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  • Nonequilibrium Thermodynamics in Cell Biology: Extending Equilibrium Formalism to Cover Living Systems.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-05-06
    Xiaona Fang,Jin Wang

    We discuss new developments in the nonequilibrium dynamics and thermodynamics of living systems, giving a few examples to demonstrate the importance of nonequilibrium thermodynamics for understanding biological dynamics and functions. We study single-molecule enzyme dynamics, in which the nonequilibrium thermodynamic and dynamic driving forces of chemical potential and flux are crucial for the emergence

    更新日期:2020-05-06
  • Gene Regulation in and out of Equilibrium.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-05-06
    Felix Wong,Jeremy Gunawardena

    Determining whether and how a gene is transcribed are two of the central processes of life. The conceptual basis for understanding such gene regulation arose from pioneering biophysical studies in eubacteria. However, eukaryotic genomes exhibit vastly greater complexity, which raises questions not addressed by this bacterial paradigm. First, how is information integrated from many widely separated

    更新日期:2020-05-06
  • Milestoning: An Efficient Approach for Atomically Detailed Simulations of Kinetics in Biophysics.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-05-06
    Ron Elber

    Recent advances in theory and algorithms for atomically detailed simulations open the way to the study of the kinetics of a wide range of molecular processes in biophysics. The theories propose a shift from the traditionally very long molecular dynamic trajectories, which are exact but may not be efficient in the study of kinetics, to the use of a large number of short trajectories. The short trajectories

    更新日期:2020-05-06
  • Insights into the Structure, Function, and Dynamics of the Bacterial Cytokinetic FtsZ-Ring.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-02-24
    Ryan McQuillen,Jie Xiao

    The FtsZ protein is a highly conserved bacterial tubulin homolog. In vivo, the functional form of FtsZ is the polymeric, ring-like structure (Z-ring) assembled at the future division site during cell division. While it is clear that the Z-ring plays an essential role in orchestrating cytokinesis, precisely what its functions are and how these functions are achieved remain elusive. In this article,

    更新日期:2020-05-06
  • Light Microscopy of Mitochondria at the Nanoscale.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-02-24
    Stefan Jakobs,Till Stephan,Peter Ilgen,Christian Brüser

    Mitochondria are essential for eukaryotic life. These double-membrane organelles often form highly dynamic tubular networks interacting with many cellular structures. Their highly convoluted contiguous inner membrane compartmentalizes the organelle, which is crucial for mitochondrial function. Since the diameter of the mitochondrial tubules is generally close to the diffraction limit of light microscopy

    更新日期:2020-05-06
  • The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-02-19
    Paul Campitelli,Tushar Modi,Sudhir Kumar,S Banu Ozkan

    Advances in sequencing techniques and statistical methods have made it possible not only to predict sequences of ancestral proteins but also to identify thousands of mutations in the human exome, some of which are disease associated. These developments have motivated numerous theories and raised many questions regarding the fundamental principles behind protein evolution, which have been traditionally

    更新日期:2020-05-06
  • RNA Droplets.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-02-10
    Kevin Rhine,Velinda Vidaurre,Sua Myong

    Liquid-liquid phase separation is emerging as the universal mechanism by which membraneless cellular granules form. Despite many previous studies on condensation of intrinsically disordered proteins and low complexity domains, we lack understanding about the role of RNA, which is the essential component of all ribonucleoprotein (RNP) granules. RNA, as an anionic polymer, is inherently an excellent

    更新日期:2020-05-06
  • Predicting Evolution Using Regulatory Architecture.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-02-04
    Philippe Nghe,Marjon G J de Vos,Enzo Kingma,Manjunatha Kogenaru,Frank J Poelwijk,Liedewij Laan,Sander J Tans

    The limits of evolution have long fascinated biologists. However, the causes of evolutionary constraint have remained elusive due to a poor mechanistic understanding of studied phenotypes. Recently, a range of innovative approaches have leveraged mechanistic information on regulatory networks and cellular biology. These methods combine systems biology models with population and single-cell quantification

