残基相互作用网络特征与木聚糖酶耐热性的关系

残基相互作用网络是体现蛋白质中残基与残基之间协同和制约关系的重要形式。残基相互作用网络的拓扑性质以及社团结构与蛋白质的功能和性质有密切的关系。本文在构建一系列耐热木聚糖酶和常温木聚糖酶的残基相互作用网络后,通过计算网络的度、聚类系数、连接强度、特征路径长度、接近中心性、介数中心性等拓扑参数来确定网络拓扑结构与木聚糖酶耐热性的关系。识别残基相互作用网络的hub点,分析hub点的亲疏水性、带电性以及各种氨基酸在hub点中所占的比例。进一步使用GA-Net算法对网络进行社团划分,并计算社团的规模、直径和密度。网络的高平均度、高连接强度、以及更短的最短路径等表明耐热木聚糖酶残基相互作用网络的结构更加紧密;耐热木聚糖酶网络中的hub节点比常温木聚糖酶网络hub节点具有更多的疏水性残基,hub点中Phe、Ile、Val的占比更高。社团检测后发现,耐热木聚糖酶网络拥有更大的社团规模、较小的社团直径和较大的社团密度。社团规模越大表明耐热木聚糖酶的氨基酸残基更倾向于形成大的社团,而较小的社团直径和较大的社团密度则表明社团内部氨基酸残基的相互作用比常温木聚糖酶更强。     

动态残基网络社团视角下的木聚糖酶耐热性分析

木聚糖酶在食品、饲料、造纸和纺织等行业有重要的应用,研究木聚糖酶的耐热性有助于挖掘其潜在的应用领域并提高经济价值。本文通过采用Louvain算法,对来自变铅青链霉菌的常温木聚糖酶(xyna_strli)和嗜热子囊菌的耐热木聚糖酶(xyna_theau)的动态残基相互作用网络进行社团检测,并分析社团演化与木聚糖酶耐热性的关系。结果表明:常温木聚糖酶的末端存在稳定相互作用;以GLU37和LEU5为中心的残基结构稳固了酶的结构。耐热木聚糖酶中,α8′、α8″上的相互作用提升了酶的热稳定性。通过分析稳定社团发现,稳定社团包含酶的末端通过稳定相互作用提高耐热性。相较于常温木聚糖酶,耐热木聚糖酶的稳定社团维持了更多短螺旋和柔性区域的稳定,其在活性位点GLU237附近的残基减少了活性位点与底物接触,提升了稳定性。     

不同类型氨基酸网络参量与蛋白质折叠的关系

理论和实验研究表明,蛋白质天然拓扑结构对其折叠过程具有重要的影响．采用复杂网络的方法分析蛋白质天然结构的拓扑特征,并探索蛋白质结构特征与折叠速率之间的内在联系．分别构建了蛋白质氨基酸网络、疏水网、亲水网、亲水-疏水网以及相应的长程网络,研究了这些网络的匹配系数(assortativity coefficient)和聚集系数(clustering coefficient)的统计特性．结果表明,除了亲水-疏水网,上述各网络的匹配系数均为正值,并且氨基酸网和疏水网的匹配系数与折叠速率表现出明显的线性正相关,揭示了疏水残基间相互作用的协同性有助于蛋白质的快速折叠．同时,研究发现疏水网的聚集系数与折叠速率有明显的线性负相关关系,这表明疏水残基间三角结构(triangle construction)的形成不利于蛋白质快速折叠．还进一步构建了相应的长程网络,发现序列上间距较远的残基接触对的形成将使蛋白质折叠进程变慢．     

