266 results match your criteria Annual Review Of Biophysics[Journal]


RNA-Mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy.

Annu Rev Biophys 2019 Apr 5. Epub 2019 Apr 5.

Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; email:

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 spectrometry allow unprecedented access to the detailed assembly mechanisms of simple virions. Read More

View Article

Download full-text PDF

Source
https://www.annualreviews.org/doi/10.1146/annurev-biophys-05
Publisher Site
http://dx.doi.org/10.1146/annurev-biophys-052118-115611DOI Listing
April 2019
8 Reads

Regulation of Transmembrane Signaling by Phase Separation.

Annu Rev Biophys 2019 Apr 5. Epub 2019 Apr 5.

Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; email: , ,

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 receptor systems: glycosylated receptors, immune receptors, cell adhesion receptors, Wnt receptors, and receptor tyrosine kinases. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115534DOI Listing

Structure and Assembly of the Nuclear Pore Complex.

Annu Rev Biophys 2019 Apr 3. Epub 2019 Apr 3.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; email: , , ,

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115308DOI Listing
April 2019
2 Reads

Hybrid Live Cell-Supported Membrane Interfaces for Signaling Studies.

Annu Rev Biophys 2019 Apr 3. Epub 2019 Apr 3.

Department of Chemistry, University of California, Berkeley, California 94720, USA; email:

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 lipid bilayer (SLB) systems, wherein a live cell interacts with a synthetic substrate supported membrane, allow interrogation of these aspects of receptor signaling. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033330DOI Listing
April 2019
1 Read

Interrogating the Structural Dynamics and Energetics of Biomolecular Systems with Pressure Modulation.

Authors:
Roland Winter

Annu Rev Biophys 2019 Apr 3. Epub 2019 Apr 3.

Faculty of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund, D-44227 Dortmund, Germany; email:

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 relaxation studies are useful tools to study the kinetics and mechanisms of biomolecular phase transitions and structural transformations, such as membrane fusion or protein and nucleic acid folding. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115601DOI Listing

Understanding the Role of Lipids in Signaling Through Atomistic and Multiscale Simulations of Cell Membranes.

Annu Rev Biophys 2019 Apr 2. Epub 2019 Apr 2.

Computational Physics Laboratory, Tampere University, FI-33014 Tampere, Finland.

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 partitioning. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115553DOI Listing
April 2019
1 Read

Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications.

Annu Rev Biophys 2019 Mar 27. Epub 2019 Mar 27.

Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA; email:

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 but also afforded opportunities to advance our understanding of fundamental intermolecular forces. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033349DOI Listing

An NMR View of Protein Dynamics in Health and Disease.

Annu Rev Biophys 2019 Mar 22. Epub 2019 Mar 22.

Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; email:

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 biomolecular dynamics in detail, even in cases where excursions involve short-lived states. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115647DOI Listing

Raman Imaging of Small Biomolecules.

Annu Rev Biophys 2019 Mar 20. Epub 2019 Mar 20.

Department of Chemistry, Columbia University, New York, NY 10027, USA; email:

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 both microscopy and tailored vibrational tags, have created exciting opportunities for noninvasive imaging of small biomolecules in living cells, tissues, and organisms. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115500DOI Listing
March 2019
1 Read

Biophysics of Chromatin Dynamics.

Annu Rev Biophys 2019 Mar 18. Epub 2019 Mar 18.

Department of Physics, Biophysics Graduate Program, Ohio State Biochemistry Graduate Program, and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210-1117, USA; email:

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 nuclear machinery. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-032847DOI Listing
March 2019
1 Read

Helicase Mechanisms During Homologous Recombination in Saccharomyces cerevisiae.

Annu Rev Biophys 2019 Mar 11. Epub 2019 Mar 11.

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; email: ,

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 the helicase protein along one strand of a nucleic acid. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115418DOI Listing

Generalized Born Implicit Solvent Models for Biomolecules.

Annu Rev Biophys 2019 Mar 11. Epub 2019 Mar 11.

Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA; email:

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 fast implicit solvent models, generalized Born (GB) models, which are widely used for molecular dynamics (MD) simulations of proteins and nucleic acids. Read More

View Article

Download full-text PDF

Source
https://www.annualreviews.org/doi/10.1146/annurev-biophys-05
Publisher Site
http://dx.doi.org/10.1146/annurev-biophys-052118-115325DOI Listing
March 2019
8 Reads

How the Genome Folds: The Biophysics of Four-Dimensional Chromatin Organization.

Annu Rev Biophys 2019 Mar 5. Epub 2019 Mar 5.

Unité Imagerie et Modélisation, CNRS UMR 3691, and C3BI (Center of Bioinformatics, Biostatistics and Integrative Biology), CNRS USR 3756, Institut Pasteur, 75015 Paris, France; email:

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 in sequencing and imaging-based techniques have enabled new views into several layers of chromatin organization. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115638DOI Listing

Giant Vesicles and Their Use in Assays for Assessing Membrane Phase State, Curvature, Mechanics, and Electrical Properties.

Authors:
Rumiana Dimova

Annu Rev Biophys 2019 Feb 27. Epub 2019 Feb 27.

Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany; email:

Giant unilamellar vesicles represent a promising and extremely useful model biomembrane system by providing the possibility 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 factors such as ions, (macro)molecules, hydrodynamic flows, or electromagnetic fields can be directly observed under the microscope. Here, we briefly review approaches for giant vesicle preparation and describe several assays used for deducing the membrane phase state and measuring a number of material properties, with further emphasis on membrane reshaping and curvature. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115342DOI Listing
February 2019

Mammalian Respiratory Complex I Through the Lens of Cryo-EM.

Annu Rev Biophys 2019 Feb 20. Epub 2019 Feb 20.

Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom; email: , , ,

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 model for mouse complex I at 3. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115704DOI Listing
February 2019
1 Read

Membrane Electroporation and Electropermeabilization: Mechanisms and Models.

Annu Rev Biophys 2019 Feb 20. Epub 2019 Feb 20.

Faculty of Electrical Engineering, University of Ljubljana , SI-1000 Ljubljana, Slovenia; email: ,

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 that changes to individual membrane lipids and proteins also contribute, substantiating the need for terminological distinction between electroporation and electropermeabilization. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115451DOI Listing
February 2019
1 Read

Split Green Fluorescent Proteins: Scope, Limitations, and Outlook.

Annu Rev Biophys 2019 Feb 20. Epub 2019 Feb 20.

Department of Chemistry, Stanford University, Stanford, California 94305, USA; email: ,

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 versatile sensors, molecular glues, optogenetic tools, and platforms for photophysical studies. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-051013-022846DOI Listing
February 2019

How Good Can Single-Particle Cryo-EM Become? What Remains Before It Approaches Its Physical Limits?

Authors:
Robert M Glaeser

Annu Rev Biophys 2019 Feb 20. Epub 2019 Feb 20.

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA; email:

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 image, and ( c) recovering the full amount of high-resolution signal in the presence of beam-induced motion of the specimen. In addition, potential for improvement is reviewed for other topics such as optimal choice of electron energy, use of aberration correctors, and quantum metrology. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-032828DOI Listing
February 2019
2 Reads

Mechanisms of Sensory Discrimination: Insights from Drosophila Olfaction.

Annu Rev Biophys 2019 Feb 20. Epub 2019 Feb 20.

Centre for Neural Circuits and Behavior, University of Oxford , Oxford OX1 3SR, United Kingdom; email:

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 response distributions in coding space, compress their variances, and combine information from sequential observations. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115655DOI Listing
February 2019

Molecular Fitness Landscapes from High-Coverage Sequence Profiling.

Annu Rev Biophys 2019 Jan 2. Epub 2019 Jan 2.

Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-052118-115333DOI Listing
January 2019

Hydrogel-Tissue Chemistry: Principles and Applications.

Annu Rev Biophys 2018 05;47:355-376

Department of Bioengineering, Stanford University, Stanford, California 94305, USA; email:

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) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons-even within vertebrate brains. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-032905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359929PMC

Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II.

