发布求助
文献互助 智能选刊 最新文献

Annual review of biophysics and biomolecular structure最新文献

筛选
英文 中文
Calculation of protein-ligand binding affinities. 蛋白质与配体结合亲和力的计算。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.36.040306.132550
Michael K Gilson, Huan-Xiang Zhou
{"title":"Calculation of protein-ligand binding affinities.","authors":"Michael K Gilson,&nbsp;Huan-Xiang Zhou","doi":"10.1146/annurev.biophys.36.040306.132550","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.040306.132550","url":null,"abstract":"<p><p>Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches. Important advances are reported in modeling protein-ligand energetics, such as the incorporation of electronic polarization and the use of quantum mechanical methods. Recent calculations suggest that changes in configurational entropy strongly oppose binding and must be included if accurate affinities are to be obtained. The linear interaction energy (LIE) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods are analyzed, as are free energy pathway methods, which show promise and may be ready for more extensive testing. Ultimately, major improvements in modeling accuracy will likely require advances on multiple fronts, as well as continued validation against experiment.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"21-42"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.36.040306.132550","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26470286","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: 821
New fluorescent tools for watching nanometer-scale conformational changes of single molecules. 用于观察单分子纳米级构象变化的新荧光工具。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.36.040306.132700
Erdal Toprak, Paul R Selvin
{"title":"New fluorescent tools for watching nanometer-scale conformational changes of single molecules.","authors":"Erdal Toprak,&nbsp;Paul R Selvin","doi":"10.1146/annurev.biophys.36.040306.132700","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.040306.132700","url":null,"abstract":"<p><p>Single-molecule biophysics has been serving biology for more than two decades. Fluorescence microscopy is one of the most commonly used tools to identify molecules of interest and to visualize biological events. Here we describe some of the most commonly used fluorescence imaging tools to measure nanoscale movements and the rotational dynamics of biomolecules.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"349-69"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.36.040306.132700","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26551310","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: 70
Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. 对称、形式和形状:大分子机器稳健性的指导原则。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102010
Florence Tama, Charles L Brooks
{"title":"Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.","authors":"Florence Tama,&nbsp;Charles L Brooks","doi":"10.1146/annurev.biophys.35.040405.102010","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102010","url":null,"abstract":"<p><p>Computational studies of large macromolecular assemblages have come a long way during the past 10 years. With the explosion of computer power and parallel computing, timescales of molecular dynamics simulations have been extended far beyond the hundreds of picoseconds timescale. However, limitations remain for studies of large-scale conformational changes occurring on timescales beyond nanoseconds, especially for large macromolecules. In this review, we describe recent methods based on normal mode analysis that have enabled us to study dynamics on the microsecond timescale for large macromolecules using different levels of coarse graining, from atomically detailed models to those employing only low-resolution structural information. Emerging from such studies is a control principle for robustness in Nature's machines. We discuss this idea in the context of large-scale functional reorganization of the ribosome, virus particles, and the muscle protein myosin.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"115-33"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26015591","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: 259
Computer-based design of novel protein structures. 基于计算机的新型蛋白质结构设计。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102046
Glenn L Butterfoss, Brian Kuhlman
{"title":"Computer-based design of novel protein structures.","authors":"Glenn L Butterfoss,&nbsp;Brian Kuhlman","doi":"10.1146/annurev.biophys.35.040405.102046","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102046","url":null,"abstract":"<p><p>Over the past 10 years there has been tremendous success in the area of computational protein design. Protein design software has been used to stabilize proteins, solubilize membrane proteins, design intermolecular interactions, and design new protein structures. A key motivation for these studies is that they test our understanding of protein energetics and structure. De novo design of novel structures is a particularly rigorous test because the protein backbone must be designed in addition to the amino acid side chains. A priori it is not guaranteed that the target backbone is even designable. To address this issue, researchers have developed a variety of methods for generating protein-like scaffolds and for optimizing the protein backbone in conjunction with the amino acid sequence. These protocols have been used to design proteins from scratch and to explore sequence space for naturally occurring protein folds.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"49-65"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102046","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26016803","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: 129