固有无序蛋白与蛋白质相互作用位点残基特征分析

本文对固有无序蛋白(IDPs)与其他蛋白质相互作用位点残基特征进行了研究.首先在数据库中选出满足条件的109条IDPs蛋白质链及与其他配体蛋白形成的299个IDPs-蛋白质复合物,然后提取复合物中作为相互作用位点的IDPs-蛋白质残基.这109条IDPs链中共含有50 031个氨基酸残基,其中处于作用位点的残基有4 822个.通过分析发现,20种氨基酸在形成IDPs-蛋白质相互作用位点残基时具有不同的倾向性,根据形成作用位点残基的倾向性,20种氨基酸可分成三大类:倾向型氨基酸(ILE、LEU、ARG、PHE、TYR、MET、TRP)、中间型氨基酸(GLN、GLU、THR、LYS、VAL、ASP、HIS)、非倾向型氨基酸(PRO、SER、GLY、ALA、ASN、CYS).研究结果还进一步表明,不同氨基酸在有序区域与无序区域形成IDPs-蛋白质作用位点残基的倾向性不同.其中,氨基酸TRP、LEU、ILE、CYS在有序和无序区域形成作用位点残基的差异性尤为明显,而氨基酸GLU、PHE、HIS、ALA则基本没有多大差别.对IDPs-蛋白质相互作用位点残基理化特征进行分析发现:疏水性强、侧链净电荷量较少、极性较小、溶剂可及性表面积较大、侧链体积较大、极化率较大的氨基酸比较倾向于形成作用位点残基.主成分分析结果显示,残基的极化率、侧链体积和溶剂可及表面积对作用位点残基影响最大.     

超氧化物歧化酶氨基酸网络与耐热性的关系研究

酶的热稳定性问题一直是生物科学领域的研究热点。构建氨基酸网络,从系统水平上研究酶热稳定性的影响因素是阐明嗜热酶耐热机制的重要途径。作者以超氧化物歧化酶(iron superoxide dismutase,Fe-SOD)的空间三维结构信息为基础,构建了不同类型的氨基酸相互作用网络。通过分析氨基酸网络的网络参数,发现热稳定性高的Fe-SOD氨基酸网络的平均度、平均连接强度及同配系数均高于常温的Fe-SOD氨基酸网络,而嗜热Fe-SOD氨基酸网络的特征路径长度小于常温的Fe-SOD氨基酸网络。此外,通过改变滑动窗口大小研究氨基酸网络中分子间相互作用区域范围,发现热稳定性高的Fe-SOD氨基酸网络中二级结构内部分子间连接紧密,二级结构之间及结构域之间的连接也较频繁。这些现象表明,嗜热Fe-SOD酶致密的内部结构缩短了氨基酸之间的距离,这更有利于稳定酶结构的作用力(如氢键和盐桥)的形成。实验结果进一步表明,通过研究氨基酸网络的网络参数可以阐述酶结构和功能之间的关系。     

为何在蛋白质相互作用网络中伪hub没有致命性?（英文）

在系统生物学中,中心性-致命性法则的机制至今仍是一个有争议的问题。但是,在蛋白质-蛋白质相互作用网络中,存在很多伪hub,它们并不具有致命性。为了解释这一现象,作者提出了三个新的度量标准:n-neighbor、n-ip和n-ibep,并从拓扑和功能两方面将伪hub与致命性hub进行比较,发现两者所有的区别都具有统计学意义。实验结果显示伪hub具有更高的进化速率,参与了较少的子图且倾向于与非致命性蛋白质发生相互作用。     

蛋白质相互作用热点残基的预测北大核心CSCD

氨基酸突变扫描实验揭示了在蛋白质相互作用的结合过程中大部分的结合自由能是由极少数热点残基贡献的,通常定义结合自由能变化△△G≥2.0 kcal/mol的蛋白质残基为热点残基。热点残基对蛋白质相互作用具有重要意义。因此,如何有效进行热点残基的预测,仍然是一个研究课题。综合蛋白质氨基酸理化属性的加权疏水性、加权残基接触数、结构属性溶剂可接近面积和残基突出指数等特征,提出利用机器学习支持向量机算法来预测热点残基的方法。所提方法在丙氨酸热力学数据库数据和结合界面数据库选定的数据集上有很好的效果。在一定程度上对以后的研究发展有所帮助。     

