Annual review of biophysics and biomolecular structure最新文献_第5页

Spinach on the ceiling: a theoretical chemist's return to biology. 天花板上的菠菜:一位理论化学家回归生物学。

Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.33.110502.133350

Martin Karplus

引用次数: 44

Quantitative fluorescent speckle microscopy of cytoskeleton dynamics. 细胞骨架动力学的定量荧光散斑显微镜。

Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102114

Gaudenz Danuser, Clare M Waterman-Storer

引用次数: 210

Chemical synthesis of proteins. 蛋白质的化学合成。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144700

Bradley L Nilsson, Matthew B Soellner, Ronald T Raines

引用次数: 205

Modeling water, the hydrophobic effect, and ion solvation. 模拟水，疏水效应，和离子溶剂化。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144517

Ken A Dill, Thomas M Truskett, Vojko Vlachy, Barbara Hribar-Lee

{"title":"Modeling water, the hydrophobic effect, and ion solvation.","authors":"Ken A Dill, Thomas M Truskett, Vojko Vlachy, Barbara Hribar-Lee","doi":"10.1146/annurev.biophys.34.040204.144517","DOIUrl":"https://doi.org/10.1146/annurev.biophys.34.040204.144517","url":null,"abstract":"Water plays a central role in the structures and properties of biomolecules--proteins, nucleic acids, and membranes--and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global properties-water's thermodynamics, phase diagram, and solvation properties, for example-and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of water-as a pure liquid and as a solvent-derive from the geometric and hydrogen bonding properties of water.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"34 ","pages":"173-99"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.34.040204.144517","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25090625","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: 336

Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: high-speed single-molecule tracking of membrane molecules. 质膜概念从二维连续流体到分割流体的范式转换:膜分子的高速单分子跟踪。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144637

Akihiro Kusumi, Chieko Nakada, Ken Ritchie, Kotono Murase, Kenichi Suzuki, Hideji Murakoshi, Rinshi S Kasai, Junko Kondo, Takahiro Fujiwara

{"title":"Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: high-speed single-molecule tracking of membrane molecules.","authors":"Akihiro Kusumi, Chieko Nakada, Ken Ritchie, Kotono Murase, Kenichi Suzuki, Hideji Murakoshi, Rinshi S Kasai, Junko Kondo, Takahiro Fujiwara","doi":"10.1146/annurev.biophys.34.040204.144637","DOIUrl":"https://doi.org/10.1146/annurev.biophys.34.040204.144637","url":null,"abstract":"Recent advancements in single-molecule tracking methods with nanometer-level precision now allow researchers to observe the movement, recruitment, and activation of single molecules in the plasma membrane in living cells. In particular, on the basis of the observations by high-speed single-particle tracking at a frame rate of 40,000 frames s(1), the partitioning of the fluid plasma membrane into submicron compartments throughout the cell membrane and the hop diffusion of virtually all the molecules have been proposed. This could explain why the diffusion coefficients in the plasma membrane are considerably smaller than those in artificial membranes, and why the diffusion coefficient is reduced upon molecular complex formation (oligomerization-induced trapping). In this review, we first describe the high-speed single-molecule tracking methods, and then we critically review a new model of a partitioned fluid plasma membrane and the involvement of the actin-based membrane-skeleton \"fences\" and anchored-transmembrane protein \"pickets\" in the formation of compartment boundaries.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"34 ","pages":"351-78"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.34.040204.144637","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25091039","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: 1079

Membrane-protein interactions in cell signaling and membrane trafficking. 细胞信号传导和膜运输中的膜-蛋白相互作用。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.33.110502.133337

Wonhwa Cho, Robert V Stahelin

{"title":"Membrane-protein interactions in cell signaling and membrane trafficking.","authors":"Wonhwa Cho, Robert V Stahelin","doi":"10.1146/annurev.biophys.33.110502.133337","DOIUrl":"https://doi.org/10.1146/annurev.biophys.33.110502.133337","url":null,"abstract":"Research in the past decade has revealed that many cytosolic proteins are recruited to different cellular membranes to form protein-protein and lipid-protein interactions during cell signaling and membrane trafficking. Membrane recruitment of these peripheral proteins is mediated by a growing number of modular membrane-targeting domains, including C1, C2, PH, FYVE, PX, ENTH, ANTH, BAR, FERM, and tubby domains, that recognize specific lipid molecules in the membranes. Structural studies of these membrane-targeting domains demonstrate how they specifically recognize their cognate lipid ligands. However, the mechanisms by which these domains and their host proteins are recruited to and interact with various cell membranes are only beginning to unravel with recent computational studies, in vitro membrane binding studies using model membranes, and cellular translocation studies using fluorescent protein-tagged proteins. This review summarizes the recent progress in our understanding of how the kinetics and energetics of membrane-protein interactions are regulated during the cellular membrane targeting and activation of peripheral proteins.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"34 ","pages":"119-51"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.33.110502.133337","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25091611","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: 569

Toward predictive models of mammalian cells. 哺乳动物细胞的预测模型。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144415

Avi Ma'ayan, Robert D Blitzer, Ravi Iyengar

{"title":"Toward predictive models of mammalian cells.","authors":"Avi Ma'ayan, Robert D Blitzer, Ravi Iyengar","doi":"10.1146/annurev.biophys.34.040204.144415","DOIUrl":"https://doi.org/10.1146/annurev.biophys.34.040204.144415","url":null,"abstract":"Progress in experimental and theoretical biology is likely to provide us with the opportunity to assemble detailed predictive models of mammalian cells. Using a functional format to describe the organization of mammalian cells, we describe current approaches for developing qualitative and quantitative models using data from a variety of experimental sources. Recent developments and applications of graph theory to biological networks are reviewed. The use of these qualitative models to identify the topology of regulatory motifs and functional modules is discussed. Cellular homeostasis and plasticity are interpreted within the framework of balance between regulatory motifs and interactions between modules. From this analysis we identify the need for detailed quantitative models on the basis of the representation of the chemistry underlying the cellular process. The use of deterministic, stochastic, and hybrid models to represent cellular processes is reviewed, and an initial integrated approach for the development of large-scale predictive models of a mammalian cell is presented.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"34 ","pages":"319-49"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.34.040204.144415","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25091040","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: 106

Single-molecule RNA science. 单分子RNA科学。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144641

Xiaowei Zhuang

引用次数: 156

Tracking topoisomerase activity at the single-molecule level. 在单分子水平上跟踪拓扑异构酶活性。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144433

G Charvin, T R Strick, D Bensimon, V Croquette

引用次数: 92

Use of EPR power saturation to analyze the membrane-docking geometries of peripheral proteins: applications to C2 domains. 使用EPR功率饱和分析外周蛋白的膜对接几何形状:在C2结构域的应用。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144534

Nathan J Malmberg, Joseph J Falke

引用次数: 65