    更新日期:2020-05-06
  • Temperature, Dynamics, and Enzyme-Catalyzed Reaction Rates.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-02-04
    Vickery L Arcus,Adrian J Mulholland

    We review the adaptations of enzyme activity to different temperatures. Psychrophilic (cold-adapted) enzymes show significantly different activation parameters (lower activation enthalpies and entropies) from their mesophilic counterparts. Furthermore, there is increasing evidence that the temperature dependence of many enzyme-catalyzed reactions is more complex than is widely believed. Many enzymes

    更新日期:2020-05-06
  • Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-01-31
    Jeong-Mo Choi,Alex S Holehouse,Rohit V Pappu

    Many biomolecular condensates appear to form via spontaneous or driven processes that have the hallmarks of intracellular phase transitions. This suggests that a common underlying physical framework might govern the formation of functionally and compositionally unrelated biomolecular condensates. In this review, we summarize recent work that leverages a stickers-and-spacers framework adapted from the

    更新日期:2020-05-06
  • Multifunctional Chaperone and Quality Control Complexes in Adaptive Immunity.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-01-31
    Simon Trowitzsch,Robert Tampé

    The fundamental process of adaptive immunity relies on the differentiation of self from nonself. Nucleated cells are continuously monitored by effector cells of the immune system, which police the peptide status presented via cell surface molecules. Recent integrative structural approaches have provided insights toward our understanding of how sophisticated cellular machineries shape such hierarchical

    更新日期:2020-05-06
  • Enhanced Diffusion and Chemotaxis of Enzymes.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-01-27
    Mudong Feng,Michael K Gilson

    Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these phenomena, termed enhanced enzyme diffusion (EED) and enzyme chemotaxis, respectively, lead to a novel view of enzymes as active matter. Enzyme chemotaxis and EED may be important in biology and could have practical applications in biotechnology

    更新日期:2020-05-06
  • Mitochondria-Associated Proteostasis.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-01-13
    Linhao Ruan,Yuhao Wang,Xi Zhang,Alexis Tomaszewski,Joshua T McNamara,Rong Li

    Mitochondria are essential organelles in eukaryotes. Most mitochondrial proteins are encoded by the nuclear genome and translated in the cytosol. Nuclear-encoded mitochondrial proteins need to be imported, processed, folded, and assembled into their functional states. To maintain protein homeostasis (proteostasis), mitochondria are equipped with a distinct set of quality control machineries. Deficiencies

    更新日期:2020-05-06
  • The Physics of Cellular Decision Making During Epithelial-Mesenchymal Transition.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-01-08
    Shubham Tripathi,Herbert Levine,Mohit Kumar Jolly

    The epithelial-mesenchymal transition (EMT) is a process by which cells lose epithelial traits, such as cell-cell adhesion and apico-basal polarity, and acquire migratory and invasive traits. EMT is crucial to embryonic development and wound healing. Misregulated EMT has been implicated in processes associated with cancer aggressiveness, including metastasis. Recent experimental advances such as single-cell

    更新日期:2020-05-06
  • Principles and Applications of Biological Membrane Organization.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2020-01-08
    Wade F Zeno,Kasey J Day,Vernita D Gordon,Jeanne C Stachowiak

    Many critical biological events, including biochemical signaling, membrane traffic, and cell motility, originate at membrane surfaces. Each such event requires that members of a specific group of proteins and lipids rapidly assemble together at a specific site on the membrane surface. Understanding the biophysical mechanisms that stabilize these assemblies is critical to decoding and controlling cellular

    更新日期:2020-05-06
  • Hybrid Live Cell-Supported Membrane Interfaces for Signaling Studies.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Kabir H Biswas,Jay T Groves

    A wide range of cell-microenvironmental interactions are mediated by membrane-localized receptors that bind ligands present on another cell or the extracellular matrix. This situation introduces a number of physical effects including spatial organization of receptor-ligand complexes and development of mechanical forces in cells. Unlike traditional experimental approaches, hybrid live cell-supported

