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Annual review of biophysics and biomolecular structure最新文献

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Lessons from lactose permease. 乳糖渗透酶的教训。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102005
Lan Guan, H Ronald Kaback
{"title":"Lessons from lactose permease.","authors":"Lan Guan,&nbsp;H Ronald Kaback","doi":"10.1146/annurev.biophys.35.040405.102005","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102005","url":null,"abstract":"<p><p>An X-ray structure of the lactose permease of Escherichia coli (LacY) in an inward-facing conformation has been solved. LacY contains N- and C-terminal domains, each with six transmembrane helices, positioned pseudosymmetrically. Ligand is bound at the apex of a hydrophilic cavity in the approximate middle of the molecule. Residues involved in substrate binding and H+ translocation are aligned parallel to the membrane at the same level and may be exposed to a water-filled cavity in both the inward- and outward-facing conformations, thereby allowing both sugar and H+ release directly into either cavity. These structural features may explain why LacY catalyzes galactoside/H+ symport in both directions utilizing the same residues. A working model for the mechanism is presented that involves alternating access of both the sugar- and H+-binding sites to either side of the membrane.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"67-91"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26016805","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: 324
The ESCRT complexes: structure and mechanism of a membrane-trafficking network. ESCRT复合物:膜转运网络的结构和机制。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102126
James H Hurley, Scott D Emr
{"title":"The ESCRT complexes: structure and mechanism of a membrane-trafficking network.","authors":"James H Hurley,&nbsp;Scott D Emr","doi":"10.1146/annurev.biophys.35.040405.102126","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102126","url":null,"abstract":"<p><p>The ESCRT complexes and associated proteins comprise a major pathway for the lysosomal degradation of transmembrane proteins and are critical for receptor downregulation, budding of the HIV virus, and other normal and pathological cell processes. The ESCRT system is conserved from yeast to humans. The ESCRT complexes form a network that recruits monoubiquitinated proteins and drives their internalization into lumenal vesicles within a type of endosome known as a multivesicular body. The structures and interactions of many of the components have been determined over the past three years, revealing mechanisms for membrane and cargo recruitment and for complex assembly.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"277-98"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102126","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26014800","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: 556
Single-molecule analysis of RNA polymerase transcription. RNA聚合酶转录的单分子分析。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.010406.150153
Lu Bai, Thomas J Santangelo, Michelle D Wang
{"title":"Single-molecule analysis of RNA polymerase transcription.","authors":"Lu Bai,&nbsp;Thomas J Santangelo,&nbsp;Michelle D Wang","doi":"10.1146/annurev.biophys.35.010406.150153","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.010406.150153","url":null,"abstract":"<p><p>The kinetics and mechanisms of transcription are now being investigated by a repertoire of single-molecule techniques, including optical and magnetic tweezers, high-sensitivity fluorescence techniques, and atomic force microscopy. Single-molecule techniques complement traditional biochemical and crystallographic approaches, are capable of detecting the motions and dynamics of individual RNAP molecules and transcription complexes in real time, and make it possible to directly measure RNAP binding to and unwinding of template DNA, as well as RNAP translocation along the DNA during transcript synthesis.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"343-60"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.010406.150153","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26014802","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: 131
Fusion pores and fusion machines in Ca2+-triggered exocytosis. Ca2+触发胞吐作用中的融合孔和融合机。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.101958
Meyer B Jackson, Edwin R Chapman
{"title":"Fusion pores and fusion machines in Ca2+-triggered exocytosis.","authors":"Meyer B Jackson,&nbsp;Edwin R Chapman","doi":"10.1146/annurev.biophys.35.040405.101958","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.101958","url":null,"abstract":"<p><p>Exocytosis is initiated within a highly localized region of contact between two biological membranes. Small areas of these membranes draw close, molecules on the two surfaces interact, and structural transformations take place. Membrane fusion requires the action of proteins specialized for this task, and these proteins act as a fusion machine. At a critical point in this process, a fusion pore forms within the membrane contact site and then expands as the spherical vesicle merges with the flat target membrane. Hence, the operation of a fusion machine must be realized through the formation and expansion of a fusion pore. Delineating the relation between the fusion machine and the fusion pore thus emerges as a central goal in elucidating the mechanisms of membrane fusion. We summarize present knowledge of fusion machines and fusion pores studied in vitro, in neurons, and in neuroendocrine cells, and synthesize this knowledge into some specific and detailed hypotheses for exocytosis.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"135-60"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.101958","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26015592","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: 190
