Annual review of biophysics and biomolecular structure最新文献_第7页

Annual review of biophysics and biomolecular structure Pub Date : 2004-05-25 DOI: 10.1146/ANNUREV.BB.33.051304.100011

D. Rees

引用次数: 1

Spin distribution and the location of protons in paramagnetic proteins. 顺磁性蛋白质中的自旋分布和质子位置。

Annual review of biophysics and biomolecular structure Pub Date : 2004-01-01 DOI: 10.1146/annurev.biophys.33.110502.140344

D Goldfarb, D Arieli

{"title":"Spin distribution and the location of protons in paramagnetic proteins.","authors":"D Goldfarb, D Arieli","doi":"10.1146/annurev.biophys.33.110502.140344","DOIUrl":"https://doi.org/10.1146/annurev.biophys.33.110502.140344","url":null,"abstract":"Two current frontiers in EPR research are high-field ( nu0 > 70 GHz, B0 > 2.5 T ) electron paramagnetic resonance (EPR) and high-field electron-nuclear double resonance (ENDOR). This review focuses on recent advances in high-field ENDOR and its applications to the study of proteins containing native paramagnetic sites. It concentrates on two aspects; the first concerns the determination of the location of protons and is related to the site geometry, and the second focuses on the spin density distribution within the site, which is inherent to the electronic structure. Both spin density and proton locations can be derived from ligand hyperfine couplings determined by ENDOR measurements. A brief description of the experimental methods is presented along with a discussion of the advantages and disadvantages of high-field ENDOR compared with conventional X-band (~ 9.5 GHz) experiments. Specific examples of both protein single crystals and frozen solutions are then presented. These include the determination of the coordinates of water ligand protons in the Mn(II) site of concanavalin A, the detection of hydrogen bonds in a quinone radical in the bacterial photosynthetic reaction center as well as in the tyrosyl radical in ribonuclease reductase, and the study of the spin distribution in copper proteins. The copper proteins discussed are the type I copper of azurin and the binuclear CuA center in a number of proteins. The last part of the review presents a brief discussion of the interpretation of hyperfine couplings using quantum chemical calculations, primarily density functional theory (DFT) methods. Such methods are becoming an integral part of the data analysis tools, as they can facilitate signal assignment and provide the ultimate relation between the experimental hyperfine couplings and the electronic wave function.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"33 ","pages":"441-68"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.33.110502.140344","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24515203","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: 35

Three-dimensional electron microscopy at molecular resolution. 分子分辨率的三维电子显微镜。

Annual review of biophysics and biomolecular structure Pub Date : 2004-01-01 DOI: 10.1146/annurev.biophys.33.110502.140339

Sriram Subramaniam, Jacqueline L S Milne

引用次数: 76

Residual dipolar couplings in NMR structure analysis. 核磁共振结构分析中的残余偶极耦合。

Annual review of biophysics and biomolecular structure Pub Date : 2004-01-01 DOI: 10.1146/annurev.biophys.33.110502.140306

Rebecca S Lipsitz, Nico Tjandra

引用次数: 157

Molecules of the bacterial cytoskeleton. 细菌细胞骨架的分子。

Annual review of biophysics and biomolecular structure Pub Date : 2004-01-01 DOI: 10.1146/annurev.biophys.33.110502.132647

Jan Löwe, Fusinita van den Ent, Linda A Amos

{"title":"Molecules of the bacterial cytoskeleton.","authors":"Jan Löwe, Fusinita van den Ent, Linda A Amos","doi":"10.1146/annurev.biophys.33.110502.132647","DOIUrl":"https://doi.org/10.1146/annurev.biophys.33.110502.132647","url":null,"abstract":"The structural elucidation of clear but distant homologs of actin and tubulin in bacteria and GFP labeling of these proteins promises to reinvigorate the field of prokaryotic cell biology. FtsZ (the tubulin homolog) and MreB/ParM (the actin homologs) are indispensable for cellular tasks that require the cell to accurately position molecules, similar to the function of the eukaryotic cytoskeleton. FtsZ is the organizing molecule of bacterial cell division and forms a filamentous ring around the middle of the cell. Many molecules, including MinCDE, SulA, ZipA, and FtsA, assist with this process directly. Recently, genes much more similar to tubulin than to FtsZ have been identified in Verrucomicrobia. MreB forms helices underneath the inner membrane and probably defines the shape of the cell by positioning transmembrane and periplasmic cell wall-synthesizing enzymes. Currently, no interacting proteins are known for MreB and its relatives that help these proteins polymerize or depolymerize at certain times and places inside the cell. It is anticipated that MreB-interacting proteins exist in analogy to the large number of actin binding proteins in eukaryotes. ParM (a plasmid-borne actin homolog) is directly involved in pushing certain single-copy plasmids to the opposite poles by ParR/parC-assisted polymerization into double-helical filaments, much like the filaments formed by actin, F-actin. Mollicutes seem to have developed special systems for cell shape determination and motility, such as the fibril protein in Spiroplasma.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"33 ","pages":"177-98"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.33.110502.132647","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24515840","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: 139

