Annual review of biophysics and biomolecular structure最新文献_第2页

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

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, 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":"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.","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

引用次数: 275

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

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, 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":"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.","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

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

引用次数: 0

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, Petra Schwille","doi":"10.1146/annurev.biophys.36.040306.132612","DOIUrl":"https://doi.org/10.1146/annurev.biophys.36.040306.132612","url":null,"abstract":"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.","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

引用次数: 141

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

引用次数: 324

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, 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":"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.","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