NMR techniques for very large proteins and rnas in solution. 溶液中非常大的蛋白质和rna的核磁共振技术。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102034
Andreas G Tzakos, Christy R R Grace, Peter J Lukavsky, Roland Riek
{"title":"NMR techniques for very large proteins and rnas in solution.","authors":"Andreas G Tzakos,&nbsp;Christy R R Grace,&nbsp;Peter J Lukavsky,&nbsp;Roland Riek","doi":"10.1146/annurev.biophys.35.040405.102034","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102034","url":null,"abstract":"<p><p>Three-dimensional structure determination of small proteins and oligonucleotides by solution NMR is established. With the development of novel NMR and labeling techniques, structure determination is now feasible for proteins with a molecular mass of up to approximately 100 kDa and RNAs of up to 35 kDa. Beyond these molecular masses special techniques and approaches are required for applying NMR as a multiprobe method for structural investigations of proteins and RNAs. It is the aim of this review to summarize the NMR techniques and approaches available to advance the molecular mass limit of NMR both for proteins (up to 1 MDa) and RNAs (up to 100 kDa). Physical pictures of the novel techniques, their experimental applications, as well as labeling and assignment strategies are discussed and accompanied by future perspectives.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"319-42"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102034","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26014801","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: 102
Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes. 用质谱法探测大分子复合物结构的辐射分解蛋白足迹。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102050
Keiji Takamoto, Mark R Chance
{"title":"Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes.","authors":"Keiji Takamoto,&nbsp;Mark R Chance","doi":"10.1146/annurev.biophys.35.040405.102050","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102050","url":null,"abstract":"<p><p>Structural proteomics approaches using mass spectrometry are increasingly used in biology to examine the composition and structure of macromolecules. Hydroxyl radical-mediated protein footprinting using mass spectrometry has recently been developed to define structure, assembly, and conformational changes of macromolecules in solution based on measurements of reactivity of amino acid side chain groups with covalent modification reagents. Accurate measurements of side chain reactivity are achieved using quantitative liquid-chromatography-coupled mass spectrometry, whereas the side chain modification sites are identified using tandem mass spectrometry. In addition, the use of footprinting data in conjunction with computational modeling approaches is a powerful new method for testing and refining structural models of macromolecules and their complexes. In this review, we discuss the basic chemistry of hydroxyl radical reactions with peptides and proteins, highlight various approaches to map protein structure using radical oxidation methods, and describe state-of-the-art approaches to combine computational and footprinting data.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"251-76"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102050","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26015597","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: 233
Continuous membrane-cytoskeleton adhesion requires continuous accommodation to lipid and cytoskeleton dynamics. 连续的膜-细胞骨架粘附需要持续适应脂质和细胞骨架动力学。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102017
Michael P Sheetz, Julia E Sable, Hans-Günther Döbereiner
{"title":"Continuous membrane-cytoskeleton adhesion requires continuous accommodation to lipid and cytoskeleton dynamics.","authors":"Michael P Sheetz,&nbsp;Julia E Sable,&nbsp;Hans-Günther Döbereiner","doi":"10.1146/annurev.biophys.35.040405.102017","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102017","url":null,"abstract":"<p><p>The plasma membrane of most animal cells conforms to the cytoskeleton and only occasionally separates to form blebs. Previous studies indicated that many weak interactions between cytoskeleton and the lipid bilayer kept the surfaces together to counteract the normal outward pressure of cytoplasm. Either the loss of adhesion strength or the formation of gaps in the cytoskeleton enables the pressure to form blebs. Membrane-associated cytoskeleton proteins, such as spectrin and filamin, can control the movement and aggregation of membrane proteins and lipids, e.g., phosphoinositol phospholipids (PIPs), as well as blebbing. At the same time, lipids (particularly PIPs) and membrane proteins affect cytoskeleton and signaling dynamics. We consider here the roles of the major phosphatidylinositol-4,5-diphosphate (PIP2) binding protein, MARCKS, and PIP2 levels in controlling cytoskeleton dynamics. Further understanding of dynamics will provide important clues about how membrane-cytoskeleton adhesion rapidly adjusts to cytoskeleton and membrane dynamics.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"417-34"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26014805","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: 272