    更新日期:2020-04-21
  • Structure and Assembly of the Nuclear Pore Complex.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Bernhard Hampoelz,Amparo Andres-Pons,Panagiotis Kastritis,Martin Beck

    Nuclear pore complexes (NPCs) mediate nucleocytoplasmic exchange. They are exceptionally large protein complexes that fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. About 30 different protein components, termed nucleoporins, assemble in multiple copies into an intricate cylindrical architecture. Here, we review our current knowledge of the structure of nucleoporins

    更新日期:2020-04-21
  • RNA-Mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Reidun Twarock,Peter G Stockley

    Viruses, entities composed of nucleic acids, proteins, and in some cases lipids lack the ability to replicate outside their target cells. Their components self-assemble at the nanoscale with exquisite precision-a key to their biological success in infection. Recent advances in structure determination and the development of biophysical tools such as single-molecule spectroscopy and noncovalent mass

    更新日期:2020-04-21
  • Regulation of Transmembrane Signaling by Phase Separation.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-04-05
    Lindsay B Case,Jonathon A Ditlev,Michael K Rosen

    Cell surface transmembrane receptors often form nanometer- to micrometer-scale clusters to initiate signal transduction in response to environmental cues. Extracellular ligand oligomerization, domain-domain interactions, and binding to multivalent proteins all contribute to cluster formation. Here we review the current understanding of mechanisms driving cluster formation in a series of representative

    更新日期:2020-04-21
  • Interrogating the Structural Dynamics and Energetics of Biomolecular Systems with Pressure Modulation.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Roland Winter

    High hydrostatic pressure affects the structure, dynamics, and stability of biomolecular systems and is a key parameter in the context of the exploration of the origin and the physical limits of life. This review lays out the conceptual framework for exploring the conformational fluctuations, dynamical properties, and activity of biomolecular systems using pressure perturbation. Complementary pressure-jump

    更新日期:2020-04-21
  • Understanding the Role of Lipids in Signaling Through Atomistic and Multiscale Simulations of Cell Membranes.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Moutusi Manna,Tuomo Nieminen,Ilpo Vattulainen

    Cell signaling controls essentially all cellular processes. While it is often assumed that proteins are the key architects coordinating cell signaling, recent studies have shown more and more clearly that lipids are also involved in signaling processes in a number of ways. Lipids do, for instance, act as messengers, modulate membrane receptor conformation and dynamics, and control membrane receptor

    更新日期:2020-04-21
  • Programming Structured DNA Assemblies to Probe Biophysical Processes
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Eike-Christian Wamhoff; James L. Banal; William P. Bricker; Tyson R. Shepherd; Molly F. Parsons; Rémi Veneziano; Matthew B. Stone; Hyungmin Jun; Xiao Wang; Mark Bathe

    Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to

    更新日期:2020-04-21
  • Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-03-27
    Zhifeng Jing,Chengwen Liu,Sara Y Cheng,Rui Qi,Brandon D Walker,Jean-Philip Piquemal,Pengyu Ren

    Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights

    更新日期:2020-04-21
  • Raman Imaging of Small Biomolecules.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Yihui Shen,Fanghao Hu,Wei Min

    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 important participants in biological processes. Recent developments in Raman imaging, including

    更新日期:2020-04-21
  • Biophysics of Chromatin Dynamics.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Beat Fierz,Michael G Poirier

    Nucleosomes and chromatin control eukaryotic genome accessibility and thereby regulate DNA processes, including transcription, replication, and repair. Conformational dynamics within the nucleosome and chromatin structure play a key role in this regulatory function. Structural fluctuations continuously expose internal DNA sequences and nucleosome surfaces, thereby providing transient access for the

    更新日期:2020-04-21
  • An NMR View of Protein Dynamics in Health and Disease.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Ashok Sekhar,Lewis E Kay

