胶原蛋白与Ⅵ型胶原蛋白的结构概述

描述了胶原蛋白的结构和Ⅵ型胶原蛋白的结构以及胶原蛋白的应用 ,并对人类胶原蛋白的生产进行了展望。     

蛋白质结构中卷曲螺旋的研究进展

卷曲螺旋 (coiledcoil)是存在于多种天然蛋白质中的结构模式 .近年来 ,通过对天然蛋白质中卷曲螺旋结构以及根据已有知识设计合成的卷曲螺旋结构的研究 ,已基本掌握了这类结构模式的特点 ,并将特异的卷曲螺旋结构应用于生化分析、工业、医药卫生等领域 .本文主要从天然蛋白质中卷曲螺旋的主要存在形式及其生物学功能、卷曲螺旋的主要结构特点、影响卷曲螺旋稳定性和结构特异性的因素、卷曲螺旋结构设计及其应用以及今后卷曲螺旋研究的主要发展方向等几个方面对近年来卷曲螺旋结构的研究进展情况进行了综述 .     

被子植物叶绿体基因组的结构变异研究进展

叶绿体是绿色植物特有的细胞器,其基因组信息被广泛应用于植物系统发育和比较基因组学研究。目前,越来越多的物种有了叶绿体全基因组序列,人们对叶绿体基因组的结构及其变异规律有了更深入的了解。该文对近年来国内外有关被子植物叶绿体基因组插入/缺失、短片段倒位与重复、基因组结构重排以及基因丢失等结构变异式样的研究进展进行综述,并分析了叶绿体基因组结构研究中仍存在的问题以及该领域未来的发展趋势。     

蛙科精子形态结构研究进展

本文对已有的蛙科精子形态结构的研究进行总结,归纳了蛙科精子形态结构及量度的特征和类型,以及蛙科精子结构与其它两栖类精子结构的异同,探讨蛙科精子形态结构研究中存在和亟待解决的问题。     

中药中寡糖分离分析方法研究进展CSCD

糖链结构与功能研究是未来糖生物学研究的重要方向,必将为人类疾病的研究和治疗带来新的希望。随着对糖类研究的不断深入,寡糖因其所具有的多种药理活性受到了国内外学者的广泛关注。寡糖结构受连接位点、糖环结构和分支等因素的影响而呈现复杂性和多样性,这为其提取,纯化、分离分析以及结构表征带来巨大了挑战。本文综述了近年来国内外在中药寡糖提取纯化、分离分析以及结构表征这三方面的研究内容,以期为寡糖的现代药物研究和临床应用以及功效产品创制提供科学参考。     

黑果枸杞花青素结构差异对其稳定性及细胞抗氧化活性的影响

本文研究了黑果枸杞花青素化合物结构对其稳定性和细胞抗氧化活性的影响。通过半制备型HPLC分离纯化得到了4种黑果枸杞花青素化合物并鉴定结构,利用比色法评价了化合物的稳定性、细胞毒实验以及H₂O₂诱导的SH-SY5Y细胞损伤模型评价了细胞抗氧化活性,并讨论了化学结构对其影响。结果表明反式结构比顺式结构在中性和弱碱性条件下有更好的稳定性,反式结构、糖基的增加以及母核B环上的甲氧基取代均可以通过缩短母核与糖链的分子距离从而提高稳定性,糖基的增加能显著地降低损伤细胞中的乳酸脱氢酶水平,且反式结构较顺式结构更有活性优势。综上所述,黑果枸杞花青素的结构影响稳定性和细胞抗氧化活性,但糖基的增加和酰基的反式异构对二者有更积极的意义。     

作物籽粒淀粉结构的形成与相关酶关系的研究进展

本文综述了前人关于作物籽粒淀粉结构形成以及相关酶的分子生物学研究进展,分析讨论了淀粉结构的形成与酶活性之间的关系,酶对淀粉结构形成的调控机理,为进一步开展作物籽粒淀粉品质改良研究提供理论依据。     

核糖体模型研究进展

随着低温电子显微镜、X射线晶体衍射等技术的发展以及有关核糖体各组分结构数据的增多,高分辨率的E.coli核糖体模型已经被建立.对该模型作了概要介绍,包括了对mRNA通道,A、P位点tRNA,肽基转位酶,肽通道等在核糖体中的定位以及它们与核糖体的相互作用.有助于提高对核糖体结构、功能、及翻译过程的理解.     