淀粉酶的同源性研究

对α－淀粉酶、麦芽四糖淀粉酶和葡萄糖淀粉酶进行的氨基酸序列比较表明,它们之间的氨基酸等同性相当低。本文在对这三种淀粉酶的氨基酸残基进行疏水性分析的基础上,采用国际上近期发展的疏水簇分析方法对这三种淀粉酶的氨基酸序列进行了二维描述,其结果清楚地显示了它们之间的同源性差异。这也被测定的三维结构所证实。这一研究结果表明,与蛋白质三维结构密切相关的蛋白质的二级结构及其相互配置主要取决于蛋白质序列中不同类型氨基酸残基的排列。     

嗜热与嗜常温微生物的蛋白质氨基酸组成比较

嗜热微生物的嗜热特性与其蛋白质的高度热稳定性紧密相关。为了探索嗜热蛋白质的热稳定机制,比较嗜热和嗜常温微生物的蛋白质在氨基酸组成上的差别,收集110对分别来自嗜热和嗜常温微生物的同源蛋白质序列,比较两组蛋白质各种氨基酸含量以及疏水性氨基酸组成、疏水性指数和荷电氨基酸组成的差别,结果两者在多种氨基酸含量上存在微小但统计学上显著的差别,嗜热蛋白质比嗜常温蛋白质具有较高的平均疏水性和荷电氨基酸组成。对两组蛋白质的“脂肪族氨基酸指数”进行分析,证明嗜热蛋白质之所以具有较高的脂肪族氨基酸指数是由于其亮氨酸含量较高,与影响该指数的其它几种氨基酸无关;从而认为该指数的意义值得怀疑。通过对大量同源嗜热蛋白质和嗜常温蛋白质氨基酸组成的比较,能够揭示一些有关蛋白质热稳定性的普遍规律。     

从胰岛素研究看等构相互作用在分子识别中的作用

蛋白质分子识别的结构基础是蛋白质的三维结构或折叠,其信息存在于氨基酸序列中。在比较功能已知或未知蛋白质的结构同源性时,常常是根据氨基酸残基的疏水性或亲水性。胰岛素定位突变的研究显示出了“等构相互作用”＾＃在考虑蛋白质同源性中的重要性。“等构相互作用”这一概念使得蛋白质结构与功能研究的视野更加开阔,同时在制药工业中开发多肽与蛋白质的类似物或模拟物有更多的选择。     

A network representation of protein structures: implications for protein stability

This study views each protein structure as a network of noncovalent connections between amino acid side chains. Each amino acid in a protein structure is a node, and the strength of the noncovalent interactions between two amino acids is evaluated for edge determination. The protein structure graphs (PSGs) for 232 proteins have been constructed as a function of the cutoff of the amino acid interaction strength at a few carefully chosen values. Analysis of such PSGs constructed on the basis of edge weights has shown the following: 1), The PSGs exhibit a complex topological network behavior, which is dependent on the interaction cutoff chosen for PSG construction. 2), A transition is observed at a critical interaction cutoff, in all the proteins, as monitored by the size of the largest cluster (giant component) in the graph. Amazingly, this transition occurs within a narrow range of interaction cutoff for all the proteins, irrespective of the size or the fold topology. And 3), the amino acid preferences to be highly connected (hub frequency) have been evaluated as a function of the interaction cutoff. We observe that the aromatic residues along with arginine, histidine, and methionine act as strong hubs at high interaction cutoffs, whereas the hydrophobic leucine and isoleucine residues get added to these hubs at low interaction cutoffs, forming weak hubs. The hubs identified are found to play a role in bringing together different secondary structural elements in the tertiary structure of the proteins. They are also found to contribute to the additional stability of the thermophilic proteins when compared to their mesophilic counterparts and hence could be crucial for the folding and stability of the unique three-dimensional structure of proteins. Based on these results, we also predict a few residues in the thermophilic and mesophilic proteins that can be mutated to alter their thermal stability.     

