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Annual Review of Biophysics

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https://www.readbyqxmd.com/read/29792820/hydrogel-tissue-chemistry-principles-and-applications
#1
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) 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...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29792819/distinct-mechanisms-of-transcription-initiation-by-rna-polymerases-i-and-ii
#2
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 II. Recent structural studies of Pol I complexes with transcription initiation factors provided insights into how the polymerase recognizes its specific promoter DNA, how it may open DNA, and how initiation may be regulated...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29792818/substrate-induced-formation-of-ribosomal-decoding-center-for-accurate-and-rapid-genetic-code-translation
#3
Michael Y Pavlov, Måns Ehrenberg
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 ( T3 ) 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 T3 ...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29792817/macroscopic-theory-for-evolving-biological-systems-akin-to-thermodynamics
#4
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 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...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29792816/the-physics-of-the-metaphase-spindle
#5
David Oriola, Daniel J Needleman, Jan Brugués
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...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29792815/molecular-mechanisms-of-fast-neurotransmitter-release
#6
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 neurotransmitter release. Structural and functional studies of the synaptic fusion machinery suggest new molecular models of synaptic vesicle priming and Ca2+ -triggered fusion...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29618220/the-physical-properties-of-ceramides-in-membranes
#7
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 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...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29618219/behavioral-variability-and-phenotypic-diversity-in-bacterial-chemotaxis
#8
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 they diversify cellular responses to identical signals. Here, we review recent experimental and theoretical advances in understanding the mechanistic origin and functional consequences of such variation in Escherichia coli chemotaxis-a well-understood model of signal transduction and behavior...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29595998/single-molecule-view-of-small-rna-guided-target-search-and-recognition
#9
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. This review focuses on single-molecule advances studying the target search and recognition mechanism of Argonaute and CRISPR (clustered regularly interspaced short palindromic repeats) systems...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29570353/dynamics-of-bacterial-gene-regulatory-networks
#10
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 networks. Here, we review how the combination of local and global factors affect dynamical responses of gene regulatory networks...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29561628/dynamic-neutron-scattering-by-biological-systems
#11
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 detectable using neutrons in biological systems at physiological temperatures. New techniques for deriving information on collective motions using coherent scattering are also reviewed...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29547341/understanding-biological-regulation-through-synthetic-biology
#12
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, each turn of the engineering cycle can force a resynthesis in understanding of natural network function...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29543504/serial-femtosecond-crystallography-of-g-protein-coupled-receptors
#13
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. 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...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29517919/modeling-cell-size-regulation-from-single-cell-level-statistics-to-molecular-mechanisms-and-population-level-effects
#14
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, and population growth, all in relation to size regulation. Finally, we discuss several future directions for developing understanding beyond phenomenological models of cell size regulation...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29505727/the-molecular-origin-of-enthalpy-entropy-compensation-in-biomolecular-recognition
#15
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 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...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29498890/structure-and-dynamics-of-membrane-proteins-from-solid-state-nmr
#16
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 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...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29494253/cryo-em-studies-of-pre-mrna-splicing-from-sample-preparation-to-model-visualization
#17
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 the RNA-based active site and to mediate the pre-mRNA branching and ligation reactions. In the past two years, cryo-electron microscopy (cryo-EM) structures of spliceosomes captured in different assembly and catalytic states have greatly advanced our understanding of its mechanism...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29494252/hemagglutinin-mediated-membrane-fusion-a-biophysical-perspective
#18
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 barriers and proceeds through several intermediate states. Here, we provide a biophysical description of the membrane fusion process, relating its kinetic and thermodynamic properties to the large conformational changes taking place in HA and placing these in the context of multiple HA proteins working together to mediate fusion...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29345990/imaging-mrna-in-vivo-from-birth-to-death
#19
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 in both fixed and live cells. By describing the application of these imaging tools, we follow the journey of mRNA from transcription to decay in single cells, with single-molecule resolution...
May 20, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29345989/assembly-of-copi-and-copii-vesicular-coat-proteins-on-membranes
#20
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 to form a bud. A multitude of structural elements of coat proteins have been solved by X-ray crystallography...
May 20, 2018: Annual Review of Biophysics
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