基质金属蛋白酶

基质金属蛋白酶是一类分解细胞外基质组分的锌蛋白酶⒚它们在有机体生长发育中的细胞外基质逆转与重塑以及疾病中的病理损害起着极为重要的作用⒚基质金属蛋白酶的表达和活性在不同细胞水平受到严密调控,如细胞因子、生长因子以及激素的调节⒚基质金属蛋白酶以酶原形式分泌,随后被其它蛋白酶如胞浆素或非蛋白酶类化学物质如有机汞所激活⒚所有基质金属蛋白酶都受到天然抑制剂 金属蛋白酶组织抑制剂所抑制⒚两者的不平衡导致许多疾病的发生,如肿瘤侵入及转移⒚合成基质金属蛋白酶组织抑制剂所抑制,如 Ｍ ａｒｉｍ ａｓｔａｔ 能控制肿瘤转移的发生及进一步扩散⒚本文将对基质金属蛋白酶的特征、分子区域结构、底物特性、激活机制、调控方式等方面进行最新概述⒚     

Kazal型蛋白酶抑制剂结构与功能研究进展

蛋白酶抑制剂广泛存在于生物体内,在许多生命活动过程中发挥必不可少的作用,特别是对蛋白酶活性进行精确调控。其中Kazal型蛋白酶抑制剂是最重要的、研究最为广泛的酶抑制剂之一,该类抑制剂一般由一个或几个结构域组成,每一个结构域具有保守的序列和分子构象,同时发现该类抑制剂与蛋白酶作用的结合部位高度易变,它们大多数暴露于与溶剂接触的环上,其中P1部位是抑制作用的关键部位,抑制剂的专一性由P1部位氨基酸残基的性质决定,其它残基取代结合部位残基对抑制剂-酶的结合常数有显著的影响。Laskowski算法可直接从Kazal型丝氨酸蛋白酶抑制剂的序列推测其与6种丝氨酸蛋白酶之间的抑制常数(Ki)。目前在生物体内发现大量的Kazal型蛋白酶抑制剂,并证实其有重要的生物学功能。     

Kunitz 型丝氨酸蛋白酶抑制剂结构与功能研究

蛋白酶抑制剂在酶学及蛋白质的结构与功能关系研究中有重要意义,Kunitz型丝氨酸蛋白酶抑制剂是其中最重要的,也是研究最广泛的蛋白酶抑制剂之一．该类蛋白酶抑制剂三维结构高度保守：由一个明显的疏水核心、三对高度保守的二硫键桥、三链β-折叠和一个N端3 10螺旋及一个C端α-螺旋组成．3对二硫键对分子空间结构的稳定起着非常重要的作用．这一类型抑制剂有5个主要的活性位点：P1、P1’、P3、P3’、P4,它们都位于一个溶剂暴露的环上．P1位点是抑制作用的关键活性位点,抑制剂的专一性由P1位点氨基酸残基的性质决定;P1’位点氨基酸残基的侧链大小对抑制剂．酶的结合常数有很大影响,用大的侧链残基取代会导致结合常数降低;P4位点残基被取代经常产生负效应,会导致活性区域环的构象发生很大改变,从而影响酶与抑制剂的结合．     

Kunitz型丝氨酸蛋白酶抑制剂研究进展

Kunitz型丝氨酸蛋白酶抑制剂是一类普遍存在的蛋白酶抑制剂,在体内各项生命活动中扮演着重要角色。这类抑制剂结构稳定且富有特色,通常具有一个或几个串联存在的Kunitz结构域,能够以类似底物的方式与丝氨酸蛋白酶结合,从而抑制酶的活性。在功能方面,Kunitz型丝氨酸蛋白酶抑制剂参与凝血和纤维蛋白溶解、肿瘤免疫、炎症调节以及抵抗细菌、真菌感染等过程。文中就Kunitz型丝氨酸蛋白酶抑制剂研究进展作一综述,为新型Kunitz型丝氨酸蛋白酶抑制剂的开发提供研究思路。     

