Abstract:
:Self-cleaving hammerhead, hairpin, hepatitis delta virus, and glmS ribozymes comprise a family of small catalytic RNA motifs that catalyze the same reversible phosphodiester cleavage reaction, but each motif adopts a unique structure and displays a unique array of biochemical properties. Recent structural, biochemical, and biophysical studies of these self-cleaving RNAs have begun to reveal how active site nucleotides exploit general acid-base catalysis, electrostatic stabilization, substrate destabilization, and positioning and orientation to reduce the free energy barrier to catalysis. Insights into the variety of catalytic strategies available to these model RNA enzymes are likely to have important implications for understanding more complex RNA-catalyzed reactions fundamental to RNA processing and protein synthesis.
journal_name
Annu Rev Biophysjournal_title
Annual review of biophysicsauthors
Fedor MJdoi
10.1146/annurev.biophys.050708.133710subject
Has Abstractpub_date
2009-01-01 00:00:00pages
271-99eissn
1936-122Xissn
1936-1238journal_volume
38pub_type
杂志文章,评审abstract::Proteins and other macromolecules can act as molecular machines that convert energy from one form to another through cycles of conformational transitions. In a macroscopically fluctuating environment or at the single-molecule level, the probability for a molecule to be in any state j fluctuates, and the probability cu...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-042910-155355
更新日期:2011-01-01 00:00:00
abstract::Cells actively sense the mechanical properties of the extracellular matrix, such as its rigidity, morphology, and deformation. The cell-matrix interaction influences a range of cellular processes, including cell adhesion, migration, and differentiation, among others. This article aims to review some of the recent prog...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-051013-023102
更新日期:2015-01-01 00:00:00
abstract::Helicases are enzymes that move, manage, and manipulate nucleic acids. They can be subdivided into six super families and are required for all aspects of nucleic acid metabolism. In general, all helicases function by converting the chemical energy stored in the bond between the gamma and beta phosphates of adenosine t...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-052118-115418
更新日期:2019-05-06 00:00:00
abstract::This review deals with two important concepts-protein intrinsic disorder and proteinaceous membrane-less organelles (PMLOs). The past 20 years have seen an upsurge of scientific interest in these phenomena. However, neither are new discoveries made in this century, but instead are timely reincarnations of old ideas th...
journal_title:Annual review of biophysics
pub_type: 杂志文章
doi:10.1146/annurev-biophys-062920-063704
更新日期:2021-01-27 00:00:00
abstract::NF-κB (nuclear factor kappa B) family transcription factors are master regulators of immune and inflammatory processes in response to both injury and infection. In the latent state, NF-κBs are sequestered in the cytosol by their inhibitor IκB (inhibitor of NF-κB) proteins. Upon stimulations of innate immune receptors ...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-083012-130338
更新日期:2013-01-01 00:00:00
abstract::Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial p...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-070317-032905
更新日期:2018-05-20 00:00:00
abstract::Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the struc...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-070816-034125
更新日期:2017-05-22 00:00:00
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journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev.biophys.36.040306.132755
更新日期:2008-01-01 00:00:00
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journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev.biophys.050708.133634
更新日期:2009-01-01 00:00:00
abstract::My research began with theory and methods for ultracentrifugal studies of proteins, first at the University of Wisconsin, Madison, with Bob Alberty and Jack Williams, then at Oxford University with A.G. ("Sandy") Ogston, and finally back at Wisconsin with Williams and Lou Gosting. In 1959 I joined Arthur Kornberg's Bi...