Search for structural factors responsible for the stability of proteins from thermophilic organisms

Database including 392 homologous pairs of proteins from thermophilic and mesophilic organisms was created. Using this database we have found that proteins from termophilic organisms contain more atom-atom contacts per residue in comparison with mesophilic homologues. Contribution to increase of the number of contacts gives exterior amino acid residues, accessible for the solvent. Amino acid composition of interior, inaccessible for the solvent, and exterior amino acid residues of proteins from thermophilic and mesophilic organisms were analyzed. We have obtained that exterior residues of proteins from thermophilic organisms contain more such amino acid residues as Lys, Arg and Glu and smaller such amino acid residues as Ala, Asp, Asn. Gln, Ser, and Thr in comparison with proteins from mesophilic organisms. Amino acid compositions of interior residues of considered proteins are not different.     

Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins

Summary. Thermophilic proteins show substantially higher intrinsic thermal stability than their mesophilic counterparts. Amino acid composition is believed to alter the intrinsic stability of proteins. Several investigations and mutagenesis experiment have been carried out to understand the amino acid composition for the thermostability of proteins. This review presents some generalized features of amino acid composition found in thermophilic proteins, including an increase in residue hydrophobicity, a decrease in uncharged polar residues, an increase in charged residues, an increase in aromatic residues, certain amino acid coupling patterns and amino acid preferences for thermophilic proteins. The differences of amino acids composition between thermophilic and mesophilic proteins are related to some properties of amino acids. These features provide guidelines for engineering mesophilic protein to thermophilic protein. Authors’ addresses: Yuan-Jiang Pan, Institute of Chemical Biology and Pharmaceutical Chemistry, Zhejiang University, Zhejiang University Road 38, Hangzhou 310027, China; Wei-Fen Li, Microbiology Division, College of Animal Science, Zhejiang University, Hangzhou 310029, China     

Temperature adaptation of lactate dehydrogenase. Structural, functional and genetic aspects

Comparison of the primary structures of thermophilic, mesophilic and psychrophilic lactate dehydrogenase (LDH) reveals a multitude of temperature-related amino acid substitutions. In the substitutions amino acid residues occurring preferentially in thermophilic, mesophilic (psychrophilic) LDH were found. On this basis, amino acid residues could be classified in an order from typical thermophilic (thermostabilizing) to typical mesophilic (thermolabilizing, increasing dynamics of the enzyme molecule) residues. The temperature-dependent ratio between thermostabilizing and thermolabilizing amino acid residues forms the basis for the specific structural and functional properties of thermophilic or mesophilic LDH. It is interesting that there appears to be a relationship between this order from thermophilic to mesophilic amino acid residues and the type of bases coding for these individual residues in the translation step of protein biosynthesis. Temperature-related amino acid substitutions are based on temperature-related base substitutions. A possible mechanism of temperature adaptation of LDH through alternative selection of thermophilic and mesophilic amino acid residues at the level of tRNA (anticodon)-mRNA (codon) interactions is discussed. These temperature-adaptation processes are evolutionary events in which the evolution and structure of the genetic code are involved.     

A search for structural factors responsible for the stability of proteins from thermophilic organisms

A database was designed to include 392 pairs of homologous proteins from thermophilic and mesophilic organisms. Proteins from thermophilic organisms proved to contain more atom-atom contacts per residue as compared with their mesophilic homologs. Solvent-accessible exterior amino acid residues contribute to the increase in the number of contacts. The amino acid composition was analyzed for internal (solvent-inaccessible) and exterior amino acid residues of thermophilic and mesophilic proteins. The exterior residues of thermophils have higher contents of Lys, Arg, and Glu and lower contents of Ala, Asp, Asn, Gln, Ser, and Thr as compared with mesophilic proteins. Interior protein regions did not differ in amino acid composition.     