基质金属蛋白酶及其组织抑制剂研究进展

基质金属蛋白酶家族是细胞外基质降解过程中的重要酶类,组织金属蛋白酶抑制剂是基质金属蛋白酶的天然抑制物。研究证实,细胞外基质中基质金属蛋白酶及其组织抑制剂的失衡与多种病理机制有关,尤其与肿瘤的侵袭和转移密切相关。本就基质金属蛋白酶及其组织抑制剂的性质、结构以及功能进行了综述。     

应用定点突变与分子模建方法研究蛋白酶抑制剂eglin C突变体对蛋白酶furin和kexin的抑制活力

蛋白质前体加工酶参与许多重要蛋白质闪体的加工成熟过程,哺乳动物来源的furin和酵母中的kexin是该家族的重要成员。首先人工合成了编码枯草杆菌蛋白酶抑制剂eglin C的基因片段,组装后在大肠杆菌中得到表达。以定点突变方法在野生型eglin C抑制活性中心的P1、P2和P4位引入碱性氨基酸残基可以将其改造为很强的furin抑制剂（Ki约10^-9mol/L）,和kexin抑制剂（Ki约10^-11mol/L）。同时根据枯草杆菌蛋白酶和eglin C复合物的晶体结构,计算机同源模建了前体加工酶与eglin C突变体结构之间的相互作用,并结合实验数据得到以下结果：（1）P1位引入的碱性残基是该抑制剂活力的前提;（2）P4位碱性残基的引入可以极大地提高抑制剂活力约两个数量级;（3）P2 的碱性残基将有效提高抑制剂的活力。然而同时可以破坏抑制剂本身的稳定性。（4）野生型P3位的疏水性残基参与抑制剂活性环附近疏水核心的构成。     

蛋白酶抑制剂反应环区的结构研究

蛋白质分子表面环区常在蛋白质功能和行为中起重要作用.我们对一些丝氨酸蛋白酶抑制剂的反应环区和已知的限制性水解部位做了结构比较研究.研究结果表明,蛋白质抑制剂反应部位所处的环区具有独特的结构,使其能够对相应蛋白酶发挥很高的抑制作用.     

登革病毒NS3蛋白酶研究进展

登革病毒的非结构蛋白NS3是一个三功能蛋白,其N端1／3具有丝氨酸样蛋白酶活性。该蛋白酶对聚蛋白前体的切割于关重要,故该蛋白已成为研制登革类疾病治疗试剂的重要靶标。本文对NS3蛋白酶的结构,功能,辅助因子和蛋白酶抑制剂等进行了综述。     

几种蛋白酶活力测定新方法

几种蛋白酶活力测定新方法陈安和（西南师范大学生化教研室,重庆６３０７１５）关键词蛋白酶活力测定近年来,蛋白酶特别是丝氨酸蛋白酶及其抑制剂已成为研究热点。众多研究表明,蛋白酶在许多重要的生命活动过程中发挥着十分重要的作用。蛋白酶参与蛋白质的水解、消化、...     

胱蛋白酶抑制剂C与肌酐评价儿童肾小球滤过功能中的作用比较

用胱蛋白酶抑制剂C与肌酐、内生肌酐清除率评价儿童肾小球滤过功能,并将其作用进行比较,确定胱蛋白酶抑制剂C在儿童中的正常参考范围。采用颗粒增强散射免疫比浊法检测150例出生后2d～13岁正常儿童及90例1～16岁患不同程度肾脏疾病的儿童血清中胱蛋白酶抑制剂C和血肌酐的浓度,并比较胱蛋白酶抑制剂C与血肌酐的相关性。结果发现胱蛋白酶抑制剂C在出生后四个月内水平明显高于成人,但在出生5个月以后下降至接近成人参考范围。血清胱蛋白酶抑制剂浓度C与尿素清除率之间有显著相关性(P<0.01)。此外,在内生肌酐清除率CCr>80(属于正常参考范围)的肾脏疾病的患儿中有56%胱蛋白酶抑制剂C异常,说明胱蛋白酶抑制剂C比血肌酐更能够敏感地反应儿童肾小球滤过功能的损伤,建议用胱蛋白酶抑制剂C作为儿童肾脏疾病的患者肾小球滤过功能的损伤指标。     

