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- Volume 46, 2017
Annual Review of Biophysics - Volume 46, 2017
Volume 46, 2017
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Progress and Potential of Electron Cryotomography as Illustrated by Its Application to Bacterial Chemoreceptor Arrays
Vol. 46 (2017), pp. 1–21More LessElectron 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 s Read More
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Geometric Principles for Designing Highly Symmetric Self-Assembling Protein Nanomaterials
Vol. 46 (2017), pp. 23–42More LessEmerging 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, acc Read More
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Weighted Ensemble Simulation: Review of Methodology, Applications, and Software
Vol. 46 (2017), pp. 43–57More LessThe 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 Read More
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Structural Insights into the Eukaryotic Transcription Initiation Machinery
Vol. 46 (2017), pp. 59–83More LessEukaryotic 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 conformation Read More
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Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence
Vol. 46 (2017), pp. 85–103More LessFor decades, rates of protein evolution have been interpreted in terms of the vague concept of functional importance. Slowly evolving proteins or sites within proteins were assumed to be more functionally important and thus subject to stronger selection pressure. More recently, biophysical models of protein evolution, which combine evolutionary theory with protein biophysics, have completely revolutionized our view of the f Read More
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Rate Constants and Mechanisms of Protein–Ligand Binding
Vol. 46 (2017), pp. 105–130More LessWhereas 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 Read More
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Integration of Bacterial Small RNAs in Regulatory Networks
Vol. 46 (2017), pp. 131–148More LessSmall 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 s Read More
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Recognition of Client Proteins by the Proteasome
Vol. 46 (2017), pp. 149–173More LessThe 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 Read More
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What Do Structures Tell Us About Chemokine Receptor Function and Antagonism?
Vol. 46 (2017), pp. 175–198More LessChemokines 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 Read More
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Progress in Human and Tetrahymena Telomerase Structure Determination
Vol. 46 (2017), pp. 199–225More LessTelomerase is an RNA–protein complex that extends the 3′ ends of linear chromosomes, using a unique telomerase reverse transcriptase (TERT) and template in the telomerase RNA (TR), thereby helping to maintain genome integrity. TR assembles with TERT and species-specific proteins, and telomerase function in vivo requires interaction with telomere-associated proteins. Over the past two decades, structures of domains of Read More
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Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules
Vol. 46 (2017), pp. 227–246More LessIn addition to continuous rapid progress in RNA structure determination, probing, and biophysical studies, the past decade has seen remarkable advances in the development of a new generation of RNA folding theories and models. In this article, we review RNA structure prediction models and models for ion–RNA and ligand–RNA interactions. These new models are becoming increasingly important for a mechanistic underst Read More
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Reconstructing Ancient Proteins to Understand the Causes of Structure and Function
Vol. 46 (2017), pp. 247–269More LessA central goal in biochemistry is to explain the causes of protein sequence, structure, and function. Mainstream approaches seek to rationalize sequence and structure in terms of their effects on function and to identify function's underlying determinants by comparing related proteins to each other. Although productive, both strategies suffer from intrinsic limitations that have left important aspects of many proteins unexp Read More
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Imaging and Optically Manipulating Neuronal Ensembles
Vol. 46 (2017), pp. 271–293More LessThe 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 t Read More
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Matrix Mechanosensing: From Scaling Concepts in ’Omics Data to Mechanisms in the Nucleus, Regeneration, and Cancer
Vol. 46 (2017), pp. 295–315More LessMany 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 comp Read More
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Structures of Large Protein Complexes Determined by Nuclear Magnetic Resonance Spectroscopy
Vol. 46 (2017), pp. 317–336More LessNuclear 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 Read More
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How Active Mechanics and Regulatory Biochemistry Combine to Form Patterns in Development
Vol. 46 (2017), pp. 337–356More LessThe 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 Read More
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Single-Molecule Studies of Telomeres and Telomerase
Vol. 46 (2017), pp. 357–377More LessTelomeres 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 telom Read More
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Soft Matter in Lipid–Protein Interactions
Vol. 46 (2017), pp. 379–410More LessMembrane 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 oligo Read More
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Single-Molecule Analysis of Bacterial DNA Repair and Mutagenesis
Vol. 46 (2017), pp. 411–432More LessUbiquitous 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-fou Read More
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High-Dimensional Mutant and Modular Thermodynamic Cycles, Molecular Switching, and Free Energy Transduction
Vol. 46 (2017), pp. 433–453More LessUnderstanding 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 Read More
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Previous Volumes
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Volume 53 (2024)
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Volume 52 (2023)
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Volume 51 (2022)
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Volume 50 (2021)
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Volume 49 (2020)
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Volume 48 (2019)
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Volume 47 (2018)
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Volume 46 (2017)
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Volume 45 (2016)
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Volume 44 (2015)
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Volume 43 (2014)
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Volume 42 (2013)
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Volume 41 (2012)
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Volume 40 (2011)
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Volume 39 (2010)
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Volume 38 (2009)
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Volume 37 (2008)
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Volume 36 (2007)
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Volume 35 (2006)
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Volume 34 (2005)
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Volume 33 (2004)
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Volume 32 (2003)
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Volume 31 (2002)
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Volume 30 (2001)
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Volume 29 (2000)
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Volume 28 (1999)
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Volume 27 (1998)
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Volume 26 (1997)
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Volume 25 (1996)
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Volume 24 (1995)
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Volume 23 (1994)
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Volume 22 (1993)
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Volume 21 (1992)
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Volume 20 (1991)
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Volume 19 (1990)
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Volume 18 (1989)
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Volume 17 (1988)
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Volume 16 (1987)
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Volume 15 (1986)
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Volume 14 (1985)
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Volume 13 (1984)
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Volume 12 (1983)
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Volume 11 (1982)
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Volume 10 (1981)
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Volume 9 (1980)
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Volume 8 (1979)
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Volume 7 (1978)
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Volume 6 (1977)
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Volume 5 (1976)
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Volume 4 (1975)
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Volume 3 (1974)
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Volume 2 (1973)
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Volume 1 (1972)
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Volume 0 (1932)