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Annual review of biophysics and biomolecular structure最新文献

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Molecular recognition and docking algorithms. 分子识别和对接算法。
Annual review of biophysics and biomolecular structure Pub Date : 2003-01-01 Epub Date: 2003-01-28 DOI: 10.1146/annurev.biophys.32.110601.142532
Natasja Brooijmans, Irwin D Kuntz
{"title":"Molecular recognition and docking algorithms.","authors":"Natasja Brooijmans,&nbsp;Irwin D Kuntz","doi":"10.1146/annurev.biophys.32.110601.142532","DOIUrl":"https://doi.org/10.1146/annurev.biophys.32.110601.142532","url":null,"abstract":"<p><p>Molecular docking is an invaluable tool in modern drug discovery. This review focuses on methodological developments relevant to the field of molecular docking. The forces important in molecular recognition are reviewed and followed by a discussion of how different scoring functions account for these forces. More recent applications of computational chemistry tools involve library design and database screening. Last, we summarize several critical methodological issues that must be addressed in future developments.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.32.110601.142532","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22234814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 677
Volumetric properties of proteins. 蛋白质的体积特性。
Annual review of biophysics and biomolecular structure Pub Date : 2003-01-01 Epub Date: 2003-01-16 DOI: 10.1146/annurev.biophys.32.110601.141709
Tigran V Chalikian
{"title":"Volumetric properties of proteins.","authors":"Tigran V Chalikian","doi":"10.1146/annurev.biophys.32.110601.141709","DOIUrl":"https://doi.org/10.1146/annurev.biophys.32.110601.141709","url":null,"abstract":"<p><p>Structural and thermodynamic characterizations of a variety of intra- and intermolecular interactions stabilizing/destabilizing protein systems represent a major part of multidisciplinary efforts aimed at solving the problems of protein folding and binding. To this end, volumetric techniques have been successfully used to gain insights into protein hydration and intraglobular packing. Despite the fact that the use of volumetric measurements in protein-related studies dates back to the 1950s, such measurements still represent a relatively untapped yet potentially informative means for tackling the problems of protein folding and binding. This notion has been further emphasized by recent advances in the development of highly sensitive volumetric instrumentation that has led to intensifying volumetric investigations of protein systems. This paper reviews the volumetric properties of proteins and their low-molecular-weight analogs, in particular, discussing the recent progress in the use of volumetric data for studying conformational transitions of proteins as well as protein-ligand, protein-protein, and protein-nucleic acid interactions.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.32.110601.141709","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22209828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 280
Nucleic acid recognition by OB-fold proteins. OB-fold蛋白的核酸识别。
Annual review of biophysics and biomolecular structure Pub Date : 2003-01-01 Epub Date: 2003-02-18 DOI: 10.1146/annurev.biophys.32.110601.142506
Douglas L Theobald, Rachel M Mitton-Fry, Deborah S Wuttke
{"title":"Nucleic acid recognition by OB-fold proteins.","authors":"Douglas L Theobald,&nbsp;Rachel M Mitton-Fry,&nbsp;Deborah S Wuttke","doi":"10.1146/annurev.biophys.32.110601.142506","DOIUrl":"https://doi.org/10.1146/annurev.biophys.32.110601.142506","url":null,"abstract":"<p><p>The OB-fold domain is a compact structural motif frequently used for nucleic acid recognition. Structural comparison of all OB-fold/nucleic acid complexes solved to date confirms the low degree of sequence similarity among members of this family while highlighting several structural sequence determinants common to most of these OB-folds. Loops connecting the secondary structural elements in the OB-fold core are extremely variable in length and in functional detail. However, certain features of ligand binding are conserved among OB-fold complexes, including the location of the binding surface, the polarity of the nucleic acid with respect to the OB-fold, and particular nucleic acid-protein interactions commonly used for recognition of single-stranded and unusually structured nucleic acids. Intriguingly, the observation of shared nucleic acid polarity may shed light on the longstanding question concerning OB-fold origins, indicating that it is unlikely that members of this family arose via convergent evolution.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.32.110601.142506","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22256654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 462
X-ray crystallographic analysis of lipid-protein interactions in the bacteriorhodopsin purple membrane. 细菌紫紫质膜中脂质-蛋白相互作用的x射线晶体学分析。
Annual review of biophysics and biomolecular structure Pub Date : 2003-01-01 Epub Date: 2003-02-10 DOI: 10.1146/annurev.biophys.32.110601.142516
Jean-Philippe Cartailler, Hartmut Luecke