Influence of DNA structures on the conversion of sanguinarine alkanolamine form to iminium form

Sanguinarine exhibits pH dependent structural equilibrium between iminium form (structure I) and alkanolamine form (structure II) with a pKa of 7.4 as revealed from spectrophotometric titration. The titration data show that the compound exists almost exclusively as structure I and structure II in the pH range 1 to 6 and 8.5 to 11, respectively. The interaction of structure I and structure II to several B-form natural and synthetic double and single stranded DNAs has been studied by spectrophotometric, spectrofluorimetric and circular dichroic measurements in buffers of pH 5.2 and pH 10.4 where the physicochemical properties of DNA remain in B-form structure. The results show that structure I bind strongly to all B-form DNA structures showing typical hypochromism and bathochromism of the alkaloid's absorption maximum, quenching of steady-state fluorescence intensity and perturbations in circular dichroic spectrum. The structure II does not bind to DNA, but in presence of large amount of DNA significant population of structure I is generated, which binds to DNA and forms a structure I-DNA intercalated complex. The nature and magnitude of the spectral pattern are very much dependent on the structure as well as base composition of each DNA. The generation of the structure I from structure II is significantly affected by increasing ionic strength of the medium. The conversion of structure II to structure I in presence of high concentration of DNA in solution is explained through formation of a binding equilibrium process between structure II and structure I-DNA intercalated complex.     

RNA-SSPT: RNA Secondary Structure Prediction Tools

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.     

Asymmetric stability among the transmembrane helices of lactose permease

Combining structure determinations from nuclear magnetic resonance (NMR) data and molecular dynamics simulations (MD) under the same environmental conditions revealed a startling asymmetry in the intrinsic conformational stability of secondary structure in the transmembrane domain of lactose permease (LacY). Eleven fragments, corresponding to transmembrane segments (TMs) of LacY, were synthesized, and their secondary structure in solution was determined by NMR. Eight of the TMs contained significant regions of helical structure. MD simulations, both in DMSO and in a DMPC bilayer, showed sites of local stability of helical structure in these TMs, punctuated by regions of conformational instability, in substantial agreement with the NMR data. Mapping the stable regions onto the crystal structure of LacY reveals a marked asymmetry, contrasting with the pseudosymmetry in the static structure: the secondary structure in the C-terminal half is more stable than in the N-terminal half. The relative stability of secondary structure is likely exploited in the transport mechanism of LacY. Residues supporting proton conduction are in more stable regions of secondary structure, while residues key to substrate binding are found in considerably unstable regions of secondary structure.     

Fully automated ab initio protein structure prediction using I-SITES,HMMSTR and ROSETTA

MOTIVATION: The Monte Carlo fragment insertion method for protein tertiary structure prediction (ROSETTA) of Baker and others, has been merged with the I-SITES library of sequence structure motifs and the HMMSTR model for local structure in proteins, to form a new public server for the ab initio prediction of protein structure. The server performs several tasks in addition to tertiary structure prediction, including a database search, amino acid profile generation, fragment structure prediction, and backbone angle and secondary structure prediction. Meeting reasonable service goals required improvements in the efficiency, in particular for the ROSETTA algorithm. RESULTS: The new server was used for blind predictions of 40 protein sequences as part of the CASP4 blind structure prediction experiment. The results for 31 of those predictions are presented here. 61% of the residues overall were found in topologically correct predictions, which are defined as fragments of 30 residues or more with a root-mean-square deviation in superimposed alpha carbons of less than 6A. HMMSTR 3-state secondary structure predictions were 73% correct overall. Tertiary structure predictions did not improve the accuracy of secondary structure prediction.     