Annu Rev Biophys 2018 05;47:425-446

Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; email:

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 II. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033058DOI Listing
May 2018
3 Reads

Substrate-Induced Formation of Ribosomal Decoding Center for Accurate and Rapid Genetic Code Translation.

Annu Rev Biophys 2018 05;47:525-548

Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden; email:

Accurate translation of genetic information is crucial for synthesis of functional proteins in all organisms. We use recent experimental data to discuss how induced fit affects accuracy of initial codon selection on the ribosome by aminoacyl transfer RNA in ternary complex ( T) with elongation factor Tu (EF-Tu) and guanosine-5'-triphosphate (GTP). We define actual accuracy ([Formula: see text]) of a particular protein synthesis system as its current accuracy and the effective selectivity ([Formula: see text]) as [Formula: see text] in the limit of zero ribosomal binding affinity for T. Read More

View Article

Download full-text PDF

Source
https://www.annualreviews.org/doi/10.1146/annurev-biophys-06
Publisher Site
http://dx.doi.org/10.1146/annurev-biophys-060414-034148DOI Listing
May 2018
1 Read

Macroscopic Theory for Evolving Biological Systems Akin to Thermodynamics.

Annu Rev Biophys 2018 05;47:273-290

Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; email:

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 rate as a consequence of the steady growth of cells. We further demonstrate that this relationship is supported through adaptation experiments of bacteria, perhaps too well as this proportionality is held even across cultures of different types of conditions. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033155DOI Listing

The Physics of the Metaphase Spindle.

Annu Rev Biophys 2018 05;47:655-673

Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany; email:

The assembly of the mitotic spindle and the subsequent segregation of sister chromatids are based on the self-organized action of microtubule filaments, motor proteins, and other microtubule-associated proteins, which constitute the fundamental force-generating elements in the system. Many of the components in the spindle have been identified, but until recently it remained unclear how their collective behaviors resulted in such a robust bipolar structure. Here, we review the current understanding of the physics of the metaphase spindle that is only now starting to emerge. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-060414-034107DOI Listing
May 2018
1 Read

Molecular Mechanisms of Fast Neurotransmitter Release.

Annu Rev Biophys 2018 05;47:469-497

Department of Molecular and Cellular Physiology, Department of Neurology and Neurological Sciences, Department of Structural Biology, Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA; email:

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 neurotransmitter release. Structural and functional studies of the synaptic fusion machinery suggest new molecular models of synaptic vesicle priming and Ca-triggered fusion. These studies will be a stepping-stone toward answering the question of how the synaptic vesicle fusion machinery achieves such high speed and sensitivity. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070816-034117DOI Listing
May 2018
1 Read

The Physical Properties of Ceramides in Membranes.

Annu Rev Biophys 2018 05 4;47:633-654. Epub 2018 Apr 4.

I nstituto Biofisika [University of the Basque Country and Spanish National Research Council (CSIC)], 48940 Leioa, Spain.

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 in membranes; ( c) give rise to lateral phase separation and domain formation in phospholipid bilayers; ( d) possess a marked intrinsic negative curvature that facilitates formation of inverted hexagonal phases; ( e) make bilayers and cell membranes permeable to small and large (i.e. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033309DOI Listing

Behavioral Variability and Phenotypic Diversity in Bacterial Chemotaxis.

Annu Rev Biophys 2018 05 4;47:595-616. Epub 2018 Apr 4.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520; email:

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 they diversify cellular responses to identical signals. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-062215-010954DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989721PMC
May 2018
1 Read

Single-Molecule View of Small RNA-Guided Target Search and Recognition.

Annu Rev Biophys 2018 05 29;47:569-593. Epub 2018 Mar 29.

Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands; email: , ,

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. Read More

View Article

Download full-text PDF

Source
https://www.annualreviews.org/doi/10.1146/annurev-biophys-07
Publisher Site
http://dx.doi.org/10.1146/annurev-biophys-070317-032923DOI Listing
May 2018
1 Read

Structure and Immune Recognition of the HIV Glycan Shield.

Annu Rev Biophys 2018 Mar 29. Epub 2018 Mar 29.

