. We propose a general mechanism in which the isolated charges on the various buried, desolvated ionic groups are stabilized by the polarized peptide units. This mechanism also has broad application to processes requiring binding of uncompensated ions and charged ligands and stabilization of enzyme reaction charged intermediates, as well as activation of catalytic residues.