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Annual Review of Biophysics

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https://www.readbyqxmd.com/read/28532217/integration-of-bacterial-small-rnas-in-regulatory-networks
#1
REVIEW
Mor Nitzan, Rotem Rehani, Hanah Margalit
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. We describe the global characteristics of the sRNA-target networks in bacteria using graph-theoretic approaches and review the local integration of sRNAs in mixed regulatory circuits, including feed-forward loops and their combinations, feedback loops, and circuits made of an sRNA and another regulator, both derived from the same transcript...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28532216/structural-insights-into-the-eukaryotic-transcription-initiation-machinery
#2
REVIEW
Eva Nogales, Robert K Louder, Yuan He
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...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28532215/matrix-mechanosensing-from-scaling-concepts-in-omics-data-to-mechanisms-in-the-nucleus-regeneration-and-cancer
#3
REVIEW
Dennis E Discher, Lucas Smith, Sangkyun Cho, Mark Colasurdo, Andrés J García, Sam Safran
Many of the most important molecules of life are polymers. In animals, the most abundant of the proteinaceous polymers are the collagens, which constitute the fibrous matrix outside cells and which can also self-assemble into gels. The physically measurable stiffness of gels, as well as tissues, increases with the amount of collagen, and cells seem to sense this stiffness. An understanding of this mechanosensing process in complex tissues, including fibrotic disease states with high collagen, is now utilizing 'omics data sets and is revealing polymer physics-type, nonlinear scaling relationships between concentrations of seemingly unrelated biopolymers...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28532214/how-active-mechanics-and-regulatory-biochemistry-combine-to-form-patterns-in-development
#4
REVIEW
Peter Gross, K Vijay Kumar, Stephan W Grill
The development of organisms starting from their zygotic state involves a tight integration of the myriad biochemical signaling interactions with the mechanical forces that eventually pattern and shape the resulting embryo. In the past decade, it has become increasingly evident that several important developmental processes involve mechanical forces in an essential manner. In this review, we highlight the multifaceted role of mechanics in pattern formation, from protein and cell sorting to the generation of tissue shape...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28532213/what-do-structures-tell-us-about-chemokine-receptor-function-and-antagonism
#5
REVIEW
Irina Kufareva, Martin Gustavsson, Yi Zheng, Bryan S Stephens, Tracy M Handel
Chemokines and their cell surface G protein-coupled receptors are critical for cell migration, not only in many fundamental biological processes but also in inflammatory diseases and cancer. Recent X-ray structures of two chemokines complexed with full-length receptors provided unprecedented insight into the atomic details of chemokine recognition and receptor activation, and computational modeling informed by new experiments leverages these insights to gain understanding of many more receptor:chemokine pairs...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28532212/soft-matter-in-lipid-protein-interactions
#6
REVIEW
Michael F Brown
Membrane lipids and cellular water (soft matter) are becoming increasingly recognized as key determinants of protein structure and function. Their influences can be ascribed to modulation of the bilayer properties or to specific binding and allosteric regulation of protein activity. In this review, we first consider hydrophobic matching of the intramembranous proteolipid boundary to explain the conformational changes and oligomeric states of proteins within the bilayer. Alternatively, membranes can be viewed as complex fluids, whose properties are linked to key biological functions...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28399632/predicting-binding-free-energies-frontiers-and-benchmarks
#7
REVIEW
David L Mobley, Michael K Gilson
Binding free energy calculations based on molecular simulations provide predicted affinities for biomolecular complexes. These calculations begin with a detailed description of a system, including its chemical composition and the interactions among its components. Simulations of the system are then used to compute thermodynamic information, such as binding affinities. Because of their promise for guiding molecular design, these calculations have recently begun to see widespread applications in early-stage drug discovery...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28375736/structures-of-large-protein-complexes-determined-by-nuclear-magnetic-resonance-spectroscopy
#8
REVIEW
Chengdong Huang, Charalampos G Kalodimos
Nuclear magnetic resonance (NMR) spectroscopy has been instrumental during the past two decades in providing high-resolution structures of protein complexes. It has been the method of choice for determining the structure of dynamic protein complexes, which are typically recalcitrant to other structural techniques. Until recently, NMR spectroscopy has yielded structures of small or medium-sized protein complexes, up to approximately 30-40 kDa. Major breakthroughs during the past decade, especially in isotope-labeling techniques, have enabled NMR characterization of large protein systems with molecular weights of hundreds of kDa...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28375735/single-molecule-studies-of-telomeres-and-telomerase
#9
REVIEW
Joseph W Parks, Michael D Stone
Telomeres are specialized chromatin structures that protect chromosome ends from dangerous processing events. In most tissues, telomeres shorten with each round of cell division, placing a finite limit on cell growth. In rapidly dividing cells, including the majority of human cancers, cells bypass this growth limit through telomerase-catalyzed maintenance of telomere length. The dynamic properties of telomeres and telomerase render them difficult to study using ensemble biochemical and structural techniques...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28375734/high-dimensional-mutant-and-modular-thermodynamic-cycles-molecular-switching-and-free-energy-transduction
#10
REVIEW
Charles W Carter
Understanding how distinct parts of proteins produce coordinated behavior has driven and continues to drive advances in protein science and enzymology. However, despite consensus about the conceptual basis for allostery, the idiosyncratic nature of allosteric mechanisms resists general approaches. Computational methods can identify conformational transition states from structural changes, revealing common switching mechanisms that impose multistate behavior. Thermodynamic cycles use factorial perturbations to measure coupling energies between side chains in molecular switches that mediate shear during domain motion...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28375733/single-molecule-analysis-of-bacterial-dna-repair-and-mutagenesis