    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 magnetic resonance (NMR) spectroscopy has emerged as a powerful method for characterizing

    更新日期:2020-04-21
  • Generalized Born Implicit Solvent Models for Biomolecules.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Alexey V Onufriev,David A Case

    It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation and can be very efficient compared to the explicit treatment of the solvent. Here, we review a particular class of so-called

    更新日期:2020-04-21
  • Helicase Mechanisms During Homologous Recombination in Saccharomyces cerevisiae.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-03-11
    J Brooks Crickard,Eric C Greene

    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 triphosphate into mechanical work, which results in the unidirectional movement of

    更新日期:2020-04-21
  • How the Genome Folds: The Biophysics of Four-Dimensional Chromatin Organization.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Jyotsana J Parmar,Maxime Woringer,Christophe Zimmer

    The genetic information that instructs transcription and other cellular functions is carried by the chromosomes, polymers of DNA in complex with histones and other proteins. These polymers are folded inside nuclei five orders of magnitude smaller than their linear length, and many facets of this folding correlate with or are causally related to transcription and other cellular functions. Recent advances

    更新日期:2020-04-21
  • Mechanisms of Sensory Discrimination: Insights from Drosophila Olfaction.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Lukas N Groschner,Gero Miesenböck

    All an animal can do to infer the state of its environment is to observe the sensory-evoked activity of its own neurons. These inferences about the presence, quality, or similarity of objects are probabilistic and inform behavioral decisions that are often made in close to real time. Neural systems employ several strategies to facilitate sensory discrimination: Biophysical mechanisms separate the neuronal

    更新日期:2020-04-21
  • Single-Molecule Studies on the Protein Translocon.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Anne-Bart Seinen,Arnold J M Driessen

    Single-molecule studies provide unprecedented details about processes that are difficult to grasp by bulk biochemical assays that yield ensemble-averaged results. One of these processes is the translocation and insertion of proteins across and into the bacterial cytoplasmic membrane. This process is facilitated by the universally conserved secretion (Sec) system, a multi-subunit membrane protein complex

    更新日期:2020-04-21
  • Mammalian Respiratory Complex I Through the Lens of Cryo-EM.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Ahmed-Noor A Agip,James N Blaza,Justin G Fedor,Judy Hirst

    Single-particle electron cryomicroscopy (cryo-EM) has led to a revolution in structural work on mammalian respiratory complex I. Complex I (mitochondrial NADH:ubiquinone oxidoreductase), a membrane-bound redox-driven proton pump, is one of the largest and most complicated enzymes in the mammalian cell. Rapid progress, following the first 5-Å resolution data on bovine complex I in 2014, has led to a

    更新日期:2020-04-21
  • Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Rob Phillips,Nathan M Belliveau,Griffin Chure,Hernan G Garcia,Manuel Razo-Mejia,Clarissa Scholes

    It is tempting to believe that we now own the genome. The ability to read and rewrite it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles' heel exposed by all of the genomic data that has accrued: We still do not know how to interpret them. Many genes are subject to sophisticated programs of transcriptional regulation, mediated by DNA sequences that

    更新日期:2020-04-21
  • Giant Vesicles and Their Use in Assays for Assessing Membrane Phase State, Curvature, Mechanics, and Electrical Properties.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Rumiana Dimova

    Giant unilamellar vesicles represent a promising and extremely useful model biomembrane system for systematic measurements of mechanical, thermodynamic, electrical, and rheological properties of lipid bilayers as a function of membrane composition, surrounding media, and temperature. The most important advantage of giant vesicles over other model membrane systems is that the membrane responses to external

    更新日期:2020-04-21
  • Membrane Electroporation and Electropermeabilization: Mechanisms and Models.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Tadej Kotnik,Lea Rems,Mounir Tarek,Damijan Miklavčič