The use of in vitro peptide-library screens in the analysis of phosphoserine/threonine-binding domain structure and function. 利用体外肽库筛选分析磷丝氨酸/苏氨酸结合域的结构和功能。

Annual review of biophysics and biomolecular structure Pub Date : 2004-01-01 DOI: 10.1146/annurev.biophys.33.110502.133346

Michael B Yaffe, Stephen J Smerdon

{"title":"The use of in vitro peptide-library screens in the analysis of phosphoserine/threonine-binding domain structure and function.","authors":"Michael B Yaffe, Stephen J Smerdon","doi":"10.1146/annurev.biophys.33.110502.133346","DOIUrl":"https://doi.org/10.1146/annurev.biophys.33.110502.133346","url":null,"abstract":"Phosphoserine/threonine-binding domains integrate intracellular signal transduction events by forming multiprotein complexes with substrates of protein serine/threonine kinases. These phosphorylation-dependent molecular recognition events are responsible for coordinating the precise temporal and spatial response of cells to a wide range of stimuli, particularly those involved in cell cycle control and the response to DNA damage. The known families of phosphoserine/threonine-binding modules include 14-3-3 proteins, WW domains, FHA domains, WD40 repeats, and the Polo-box domains of Polo-like kinases. Peptide-library experiments reveal the optimal sequence motifs recognized by these domains, and facilitate high-resolution structural studies elucidating the mechanisms of phospho-dependent binding and the molecular basis for domain function within intricate signaling networks. Information emerging from these studies is critical for the design of novel experimental and therapeutic tools aimed at altering signal transduction cascades in normal and diseased cells.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"33 ","pages":"225-44"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.33.110502.133346","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24515842","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: 89

Force as a useful variable in reactions: unfolding RNA. 力是反应中有用的变量:展开RNA。

Annual review of biophysics and biomolecular structure Pub Date : 2004-01-01 DOI: 10.1146/annurev.biophys.33.110502.140418

Ignacio Tinoco

引用次数: 65

Structure, dynamics, and catalytic function of dihydrofolate reductase. 二氢叶酸还原酶的结构、动力学和催化功能。

Annual review of biophysics and biomolecular structure Pub Date : 2004-01-01 DOI: 10.1146/annurev.biophys.33.110502.133613

Jason R Schnell, H Jane Dyson, Peter E Wright

{"title":"Structure, dynamics, and catalytic function of dihydrofolate reductase.","authors":"Jason R Schnell, H Jane Dyson, Peter E Wright","doi":"10.1146/annurev.biophys.33.110502.133613","DOIUrl":"https://doi.org/10.1146/annurev.biophys.33.110502.133613","url":null,"abstract":"Molecular motions are widely regarded as contributing factors in many aspects of protein function. The enzyme dihydrofolate reductase (DHFR), and particularly that from Escherichia coli, has become an important system for investigating the linkage between protein dynamics and catalytic function, both because of the location and timescales of the motions observed and because of the availability of a large amount of structural and mechanistic data that provides a detailed context within which the motions can be interpreted. Changes in protein dynamics in response to ligand binding, conformational change, and mutagenesis have been probed using numerous experimental and theoretical approaches, including X-ray crystallography, fluorescence, nuclear magnetic resonance (NMR), molecular dynamics simulations, and hybrid quantum/classical dynamics methods. These studies provide a detailed map of changes in conformation and dynamics throughout the catalytic cycle of DHFR and give new insights into the role of protein motions in the catalytic activity of this enzyme.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"33 ","pages":"119-40"},"PeriodicalIF":0.0,"publicationDate":"2004-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.33.110502.133613","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"24515922","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: 453

Tethering: fragment-based drug discovery. Tethering:基于碎片的药物发现。

Annual review of biophysics and biomolecular structure Pub Date : 2004-01-01 DOI: 10.1146/annurev.biophys.33.110502.140409

Daniel A Erlanson, James A Wells, Andrew C Braisted

引用次数: 325

The role of water in protein-DNA recognition. 水在蛋白质- dna识别中的作用。

Annual review of biophysics and biomolecular structure Pub Date : 2004-01-01 DOI: 10.1146/annurev.biophys.33.110502.140414

B Jayaram, Tarun Jain

引用次数: 188