Department of Integrative Structural and Computational Biology, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, International AIDS Vaccine Initiative Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California 92037, USA; email: ,

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 on the Env protein. Because Env is heavily glycosylated compared to host glycoproteins, the glycans have become targets for the antibody response. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-060414-034156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6163090PMC

Dynamics of Bacterial Gene Regulatory Networks.

Annu Rev Biophys 2018 05 23;47:447-467. Epub 2018 Mar 23.

Department of Biosciences, Rice University, Houston, Texas 77005, USA; email:

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 networks. Here, we review how the combination of local and global factors affect dynamical responses of gene regulatory networks. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-032947DOI Listing
May 2018
1 Read

Dynamic Neutron Scattering by Biological Systems.

Annu Rev Biophys 2018 05 21;47:335-354. Epub 2018 Mar 21.

School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.

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 detectable using neutrons in biological systems at physiological temperatures. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033358DOI Listing
May 2018
1 Read

Understanding Biological Regulation Through Synthetic Biology.

Annu Rev Biophys 2018 05 16;47:399-423. Epub 2018 Mar 16.

Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; email: ,

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, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070816-033903DOI Listing

Serial Femtosecond Crystallography of G Protein-Coupled Receptors.

Annu Rev Biophys 2018 05 15;47:377-397. Epub 2018 Mar 15.

Department of Chemistry and Bridge Institute, University of Southern California, Los Angeles, California 90089, USA; email: ,

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. The recent emergence of X-ray free-electron lasers (XFELs) has further accelerated structural studies of GPCRs and other challenging proteins by overcoming radiation damage and providing access to high-resolution structures and dynamics using micrometer-sized crystals. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6290114PMC
May 2018
3 Reads

High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery.

Annu Rev Biophys 2018 Mar 14. Epub 2018 Mar 14.

Center for Proteomics and Bioinformatics, and Department of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106, USA; email:

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, additional specific and nonspecific labeling reagents have been introduced to extend the approach. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033123DOI Listing
March 2018
1 Read

Photoreceptors Take Charge: Emerging Principles for Light Sensing.

Annu Rev Biophys 2018 Mar 14. Epub 2018 Mar 14.

Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, USA; email:

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 of proton and electron transfer in photosensory proteins and their involvement both in primary photochemistry and subsequent processes that lead to the formation of the signaling state. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033047DOI Listing
March 2018
2 Reads

Modeling Cell Size Regulation: From Single-Cell-Level Statistics to Molecular Mechanisms and Population-Level Effects.

Annu Rev Biophys 2018 05 8;47:251-271. Epub 2018 Mar 8.

John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA; email:

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-032955DOI Listing
May 2018
25 Reads

The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition.

Annu Rev Biophys 2018 05 5;47:223-250. Epub 2018 Mar 5.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA; email: , ,

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 interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070816-033743DOI Listing

Structure and Dynamics of Membrane Proteins from Solid-State NMR.

Annu Rev Biophys 2018 05 2;47:201-222. Epub 2018 Mar 2.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; email:

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 helix proteins. Research has also identified conformational plasticity underlying virus-cell membrane fusions by complex protein machineries, and β-sheet folding and assembly by amyloidogenic proteins bound to lipid membranes. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070816-033712DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6312106PMC
May 2018
1 Read

Structural Basis for G Protein-Coupled Receptor Signaling.

Annu Rev Biophys 2018 Mar 2. Epub 2018 Mar 2.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA; email: , ,

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 receptors in unprecedented atomic detail. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-032931DOI Listing
March 2018
2 Reads

The Jigsaw Puzzle of mRNA Translation Initiation in Eukaryotes: A Decade of Structures Unraveling the Mechanics of the Process.

Annu Rev Biophys 2018 Mar 1. Epub 2018 Mar 1.

Department of Biological Sciences, Columbia University, New York, NY 10032, USA; email:

Translation initiation in eukaryotes is a highly regulated and rate-limiting process. It results in the assembly and disassembly of numerous transient and intermediate complexes involving over a dozen eukaryotic initiation factors (eIFs). This process culminates in the accommodation of a start codon marking the beginning of an open reading frame at the appropriate ribosomal site. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070816-034034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318078PMC
March 2018
4 Reads

Nanodiscs: A Controlled Bilayer Surface for the Study of Membrane Proteins.