Cryo-electron microscopy of spliceosomal components. 剪接体成分的低温电子显微镜。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.101953
Holger Stark, Reinhard Lührmann
{"title":"Cryo-electron microscopy of spliceosomal components.","authors":"Holger Stark,&nbsp;Reinhard Lührmann","doi":"10.1146/annurev.biophys.35.040405.101953","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.101953","url":null,"abstract":"<p><p>Splicing is an essential step of gene expression in which introns are removed from pre-mRNA to generate mature mRNA that can be translated by the ribosome. This reaction is catalyzed by a large and dynamic macromolecular RNP complex called the spliceosome. The spliceosome is formed by the stepwise integration of five snRNPs composed of U1, U2, U4, U5, and U6 snRNAs and more than 150 proteins binding sequentially to pre-mRNA. To study the structure of this particularly dynamic RNP machine that undergoes many changes in composition and conformation, single-particle cryo-electron microscopy (cryo-EM) is currently the method of choice. In this review, we present the results of these cryo-EM studies along with some new perspectives on structural and functional aspects of splicing, and we outline the perspectives and limitations of the cryo-EM technique in obtaining structural information about macromolecular complexes, such as the spliceosome, involved in splicing.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"435-57"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.101953","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26014806","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: 107
Roles of bilayer material properties in function and distribution of membrane proteins. 双层材料性质在膜蛋白功能和分布中的作用。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102022
Thomas J McIntosh, Sidney A Simon
{"title":"Roles of bilayer material properties in function and distribution of membrane proteins.","authors":"Thomas J McIntosh,&nbsp;Sidney A Simon","doi":"10.1146/annurev.biophys.35.040405.102022","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102022","url":null,"abstract":"<p><p>Structural, compositional, and material (elastic) properties of lipid bilayers exert strong influences on the interactions of water-soluble proteins and peptides with membranes, the distribution of transmembrane proteins in the plane of the membrane, and the function of specific membrane channels. Theoretical and experimental studies show that the binding of either cytoplasmic proteins or extracellular peptides to membranes is regulated by the presence of charged lipids and that the sorting of transmembrane proteins into or out of membrane microdomains (rafts) depends on several factors, including bilayer material properties governed by the presence of cholesterol. Recent studies have also shown that bilayer material properties modify the permeability of membrane pores, formed either by protein channels or by cell-lytic peptides.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"177-98"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102022","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26015594","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: 229
Evolutionary relationships and structural mechanisms of AAA+ proteins. AAA+蛋白的进化关系及结构机制。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.101933
Jan P Erzberger, James M Berger
{"title":"Evolutionary relationships and structural mechanisms of AAA+ proteins.","authors":"Jan P Erzberger,&nbsp;James M Berger","doi":"10.1146/annurev.biophys.35.040405.101933","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.101933","url":null,"abstract":"<p><p>Complex cellular events commonly depend on the activity of molecular \"machines\" that efficiently couple enzymatic and regulatory functions within a multiprotein assembly. An essential and expanding subset of these assemblies comprises proteins of the ATPases associated with diverse cellular activities (AAA+) family. The defining feature of AAA+ proteins is a structurally conserved ATP-binding module that oligomerizes into active arrays. ATP binding and hydrolysis events at the interface of neighboring subunits drive conformational changes within the AAA+ assembly that direct translocation or remodeling of target substrates. In this review, we describe the critical features of the AAA+ domain, summarize our current knowledge of how this versatile element is incorporated into larger assemblies, and discuss specific adaptations of the AAA+ fold that allow complex molecular manipulations to be carried out for a highly diverse set of macromolecular targets.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"93-114"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.101933","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26016804","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: 726
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：481959085
Book学术官方微信