    Exposure of biological cells to high-voltage, short-duration electric pulses causes a transient increase in their plasma membrane permeability, allowing transmembrane transport of otherwise impermeant molecules. In recent years, large steps were made in the understanding of underlying events. Formation of aqueous pores in the lipid bilayer is now a widely recognized mechanism, but evidence is growing

    更新日期:2020-04-21
  • How Good Can Single-Particle Cryo-EM Become? What Remains Before It Approaches Its Physical Limits?
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Robert M Glaeser

    Impressive though the achievements of single-particle cryo-electron microscopy are today, a substantial gap still remains between what is currently accomplished and what is theoretically possible. As is reviewed here, twofold or more improvements are possible as regards (a) the detective quantum efficiency of cameras at high resolution, (b) converting phase modulations to intensity modulations in the

    更新日期:2020-04-21
  • Split Green Fluorescent Proteins: Scope, Limitations, and Outlook.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Matthew G Romei,Steven G Boxer

    Many proteins can be split into fragments that spontaneously reassemble, without covalent linkage, into a functional protein. For split green fluorescent proteins (GFPs), fragment reassembly leads to a fluorescent readout, which has been widely used to investigate protein-protein interactions. We review the scope and limitations of this approach as well as other diverse applications of split GFPs as

    更新日期:2020-04-21
  • Molecular Fitness Landscapes from High-Coverage Sequence Profiling.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2019-05-14
    Celia Blanco,Evan Janzen,Abe Pressman,Ranajay Saha,Irene A Chen

    The function of fitness (or molecular activity) in the space of all possible sequences is known as the fitness landscape. Evolution is a random walk on the fitness landscape, with a bias toward climbing hills. Mapping the topography of real fitness landscapes is fundamental to understanding evolution, but previous efforts were hampered by the difficulty of obtaining large, quantitative data sets. The

    更新日期:2020-04-21
  • Biophysics. Introduction.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2013-06-27
    Ken A Dill

    更新日期:2019-11-01
  • Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Huan-Xiang Zhou,Germán Rivas,Allen P Minton

    Expected and observed effects of volume exclusion on the free energy of rigid and flexible macromolecules in crowded and confined systems, and consequent effects of crowding and confinement on macromolecular reaction rates and equilibria are summarized. Findings from relevant theoretical/simulation and experimental literature published from 2004 onward are reviewed. Additional complexity arising from

    更新日期:2019-11-01
  • RNA folding: conformational statistics, folding kinetics, and ion electrostatics.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Shi-Jie Chen

    RNA folding is a remarkably complex problem that involves ion-mediated electrostatic interaction, conformational entropy, base pairing and stacking, and noncanonical interactions. During the past decade, results from a variety of experimental and theoretical studies pointed to (a) the potential ion correlation effect in Mg2+-RNA interactions, (b) the rugged energy landscapes and multistate RNA folding

    更新日期:2019-11-01
  • Bimolecular fluorescence complementation (BiFC) analysis as a probe of protein interactions in living cells.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Tom K Kerppola

    Protein interactions are a fundamental mechanism for the generation of biological regulatory specificity. The study of protein interactions in living cells is of particular significance because the interactions that occur in a particular cell depend on the full complement of proteins present in the cell and the external stimuli that influence the cell. Bimolecular fluorescence complementation (BiFC)

    更新日期:2019-11-01
  • Multiple routes and structural heterogeneity in protein folding.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Jayant B Udgaonkar

    Experimental studies show that many proteins fold along sequential pathways defined by folding intermediates. An intermediate may not always be a single population of molecules but may consist of subpopulations that differ in their average structure. These subpopulations are likely to fold via independent pathways. Parallel folding and unfolding pathways appear to arise because of structural heterogeneity

    更新日期:2019-11-01
  • Structural principles from large RNAs.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Stephen R Holbrook

    Since the year 2000 a number of large RNA three-dimensional structures have been determined by X-ray crystallography. Structures composed of more than 100 nucleotide residues include the signal recognition particle RNA, group I intron, the GlmS ribozyme, RNAseP RNA, and ribosomal RNAs from Haloarcula morismortui, Escherichia coli, Thermus thermophilus, and Deinococcus radiodurans. These large RNAs

