- Home
- A-Z Publications
- Annual Review of Biophysics
- Previous Issues
- Volume 40, 2011
Annual Review of Biophysics - Volume 40, 2011
Volume 40, 2011
-
-
Respice, Adspice, and Prospice
Vol. 40 (2011), pp. 1–39More LessThe title, “Look to the past, Look to the present, and Look to the future,” the motto of City College of New York, expresses how my family life and education led me to an academic career in physical chemistry and ultimately to a study of proteins. The economic depression of the 1930s left a lasting impression on my outlook and career aspirations. With fortunate experiences at several stages in my life, I was able to participate in the great adventure of the last half of the twentieth century: the revolution in biology that advanced the field of protein chemistry to so great an extent. The future is bright and limitless, with greater understanding of biology yet to come.
-
-
-
Equilibrium Sampling in Biomolecular Simulations
Vol. 40 (2011), pp. 41–62More LessEquilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to parallelization to novel uses of hardware. Special focus is placed on classifying algorithms—most of which are underpinned by a few key ideas—in order to understand their fundamental strengths and limitations. Although algorithms have proliferated, progress resulting from novel hardware use appears to be more clear-cut than from algorithms alone, due partly to the lack of widely used sampling measures.
-
-
-
Decision Making in Living Cells: Lessons from a Simple System
Vol. 40 (2011), pp. 63–80More LessThe life cycle of bacteriophage lambda serves as a simplified paradigm for cell-fate decisions. The ongoing quantitative, high-resolution experimental investigation of this life cycle has produced some important insights in recent years. These insights have to do with the way cells choose among alternative fates, how they maintain long-term memory of their gene-expression state, and how they switch from one stable state to another. The recent studies have highlighted the role of spatiotemporal effects in cellular processes and the importance of distinguishing chemical stochasticity from possible hidden variables in cellular decision making.
-
-
-
High-Pressure Protein Crystallography and NMR to Explore Protein Conformations
Vol. 40 (2011), pp. 81–98More LessHigh-pressure methods for solving protein structures by X-ray crystallography and NMR are maturing. These techniques are beginning to impact our understanding of thermodynamic and structural features that define not only the protein's native conformation, but also the higher free energy conformations. The ability of high-pressure methods to visualize these mostly unexplored conformations provides new insight into protein function and dynamics. In this review, we begin with a historical discussion of high-pressure structural studies, with an eye toward early results that paved the way to mapping the multiple conformations of proteins. This is followed by an examination of several recent studies that emphasize different strengths and uses of high-pressure structural studies, ranging from basic thermodynamics to the suggestion of high-pressure structural methods as a tool for protein engineering.
-
-
-
Nucleosome Structure(s) and Stability: Variations on a Theme
Vol. 40 (2011), pp. 99–117More LessChromatin is a highly regulated, modular nucleoprotein complex that is central to many processes in eukaryotes. The organization of DNA into nucleosomes and higher-order structures has profound implications for DNA accessibility. Alternative structural states of the nucleosome, and the thermodynamic parameters governing its assembly and disassembly, need to be considered in order to understand how access to nucleosomal DNA is regulated. In this review, we provide a brief historical account of how the overriding perception regarding aspects of nucleosome structure has changed over the past thirty years. We discuss recent technical advances regarding nucleosome structure and its physical characterization and review the evidence for alternative nucleosome conformations and their implications for nucleosome and chromatin dynamics.
-
-
-
Molecular Mechanisms of Ubiquitin-Dependent Membrane Traffic
Vol. 40 (2011), pp. 119–142More LessOver the past 14 years, ubiquitination has emerged as a centrally important mechanism governing the subcellular trafficking of proteins. Ubiquitination, interaction with sorting factors that contain ubiquitin-binding domains, and deubiquitination govern the itineraries of cargo proteins that include yeast carboxypeptidase S, the epithelial sodium channel ENaC, and epidermal growth factor receptor. The molecular structures and mechanisms of the paradigmatic HECT and RING domain ubiquitin ligases, of JAMM- and USP-domain-deubiquitinating enzymes, and of numerous ubiquitin-binding domains involved in these pathways have been worked out in recent years and are described.