#11
REVIEW
Stephan Uphoff, David J Sherratt
Ubiquitous conserved processes that repair DNA damage are essential for the maintenance and propagation of genomes over generations. Then again, inaccuracies in DNA transactions and failures to remove mutagenic lesions cause heritable genome changes. Building on decades of research using genetics and biochemistry, unprecedented quantitative insight into DNA repair mechanisms has come from the new-found ability to measure single proteins in vitro and inside individual living cells. This has brought together biologists, chemists, engineers, physicists, and mathematicians to solve long-standing questions about the way in which repair enzymes search for DNA lesions and form protein complexes that act in DNA repair pathways...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28375732/rate-constants-and-mechanisms-of-protein-ligand-binding
#12
REVIEW
Xiaodong Pang, Huan-Xiang Zhou
Whereas protein-ligand binding affinities have long-established prominence, binding rate constants and binding mechanisms have gained increasing attention in recent years. Both new computational methods and new experimental techniques have been developed to characterize the latter properties. It is now realized that binding mechanisms, like binding rate constants, can and should be quantitatively determined. In this review, we summarize studies and synthesize ideas on several topics in the hope of providing a coherent picture of and physical insight into binding kinetics...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28375731/crispr-cas9-structures-and-mechanisms
#13
REVIEW
Fuguo Jiang, Jennifer A Doudna
Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems employ the dual RNA-guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific double-stranded breaks in target DNA. Target recognition strictly requires the presence of a short protospacer adjacent motif (PAM) flanking the target site, and subsequent R-loop formation and strand scission are driven by complementary base pairing between the guide RNA and target DNA, Cas9-DNA interactions, and associated conformational changes...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28375730/rna-structure-advances-and-assessment-of-3d-structure-prediction
#14
REVIEW
Zhichao Miao, Eric Westhof
Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28375729/long-range-interactions-in-riboswitch-control-of-gene-expression
#15
REVIEW
Christopher P Jones, Adrian R Ferré-D'Amaré
Riboswitches are widespread RNA motifs that regulate gene expression in response to fluctuating metabolite concentrations. Known primarily from bacteria, riboswitches couple specific ligand binding and changes in RNA structure to mRNA expression in cis. Crystal structures of the ligand binding domains of most of the phylogenetically widespread classes of riboswitches, each specific to a particular metabolite or ion, are now available. Thus, the bound states-one end point-have been thoroughly characterized, but the unbound states have been more elusive...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28301774/geometric-principles-for-designing-highly-symmetric-self-assembling-protein-nanomaterials
#16
REVIEW
Todd O Yeates
Emerging protein design strategies are enabling the creation of diverse, self-assembling supramolecular structures with precision on the atomic scale. The design possibilities include various types of architectures: finite cages or shells, essentially unbounded two-dimensional and three-dimensional arrays (i.e., crystals), and linear or tubular filaments. In nature, structures of those types are generally symmetric, and, accordingly, symmetry provides a powerful guide for developing new design approaches. Recent design studies have produced numerous protein assemblies in close agreement with geometric specifications...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28301773/progress-and-potential-of-electron-cryotomography-as-illustrated-by-its-application-to-bacterial-chemoreceptor-arrays
#17
REVIEW
Ariane Briegel, Grant Jensen
Electron cryotomography (ECT) can produce three-dimensional images of biological samples such as intact cells in a near-native, frozen-hydrated state to macromolecular resolution (∼4 nm). Because one of its first and most common applications has been to bacterial chemoreceptor arrays, ECT's contributions to this field illustrate well its past, present, and future. While X-ray crystallography and nuclear magnetic resonance spectroscopy have revealed the structures of nearly all the individual components of chemoreceptor arrays, ECT has revealed the mesoscale information about how the components are arranged within cells...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28301772/weighted-ensemble-simulation-review-of-methodology-applications-and-software
#18
REVIEW
Daniel M Zuckerman, Lillian T Chong
The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling-the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28301771/recognition-of-client-proteins-by-the-proteasome
#19
REVIEW
Houqing Yu, Andreas Matouschek
The ubiquitin proteasome system controls the concentrations of regulatory proteins and removes damaged and misfolded proteins from cells. Proteins are targeted to the protease at the center of this system, the proteasome, by ubiquitin tags, but ubiquitin is also used as a signal in other cellular processes. Specificity is conferred by the size and structure of the ubiquitin tags, which are recognized by receptors associated with the different cellular processes. However, the ubiquitin code remains ambiguous, and the same ubiquitin tag can target different proteins to different fates...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28301770/imaging-and-optically-manipulating-neuronal-ensembles
#20
REVIEW
Luis Carrillo-Reid, Weijian Yang, Jae-Eun Kang Miller, Darcy S Peterka, Rafael Yuste
The neural code that relates the firing of neurons to the generation of behavior and mental states must be implemented by spatiotemporal patterns of activity across neuronal populations. These patterns engage selective groups of neurons, called neuronal ensembles, which are emergent building blocks of neural circuits. We review optical and computational methods, based on two-photon calcium imaging and two-photon optogenetics, to detect, characterize, and manipulate neuronal ensembles in three dimensions. We review data using these methods in the mammalian cortex that demonstrate the existence of neuronal ensembles in the spontaneous and evoked cortical activity in vitro and in vivo...
May 22, 2017: Annual Review of Biophysics
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