    更新日期:2019-11-01
  • Single-molecule approach to molecular biology in living bacterial cells.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    X Sunney Xie,Paul J Choi,Gene-Wei Li,Nam Ki Lee,Giuseppe Lia

    Recent developments on fluorescent proteins and microscopy techniques have allowed the probing of single molecules in a living bacterial cell with high specificity, millisecond time resolution, and nanometer spatial precision. Recording movies and analyzing dynamics of individual macromolecules have brought new insights into the mechanisms of many processes in molecular biology, such as DNA-protein

    更新日期:2019-11-01
  • Biophysics of catch bonds.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Wendy E Thomas,Viola Vogel,Evgeni Sokurenko

    Receptor-ligand bonds strengthened by tensile mechanical force are referred to as catch bonds. This review examines experimental data and biophysical theory to analyze why mechanical force prolongs the lifetime of these bonds rather than shortens the lifetime by pulling the ligand out of the binding pocket. Although many mathematical models can explain catch bonds, experiments using structural variants

    更新日期:2019-11-01
  • Structure-based view of epidermal growth factor receptor regulation.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Kathryn M Ferguson

    High-resolution X-ray crystal structures determined in the past six years dramatically influence our view of ligand-induced activation of the epidermal growth factor receptor (EGFR) family of receptor tyrosine kinases. Ligand binding to the extracellular region of EGFR promotes a major domain reorganization, plus local conformational changes, that are required to generate an entirely receptor-mediated

    更新日期:2019-11-01
  • Structure of eukaryotic RNA polymerases.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    P Cramer,K-J Armache,S Baumli,S Benkert,F Brueckner,C Buchen,G E Damsma,S Dengl,S R Geiger,A J Jasiak,A Jawhari,S Jennebach,T Kamenski,H Kettenberger,C-D Kuhn,E Lehmann,K Leike,J F Sydow,A Vannini

    The eukaryotic RNA polymerases Pol I, Pol II, and Pol III are the central multiprotein machines that synthesize ribosomal, messenger, and transfer RNA, respectively. Here we provide a catalog of available structural information for these three enzymes. Most structural data have been accumulated for Pol II and its functional complexes. These studies have provided insights into many aspects of the transcription

    更新日期:2019-11-01
  • The protein folding problem.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Ken A Dill,S Banu Ozkan,M Scott Shell,Thomas R Weikl

    The "protein folding problem" consists of three closely related puzzles: (a) What is the folding code? (b) What is the folding mechanism? (c) Can we predict the native structure of a protein from its amino acid sequence? Once regarded as a grand challenge, protein folding has seen great progress in recent years. Now, foldable proteins and nonbiological polymers are being designed routinely and moving

    更新日期:2019-11-01
  • Translocation and unwinding mechanisms of RNA and DNA helicases.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Anna Marie Pyle

    Helicases and remodeling enzymes are ATP-dependent motor proteins that play a critical role in every aspect of RNA and DNA metabolism. Most RNA-remodeling enzymes are members of helicase superfamily 2 (SF2), which includes many DNA helicase enzymes that display similar structural and mechanistic features. Although SF2 enzymes are typically called helicases, many of them display other types of functions

    更新日期:2019-11-01
  • Nanobiotechnology and cell biology: micro- and nanofabricated surfaces to investigate receptor-mediated signaling.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Alexis J Torres,Min Wu,David Holowka,Barbara Baird

    Advances in microfabrication and nanofabrication are opening new opportunities to investigate complicated questions of cell biology in ways not before possible. In particular, the spatial regulation of cellular processes can be examined by engineering the chemical and physical environment to which the cell responds. Lithographic methods and selective chemical modification schemes can provide biocompatible

    更新日期:2019-11-01
  • Crowding effects on diffusion in solutions and cells.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    James A Dix,A S Verkman

