Biophysical Journal back issues from June 2008:
Amplification of Diacylglycerol Activation of Protein Kinase C by Cholesterol
Jun 15, 2008; ... ABSTRACT The combined effects of cholesterol, a major cell membrane component, and the lipid second messenger diacylglycerol on the activity of protein kinase C (PK-C) and the structure of phosphatidylcholine/phosphatidylserine bilayers were investigated using specific PK-C assays and ...
Salt-Mediated Electrostatics in the Association of TATA Binding Proteins to DNA: A Combined Molecular Mechanics/Poisson-Boltzmann Study
Jun 15, 2008; ... ABSTRACT The TATA-binding protein (TBP) is a key component of the archaea ternary preinitiation transcription assembly. The archaeon TBP, from the halophile/hyperthermophile organism Pyrococcus woesei, is adapted to high concentrations of salt and high-temperature environments. Although ...
Effects of Posttranslational Modifications on the Structure and Dynamics of Histone H3 N-Terminal Peptide
Jun 15, 2008; ... ABSTRACT The highly conserved signature N-terminal peptide of histone protein H3 plays crucial roles in gene expression controls. We investigated the conformational changes of the peptide caused by lysine dimethylation and acetylation of the histone H3 N-terminal tail by molecular ...
The Allosteric Role of the Ca^sup 2+^ Switch in Adhesion and Elasticity of C-Cadherin
Jun 15, 2008; ... ABSTRACT Modular proteins such as titin, fibronectin, and cadherin are ubiquitous components of living cells. Often involved in signaling and mechanical processes, their architecture is characterized by domains containing a variable number of heterogeneous "repeats" arranged in series, ...
Pathway and Endpoint Free Energy Calculations for Cyclic Nucleotide Binding to HCN Channels
Jun 15, 2008; ... ABSTRACT cAMP and cGMP differentially bind to and regulate a variety of proteins, including cyclic nucleotide-gated (CNG) channels and hyperpolarization-activated cyclic nucleotide-regulated (HCN) channels. Previous site-directed mutagenesis studies have isolated two conserved residues ...
Molecular Models Need to be Tested: The Case of a Solar Flares Discoidal HDL Model
Jun 15, 2008; ... ABSTRACT In the absence of atomic structures of high-density lipoproteins in their lipid-bound states, many molecular models have been produced based on experimental data. Using molecular dynamics, we show that a recently proposed "solar-flares" model of discoidal high-density ...
Protein Unfolding Behavior Studied by Elastic Network Model
Jun 15, 2008; ... ABSTRACT Experimental and theoretical studies have showed that the native-state topology conceals a wealth of information about protein folding/unfolding. In this study, a method based on the Gaussian network model (GNM) is developed to study some properties of protein unfolding and ...
Confirming the Revised C-Terminal Domain of the MscL Crystal Structure
Jun 15, 2008; ... ABSTRACT The structure of the C-terminal domain of the mechanosensitive channel of large conductance (MscL) has generated significant controversy. As a result, several structures have been proposed for this region: the original crystal structure (1MSL) of the Mycobacterium tuberculosis ...
AFM Study on the Electric-Field Effects on Supported Bilayer Lipid Membranes
Jun 15, 2008; ... ABSTRACT Electric-field induced changes in structure and conductivity of supported bilayer lipid membranes (SLM) have been studied at submicroscoptc resolution using atomic force microscopy and electrochemical impedance spectroscopy. The SLMs are formed on gold surfaces modified with ...
Urea and Guanidinium Chloride Denature Protein L in Different Ways in Molecular Dynamics Simulations
Jun 15, 2008; ... ABSTRACT In performing protein-denaturation experiments, it is common to employ different kinds of denaturants interchangeably. We make use of molecular dynamics simulations of Protein L in water, in urea, and in guanidinium chloride (GdmCl) to ascertain if there are any structural ...
Primary Charge Separation in the Photosystem II Core from Synechocystis: A Comparison of Femtosecond Visible/Midinfrared Pump-Probe Spectra of Wild-Type and Two P^sub 680^ Mutants
Jun 15, 2008; ... ABSTRACT It is now quite well accepted that charge separation in PS2 reaction centers starts predominantly from the accessory chlorophyll B^sub A^ and not from the special pair P^sub 680^. To identify spectral signatures of B^sub A^, and to further clarify the process of primary charge ...