{"title":"X-ray crystallographic analysis of lipid-protein interactions in the bacteriorhodopsin purple membrane.","authors":"Jean-Philippe Cartailler,&nbsp;Hartmut Luecke","doi":"10.1146/annurev.biophys.32.110601.142516","DOIUrl":"https://doi.org/10.1146/annurev.biophys.32.110601.142516","url":null,"abstract":"<p><p>The past decade has witnessed increasingly detailed insights into the structural mechanism of the bacteriorhodopsin photocycle. Concurrently, there has been much progress within our knowledge pertaining to the lipids of the purple membrane, including the discovery of new lipids and the overall effort to localize and identify each lipid within the purple membrane. Therefore, there is a need to classify this information to generalize the findings. We discuss the properties and roles of haloarchaeal lipids and present the structural data as individual case studies. Lipid-protein interactions are discussed in the context of structure-function relationships. A brief discussion of the possibility that bacteriorhodopsin functions as a light-driven inward hydroxide pump rather than an outward proton pump is also presented.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.32.110601.142516","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22256655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 62
The binding of cofactors to photosystem I analyzed by spectroscopic and mutagenic methods. 用光谱学和诱变方法分析了辅助因子与光系统的结合。
Annual review of biophysics and biomolecular structure Pub Date : 2003-01-01 Epub Date: 2003-01-08 DOI: 10.1146/annurev.biophys.32.110601.142356
John H Golbeck
{"title":"The binding of cofactors to photosystem I analyzed by spectroscopic and mutagenic methods.","authors":"John H Golbeck","doi":"10.1146/annurev.biophys.32.110601.142356","DOIUrl":"https://doi.org/10.1146/annurev.biophys.32.110601.142356","url":null,"abstract":"<p><p>This review focuses on cofactor-ligand and protein-protein interactions within the photosystem I reaction center. The topics include a description of the electron transfer cofactors, the mode of binding of the cofactors to protein-bound ligands, and a description of intraprotein contacts that ultimately allow photosystem I to be assembled (in cyanobacteria) from 96 chlorophylls, 22 carotenoids, 2 phylloquinones, 3 [4Fe-4S] clusters, and 12 polypeptides. During the 15 years that have elapsed from the first report of crystals to the atomic-resolution X-ray crystal structure, cofactor-ligand interactions and protein-protein interactions were systematically being explored by spectroscopic and genetic methods. This article charts the interplay between these disciplines and assesses how good the early insights were in light of the current structure of photosystem I.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.32.110601.142356","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22191660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 49
Proteome analysis by mass spectrometry. 质谱分析蛋白质组学。
Annual review of biophysics and biomolecular structure Pub Date : 2003-01-01 Epub Date: 2003-01-28 DOI: 10.1146/annurev.biophys.32.110601.141854
P Lee Ferguson, Richard D Smith
{"title":"Proteome analysis by mass spectrometry.","authors":"P Lee Ferguson,&nbsp;Richard D Smith","doi":"10.1146/annurev.biophys.32.110601.141854","DOIUrl":"https://doi.org/10.1146/annurev.biophys.32.110601.141854","url":null,"abstract":"<p><p>The coupling of high-performance mass spectrometry instrumentation with highly efficient chromatographic and electrophoretic separations has enabled rapid qualitative and quantitative analysis of thousands of proteins from minute samples of biological materials. Here, we review recent progress in the development and application of mass spectrometry-based techniques for the qualitative and quantitative analysis of global proteome samples derived from whole cells, tissues, or organisms. Techniques such as multidimensional peptide and protein separations coupled with mass spectrometry, accurate mass measurement of peptides from global proteome digests, and mass spectrometric characterization of intact proteins hold great promise for characterization of highly complex protein mixtures. Advances in chemical tagging and isotope labeling techniques have enabled quantitative analysis of proteomes, and highly specific isolation strategies have been developed aimed at selective analysis of posttranslationally modified proteins.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.32.110601.141854","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22234811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 135
Cations as hydrogen bond donors: a view of electrostatic interactions in DNA. 阳离子作为氢键供体:DNA静电相互作用的观点。
Annual review of biophysics and biomolecular structure Pub Date : 2003-01-01 Epub Date: 2003-02-14 DOI: 10.1146/annurev.biophys.32.110601.141726
Juan A Subirana, Montserrat Soler-Lopez
{"title":"Cations as hydrogen bond donors: a view of electrostatic interactions in DNA.","authors":"Juan A Subirana,&nbsp;Montserrat Soler-Lopez","doi":"10.1146/annurev.biophys.32.110601.141726","DOIUrl":"https://doi.org/10.1146/annurev.biophys.32.110601.141726","url":null,"abstract":"<p><p>Cations are bound to nucleic acids in a solvated state. High-resolution X-ray diffraction studies of oligonucleotides provide a detailed view of Mg2+, and occasionally other ions bound to DNA. In a survey of several such structures, certain general observations emerge. First, cations bind preferentially to the guanine base in the major groove or to phosphate group oxygen atoms. Second, cations interact with DNA most frequently via water molecules in their primary solvation shell, direct ion-DNA contacts being only rarely observed. Thus, the solvated ions should be viewed as hydrogen bond donors in addition to point charges. Finally, ion interaction sites are readily exchangeable: The same site may be occupied by any ion, including spermine, as well as by a water molecule.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.32.110601.141726","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22256650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 115