The functional significance of leaf structure: a search for generalizations

The coupling between leaf structure and function is illustrated with reference to two examples, the C₄ photosynthetic pathway and leaf pubescence. A distinction is made between function and functional significance. The latter is defined as the role, significance or consequence of a structure, whereas the former is more simply the action that a structure is capable of performing. Using the two examples, four generalizations are made concerning the relationships between structure, function and functional significance: the functional significance of leaf structure is environment-dependent; the relationship between functional significance and structure is sometimes non-intuitive; functional equivalency means that there is often more than one 'solution' to the same 'constraint'; and the consequences of leaf structure can exert profound effects at levels of organization beyond those of the individual organism and may play a critical role in determining community structure and function, through interactions with other species and trophic levels. The importance of understanding the consequences in variation in leaf structure at the global scale is illustrated with reference to the issue of global climate change.     

Prediction of RNA secondary structure by free energy minimization

RNA secondary structure is often predicted from sequence by free energy minimization. Over the past two years, advances have been made in the estimation of folding free energy change, the mapping of secondary structure and the implementation of computer programs for structure prediction. The trends in computer program development are: efficient use of experimental mapping of structures to constrain structure prediction; use of statistical mechanics to improve the fidelity of structure prediction; inclusion of pseudoknots in secondary structure prediction; and use of two or more homologous sequences to find a common structure.     

Transformation of an alpha-helix peptide into a beta-hairpin induced by addition of a fragment results in creation of a coexisting state

Intrinsic rules of determining the tertiary structure of a protein have been unknown partly because physicochemical factors that contribute to stabilization of a protein structure cannot be represented as a linear combination of local interactions. To clarify the rules on the nonlinear term caused by nonlocal interaction in a protein, we tried to transform a peptide that has a fully helical structure (Target Peptide or TP) into a peptide that has a beta-hairpin structure (Designed Peptide or DP) by adding seven residues to the C terminus of TP. According to analyses of nuclear magnetic resonance measurements, while the beta-hairpin structure is stabilized in some DPs, it is evident that the helical structure observed in TP is also persistent and even extended throughout the length of the molecule. As a result, we have produced a peptide molecule that contains both the alpha-helix and beta-hairpin conformation at an almost equally populated level. The helical structures contained in these DPs were more stable than the helix in TP, suggesting that stabilizing one conformation does not result in destabilizing the other conformation. These DPs can thus be regarded as an isolated peptide version of the chameleon sequence, which has the capability of changing the secondary structure depending on the context of the surrounding environment in a protein structure. The fact that the transformation of one secondary structure caused stabilization of both the original and the induced structure would shed light on the mechanism of protein folding.     

融入植被结构因子的生态单元制图法在城市生物多样性信息采集中的应用

以前所使用的生态单元制图模型中没有涉及植被时间和空间结构因子,然而一些研究结果显示植被的时空结构对于生物多样性有着重要的影响。因此,设计一个融入植被结构因子的改良城市生态单元制图模型,并且将其应用于瑞典赫尔辛堡市的绿色空间个案研究中,以期能够获得有关生物多样性方面的信息。这个改良的制图方法基于一个生态单元分类系统,此分类系统融入了4个植被结构因子,分别是:植被覆盖的连续性因子、优势乔木种的年龄因子、横向结构因子以及竖向结构因子。公共绿色空间信息的采集借助于全彩色航空照片的分析以及实地调查,生态单元图谱的绘制基于各个层级的生态单元分类重点。通过使用原生林地指示种或林地连续性指示种(AWIS)鉴定林地的连续性以及观测不同的植被结构下动物的分布情况得出,一些含有AWIS的生态单元是长连续性的林地,并且其含有较高的或潜在高的生物多样性;同时,植被的横向和竖向结构以及树木的年龄结构影响着鸟类和哺乳动物的分布、丰富度和多样性。得出融入植被时空结构的生态单元制图法是一个重要的调查城市生物多样性的方法,图谱能够显示出各个生态单元含有生物多样性价值的信息,基于此可以对今后的城市生物多样性保护和提高提出相应的策略。