Initial Reaction Dynamics of Proteorhodopsin Observed by Femtosecond Infrared and Visible Spectroscopy
Jun 15, 2008; ... ABSTRACT We present a comparative study using femtosecond pump/probe spectroscopy in the visible and infrared of the early photodynamics of solubilized proteorhodopsin (green absorbing variant) in D^sub 2^O with deprotonated (pD 9.2) and protonated (pD 6.4) primary proton acceptor ...
Interaction of LL-37 with Model Membrane Systems of Different Complexity: Influence of the Lipid Matrix
Jun 15, 2008; ... ABSTRACT As the main difference between bacterial and mammalian cell membranes is their net charge, the focal point of consideration in many model membrane experiments with antimicrobial peptides is lipid headgroup charge. We studied the interaction of the human multifunctional peptide ...
ARVC-Related Mutations in Divergent Region 3 Alter Functional Properties of the Cardiac Ryanodine Receptor
Jun 15, 2008; ... ABSTRACT Two single-nucleotide polymorphisms in the type 2 ryanodine receptor (RyR2) leading to the nonsynonymous amino acid replacements G1885E and G1886S are associated with arrhythmogenic right ventricular cardiomyopathy in patients who are carrying both of the corresponding RyR2 ...
Subunit-Specific Effect of the Voltage Sensor Domain on Ca^sup 2+^ Sensitivity of BK Channels
Jun 15, 2008; ... ABSTRACT Large conductance Ca^sup 2+^ - and voltage-activated K+ (BK) channels, composed of pore-forming α-subunits and auxiliary β-subunits, play important roles in diverse physiological processes. The differences in BK channel phenotypes are primarily due to the ...
Molecular Force Balance Measurements Reveal that Double-Stranded DNA Unbinds Under Force in Rate-Dependent Pathways
Jun 15, 2008; ... ABSTRACT Strand separation of double-stranded DNA is a crucial step for essential cellular processes such as recombination and transcription. By means of a molecular force balance, we have analyzed the impact of different pulling directions and different force-loading rates on the ...
Interaction of the Most Membranotropic Region of the HCV E2 Envelope Glycoprotein with Membranes. Biophysical Characterization
Jun 15, 2008; ... ABSTRACT The previously identified membrane-active regions of the hepatitis C virus (HCV) E1 and E2 envelope glycoproteins led us to identify different segments that might be implicated in viral membrane fusion, membrane interaction, and/or protein-protein binding. HCV E2 glycoprotein ...
Protein Dynamics and Stability: The Distribution of Atomic Fluctuations in Thermophilic and Mesophilic Dihydrofolate Reductase Derived Using Elastic Incoherent Neutron Scattering
Jun 15, 2008; ... ABSTRACT The temperature dependence of the dynamics of mesophilic and thermophilic dihydrofolate reductase is examined using elastic incoherent neutron scattering. It is demonstrated that the distribution of atomic displacement amplitudes can be derived from the elastic scattering data ...
The Mycobacterium tuberculosis Virulence Factor Trehalose Dimycolate Imparts Desiccation Resistance to Model Mycobacterial Membranes
Jun 15, 2008; ... ABSTRACT Mycobacteria, including persistent pathogens like Mycobacterium tuberculosis, have an unusual membrane structure in which, outside the plasma membrane, a nonfluid hydrophobic fatty acid layer supports a fluid monolayer rich in glycolipids such as trehalose 6,6'-dimycolate (TDM; ...
Attractive Forces between Cation Condensed DNA Double Helices
Jun 15, 2008; ... ABSTRACT By combining single-molecule magnetic tweezers and osmotic stress on DNA assemblies, we separate attractive and repulsive components of the total intermolecular interaction between multivalent cation condensed DNA. Based on measurements of several different cations, we identify ...
Elasticity, Strength, and Water Permeability of Bilayers that Contain Raft Microdomain-Forming Lipids
Jun 15, 2008; ... ABSTRACT Bilayers composed of phosphatidylcholine (PC), sphingomyelin (SM), and cholesterol (CHOL) are commonly used as systems to model the raft-lipid domain structure believed to compartmentalize particular cell membrane proteins. In this work, micropipette aspiration of giant ...