甘油醛-3-磷酸脱氢酶结构的保守性

对中国南海龙虾等五种种属的甘油醛－３－磷酸脱氢酶晶体结构进行了比较,结果显示该酶三维结构的高度保守性。结构类似性包括酶活性中心、与辅酶结合部位、二级结构、结构域组织、亚基排列以及许多有序水结构。位于分子中心的Ｓ－ｌｏｏｐ区存在两种略有差别的构象,分别对应于耐热酶与不耐热酶。对其它细小的结构差别也进行了分析与讨论。     

DMPC单分子层膜及细胞色素C氧化酶重组脂质体表面的扫描隧道显微镜观察

本文报导了扫描隧道显微镜对固相磷脂单分子层膜以及重组了细胞色素C氧化酶后的脂质体表面结构的观察.对DMPC单分子层著,得到了有关磷脂头部形态,大小及排态状况等结构信息,达到分子水平分辨;对重组酶后的脂质体表面,也得到了氧化酶分子在膜上的结构信息.     

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.     

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.     

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 homologous protein structures based on conformational searches and energetics

A "knowledge-based" method of predicting the unknown structure of a protein from a homologous known structure using energetics to determine a sidechain conformation is proposed. The method consists of exchanging the residues in the known structure for the sequence of the unknown protein. Then a conformational search with molecular mechanics energy minimization is done on the exchanged residues. The lowest energy conformer is the one picked to be the predicted structure. In the structure of bovine trypsin, the importance of including a solvation energy term in the search is demonstrated for solvent accessible residues, while molecular mechanics alone is enough to correctly predict the conformation of internal residues. The correctness of the model is assessed by a volume error overlap of the predicted structure compared to the crystal structure. Finally, the structure of rat trypsin is predicted from the crystal structure of bovine trypsin. The sequences of these two proteins are 74% identical and all of the significant changes between them are on external residues. Thus, the inclusion of solvation energy in the conformational search is necessary to accurately predict the structure of the exchanged residues.     

Adsorption and folding dynamics of MPER of HIV‐1 gp41 in the presence of dpc micelle

Membrane‐proximal ectodomain region (MPER) of HIV‐1 gp41 is known to have several epitopes of monoclonal antibodies. It also plays an important role in the membrane fusion process that is well‐evidenced, though not well‐elucidated. There are also disputes over the true structure of MPER. In this study, MPER NMR structure in the presence of dodecylphosphatidylcholine micelle is used in the molecular dynamic simulation to elucidate structural dynamics and adsorption to model MPER interaction in a membrane environment. Polarized protein‐specific charge derived from its NMR structure is found to better preserve the helical structure found in the NMR structure compared to AMBER03 calculation. The preserved helical structure also adsorb to the micelle using the hydrophobic side‐chains, consistent to the NMR structure. Ab initio folding of MPER predicts a structure quite in well agreement with the NMR structure (RMSd 3.9 Å) and shows that the micelle plays a role in the folding process. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

Hydrography and population genetic structure in brook charr (Salvelinus fontinalis, Mitchill) from eastern Canada

Despite the abundance of studies of genetic diversity in freshwater fishes, few have specifically addressed the role of habitat structure in partitioning genetic variance within and among populations. In this study, we analysed the variability of six microsatellite loci among 24 brook charr population samples in order to correlate hydrographic structure with genetic organization. These populations originated from three Canadian National parks (Kouchibouguac, Fundy and Forillon) that showed distinct hydrographic structure. Considering the general characteristics of these habitats, we formulated specific hypotheses in regard to genetic structure, which were principally based on the potential for gene flow and population size associated with each habitat. The hierarchical analysis of molecular variance and the genetic distances computed among populations revealed that habitat structure analyses constitute an important, but insufficient, predictor of genetic structure. We discuss the importance of habitat complexity on genetic structure in the context of management and conservation.