-
-
-
The Cyanobacterial Circadian System: From Biophysics to Bioevolution
Vol. 40 (2011), pp. 143–167More LessRecent studies have unveiled the molecular machinery responsible for the biological clock in cyanobacteria and found that it exerts pervasive control over cellular processes including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topology/compaction! The circadian system comprises both a posttranslational oscillator (PTO) and a transcriptional/translational feedback loop (TTFL). The PTO can be reconstituted in vitro with three purified proteins (KaiA, KaiB, and KaiC) and ATP. These are the only circadian proteins for which high-resolution structures are available. Phase in this nanoclockwork has been associated with key phosphorylations of KaiC. Structural considerations illuminate the mechanism by which the KaiABC oscillator ratchets unidirectionally. Models of the complete in vivo system have important implications for our understanding of circadian clocks in higher organisms, including mammals. The conjunction of structural, biophysical, and biochemical approaches to this system has brought our understanding of the molecular mechanisms of biological timekeeping to an unprecedented level.
-
-
-
Actin Structure and Function
Vol. 40 (2011), pp. 169–186More LessActin is the most abundant protein in most eukaryotic cells. It is highly conserved and participates in more protein-protein interactions than any known protein. These properties, along with its ability to transition between monomeric (G-actin) and filamentous (F-actin) states under the control of nucleotide hydrolysis, ions, and a large number of actin-binding proteins, make actin a critical player in many cellular functions, ranging from cell motility and the maintenance of cell shape and polarity to the regulation of transcription. Moreover, the interaction of filamentous actin with myosin forms the basis of muscle contraction. Owing to its central role in the cell, the actin cytoskeleton is also disrupted or taken over by numerous pathogens. Here we review structures of G-actin and F-actin and discuss some of the interactions that control the polymerization and disassembly of actin.
-
-
-
Molecular Origin of the Hierarchical Elasticity of Titin: Simulation, Experiment, and Theory
Vol. 40 (2011), pp. 187–203More LessThis review uses the giant muscle protein titin as an example to showcase the capability of molecular dynamics simulations. Titin is responsible for the passive elasticity in muscle and is a chain composed of immunoglobulin (Ig)-like and fibronectin III (FN-III)-like domains, as well as PEVK segments rich in proline (P), glutamate (E), valine (V), and lysine (K). The elasticity of titin is derived in stages of extension under increasing external force: Ig domain straightening occurs first (termed tertiary structure elasticity), followed by the extension of the disordered PEVK segments. At larger extension and force, Ig domains unfold one by one (termed secondary structure elasticity). With the availability of crystal structures of single and connected Ig domains, the tertiary and secondary structure elasticity of titin was investigated through molecular dynamics simulations, unveiling the molecular origin of titin's elasticity.
-
-
-
Proton-Pumping Mechanism of Cytochrome c Oxidase
Vol. 40 (2011), pp. 205–223More LessCytochrome c oxidase (CcO), as the terminal oxidase of cellular respiration, coupled with a proton-pumping process, reduces molecular oxygen (O2) to water. This intriguing and highly organized chemical process represents one of the most critical aspects of cellular respiration. It employs transition metals (Fe and Cu) at the O2 reduction site and has been considered one of the most challenging research subjects in life science. Extensive X-ray structural and mutational analyses have provided two different proposals with regard to the mechanism of proton pumping. One mechanism is based on bovine CcO and includes an independent pathway for the pumped protons. The second mechanistic proposal includes a common pathway for the pumped and chemical protons and is based upon bacterial CcO. Here, recent progress in experimental evaluations of these proposals is reviewed and strategies for improving our understanding of the mechanism of this physiologically important process are discussed.
