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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
  • Assembly of COPI and COPII Vesicular Coat Proteins on Membranes
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Julien Béthune, Felix T. Wieland

    In eukaryotes, distinct transport vesicles functionally connect various intracellular compartments. These carriers mediate transport of membranes for the biogenesis and maintenance of organelles, secretion of cargo proteins and peptides, and uptake of cargo into the cell. Transport vesicles have distinct protein coats that assemble on a donor membrane where they can select cargo and curve the membrane

    更新日期:2018-05-24
  • Imaging mRNA In Vivo, from Birth to Death
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Evelina Tutucci, Nathan M. Livingston, Robert H. Singer, Bin Wu

    RNA is the fundamental information transfer system in the cell. The ability to follow single messenger RNAs (mRNAs) from transcription to degradation with fluorescent probes gives quantitative information about how the information is transferred from DNA to proteins. This review focuses on the latest technological developments in the field of single-mRNA detection and their usage to study gene expression

    更新日期:2018-05-24
  • Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Sander Boonstra, Jelle S. Blijleven, Wouter H. Roos, Patrick R. Onck, Erik van der Giessen, Antoine M. van Oijen

    Influenza hemagglutinin (HA) is a viral membrane protein responsible for the initial steps of the entry of influenza virus into the host cell. It mediates binding of the virus particle to the host-cell membrane and catalyzes fusion of the viral membrane with that of the host. HA is therefore a major target in the development of antiviral strategies. The fusion of two membranes involves high activation

    更新日期:2018-05-24
  • Cryo-EM Studies of Pre-mRNA Splicing: From Sample Preparation to Model Visualization
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Max E. Wilkinson, Pei-Chun Lin, Clemens Plaschka, Kiyoshi Nagai

    The removal of noncoding introns from pre-messenger RNA (pre-mRNA) is an essential step in eukaryotic gene expression and is catalyzed by a dynamic multi-megadalton ribonucleoprotein complex called the spliceosome. The spliceosome assembles on pre-mRNA substrates by the stepwise addition of small nuclear ribonucleoprotein particles and numerous protein factors. Extensive remodeling is required to form

    更新日期:2018-05-24
  • Structure and Dynamics of Membrane Proteins from Solid-State NMR
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Venkata S. Mandala, Jonathan K. Williams, Mei Hong

    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 mechanisms, substrate transport dynamics, and oligomeric interfaces of seven-transmembrane

    更新日期:2018-05-24
  • The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Jerome M. Fox, Mengxia Zhao, Michael J. Fink, Kyungtae Kang, George M. Whitesides

    Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes

    更新日期:2018-05-24
  • Modeling Cell Size Regulation: From Single-Cell-Level Statistics to Molecular Mechanisms and Population-Level Effects
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Po-Yi Ho, Jie Lin, Ariel Amir

    Most microorganisms regulate their cell size. In this article, we review some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics that they generate. We review the biologically relevant insights obtained from these models. We then describe cell cycle regulation and its molecular implementations, protein number regulation

    更新日期:2018-05-24
  • Macroscopic Theory for Evolving Biological Systems Akin to Thermodynamics
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Kunihiko Kaneko, Chikara Furusawa

    We present a macroscopic theory to characterize the plasticity, robustness, and evolvability of biological responses and their fluctuations. First, linear approximation in intracellular reaction dynamics is used to demonstrate proportional changes in the expression of all cellular components in response to a given environmental stress, with the proportion coefficient determined by the change in growth

    更新日期:2018-05-24
  • High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Janna Kiselar, Mark R. Chance

    Hydroxyl radical footprinting (HRF) of proteins with mass spectrometry (MS) is a widespread approach for assessing protein structure. Hydroxyl radicals react with a wide variety of protein side chains, and the ease with which radicals can be generated (by radiolysis or photolysis) has made the approach popular with many laboratories. As some side chains are less reactive and thus cannot be probed,

    更新日期:2018-05-24
  • Dynamic Neutron Scattering by Biological Systems
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Jeremy C. Smith, Pan Tan, Loukas Petridis, Liang Hong

    Dynamic neutron scattering directly probes motions in biological systems on femtosecond to microsecond timescales. When combined with molecular dynamics simulation and normal mode analysis, detailed descriptions of the forms and frequencies of motions can be derived. We examine vibrations in proteins, the temperature dependence of protein motions, and concepts describing the rich variety of motions

    更新日期:2018-05-24
  • Hydrogel-Tissue Chemistry: Principles and Applications
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Viviana Gradinaru, Jennifer Treweek, Kristin Overton, Karl Deisseroth

    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 phenotypic information regarding constituent cells and molecules (and their joint interrelationships)

    更新日期:2018-05-24
  • Serial Femtosecond Crystallography of G Protein–Coupled Receptors
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Benjamin Stauch, Vadim Cherezov

    G protein–coupled receptors (GPCRs) represent a large superfamily of membrane proteins that mediate cell signaling and regulate a variety of physiological processes in the human body. Structure-function studies of this superfamily were enabled a decade ago by multiple breakthroughs in technology that included receptor stabilization, crystallization in a membrane environment, and microcrystallography