    We review the effects of molecular crowding on solute diffusion in solution and in cellular aqueous compartments and membranes. Anomalous diffusion, in which mean squared displacement does not increase linearly with time, is predicted in simulations of solute diffusion in media crowded with fixed or mobile obstacles, or when solute diffusion is restricted or accelerated by a variety of geometric or

    更新日期:2019-11-01
  • Intrinsically disordered proteins in human diseases: introducing the D2 concept.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Vladimir N Uversky,Christopher J Oldfield,A Keith Dunker

    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 multiple partners and high-specificity/low-affinity interactions play a crucial role

    更新日期:2019-11-01
  • PIP2 is a necessary cofactor for ion channel function: how and why?
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Byung-Chang Suh,Bertil Hille

    Phosphatidylinositol 4,5-bisphosphate (PIP2) is a minority phospholipid of the inner leaflet of plasma membranes. Many plasma membrane ion channels and ion transporters require PIP2 to function and can be turned off by signaling pathways that deplete PIP2. This review discusses the dependence of ion channels on phosphoinositides and considers possible mechanisms by which PIP2 and analogues regulate

    更新日期:2019-11-01
  • Protein design by directed evolution.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Christian Jäckel,Peter Kast,Donald Hilvert

    While nature evolved polypeptides over billions of years, protein design by evolutionary mimicry is progressing at a far more rapid pace. The mutation, selection, and amplification steps of the evolutionary cycle may be imitated in the laboratory using existing proteins, or molecules created de novo from random sequence space, as starting templates. However, the astronomically large number of possible

    更新日期:2019-11-01
  • Calorimetry and thermodynamics in drug design.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Jonathan B Chaires

    Modern instrumentation for calorimetry permits direct determination of enthalpy values for binding reactions and conformational transitions in biomolecules. Complete thermodynamic profiles consisting of free energy, enthalpy, and entropy may be obtained for reactions of interest in a relatively straightforward manner. Such profiles are of enormous value in drug design because they provide information

    更新日期:2019-11-01
  • Riboswitches: emerging themes in RNA structure and function.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Rebecca K Montange,Robert T Batey

    Riboswitches are RNAs capable of binding cellular metabolites using a diverse array of secondary and tertiary structures to modulate gene expression. The recent determination of the three-dimensional structures of parts of six different riboswitches illuminates common features that allow riboswitches to be grouped into one of two types. Type I riboswitches, as exemplified by the purine riboswitch,

    更新日期:2019-11-01
  • Metal binding affinity and selectivity in metalloproteins: insights from computational studies.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Todor Dudev,Carmay Lim

    This review highlights insights gained from computational studies on protein-metal recognition. We systematically dissect the various factors governing metal binding affinity and selectivity in proteins starting from (a) the intrinsic properties of the metal and neighboring metal cations (if present), to (b) the primary coordination sphere, (c) the second coordination shell, (d) the protein matrix

    更新日期:2019-11-01
  • Mediation, modulation, and consequences of membrane-cytoskeleton interactions.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Gary J Doherty,Harvey T McMahon

    Elements of the cytoskeleton interact intimately and communicate bidirectionally with cellular membranes. Such interactions are critical for a host of cellular processes. Here we focus on the many types of interactions that exist between the cytoskeleton and the plasma membrane to illustrate why these cellular components can never truly be studied in isolation in vivo. We discuss how membrane-cytoskeleton

    更新日期:2019-11-01
  • Unique rotary ATP synthase and its biological diversity.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2008-06-25
    Christoph von Ballmoos,Gregory M Cook,Peter Dimroth

    F1F0 ATP synthases convert energy stored in an electrochemical gradient of H+ or Na+ across the membrane into mechanical rotation, which is subsequently converted into the chemical bond energy of ATP. The majority of cellular ATP is produced by the ATP synthase in organisms throughout the biological kingdom and therefore under diverse environmental conditions. The ATP synthase of each particular cell

    更新日期:2019-11-01
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