- Home
- A-Z Publications
- Annual Review of Biophysics
- Previous Issues
- Volume 47, 2018
Annual Review of Biophysics - Volume 47, 2018
Volume 47, 2018
-
-
Dynamics of Bacterial Gene Regulatory Networks
Vol. 47 (2018), pp. 447–467More LessThe 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. Our goal is to discuss the general principles that allow extrapolation from a few model bacteria to less understood microbes. We emphasize that, in addition to well-studied effects of network architecture, network dynamics are shaped by global pleiotropic effects and cell physiology.
-
-
-
Molecular Mechanisms of Fast Neurotransmitter Release
Vol. 47 (2018), pp. 469–497More LessThis 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. These studies will be a stepping-stone toward answering the question of how the synaptic vesicle fusion machinery achieves such high speed and sensitivity.
-
-
-
Structure and Immune Recognition of the HIV Glycan Shield
Vol. 47 (2018), pp. 499–523More LessVaccine 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. Therefore, considerable efforts have been made in developing and validating biophysical methods to elucidate the complex structure of the Env-spike glycoprotein, with its combination of glycan and protein epitopes. We illustrate here how the application of robust biophysical methods has transformed our understanding of the structure and function of the HIV Env spike and stimulated innovation in vaccine design strategies that takes into account the essential glycan components.
-
-
-
Substrate-Induced Formation of Ribosomal Decoding Center for Accurate and Rapid Genetic Code Translation
Vol. 47 (2018), pp. 525–548More LessAccurate 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 (
) of a particular protein synthesis system as its current accuracy and the effective selectivity (
) as
in the limit of zero ribosomal binding affinity for T3. Intrinsic selectivity (
), defined as the upper thermodynamic limit of
, is determined by the free energy difference between near-cognate and cognate T3 in the pre-GTP hydrolysis state on the ribosome.
is much larger than
, suggesting the possibility of a considerable increase in
and
at negligible kinetic cost. Induced fit increases
and
without affecting
, and aminoglycoside antibiotics reduce
and
at unaltered
.
-
-
-
The Biophysics of 3D Cell Migration
Vol. 47 (2018), pp. 549–567More LessThree-dimensional (3D) cell culture systems have gained increasing interest not only for 3D migration studies but also for their use in drug screening, tissue engineering, and ex vivo modeling of metastatic behavior in the field of cancer biology and morphogenesis in the field of developmental biology. The goal of studying cells in a 3D context is to attempt to more faithfully recapitulate the physiological microenvironment of tissues, including mechanical and structural parameters that we envision will reveal more predictive data for development programs and disease states. In this review, we discuss the pros and cons of several well-characterized 3D cell culture systems for performing 3D migration studies. We discuss the intracellular and extracellular signaling mechanisms that govern cell migration. We also describe the mathematical models and relevant assumptions that can be used to describe 3D cell movement.
-
-
-
Single-Molecule View of Small RNA–Guided Target Search and Recognition
Vol. 47 (2018), pp. 569–593More LessMost 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. We discuss different steps involved in search and recognition, from the initial complex prearrangement into the target-search competent state to the final proofreading steps. We focus on target search mechanisms that range from weak interactions, to one- and three-dimensional diffusion, to conformational proofreading. We compare the mechanisms of Argonaute and CRISPR with a well-studied target search system, RecA.
-
-
-
Behavioral Variability and Phenotypic Diversity in Bacterial Chemotaxis
Vol. 47 (2018), pp. 595–616More LessLiving 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. After briefly summarizing the architecture and logic of the chemotaxis system, we discuss determinants of behavior and chemotactic performance of individual cells. Then, we review how cell-to-cell differences in protein abundance map onto differences in individual chemotactic abilities and how phenotypic variability affects the performance of the population. We conclude with open questions to be addressed by future research.
-
-
-
Mechanotransduction by the Actin Cytoskeleton: Converting Mechanical Stimuli into Biochemical Signals
Vol. 47 (2018), pp. 617–631More LessForce transmission through the actin cytoskeleton plays a central role in cell movements, shape change, and internal organization. Dynamic reorganization of actin filaments by an array of specialized binding proteins creates biochemically and architecturally distinct structures, many of which are finely tuned to exert or resist mechanical loads. The molecular complexity of the actin cytoskeleton continues to be revealed by detailed biochemical assays, and the architectural diversity and dynamics of actin structures are being uncovered by advances in super-resolution fluorescence microscopy and electron microscopy. However, our understanding of how mechanical forces feed back on cytoskeletal architecture and actin-binding protein organization is comparatively limited. In this review, we discuss recent work investigating how mechanical forces applied to cytoskeletal proteins are transduced into biochemical signals. We explore multiple mechanisms for mechanical signal transduction, including the mechanosensitive behavior of actin-binding proteins, the effect of mechanical force on actin filament dynamics, and the influence of mechanical forces on the structure of single actin filaments. The emerging picture is one in which the actin cytoskeleton is defined not only by the set of proteins that constitute a network but also by the constant interplay of mechanical forces and biochemistry.
-
-
-
The Physical Properties of Ceramides in Membranes
Vol. 47 (2018), pp. 633–654More LessCeramides 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., protein-size) solutes; and (f) promote transmembrane (flip-flop) lipid motion. Unfortunately, there is hardly any link between the physical studies reviewed here and the mass of biological and clinical studies on the effects of ceramides in health and disease.
-
-
-
The Physics of the Metaphase Spindle
Vol. 47 (2018), pp. 655–673More LessThe 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.
-
Previous Volumes
-
Volume 53 (2024)
-
Volume 52 (2023)
-
Volume 51 (2022)
-
Volume 50 (2021)
-
Volume 49 (2020)
-
Volume 48 (2019)
-
Volume 47 (2018)
-
Volume 46 (2017)
-
Volume 45 (2016)
-
Volume 44 (2015)
-
Volume 43 (2014)
-
Volume 42 (2013)
-
Volume 41 (2012)
-
Volume 40 (2011)
-
Volume 39 (2010)
-
Volume 38 (2009)
-
Volume 37 (2008)
-
Volume 36 (2007)
-
Volume 35 (2006)
-
Volume 34 (2005)
-
Volume 33 (2004)
-
Volume 32 (2003)
-
Volume 31 (2002)
-
Volume 30 (2001)
-
Volume 29 (2000)
-
Volume 28 (1999)
-
Volume 27 (1998)
-
Volume 26 (1997)
-
Volume 25 (1996)
-
Volume 24 (1995)
-
Volume 23 (1994)
-
Volume 22 (1993)
-
Volume 21 (1992)
-
Volume 20 (1991)
-
Volume 19 (1990)
-
Volume 18 (1989)
-
Volume 17 (1988)
-
Volume 16 (1987)
-
Volume 15 (1986)
-
Volume 14 (1985)
-
Volume 13 (1984)
-
Volume 12 (1983)
-
Volume 11 (1982)
-
Volume 10 (1981)
-
Volume 9 (1980)
-
Volume 8 (1979)
-
Volume 7 (1978)
-
Volume 6 (1977)
-
Volume 5 (1976)
-
Volume 4 (1975)
-
Volume 3 (1974)
-
Volume 2 (1973)
-
Volume 1 (1972)
-
Volume 0 (1932)