Unloaded Speed of Shortening in Voltage-Clamped Intact Skeletal Muscle Fibers from wt, mdx, and Transgenic Minidystrophin Mice Using a Novel High-Speed Acquisition System
Jun 15, 2008; ... ABSTRACT Skeletal muscle unloaded shortening has been indirectly determined in the past. Here, we present a novel high-speed optical tracking technique that allows recording of unloaded shortening in single intact, voltage-clamped mammalian skeletal muscle fibers with 2-ms time ...
Femtosecond Spectroscopy of Native and Carotenoidless Purple-Bacterial LH2 Clarifies Functions of Carotenoids
Jun 15, 2008; ... ABSTRACT EET between the two circular bacteriochlorophyll compartments B800 and B850 in native (containing the carotenoid rhodopin) and carotenoidless LH2 isolated from the photosynthetic purple sulfur bacterium Allochromatium minutissimum was investigated by femtosecond time-resolved ...
Using Fluorescence Correlation Spectroscopy to Study Conformational Changes in Denatured Proteins
Jun 15, 2008; ... ABSTRACT Fluorescence correlation spectroscopy (FCS) is a sensitive analytical tool that allows dynamics and hydrodynamics of biomolecules to be studied under a broad range of experimental conditions. One application of FCS of current interest is the determination of the size of protein ...
Global and Local Structural Changes of Cytochrome c and Lysozyme Characterized by a Multigroup Unfolding Process
Jun 15, 2008; ... ABSTRACT Equilibrium unfolding behaviors of cytochrome c and lysozyme induced by the presence of urea (0-10 M) as well as changes in temperature (295-363 K) or pH (1.8-7) are examined via small-angle x-ray scattering and spectroscopic techniques, including circular dichroism and optical ...
Observation of Noncooperative Folding Thermodynamics in Simulations of 1BBL
Jun 15, 2008; ... ABSTRACT One of the predictions of the energy landscape theory of protein folding is the possibility of barrierless, "downhill" folding under certain conditions. The protein 1BBL has been proposed to fold by such a downhill mechanism, though this is a matter of some dispute. We carried ...
Differences in Internal Dynamics of Actin under Different Structural States Detected by Neutron Scattering
Jun 15, 2008; ... ABSTRACT F-actin, a helical polymer formed by polymerization of the monomers (G-actin), plays crucial roles in various aspects of cell motility. Flexibility of F-actin has been suggested to be important for such a variety of functions. Understanding the flexibility of F-actin requires ...
Arp2/3 Controls the Motile Behavior of N-WASP-Functionalized GUVs and Modulates N-WASP Surface Distribution by Mediating Transient Links with Actin Filaments
Jun 15, 2008; ... ABSTRACT Spatially controlled assembly of actin in branched filaments generates cell protrusions or the propulsion of intracellular vesicles and pathogens. The propulsive movement of giant unilamellar vesicles (GUVs) functionalized by N-WASP (full-length or truncated) is reconstituted in ...
Label-Free, High-Throughput Measurements of Dynamic Changes in Cell Nuclei Using Angle-Resolved Low Coherence Interferometry
Jun 15, 2008; ... ABSTRACT Accurate measurements of nuclear deformation, i.e., structural changes of the nucleus in response to environmental stimuli, are important for signal transduction studies. Traditionally, these measurements require labeling and imaging, and then nuclear measurement using image ...
Three-Dimensional Resolution Doubling in Wide-Field Fluorescence Microscopy by Structured Illumination
Jun 15, 2008; ... ABSTRACT Structured illumination microscopy is a method that can increase the spatial resolution of wide-field fluorescence microscopy beyond its classical limit by using spatially structured illumination light. Here we describe how this method can be applied in three dimensions to ...
I^sup 5^S: Wide-Field Light Microscopy with 100-nm-Scale Resolution in Three Dimensions
Jun 15, 2008; ... ABSTRACT A new type of wide-field fluorescence microscopy is described, which produces 100-nm-scale spatial resolution in all three dimensions, by using structured illumination in a microscope that has two opposing objective lenses. Illumination light is split by a grating and a beam ...
Micropatterning of Single Endothelial Cell Shape Reveals a Tight Coupling between Nuclear Volume in G1 and Proliferation
Jun 15, 2008; ... ABSTRACT Shape-dependent local differentials in cell proliferation are considered to be a major driving mechanism of structuring processes in vivo, such as embryogenesis, wound healing, and angiogenesis. However, the specific biophysical signaling by which changes in cell shape ...
