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Annual review of biophysics and biomolecular structure最新文献

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Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins. 泛素样蛋白翻译后修饰的结构机制。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.36.040306.132820
Billy T Dye, Brenda A Schulman
{"title":"Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins.","authors":"Billy T Dye,&nbsp;Brenda A Schulman","doi":"10.1146/annurev.biophys.36.040306.132820","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.040306.132820","url":null,"abstract":"<p><p>Covalent attachment of ubiquitin-like proteins (Ubls) is a predominant mechanism for regulating protein function in eukaryotes. Several structurally related Ubls, such as ubiquitin, SUMO, NEDD8, and ISG15, modify a vast number of proteins, altering their functions in a variety of ways. Ubl modifications can affect the target's half-life, subcellular localization, enzymatic activity, or ability to interact with protein or DNA partners. Generally, these diverse Ubls are covalently attached via their C termini to their targets by parallel, but specific, cascades involving three classes of enzymes known as E1, E2, and E3. Structures are now available for many protein complexes in E1-E2-E3 cascades, revealing a series of modular building blocks and providing mechanistic insights into their functions.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"131-50"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.36.040306.132820","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26702977","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: 264
Bilayer thickness and membrane protein function: an energetic perspective. 双层厚度与膜蛋白功能:能量视角。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.36.040306.132643
Olaf S Andersen, Roger E Koeppe
{"title":"Bilayer thickness and membrane protein function: an energetic perspective.","authors":"Olaf S Andersen,&nbsp;Roger E Koeppe","doi":"10.1146/annurev.biophys.36.040306.132643","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.040306.132643","url":null,"abstract":"<p><p>The lipid bilayer component of biological membranes is important for the distribution, organization, and function of bilayer-spanning proteins. This regulation is due to both specific lipid-protein interactions and general bilayer-protein interactions, which modulate the energetics and kinetics of protein conformational transitions, as well as the protein distribution between different membrane compartments. The bilayer regulation of membrane protein function arises from the hydrophobic coupling between the protein's hydrophobic domains and the bilayer hydrophobic core, which causes protein conformational changes that involve the protein/bilayer boundary to perturb the adjacent bilayer. Such bilayer perturbations, or deformations, incur an energetic cost, which for a given conformational change varies as a function of the bilayer material properties (bilayer thickness, intrinsic lipid curvature, and the elastic compression and bending moduli). Protein function therefore is regulated by changes in bilayer material properties, which determine the free-energy changes caused by the protein-induced bilayer deformation. The lipid bilayer thus becomes an allosteric regulator of membrane function.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"107-30"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.36.040306.132643","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26522005","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: 754
Small-angle X-ray scattering from RNA, proteins, and protein complexes. RNA、蛋白质和蛋白质复合物的小角度x射线散射。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.36.040306.132655
Jan Lipfert, Sebastian Doniach
{"title":"Small-angle X-ray scattering from RNA, proteins, and protein complexes.","authors":"Jan Lipfert,&nbsp;Sebastian Doniach","doi":"10.1146/annurev.biophys.36.040306.132655","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.040306.132655","url":null,"abstract":"<p><p>Small-angle X-ray scattering (SAXS) is increasingly used to characterize the structure and interactions of biological macromolecules and their complexes in solution. Although still a low-resolution technique, the advent of high-flux synchrotron sources and the development of algorithms for the reconstruction of 3-D electron density maps from 1-D scattering profiles have made possible the generation of useful low-resolution molecular models from SAXS data. Furthermore, SAXS is well suited for the study of unfolded or partially folded conformational ensembles as a function of time or solution conditions. Here, we review recently developed algorithms for 3-D structure modeling and applications to protein complexes. Furthermore, we discuss the emerging use of SAXS as a tool to study membrane protein-detergent complexes. SAXS is proving useful to study the folding of functional RNA molecules, and finally we discuss uses of SAXS to study ensembles of denatured proteins.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"307-27"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.36.040306.132655","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26539687","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: 275
From "simple" DNA-protein interactions to the macromolecular machines of gene expression. 从“简单”的dna -蛋白质相互作用到基因表达的大分子机器。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.34.040204.144521
Peter H von Hippel
