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Annu Rev Biophys Biomol Struct 2007 ;36:451-77

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.

This review summarizes what is known about the biochemical and biophysical mechanisms that initiate the assembly of actin filaments in cells. Assembly and disassembly of these filaments contribute to many types of cellular movements. Numerous proteins regulate actin assembly, but Arp2/3 complex and formins are the focus of this review because more is known about them than other proteins that stimulate the formation of new filaments. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:413-34

Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

Within a population of genetically identical cells there can be significant variation, or noise, in gene expression. Yet even with this inherent variability, cells function reliably. This review focuses on our understanding of noise at the level of both single genes and genetic regulatory networks, emphasizing comparisons between theoretical models and experimental results whenever possible. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:261-80

Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

Globular proteins are a key component of the network of life. Over many decades much experimental data on proteins have been gathered, yet theoretical progress has been somewhat limited. We show that the results accumulated over the years inexorably lead to a unified framework for understanding proteins. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:151-69

BioTec TU Dresden, Institute for Biophysics, D-01307 Dresden, Germany.

Fluorescence correlation spectroscopy (FCS) is one of the major biophysical techniques used for unraveling molecular interactions in vitro and in vivo. It allows minimally invasive study of dynamic processes in biological specimens with extremely high temporal and spatial resolution. By recording and correlating the fluorescence fluctuations of single labeled molecules through the exciting laser beam, FCS gives information on molecular mobility and photophysical and photochemical reactions. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:131-50

Howard Hughes Medical Institute, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.

Covalent attachment of ubiquitin-like proteins (Ubls) is a predominant mechanism for regulating protein function in eukaryotes. Several structurally related Ubls, such as ubiquitin, SUMO, NEDD8, and ISG15, modify a vast number of proteins, altering their functions in a variety of ways. Ubl modifications can affect the target's half-life, subcellular localization, enzymatic activity, or ability to interact with protein or DNA partners. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:79-105

Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA.

The physicochemical concepts that underlie our present ideas on the structure and assembly of the "macromolecular machines of gene expression" are developed, starting with the structure and folding of the individual protein and DNA components, the thermodynamics and kinetics of their conformational rearrangements during complex assembly, and the molecular basis of the sequence specificity and recognition interactions of the final assemblies that include the DNA genome. The role of diffusion in reduced dimensions in the kinetics of the assembly of macromolecular machines from their components is also considered, and diffusion-driven reactions are compared with those fueled by ATP binding and hydrolysis, as well as by the specific covalent chemical modifications involved in rearranging chromatin and modifying signal transduction networks in higher organisms. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:171-90

Department of Applied Physics, Stanford University, Stanford, California 94305-5030, USA.

Many biologically important macromolecules undergo motions that are essential to their function. Biophysical techniques can now resolve the motions of single molecules down to the nanometer scale or even below, providing new insights into the mechanisms that drive molecular movements. This review outlines the principal approaches that have been used for high-resolution measurements of single-molecule motion, including centroid tracking, fluorescence resonance energy transfer, magnetic tweezers, atomic force microscopy, and optical traps. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:233-60

Department of Cellular Machines, Center of Biotechnology, Technische Universität Dresden, 01307 Dresden, Germany.

Molecular interactions are the basic language of biological processes. They establish the forces interacting between the building blocks of proteins and other macromolecules, thus determining their functional roles. Because molecular interactions trigger virtually every biological process, approaches to decipher their language are needed. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:435-50

Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003, USA.

The transport of electrically charged macromolecules such as DNA through narrow pores is a fundamental process in life. When polymer molecules are forced to navigate through pores, their transport is controlled by entropic barriers that accompany their conformational changes. During the past decade, exciting results have emerged from single-molecule electrophysiology experiments. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:329-47

Department of Biological Sciences, Columbia University, New York, New York 10027, USA.

Various algorithms are available for predicting mRNA expression and modeling gene regulatory processes. They differ in whether they rely on the existence of modules of coregulated genes or build a model that applies to all genes, whether they represent regulatory activities as hidden variables or as mRNA levels, and whether they implicitly or explicitly model the complex cis-regulatory logic of multiple interacting transcription factors binding the same DNA. The fact that functional genomics data of different types reflect the same molecular processes provides a natural strategy for integrative computational analysis. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:349-69

Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA.