All-atom contact potential approach to protein thermostability analysis

In this paper we use all-atom potential energy to define and analyze the inter-residue contacts in mesophilic and thermophilic proteins. Fifteen families of proteins are selected and each family has two representative proteins with greatly different preferred environmental temperatures. We find that both the number and energy of the contacts defined in this way show stronger correlations with the preferred temperatures of proteins than other factors used before. We also find that the charged-polar and charged-nonpolar residue contacts not only have larger contact numbers but also have lower single contact energies. Furthermore, the most important is that most of the thermophilic proteins have more charged-polar and charged-nonpolar residue contacts than their mesophilic counterparts. This suggests that they may play an important role in the thermostability of proteins, except usual charged-charged and nonpolar-nonpolar residue contacts. Charged residues may exert their profound influence by forming contacts not only with other charged residues but also with polar or nonpolar residues, thus further increasing the strength of contact network and then the thermostability of proteins.     

Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications

A fundamental role of the Hsp90 chaperone in regulating functional activity of diverse protein clients is essential for the integrity of signaling networks. In this work we have combined biophysical simulations of the Hsp90 crystal structures with the protein structure network analysis to characterize the statistical ensemble of allosteric interaction networks and communication pathways in the Hsp90 chaperones. We have found that principal structurally stable communities could be preserved during dynamic changes in the conformational ensemble. The dominant contribution of the inter-domain rigidity to the interaction networks has emerged as a common factor responsible for the thermodynamic stability of the active chaperone form during the ATPase cycle. Structural stability analysis using force constant profiling of the inter-residue fluctuation distances has identified a network of conserved structurally rigid residues that could serve as global mediating sites of allosteric communication. Mapping of the conformational landscape with the network centrality parameters has demonstrated that stable communities and mediating residues may act concertedly with the shifts in the conformational equilibrium and could describe the majority of functionally significant chaperone residues. The network analysis has revealed a relationship between structural stability, global centrality and functional significance of hotspot residues involved in chaperone regulation. We have found that allosteric interactions in the Hsp90 chaperone may be mediated by modules of structurally stable residues that display high betweenness in the global interaction network. The results of this study have suggested that allosteric interactions in the Hsp90 chaperone may operate via a mechanism that combines rapid and efficient communication by a single optimal pathway of structurally rigid residues and more robust signal transmission using an ensemble of suboptimal multiple communication routes. This may be a universal requirement encoded in protein structures to balance the inherent tension between resilience and efficiency of the residue interaction networks.     

Drivers of plant individual-based pollinator visitation network topology in an arid ecosystem

Interactions with pollinators underlie the structure and function of plant communities. Network analysis is a valuable tool for studying plant-pollinator interactions, but these networks are most frequently built by aggregating interactions at the species level. Interactions are between individuals and an advantage of individual-based networks is the ability to integrate inter-individual variation in traits and environmental context within complex ecological networks. We studied the influence of inter-individual variation on pollinator sharing among foundation shrubs and cactus in a desert ecosystem using plant individual-based pollinator visitation networks. We hypothesized that the traits that alter attractiveness of plants to pollinators will also influence an individual plant's role within the visitation network. Foundation plants growing with higher densities of nearby blooming shrubs had higher pollinator visitation rates and had greater access to the conspecific mating pool, suggesting widespread and diffuse pollination facilitation within this community. Further, shrub density influenced the role of betweenness centrality and the effective number of partners (e^H). Floral display size also influenced the effective number of interaction partners but did not directly influence the centrality measures for individual plants or other measures of network structure despite increasing visitation rates. The individual-based visitation networks were significantly modular and module membership was predicted by species identity and pollinator visitation rates. Ecological and individual context mediate the outcome of pollinator-mediated interactions and are fundamental drivers of whole community structure. This study shows that the density of immediate neighbours can influence the overall structure of plant-pollinator interaction networks. Exploring the contribution of intraspecific variation to community interaction networks will improve our understanding of drivers of community-level ecological dynamics.