journal_title:Annual review of biophysics
pub_type: 传,历史文章,杂志文章,评审
doi:10.1146/annurev.biophys.37.032807.125948
更新日期:2008-01-01 00:00:00
abstract::Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-051013-022754
更新日期:2014-01-01 00:00:00
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journal_title:Annual review of biophysics
pub_type: 杂志文章
doi:10.1146/annurev-biophys-062420-081842
更新日期:2020-12-07 00:00:00
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journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-083012-130401
更新日期:2013-01-01 00:00:00
abstract::Rhodopsin is a specialized G protein-coupled receptor (GPCR) found in vertebrate rod cells. Absorption of light by its 11-cis retinal chromophore leads to rapid photochemical isomerization and receptor activation. Recent results from protein crystallography and NMR spectroscopy show how structural changes on the extra...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-101209-104901
更新日期:2010-01-01 00:00:00
abstract::Actin is the most abundant protein in most eukaryotic cells. It is highly conserved and participates in more protein-protein interactions than any known protein. These properties, along with its ability to transition between monomeric (G-actin) and filamentous (F-actin) states under the control of nucleotide hydrolysi...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-042910-155359
更新日期:2011-01-01 00:00:00
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journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-051013-022846
更新日期:2019-05-06 00:00:00
abstract::Intrinsically disordered proteins (IDPs) lack stable tertiary and/or secondary structures under physiological conditions in vitro. They are highly abundant in nature and their functional repertoire complements the functions of ordered proteins. IDPs are involved in regulation, signaling, and control, where binding to ...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev.biophys.37.032807.125924
更新日期:2008-01-01 00:00:00
abstract::Next-generation synchrotron radiation sources, such as X-ray free-electron lasers, energy recovery linacs, and ultra-low-emittance storage rings, are catalyzing novel methods of biomolecular microcrystallography and solution scattering. These methods are described and future trends are predicted. Importantly, there is...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-060414-033813
更新日期:2015-01-01 00:00:00
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journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-070816-033647
更新日期:2017-05-22 00:00:00
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journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-052118-115342
更新日期:2019-05-06 00:00:00
abstract::As primary carriers of epigenetic information and gatekeepers of genomic DNA, nucleosomes are essential for proper growth and development of all eukaryotic cells. Although they are intrinsically dynamic, nucleosomes are actively reorganized by ATP-dependent chromatin remodelers. Chromatin remodelers contain helicase-l...
journal_title:Annual review of biophysics
pub_type: 杂志文章
doi:10.1146/annurev-biophys-082520-080201
更新日期:2021-01-04 00:00:00
abstract::Imaging techniques greatly facilitate the comprehensive knowledge of biological systems. Although imaging methodology for biomacromolecules such as protein and nucleic acids has been long established, microscopic techniques and contrast mechanisms are relatively limited for small biomolecules, which are equally import...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-052118-115500
更新日期:2019-05-06 00:00:00
abstract::We argue that the mechanical control of proteins-the notion of controlling chemical reactions and processes by mechanics-is conceptually interesting. We give a brief review of the main accomplishments so far, leading to our present approach of using DNA molecular springs to exert controlled stresses on proteins. Our f...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev.biophys.050708.133637
更新日期:2009-01-01 00:00:00
abstract::Of great interest to the academic and pharmaceutical research communities, helical transmembrane proteins are characterized by their ability to dissolve and fold in lipid bilayers--properties conferred by polypeptide spans termed transmembrane domains (TMDs). The apolar nature of TMDs necessitates the use of membrane-...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-050511-102310
更新日期:2012-01-01 00:00:00
abstract::The living cell is an incredibly complex entity, and the goal of predictively and quantitatively understanding its function is one of the next great challenges in biology. Much of what we know about the cell concerns its constituent parts, but to a great extent we have yet to decode how these parts are organized to yi...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev.biophys.050708.133652
更新日期:2010-01-01 00:00:00
abstract::Solid-state nuclear magnetic resonance (SSNMR) spectroscopy elucidates membrane protein structures and dynamics in atomic detail to yield mechanistic insights. By interrogating membrane proteins in phospholipid bilayers that closely resemble biological membranes, SSNMR spectroscopists have revealed ion conduction mech...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-070816-033712
更新日期:2018-05-20 00:00:00
abstract::Biological molecules are often highly dynamic, and this flexibility can be critical for function. The large range of sampled timescales and the fact that many of the conformers that are continually explored are only transiently formed and sparsely populated challenge current biophysical approaches. Solution nuclear ma...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-052118-115647
更新日期:2019-05-06 00:00:00
abstract::Physical factors in the local cellular microenvironment, including cell shape and geometry, matrix mechanics, external mechanical forces, and nanotopographical features of the extracellular matrix, can all have strong influences on regulating stem cell fate. Stem cells sense and respond to these insoluble biophysical ...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-042910-155306
更新日期:2012-01-01 00:00:00
abstract::In eukaryotic cells, membrane compartments are split into two by membrane fission. This ensures discontinuity of membrane containers and thus proper compartmentalization. The first proteic machinery implicated in catalyzing membrane fission was dynamin. Dynamin forms helical collars at the neck of endocytic buds. This...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-050511-102247
更新日期:2013-01-01 00:00:00
abstract::In the past decade, a concerted effort to successfully capture specific tertiary packing interactions produced specific three-dimensional structures for many de novo designed proteins that are validated by nuclear magnetic resonance and/or X-ray crystallographic techniques. However, the success rate of computational d...
journal_title:Annual review of biophysics
pub_type: 杂志文章,评审
doi:10.1146/annurev-biophys-083012-130315
更新日期:2013-01-01 00:00:00