Single-molecule biophysics has been serving biology for more than two decades. Fluorescence microscopy is one of the most commonly used tools to identify molecules of interest and to visualize biological events. Here we describe some of the most commonly used fluorescence imaging tools to measure nanoscale movements and the rotational dynamics of biomolecules. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:191

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

Controlling the differential expression of many thousands of genes is the most fundamental task of a developing organism. It requires an enormous computational device that has the capacity to process in parallel a vast number of regulatory inputs in the various cells of the embryo and come out with regulatory outputs that are tissue specific. The regulatory genome constitutes this computational device, comprising many thousands of processing units in the form of cis-regulatory modules. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:395-412

Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.

Recent experimental developments are changing the ways we interpret experimental data in protein folding, leading to a closer connection with theory and an improved understanding of some long-standing questions in the field. We now have a basic roadmap of the types of polypeptide motions and timescales that are relevant to the various folding stages. The folding barriers estimated with a variety of independent methods are consistently small, indicating that several fast-folding proteins are near or within the downhill folding regime. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:371-94

Institute of Medical Physics and Biophysics, and Center for Nanotechnology (CeNTech), University of Münster, 48149 Münster, Germany.

Recent progress in proteomics suggests that the cell can be conceived as a large network of highly refined, nanomachine-like protein complexes. This working hypothesis calls for new methods capable of analyzing individual protein complexes in living cells and tissues at high speed. Here, we examine whether single-molecule fluorescence (SMF) analysis can satisfy that demand. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:281-305

Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.

Chemically modified nucleic acids function as model systems for native DNA and RNA; as chemical probes in diagnostics or the analysis of protein-nucleic acid interactions and in high-throughput genomics and drug target validation; as potential antigene-, antisense-, or RNAi-based drugs; and as tools for structure determination (i.e., crystallographic phasing), just to name a few. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:307-27

Department of Physics, Biophysics Program, Stanford University, Stanford, California 94305, USA.

Small-angle X-ray scattering (SAXS) is increasingly used to characterize the structure and interactions of biological macromolecules and their complexes in solution. Although still a low-resolution technique, the advent of high-flux synchrotron sources and the development of algorithms for the reconstruction of 3-D electron density maps from 1-D scattering profiles have made possible the generation of useful low-resolution molecular models from SAXS data. Furthermore, SAXS is well suited for the study of unfolded or partially folded conformational ensembles as a function of time or solution conditions. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:213-31

Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, California 94305, USA.

Microfluidic large-scale integration (mLSI) refers to the development of microfluidic chips with thousands of integrated micromechanical valves and control components. This technology is utilized in many areas of biology and chemistry and is a candidate to replace today's conventional automation paradigm, which consists of fluid-handling robots. We review the basic development of mLSI and then discuss design principles of mLSI to assess the capabilities and limitations of the current state of the art and to facilitate the application of mLSI to areas of biology. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:107-30

Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021, USA.

The lipid bilayer component of biological membranes is important for the distribution, organization, and function of bilayer-spanning proteins. This regulation is due to both specific lipid-protein interactions and general bilayer-protein interactions, which modulate the energetics and kinetics of protein conformational transitions, as well as the protein distribution between different membrane compartments. The bilayer regulation of membrane protein function arises from the hydrophobic coupling between the protein's hydrophobic domains and the bilayer hydrophobic core, which causes protein conformational changes that involve the protein/bilayer boundary to perturb the adjacent bilayer. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:1-19

Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, California 91125, USA.

Synthetic circuits offer great promise for generating insights into nature's underlying design principles or forward engineering novel biotechnology applications. However, construction of these circuits is not straightforward. Synthetic circuits generally consist of components optimized to function in their natural context, not in the context of the synthetic circuit. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:21-42

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.

Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches. Important advances are reported in modeling protein-ligand energetics, such as the incorporation of electronic polarization and the use of quantum mechanical methods. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:63-77

Field of Biophysics, Cornell University, Ithaca, New York 14853, USA.

Bilayer mixtures of lipids are used by many researchers as chemically simple models for biological membranes. In particular, observations on three-component bilayer mixtures containing cholesterol show rich phase behavior, including several regions of two-phase coexistence and one region of three-phase coexistence. Yet, the relationship between these simple model mixtures and biological membranes, which contain hundreds of different proteins and lipids, is not clear. Read More

Annu Rev Biophys Biomol Struct 2007 ;36:43-62

Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.

It is becoming increasingly clear that many macromolecules are intrinsically flexible and exist in multiple conformations in solution. Single-particle reconstruction of vitrified samples (cryo-electron microscopy, or cryo-EM) is uniquely positioned to visualize this conformational flexibility in its native state. Although heterogeneity remains a significant challenge in cryo-EM single-particle analysis, recent efforts in the field point to a future where it will be possible to tap into this rich source of biological information on a routine basis. Read More

Annu Rev Biophys Biomol Struct 2006 ;35:459-88

Laboratory for Biologically Oriented Materials, Department of Materials, Swiss Federal Institute of Technology, ETH Zurich, CH-8093 Switzerland.

