Annual review of biophysics and biomolecular structure最新文献_第6页

The structure-function dilemma of the hammerhead ribozyme. 锤头核酶的结构-功能困境。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.122004.184428

Kenneth F Blount, Olke C Uhlenbeck

{"title":"The structure-function dilemma of the hammerhead ribozyme.","authors":"Kenneth F Blount, Olke C Uhlenbeck","doi":"10.1146/annurev.biophys.34.122004.184428","DOIUrl":"https://doi.org/10.1146/annurev.biophys.34.122004.184428","url":null,"abstract":"A powerful approach to understanding protein enzyme catalysis is to examine the structural context of essential amino acid side chains whose deletion or modification negatively impacts catalysis. In principle, this approach can be even more powerful for RNA enzymes, given the wide variety and subtlety of functionally modified nucleotides now available. Numerous recent success stories confirm the utility of this approach to understanding ribozyme function. An anomaly, however, is the hammerhead ribozyme, for which the structural and functional data do not agree well, preventing a unifying view of its catalytic mechanism from emerging. To delineate the hammerhead structure-function comparison, we have evaluated and distilled the large body of biochemical data into a consensus set of functional groups unambiguously required for hammerhead catalysis. By examining the context of these functional groups within available structures, we have established a concise set of disagreements between the structural and functional data. The number and relative distribution of these inconsistencies throughout the hammerhead reaffirms that an extensive conformational rearrangement from the fold observed in the crystal structure must be necessary for cleavage to occur. The nature and energetic driving force of this conformational isomerization are discussed.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"34 ","pages":"415-40"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.34.122004.184428","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25263961","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

How well can simulation predict protein folding kinetics and thermodynamics? 模拟能在多大程度上预测蛋白质折叠动力学和热力学?

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144447

Christopher D Snow, Eric J Sorin, Young Min Rhee, Vijay S Pande

引用次数: 225

Protein-DNA recognition patterns and predictions. 蛋白质- dna识别模式和预测。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144537

Akinori Sarai, Hidetoshi Kono

引用次数: 181

Structural and sequence motifs of protein (histone) methylation enzymes. 蛋白质(组蛋白)甲基化酶的结构和序列基序。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144452

Xiaodong Cheng, Robert E Collins, Xing Zhang

引用次数: 336

Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size. 环状DNA凝聚体:揭示精细结构和成核在确定大小中的作用。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144500

Nicholas V Hud, Igor D Vilfan

{"title":"Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size.","authors":"Nicholas V Hud, Igor D Vilfan","doi":"10.1146/annurev.biophys.34.040204.144500","DOIUrl":"https://doi.org/10.1146/annurev.biophys.34.040204.144500","url":null,"abstract":"Toroidal DNA condensates have attracted the attention of biophysicists, biochemists, and polymer physicists for more than thirty years. In the biological community, the quest to understand DNA toroid formation has been motivated by its relevance to gene packing in certain viruses and by the potential use of DNA toroids in artificial gene delivery (e.g., gene therapy). In the physical sciences, DNA toroids are appreciated as a superb model system for studying particle formation by the collapse of a semiflexible, polyelectrolyte polymer. This review focuses on experimental studies from the past few years that have significantly increased our understanding of DNA toroid structure and the mechanism of their formation. Highlights include structural studies that show the DNA strands within toroids to be packed in an ideal hexagonal lattice, and also in regions with a nonhexagonal lattice that are required by the topological constraints associated with winding DNA into a toroid. Recent studies of DNA toroid formation have also revealed that toroid size limits result from a complex interplay between kinetic and thermodynamic factors that govern both toroid nucleation and growth. The work discussed in this review indicates that it will ultimately be possible to obtain substantial control over DNA toroid dimensions.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"34 ","pages":"295-318"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.34.040204.144500","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25091037","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: 189

Ligand-target interactions: what can we learn from NMR? 配体-靶相互作用:我们能从核磁共振中学到什么?

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144419

Teresa Carlomagno

{"title":"Ligand-target interactions: what can we learn from NMR?","authors":"Teresa Carlomagno","doi":"10.1146/annurev.biophys.34.040204.144419","DOIUrl":"https://doi.org/10.1146/annurev.biophys.34.040204.144419","url":null,"abstract":"The conformation of the ligand in complex with a macromolecular target can be studied by nuclear magnetic resonance (NMR) in solution for both tightly and weakly forming complexes. In the weak binding regime (k(off) > 10(4) Hz), the structure of the bound ligand is accessible also for very large complexes (>100 kDa), which are not amenable to NMR studies in the tight binding regime. Here I review the state-of-the-art NMR methodology used for screening ligands and for the structural investigation of bound ligand conformations, in both tight and weak binding regimes. The advantages and disadvantages of each approach are critically described. The NMR methodology used to investigate transiently forming complexes has expanded considerably in the past few years, opening new possibilities for a detailed description of ligand-target interactions. Novel methods for the determination of the bound ligand conformation, in particular transferred cross-correlated relaxation, are thoroughly reviewed, and their advantages with respect to established methodology are discussed, using the epothilone-tubulin complex as a primary example.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"34 ","pages":"245-66"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.34.040204.144419","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25091036","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: 87

A quiet life with proteins. 有蛋白质的安静生活。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144531

David Davies

引用次数: 4

Ions and RNA folding. 离子和RNA折叠。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144511

David E Draper, Dan Grilley, Ana Maria Soto

引用次数: 411

Communication between noncontacting macromolecules. 非接触大分子之间的通信。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.33.110502.133332

Jens Völker, Kenneth J Breslauer

{"title":"Communication between noncontacting macromolecules.","authors":"Jens Völker, Kenneth J Breslauer","doi":"10.1146/annurev.biophys.33.110502.133332","DOIUrl":"https://doi.org/10.1146/annurev.biophys.33.110502.133332","url":null,"abstract":"Molecular interactions are the language that molecules use to communicate recognition, binding, and regulation, events central to biological control mechanisms. Traditionally, such interactions involve direct, atom-to-atom, noncovalent contacts, or indirect contacts bridged by relatively fixed solvent molecules. Here we discuss a third class of molecular communication that, to date, has received less experimental attention, namely solvent-mediated communication between noncontacting macromolecules. This form of communication can be understood in terms of fundamental, well-established principles (coupled equilibria and linkage thermodynamics) that govern interactions between individual polymers and their solutions. In contrast to simple solutions used in laboratory studies, biological systems contain a multitude of nominally noninteracting biopolymers within the same solution environment. The exquisite control of biological function requires some form of communication between many of these solution components, even in the absence of direct and/or indirect contacts. Such communication must be considered when describing potential mechanisms of biological regulation.","PeriodicalId":8270,"journal":{"name":"Annual review of biophysics and biomolecular structure","volume":"34 ","pages":"21-42"},"PeriodicalIF":0.0,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.biophys.33.110502.133332","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25091608","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: 25

Ion conduction and selectivity in K(+) channels. 离子在K(+)通道中的传导和选择性。

Annual review of biophysics and biomolecular structure Pub Date : 2005-01-01 DOI: 10.1146/annurev.biophys.34.040204.144655

Benoît Roux

引用次数: 146