Real-Time Cross-Correlation Image Analysis of Early Events in IgE Receptor Signaling
Jun 15, 2008; ... ABSTRACT Signaling in mast cells and basophils is mediated through IgE and its high affinity cell surface receptor, FcεRI. Crosslinking of the receptors by a cognate multivalent antigen leads to degranulation and release of mediators of the allergic immune response. Using multicolor ...
Coordination of Kinesin Motors Pulling on Fluid Membranes
Jun 15, 2008; ... ABSTRACT Intracellular transport relies on the action of motor proteins, which work collectively to either carry small vesicles or pull membranes tubes along cytoskeletal filaments. Although the individual properties of kinesin-1 motors have been extensively studied, little is known on ...
Quantification of Electroporative Uptake Kinetics and Electric Field Heterogeneity Effects in Cells
Jun 15, 2008; ... ABSTRACT We have conducted experiments quantitatively investigating electroporative uptake kinetics of a fluorescent plasma membrane integrity indicator, propidium iodide (PI), in HL60 human leukemia cells resulting from exposure to 40 µs pulsed electric fields (PEFs). These experiments ...
Low-Frequency Stimulation Induces Stable Transitions in Stereotypical Activity in Cortical Networks
Jun 15, 2008; ... ABSTRACT Reverberating spontaneous synchronized brain activity is believed to play an important role in neural information processing. Whether and how external stimuli can influence this spontaneous activity is poorly understood. Because periodic synchronized network activity is also ...
Subunit b-Dimer of the Escherichia coli ATP Synthase Can Form Left-Handed Coiled-Coils
Jun 15, 2008; ... ABSTRACT One remaining challenge to our understanding of the ATP synthase concerns the dimeric coiled-coil stator subunit b of bacterial synthases. The subunit b-dimer has been implicated in important protein interactions that appear necessary for energy conservation and that may be ...
Structure of the Cytosolic Part of the Subunit b-Dimer of Escherichia coli F^sub 0^F^sub 1^-ATP Synthase
Jun 15, 2008; ... ABSTRACT The structure of the external stalk and its function in the catalytic mechanism of the F^sub 0^F^sub 0^-ATP synthase remains one of the important questions in bioenergetics. The external stalk has been proposed to be either a rigid stator that binds F^sub 1^ or an elastic ...
Metabolic Fluxes and Stoichiometry of Glucose Metabolism
Jun 15, 2008; ... I would like to comment on a recent article by Bertram et al. titled "Interaction of Glycolysis and Mitochondrial Respiration in Metabolic Oscillations of Pancreatic Islets" (1). The article addresses two different types of oscillations of the membrane potential V and of [Ca^sup 2+^]^sub ...
Response to the Comment by F. Diederichs
Jun 15, 2008; ... The correspondent has correctly identified that our (1) model is not a biochemically complete description of β-cell metabolism. In particular, there is a phenomenological bridge between glycolysis and the electron transport chain, as we have not modeled all the steps of glycolysis or most ...
Corrections
Jun 15, 2008; ... Guanglei Cui and Kenneth M. Merz Jr. 2008. The Intrinsic Dynamics and Function of Nickel-Binding Regulatory Protein: Insights from Elastic Network Analysis. Biophys. J. 94:3769-3778. Add acknowledgment: We thank the National Institutes of Health via grant GM066859 for funding ...
Backbone Dynamics of the 18.5 kDa Isoform of Myelin Basic Protein Reveals Transient [alpha]-Helices and a Calmodulin-Binding Site
Jun 15, 2008; ... ABSTRACT The 18.5 kDa isoform of myelin basic protein (MBP) is the predominant form in adult human central nervous system myelin. It is an intrinsically disordered protein that functions both in membrane adhesion, and as a linker connecting the oligodendrocyte membrane to the underlying ...
Fluorescent N-Arylaminonaphthalene Sulfonate Probes for Amyloid Aggregation of [alpha]-Synuclein
Jun 15, 2008; ... ABSTRACT The deposition of fibrillar structures (amyloids) is characteristic of pathological conditions including Alzheimer's and Parkinson's diseases. The detection of protein deposits and the evaluation of their kinetics of aggregation are generally based on fluorescent probes such as ...