Cells can sense and transduce a broad range of mechanical forces into distinct sets of biochemical signals that ultimately regulate cellular processes, including adhesion, proliferation, differentiation, and apoptosis. Deciphering at the nanoscale the design principles by which sensory elements are integrated into structural protein motifs whose conformations can be switched mechanically is crucial to understand the process of transduction of force into biochemical signals that are then integrated to regulate mechanoresponsive pathways. While the major focus in the search for mechanosensory units has been on membrane proteins such as ion channels, integrins, and associated cytoplasmic complexes, a multimodular design of tandem repeats of various structural motifs is ubiquitously found among extracellular matrix proteins, as well as cell adhesion molecules, and among many intracellular players that physically link transmembrane proteins to the contractile cytoskeleton. Read More

Annu Rev Biophys Biomol Struct 2006 ;35:435-57

Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.

Splicing is an essential step of gene expression in which introns are removed from pre-mRNA to generate mature mRNA that can be translated by the ribosome. This reaction is catalyzed by a large and dynamic macromolecular RNP complex called the spliceosome. The spliceosome is formed by the stepwise integration of five snRNPs composed of U1, U2, U4, U5, and U6 snRNAs and more than 150 proteins binding sequentially to pre-mRNA. Read More

Annu Rev Biophys Biomol Struct 2006 ;35:417-34

Biological Sciences Department, Columbia University, New York, NY, 10027, USA.

The plasma membrane of most animal cells conforms to the cytoskeleton and only occasionally separates to form blebs. Previous studies indicated that many weak interactions between cytoskeleton and the lipid bilayer kept the surfaces together to counteract the normal outward pressure of cytoplasm. Either the loss of adhesion strength or the formation of gaps in the cytoskeleton enables the pressure to form blebs. Read More

Annu Rev Biophys Biomol Struct 2006 ;35:389-415

Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, California 92093, USA.

Water is essential for life in many ways, and without it biomolecules might no longer truly be biomolecules. In particular, water is important to the structure, stability, dynamics, and function of biological macromolecules. In protein folding, water mediates the collapse of the chain and the search for the native topology through a funneled energy landscape. Read More

Annu Rev Biophys Biomol Struct 2006 ;35:361-87

Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Fluorescent speckle microscopy (FSM) is a technology used to analyze the dynamics of macromolecular assemblies in vivo and in vitro. Speckle formation by random association of fluorophores with a macromolecular structure was originally discovered for microtubules. Since then FSM has been expanded to study other cytoskeleton and cytoskeleton-binding proteins. Read More

Annu Rev Biophys Biomol Struct 2006 ;35:343-60

Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.

The kinetics and mechanisms of transcription are now being investigated by a repertoire of single-molecule techniques, including optical and magnetic tweezers, high-sensitivity fluorescence techniques, and atomic force microscopy. Single-molecule techniques complement traditional biochemical and crystallographic approaches, are capable of detecting the motions and dynamics of individual RNAP molecules and transcription complexes in real time, and make it possible to directly measure RNAP binding to and unwinding of template DNA, as well as RNAP translocation along the DNA during transcript synthesis. Read More

Annu Rev Biophys Biomol Struct 2006 ;35:319-42

MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom.

Three-dimensional structure determination of small proteins and oligonucleotides by solution NMR is established. With the development of novel NMR and labeling techniques, structure determination is now feasible for proteins with a molecular mass of up to approximately 100 kDa and RNAs of up to 35 kDa. Beyond these molecular masses special techniques and approaches are required for applying NMR as a multiprobe method for structural investigations of proteins and RNAs. Read More

Annu Rev Biophys Biomol Struct 2006 ;35:299-317

Howard Hughes Medical Institute, Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA.

Single-particle cryo-electron microscopy (cryo-EM) is the method of choice for studying the dynamics of macromolecular machines both at a phenomenological and, increasingly, at the molecular level, with the advent of high-resolution component X-ray structures and of progressively improving fitting algorithms. Cryo-EM has shed light on the structure of the ribosome during the four steps of translation: initiation, elongation, termination, and recycling. Interpretation of cryo-EM reconstructions of the ribosome in quasi-atomic detail reveals a picture in which the ribosome uses RNA not only to catalyze chemical reactions, but also as a means for signal transduction over large distances. Read More