New insight into site-specific recombination from Flp recombinase-DNA structures. 从Flp重组酶- dna结构对位点特异性重组的新见解。
Annual review of biophysics and biomolecular structure Pub Date : 2003-01-01 Epub Date: 2003-02-11 DOI: 10.1146/annurev.biophys.32.110601.141732
Yu Chen, Phoebe A Rice
{"title":"New insight into site-specific recombination from Flp recombinase-DNA structures.","authors":"Yu Chen,&nbsp;Phoebe A Rice","doi":"10.1146/annurev.biophys.32.110601.141732","DOIUrl":"https://doi.org/10.1146/annurev.biophys.32.110601.141732","url":null,"abstract":"<p><p>The lamba integrase, or tyrosine-based family of site-specific recombinases, plays an important role in a variety of biological processes by inserting, excising, and inverting DNA segments. Flp, encoded by the yeast 2-mum plasmid, is the best-characterized eukaryotic member of this family and is responsible for maintaining the copy number of this plasmid. Over the past several years, structural and biochemical studies have shed light on the details of a common catalytic scheme utilized by these enzymes with interesting variations under different biological contexts. The emergence of new Flp structures and solution data provides insights not only into its unique mechanism of active site assembly and activity regulation but also into the specific contributions of certain protein residues to catalysis.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.32.110601.141732","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22256651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 94
Protein analysis by hydrogen exchange mass spectrometry. 氢交换质谱法分析蛋白质。
Annual review of biophysics and biomolecular structure Pub Date : 2003-01-01 Epub Date: 2003-02-18 DOI: 10.1146/annurev.biophys.32.110601.142417
Andrew N Hoofnagle, Katheryn A Resing, Natalie G Ahn
{"title":"Protein analysis by hydrogen exchange mass spectrometry.","authors":"Andrew N Hoofnagle,&nbsp;Katheryn A Resing,&nbsp;Natalie G Ahn","doi":"10.1146/annurev.biophys.32.110601.142417","DOIUrl":"https://doi.org/10.1146/annurev.biophys.32.110601.142417","url":null,"abstract":"<p><p>Mass spectrometry has provided a powerful method for monitoring hydrogen exchange of protein backbone amides with deuterium from solvent. In comparison to popular NMR approaches, mass spectrometry has the advantages of higher sensitivity, wider coverage of sequence, and the ability to analyze larger proteins. Proteolytic fragmentation of proteins following the exchange reaction provides moderate structural resolution, in some cases enabling measurements from single amides. The technique has provided new insight into protein-protein and protein-ligand interfaces, as well as conformational changes during protein folding or denaturation. In addition, recent studies illustrate the utility of hydrogen exchange mass spectrometry toward detecting protein motions relevant to allostery, covalent modifications, and enzyme function.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.32.110601.142417","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22256652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 346
The role of dynamics in enzyme activity. 动力学在酶活性中的作用。
Annual review of biophysics and biomolecular structure Pub Date : 2003-01-01 Epub Date: 2002-12-02 DOI: 10.1146/annurev.biophys.32.110601.142445
R M Daniel, R V Dunn, J L Finney, J C Smith
{"title":"The role of dynamics in enzyme activity.","authors":"R M Daniel,&nbsp;R V Dunn,&nbsp;J L Finney,&nbsp;J C Smith","doi":"10.1146/annurev.biophys.32.110601.142445","DOIUrl":"https://doi.org/10.1146/annurev.biophys.32.110601.142445","url":null,"abstract":"<p><p>Although protein function is thought to depend on flexibility, precisely how the dynamics of the molecule and its environment contribute to catalytic mechanisms is unclear. We review experimental and computational work relating to enzyme dynamics and function, including the role of solvent. The evidence suggests that fast motions on the 100 ps timescale, and any motions coupled to these, are not required for enzyme function. Proteins where the function is electron transfer, proton tunneling, or ligand binding may have different dynamical dependencies from those for enzymes, and enzymes with large turnover numbers may have different dynamical dependencies from those that turn over more slowly. The timescale differences between the fastest anharmonic fluctuations and the barrier-crossing rate point to the need to develop methods to resolve the range of motions present in enzymes on different time- and lengthscales.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.32.110601.142445","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22144599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 312
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