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. 核糖体动力学:从原子结构建模到低温电子显微镜图的见解。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.101950
Kakoli Mitra, Joachim Frank
{"title":"Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps.","authors":"Kakoli Mitra,&nbsp;Joachim Frank","doi":"10.1146/annurev.biophys.35.040405.101950","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.101950","url":null,"abstract":"<p><p>Single-particle cryo-electron microscopy (cryo-EM) is the method of choice for studying the dynamics of macromolecular machines both at a phenomenological and, increasingly, at the molecular level, with the advent of high-resolution component X-ray structures and of progressively improving fitting algorithms. Cryo-EM has shed light on the structure of the ribosome during the four steps of translation: initiation, elongation, termination, and recycling. Interpretation of cryo-EM reconstructions of the ribosome in quasi-atomic detail reveals a picture in which the ribosome uses RNA not only to catalyze chemical reactions, but also as a means for signal transduction over large distances.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"299-317"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.101950","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26015598","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: 137
Mechanotransduction involving multimodular proteins: converting force into biochemical signals. 涉及多模蛋白的机械转导:将力转化为生化信号。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102013
Viola Vogel
{"title":"Mechanotransduction involving multimodular proteins: converting force into biochemical signals.","authors":"Viola Vogel","doi":"10.1146/annurev.biophys.35.040405.102013","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102013","url":null,"abstract":"<p><p>Cells can sense and transduce a broad range of mechanical forces into distinct sets of biochemical signals that ultimately regulate cellular processes, including adhesion, proliferation, differentiation, and apoptosis. Deciphering at the nanoscale the design principles by which sensory elements are integrated into structural protein motifs whose conformations can be switched mechanically is crucial to understand the process of transduction of force into biochemical signals that are then integrated to regulate mechanoresponsive pathways. While the major focus in the search for mechanosensory units has been on membrane proteins such as ion channels, integrins, and associated cytoplasmic complexes, a multimodular design of tandem repeats of various structural motifs is ubiquitously found among extracellular matrix proteins, as well as cell adhesion molecules, and among many intracellular players that physically link transmembrane proteins to the contractile cytoskeleton. Single-molecule studies have revealed an unexpected richness of mechanosensory motifs, including force-regulated conformational changes of loop-exposed molecular recognition sites, intermediate states in the unraveling pathway that might either expose cryptic binding or phosphorylation sites, or regions that display enzymatic activity only when unmasked by force. Insights into mechanochemical signal conversion principles will also affect various technological fields, from biotechnology to tissue engineering and drug development.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"459-88"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26014807","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: 425
Electron tomography of membrane-bound cellular organelles. 膜结合细胞器的电子断层扫描。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102039
Terrence G Frey, Guy A Perkins, Mark H Ellisman
{"title":"Electron tomography of membrane-bound cellular organelles.","authors":"Terrence G Frey,&nbsp;Guy A Perkins,&nbsp;Mark H Ellisman","doi":"10.1146/annurev.biophys.35.040405.102039","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102039","url":null,"abstract":"<p><p>Electron microscope tomography produces three-dimensional reconstructions and has been used to image organelles both isolated and in situ, providing new insight into their structure and function. It is analogous to the various tomographies used in medical imaging. Compared with light microscopy, electron tomography offers an improvement in resolution of 30- to 80-fold and currently ranges from 3 to 8 nm, thus filling the gap between high-resolution structure determinations of isolated macromolecules and larger-scale studies on cells and tissues by light microscopy. Here, we provide an introduction to electron tomography and applications of the method in characterizing organelle architecture that also show its power for suggesting functional significance. Further improvements in labeling modalities, imaging tools, specimen preparation, and reconstruction algorithms promise to increase the quality and breadth of reconstructions by electron tomography and eventually to allow the mapping of the cellular proteomes onto detailed three-dimensional models of cellular structure.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"199-224"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102039","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26015595","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: 106