    更新日期:2018-05-24
  • Understanding Biological Regulation Through Synthetic Biology
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Caleb J. Bashor, James J. Collins

    Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry—biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved

    更新日期:2018-05-24
  • Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Christoph Engel, Simon Neyer, Patrick Cramer

    RNA polymerases I and II (Pol I and Pol II) are the eukaryotic enzymes that catalyze DNA-dependent synthesis of ribosomal RNA and messenger RNA, respectively. Recent work shows that the transcribing forms of both enzymes are similar and the fundamental mechanisms of RNA chain elongation are conserved. However, the mechanisms of transcription initiation and its regulation differ between Pol I and Pol

    更新日期:2018-05-24
  • Dynamics of Bacterial Gene Regulatory Networks
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    David L. Shis, Matthew R. Bennett,, Oleg A. Igoshin

    The ability of bacterial cells to adjust their gene expression program in response to environmental perturbation is often critical for their survival. Recent experimental advances allowing us to quantitatively record gene expression dynamics in single cells and in populations coupled with mathematical modeling enable mechanistic understanding on how these responses are shaped by the underlying regulatory

    更新日期:2018-05-24
  • Molecular Mechanisms of Fast Neurotransmitter Release
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Axel T. Brunger, Ucheor B. Choi, Ying Lai, Jeremy Leitz, Qiangjun Zhou

    This review summarizes current knowledge of synaptic proteins that are central to synaptic vesicle fusion in presynaptic active zones, including SNAREs (soluble N-ethylmaleimide sensitive factor attachment protein receptors), synaptotagmin, complexin, Munc18 (mammalian uncoordinated-18), and Munc13 (mammalian uncoordinated-13), and highlights recent insights in the cooperation of these proteins for

    更新日期:2018-05-24
  • Single-Molecule View of Small RNA–Guided Target Search and Recognition
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Viktorija Globyte, Sung Hyun Kim, Chirlmin Joo

    Most everyday processes in life involve a necessity for an entity to locate its target. On a cellular level, many proteins have to find their target to perform their function. From gene-expression regulation to DNA repair to host defense, numerous nucleic acid–interacting proteins use distinct target search mechanisms. Several proteins achieve that with the help of short RNA strands known as guides

    更新日期:2018-05-24
  • Behavioral Variability and Phenotypic Diversity in Bacterial Chemotaxis
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Adam James Waite, Nicholas W. Frankel, Thierry Emonet

    Living cells detect and process external signals using signaling pathways that are affected by random fluctuations. These variations cause the behavior of individual cells to fluctuate over time (behavioral variability) and generate phenotypic differences between genetically identical individuals (phenotypic diversity). These two noise sources reduce our ability to predict biological behavior because

    更新日期:2018-05-24
  • The Physical Properties of Ceramides in Membranes
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-05-24
    Alicia Alonso, Félix M. Goñi

    Ceramides are sphingolipids containing a sphingosine or a related base, to which a fatty acid is linked through an amide bond. When incorporated into a lipid bilayer, ceramides exhibit a number of properties not shared by almost any other membrane lipid: Ceramides (a) are extremely hydrophobic and thus cannot exist in suspension in aqueous media; (b) increase the molecular order (rigidity) of phospholipids

    更新日期:2018-05-24
  • Structure and Immune Recognition of the HIV Glycan Shield.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-03-29
    Max Crispin,Andrew B Ward,Ian A Wilson

    Vaccine design efforts against the human immunodeficiency virus (HIV) have been greatly stimulated by the observation that many infected patients eventually develop highly potent broadly neutralizing antibodies (bnAbs). Importantly, these bnAbs have evolved to recognize not only the two protein components of the viral envelope protein (Env) but also the numerous glycans that form a protective barrier

    更新日期:2018-05-24
  • Photoreceptors Take Charge: Emerging Principles for Light Sensing.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-03-14
    Tilman Kottke,Aihua Xie,Delmar S Larsen,Wouter D Hoff

    The first stage in biological signaling is based on changes in the functional state of a receptor protein triggered by interaction of the receptor with its ligand(s). The light-triggered nature of photoreceptors allows studies on the mechanism of such changes in receptor proteins using a wide range of biophysical methods and with superb time resolution. Here, we critically evaluate current understanding

    更新日期:2018-05-24
  • Structural Basis for G Protein-Coupled Receptor Signaling.
    Annu. Rev. Biophys. (IF 11.685) Pub Date : 2018-03-02
    Sarah C Erlandson,Conor McMahon,Andrew C Kruse

    G protein-coupled receptors (GPCRs), which mediate processes as diverse as olfaction and maintenance of metabolic homeostasis, have become the single most effective class of therapeutic drug targets. As a result, understanding the molecular basis for their activity is of paramount importance. Recent technological advances have made GPCR structural biology increasingly tractable, offering views of these

    更新日期:2018-05-24
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