{"title":"From \"simple\" DNA-protein interactions to the macromolecular machines of gene expression.","authors":"Peter H von Hippel","doi":"10.1146/annurev.biophys.34.040204.144521","DOIUrl":"https://doi.org/10.1146/annurev.biophys.34.040204.144521","url":null,"abstract":"<p><p>The physicochemical concepts that underlie our present ideas on the structure and assembly of the \"macromolecular machines of gene expression\" are developed, starting with the structure and folding of the individual protein and DNA components, the thermodynamics and kinetics of their conformational rearrangements during complex assembly, and the molecular basis of the sequence specificity and recognition interactions of the final assemblies that include the DNA genome. The role of diffusion in reduced dimensions in the kinetics of the assembly of macromolecular machines from their components is also considered, and diffusion-driven reactions are compared with those fueled by ATP binding and hydrolysis, as well as by the specific covalent chemical modifications involved in rearranging chromatin and modifying signal transduction networks in higher organisms.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"79-105"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.34.040204.144521","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26702976","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: 111
Visualizing flexibility at molecular resolution: analysis of heterogeneity in single-particle electron microscopy reconstructions. 可视化柔韧性在分子分辨率:分析异质性在单粒子电子显微镜重建。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.36.040306.132742
Andres E Leschziner, Eva Nogales
{"title":"Visualizing flexibility at molecular resolution: analysis of heterogeneity in single-particle electron microscopy reconstructions.","authors":"Andres E Leschziner,&nbsp;Eva Nogales","doi":"10.1146/annurev.biophys.36.040306.132742","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.040306.132742","url":null,"abstract":"<p><p>It is becoming increasingly clear that many macromolecules are intrinsically flexible and exist in multiple conformations in solution. Single-particle reconstruction of vitrified samples (cryo-electron microscopy, or cryo-EM) is uniquely positioned to visualize this conformational flexibility in its native state. Although heterogeneity remains a significant challenge in cryo-EM single-particle analysis, recent efforts in the field point to a future where it will be possible to tap into this rich source of biological information on a routine basis. In this article, we review the basic principles behind a few relatively new and generally applicable methods that show particular promise as tools to analyze macromolecular flexibility. We also discuss some of their recent applications to problems of biological interest.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"43-62"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.36.040306.132742","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26470284","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: 108
Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides. 从晶体学研究到核酸类似物和化学修饰的DNA和RNA寡核苷酸的结构和配对特性的见解。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.36.040306.132556
Martin Egli, Pradeep S Pallan
{"title":"Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides.","authors":"Martin Egli,&nbsp;Pradeep S Pallan","doi":"10.1146/annurev.biophys.36.040306.132556","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.040306.132556","url":null,"abstract":"<p><p>Chemically modified nucleic acids function as model systems for native DNA and RNA; as chemical probes in diagnostics or the analysis of protein-nucleic acid interactions and in high-throughput genomics and drug target validation; as potential antigene-, antisense-, or RNAi-based drugs; and as tools for structure determination (i.e., crystallographic phasing), just to name a few. Biophysical and structural investigations of chemically modified DNAs and RNAs, particularly of nucleic acid analogs with more significant alterations to the well-known base-sugar-phosphate framework (i.e., peptide or hexopyranose nucleic acids), can also provide insights into the properties of the natural nucleic acids that are beyond the reach of studies focusing on DNA or RNA alone. In this review we summarize results from crystallographic analyses of chemically modified DNAs and RNAs that are primarily of interest in the context of the discovery and development of oligonucleotide-based therapeutics. In addition, we re-examine recent structural data on nucleic acid analogs that are investigated as part of a systematic effort to rationalize nature's choice of pentose in the genetic system.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"281-305"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.36.040306.132556","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26542122","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: 57
Fluorescence correlation spectroscopy: novel variations of an established technique. 荧光相关光谱学:一种已建立的技术的新变化。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.36.040306.132612
Elke Haustein, Petra Schwille