Expanding the genetic code. 扩展遗传密码。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.101105.121507
Lei Wang, Jianming Xie, Peter G Schultz
{"title":"Expanding the genetic code.","authors":"Lei Wang,&nbsp;Jianming Xie,&nbsp;Peter G Schultz","doi":"10.1146/annurev.biophys.35.101105.121507","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.101105.121507","url":null,"abstract":"Recently, a general method was developed that makes it possible to genetically encode unnatural amino acids with diverse physical, chemical, or biological properties in Escherichia coli, yeast, and mammalian cells. More than 30 unnatural amino acids have been incorporated into proteins with high fidelity and efficiency by means of a unique codon and corresponding tRNA/aminoacyl-tRNA synthetase pair. These include fluorescent, glycosylated, metal-ion-binding, and redox-active amino acids, as well as amino acids with unique chemical and photochemical reactivity. This methodology provides a powerful tool both for exploring protein structure and function in vitro and in vivo and for generating proteins with new or enhanced properties.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"225-49"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.101105.121507","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26015596","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: 114
Water mediation in protein folding and molecular recognition. 水在蛋白质折叠和分子识别中的调解作用。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102134
Yaakov Levy, José N Onuchic
{"title":"Water mediation in protein folding and molecular recognition.","authors":"Yaakov Levy,&nbsp;José N Onuchic","doi":"10.1146/annurev.biophys.35.040405.102134","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102134","url":null,"abstract":"<p><p>Water is essential for life in many ways, and without it biomolecules might no longer truly be biomolecules. In particular, water is important to the structure, stability, dynamics, and function of biological macromolecules. In protein folding, water mediates the collapse of the chain and the search for the native topology through a funneled energy landscape. Water actively participates in molecular recognition by mediating the interactions between binding partners and contributes to either enthalpic or entropic stabilization. Accordingly, water must be included in recognition and structure prediction codes to capture specificity. Thus water should not be treated as an inert environment, but rather as an integral and active component of biomolecular systems, where it has both dynamic and structural roles. Focusing on water sheds light on the physics and function of biological machinery and self-assembly and may advance our understanding of the natural design of proteins and nucleic acids.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"389-415"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102134","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26014804","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: 822
RNA folding during transcription. 转录过程中的RNA折叠。
Annual review of biophysics and biomolecular structure Pub Date : 2006-01-01 DOI: 10.1146/annurev.biophys.35.040405.102053
Tao Pan, Tobin Sosnick
{"title":"RNA folding during transcription.","authors":"Tao Pan,&nbsp;Tobin Sosnick","doi":"10.1146/annurev.biophys.35.040405.102053","DOIUrl":"https://doi.org/10.1146/annurev.biophys.35.040405.102053","url":null,"abstract":"<p><p>The evolution of RNA sequence needs to satisfy three requirements: folding, structure, and function. Studies on folding during transcription are related directly to folding in the cell. Understanding RNA folding during transcription requires the elucidation of structure formation and structural changes of the RNA, and the consideration of intrinsic properties of the RNA polymerase and other proteins that interact with the RNA. This review summarizes the research progress in this area and outlines the enormous challenges facing this field. Significant advancement requires the development of new experimental methods and theoretical considerations in all aspects of transcription and RNA folding.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"35 ","pages":"161-75"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.35.040405.102053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26015593","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
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