-
-
-
SAXS Studies of Ion–Nucleic Acid Interactions
Vol. 40 (2011), pp. 225–242More LessPositively charged ions, atoms, or molecules compensate the high negative charge of the nucleic acid backbone. Their presence is critical to the biological function of DNA and RNA. This review focuses on experimental studies probing (a) interactions between small ions and nucleic acids and (b) ion-mediated interactions between nucleic acid duplexes. Experimental results on these simple model systems can be compared with specific theoretical models to validate their predictions. Small angle X-ray scattering (SAXS) provides unique insight into these interactions. Anomalous SAXS reports the spatial correlations of condensed (e.g., locally concentrated) counterions to individual DNA or RNA duplexes. SAXS very effectively reports interactions between nucleic acid helices, which range from strongly repulsive to strongly attractive depending on the ionic species present. The sign and strength of interparticle interactions are easily deduced from dramatic changes in the scattering profiles of interacting duplexes.
-
-
-
P-Type ATPases
Vol. 40 (2011), pp. 243–266More LessP-type ATPases form a large superfamily of cation and lipid pumps. They are remarkably simple with only a single catalytic subunit and carry out large domain motions during transport. The atomic structure of P-type ATPases in different conformations, together with ample mutagenesis evidence, has provided detailed insights into the pumping mechanism by these biological nanomachines. Phylogenetically, P-type ATPases are divided into five subfamilies, P1–P5. These subfamilies differ with respect to transported ligands and the way they are regulated.
-
-
-
Kinesin Assembly and Movement in Cells
Vol. 40 (2011), pp. 267–288More LessLong-distance transport in eukaryotic cells is driven by molecular motors that move along microtubule tracks. Molecular motors of the kinesin superfamily contain a kinesin motor domain attached to family-specific sequences for cargo binding, regulation, and oligomerization. The biochemical and biophysical properties of the kinesin motor domain have been widely studied, yet little is known about how kinesin motors work in the complex cellular environment. We discuss recent studies on the three major families involved in intracellular transport (kinesin-1, kinesin-2, and kinesin-3) that have begun to bridge the gap in knowledge between the in vitro and in vivo behaviors of kinesin motors. These studies have increased our understanding of how kinesin subunits assemble to produce a functional motor, how kinesin motors are affected by biochemical cues and obstacles present on cellular microtubules, and how multiple motors on a cargo surface can work collectively for increased force production and travel distance.
-
-
-
Stochastic Conformational Pumping: A Mechanism for Free-Energy Transduction by Molecules
Vol. 40 (2011), pp. 289–313More LessProteins and other macromolecules can act as molecular machines that convert energy from one form to another through cycles of conformational transitions. In a macroscopically fluctuating environment or at the single-molecule level, the probability for a molecule to be in any state j fluctuates, and the probability current from any other state i to state j is given as the sum of a steady-state current and a pumped current, Iij=Issij+FijdPj/dt, where Fij is the fraction of the fluctuating current into and out of state j coming directly from state i, and dPj/dt is the rate of change of the probability for the molecule to be in state j. If the fluctuations arise from an equilibrium source, microscopic reversibility guarantees that the time average of the pumped current is zero. If, however, the fluctuations arise due to the action of a nonequilibrium source, the time average of the pumped current is not in general zero and can be opposite in sign to the steady-state current. The pumped current provides a mechanism by which fluctuations, whether generated externally or arising from an internal nonequilibrium chemical reaction, can do electrical, mechanical, or chemical work on a system by coupling into the equilibrium conformational transitions of a protein. In this review I examine work elaborating the mechanism of stochastic pumping and also discuss a thermodynamically consistent approach for modeling the effects of dynamic disorder on enzymes and other proteins.