{"title":"Fluorescence correlation spectroscopy: novel variations of an established technique.","authors":"Elke Haustein,&nbsp;Petra Schwille","doi":"10.1146/annurev.biophys.36.040306.132612","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.040306.132612","url":null,"abstract":"<p><p>Fluorescence correlation spectroscopy (FCS) is one of the major biophysical techniques used for unraveling molecular interactions in vitro and in vivo. It allows minimally invasive study of dynamic processes in biological specimens with extremely high temporal and spatial resolution. By recording and correlating the fluorescence fluctuations of single labeled molecules through the exciting laser beam, FCS gives information on molecular mobility and photophysical and photochemical reactions. By using dual-color fluorescence cross-correlation, highly specific binding studies can be performed. These have been extended to four reaction partners accessible by multicolor applications. Alternative detection schemes shift accessible time frames to slower processes (e.g., scanning FCS) or higher concentrations (e.g., TIR-FCS). Despite its long tradition, FCS is by no means dated. Rather, it has proven to be a highly versatile technique that can easily be adapted to solve specific biological questions, and it continues to find exciting applications in biology and medicine.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"151-69"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.36.040306.132612","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26702978","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: 512
Physics of proteins. 蛋白质物理学。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.36.040306.132808
Jayanth R Banavar, Amos Maritan
{"title":"Physics of proteins.","authors":"Jayanth R Banavar,&nbsp;Amos Maritan","doi":"10.1146/annurev.biophys.36.040306.132808","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.040306.132808","url":null,"abstract":"<p><p>Globular proteins are a key component of the network of life. Over many decades much experimental data on proteins have been gathered, yet theoretical progress has been somewhat limited. We show that the results accumulated over the years inexorably lead to a unified framework for understanding proteins. The framework predicts the existence of a fixed menu of folds determined by geometry, clarifies the role of the amino acid sequence in selecting the native-state structure from this menu, and explains the propensity for amyloid formation. The experimental data and the new approach reveal an astonishing simplicity underlying the protein problem.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"261-80"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.36.040306.132808","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26702979","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: 141
High-resolution, single-molecule measurements of biomolecular motion. 生物分子运动的高分辨率单分子测量。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.36.101106.101451
William J Greenleaf, Michael T Woodside, Steven M Block
{"title":"High-resolution, single-molecule measurements of biomolecular motion.","authors":"William J Greenleaf,&nbsp;Michael T Woodside,&nbsp;Steven M Block","doi":"10.1146/annurev.biophys.36.101106.101451","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.101106.101451","url":null,"abstract":"<p><p>Many biologically important macromolecules undergo motions that are essential to their function. Biophysical techniques can now resolve the motions of single molecules down to the nanometer scale or even below, providing new insights into the mechanisms that drive molecular movements. This review outlines the principal approaches that have been used for high-resolution measurements of single-molecule motion, including centroid tracking, fluorescence resonance energy transfer, magnetic tweezers, atomic force microscopy, and optical traps. For each technique, the principles of operation are outlined, the capabilities and typical applications are examined, and various practical issues for implementation are considered. Extensions to these methods are also discussed, with an eye toward future application to outstanding biological problems.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"171-90"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.36.101106.101451","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26577182","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: 448
Living with noisy genes: how cells function reliably with inherent variability in gene expression. 与嘈杂的基因一起生活:细胞如何在基因表达的固有变异性下可靠地发挥作用。
Annual review of biophysics and biomolecular structure Pub Date : 2007-01-01 DOI: 10.1146/annurev.biophys.36.040306.132705
Narendra Maheshri, Erin K O'Shea
{"title":"Living with noisy genes: how cells function reliably with inherent variability in gene expression.","authors":"Narendra Maheshri,&nbsp;Erin K O'Shea","doi":"10.1146/annurev.biophys.36.040306.132705","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.040306.132705","url":null,"abstract":"<p><p>Within a population of genetically identical cells there can be significant variation, or noise, in gene expression. Yet even with this inherent variability, cells function reliably. This review focuses on our understanding of noise at the level of both single genes and genetic regulatory networks, emphasizing comparisons between theoretical models and experimental results whenever possible. To highlight the importance of noise, we particularly emphasize examples in which a stochastic description of gene expression leads to a qualitatively different outcome than a deterministic one.</p>","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"36 ","pages":"413-34"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.36.040306.132705","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26702980","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: 324
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