Annu Rev Biophys 2018 Mar 1. Epub 2018 Mar 1.

Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA; email: , ,

The study of membrane proteins and receptors presents many challenges to researchers wishing to perform biophysical measurements to determine the structure, function, and mechanism of action of such components. In most cases, to be fully functional, proteins and receptors require the presence of a native phospholipid bilayer. In addition, many complex multiprotein assemblies involved in cellular communication require an integral membrane protein as well as a membrane surface for assembly and information transfer to soluble partners in a signaling cascade. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070816-033620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6370528PMC
March 2018
2 Reads

Cryo-EM Studies of Pre-mRNA Splicing: From Sample Preparation to Model Visualization.

Annu Rev Biophys 2018 05 1;47:175-199. Epub 2018 Mar 1.

MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; email: , , ,

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 the RNA-based active site and to mediate the pre-mRNA branching and ligation reactions. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033410DOI Listing
May 2018
7 Reads

Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective.

Annu Rev Biophys 2018 05 1;47:153-173. Epub 2018 Mar 1.

School of Chemistry; Faculty of Science, Medicine and Health; University of Wollongong, Wollongong, New South Wales 2522, Australia; email:

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033018DOI Listing
May 2018
1 Read

Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions.

Annu Rev Biophys 2018 Jan 18. Epub 2018 Jan 18.

Department of Biomedical Engineering and center for Biological Systems Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA; email: ,

Proteins can collapse into compact globules or form expanded, solvent-accessible, coil-like conformations. Additionally, they can fold into well-defined three-dimensional structures or remain partially or entirely disordered. Recent discoveries have shown that the tendency for proteins to collapse or remain expanded is not intrinsically coupled to their ability to fold. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-032838DOI Listing
January 2018
1 Read

Imaging mRNA In Vivo, from Birth to Death.

Annu Rev Biophys 2018 05 18;47:85-106. Epub 2018 Jan 18.

Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205.

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 in both fixed and live cells. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033037DOI Listing
May 2018
5 Reads

Assembly of COPI and COPII Vesicular Coat Proteins on Membranes.

Annu Rev Biophys 2018 05 18;47:63-83. Epub 2018 Jan 18.

Heidelberg University Biochemistry Centre, 69120 Heidelberg, Germany; email: ,

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 to form a bud. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070317-033259DOI Listing

Measuring Entropy in Molecular Recognition by Proteins.

Annu Rev Biophys 2018 05 18;47:41-61. Epub 2018 Jan 18.

Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6059, USA; email: ,

Molecular recognition by proteins is fundamental to the molecular basis of biology. Dissection of the thermodynamic landscape governing protein-ligand interactions has proven difficult because determination of various entropic contributions is quite challenging. Nuclear magnetic resonance relaxation measurements, theory, and simulations suggest that conformational entropy can be accessed through a dynamical proxy. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-060414-034042DOI Listing

Integration of Bacterial Small RNAs in Regulatory Networks.

Annu Rev Biophys 2017 05;46:131-148

Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; email:

Small RNAs (sRNAs) are central regulators of gene expression in bacteria, controlling target genes posttranscriptionally by base pairing with their mRNAs. sRNAs are involved in many cellular processes and have unique regulatory characteristics. In this review, we discuss the properties of regulation by sRNAs and how it differs from and combines with transcriptional regulation. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070816-034058DOI Listing
May 2017
15 Reads

Structural Insights into the Eukaryotic Transcription Initiation Machinery.

Annu Rev Biophys 2017 05;46:59-83

Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500.

Eukaryotic gene transcription requires the assembly at the promoter of a large preinitiation complex (PIC) that includes RNA polymerase II (Pol II) and the general transcription factors TFIID, TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH. The size and complexity of Pol II, TFIID, and TFIIH have precluded their reconstitution from heterologous systems, and purification relies on scarce endogenous sources. Together with their conformational flexibility and the transient nature of their interactions, these limitations had precluded structural characterization of the PIC. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-biophys-070816-033751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6186020PMC
May 2017
19 Reads