-
-
-
Protein Self-Organization: Lessons from the Min System
Vol. 40 (2011), pp. 315–336More LessOne of the most fundamental features of biological systems is probably their ability to self-organize in space and time on different scales. Despite many elaborate theoretical models of how molecular self-organization can come about, only a few experimental systems of biological origin have so far been rigorously described, due mostly to their inherent complexity. The most promising strategy of modern biophysics is thus to identify minimal biological systems showing self-organized emergent behavior. One of the best-understood examples of protein self-organization, which has recently been successfully reconstituted in vitro, is represented by the oscillations of the Min proteins in Escherichia coli. In this review, we summarize the current understanding of the mechanism of Min protein self-organization in vivo and in vitro. We discuss the potential of the Min oscillations to sense the geometry of the cell and suggest that spontaneous protein waves could be a general means of intracellular organization. We hypothesize that cooperative membrane binding and unbinding, e.g., as an energy-dependent switch, may act as an important regulatory mechanism for protein oscillations and pattern formation in the cell.
-
-
-
Protein Folding at the Exit Tunnel
Vol. 40 (2011), pp. 337–359More LessOver five decades of research have yielded a large body of information on how purified proteins attain their native state when refolded in the test tube, starting from a chemically or thermally denatured state. Nevertheless, we still know little about how proteins fold and unfold in their natural biological habitat: the living cell. Indeed, a variety of cellular components, including molecular chaperones, the ribosome, and crowding of the intracellular medium, modulate folding mechanisms in physiologically relevant environments. This review focuses on the current state of knowledge in protein folding in the cell with emphasis on the early stage of a protein's life, as the nascent polypeptide traverses and emerges from the ribosomal tunnel. Given the vectorial nature of ribosome-assisted translation, the transient degree of chain elongation becomes a relevant variable expected to affect nascent protein foldability, aggregation propensity and extent of interaction with chaperones and the ribosome.
-
-
-
Mechanosignaling to the Cell Nucleus and Gene Regulation
Vol. 40 (2011), pp. 361–378More LessCells integrate physicochemical signals on the nanoscale from the local microenvironment, resulting in altered functional nuclear landscape and gene expression. These alterations regulate diverse biological processes including stem cell differentiation, establishing robust developmental genetic programs and cellular homeostatic control systems. The mechanisms by which these signals are integrated into the 3D spatiotemporal organization of the cell nucleus to elicit differential gene expression programs are poorly understood. In this review I analyze our current understanding of mechanosignal transduction mechanisms to the cell nucleus to induce differential gene regulation. A description of both physical and chemical coupling, resulting in a prestressed nuclear organization, is emphasized. I also highlight the importance of spatial dimension in chromosome assembly, as well as the temporal filtering and stochastic processes at gene promoters that may be important in understanding the biophysical design principles underlying mechanoregulation of gene transcription.
-
-
-
Amphipols From A to Z*
J.-L. Popot, T. Althoff, D. Bagnard, J.-L. Banères, P. Bazzacco, E. Billon-Denis, L.J. Catoire, P. Champeil, D. Charvolin, M.J. Cocco, G. Crémel, T. Dahmane, L.M. de la Maza, C. Ebel, F. Gabel, F. Giusti, Y. Gohon, E. Goormaghtigh, E. Guittet, J.H. Kleinschmidt, W. Kühlbrandt, C. Le Bon, K.L. Martinez, M. Picard, B. Pucci, J.N. Sachs, C. Tribet, C. van Heijenoort, F. Wien, F. Zito, and M. ZoonensVol. 40 (2011), pp. 379–408More LessAmphipols (APols) are short amphipathic polymers that can substitute for detergents to keep integral membrane proteins (MPs) water soluble. In this review, we discuss their structure and solution behavior; the way they associate with MPs; and the structure, dynamics, and solution properties of the resulting complexes. All MPs tested to date form water-soluble complexes with APols, and their biochemical stability is in general greatly improved compared with MPs in detergent solutions. The functionality and ligand-binding properties of APol-trapped MPs are reviewed, and the mechanisms by which APols stabilize MPs are discussed. Applications of APols include MP folding and cell-free synthesis, structural studies by NMR, electron microscopy and X-ray diffraction, APol-mediated immobilization of MPs onto solid supports, proteomics, delivery of MPs to preexisting membranes, and vaccine formulation.
-
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)