Biophysical Journal back issues from March 2006:
Intracellular Transport Dynamics of Endosomes Containing DNA Polyplexes along the Microtubule Network
Mar 01, 2006; ... ABSTRACT We have explored the transport of DNA polyplexes enclosed in endosomes within the cellular environment by multiple particle tracking (MPT). The polyplex-loaded endosomes demonstrate enhanced diffusion at short timescales (t < 7 s) with their mean-square displacement (MSD) ...
Structure and Dynamics of Phosphate Linkages and Sugars in an Abasic Hexaloop RNA Hairpin
Mar 01, 2006; ... ABSTRACT Hairpins containing hexaloops are well represented among the diverse conformations adopted by the RNA molecules. To investigate the intrinsic properties of a backbone submitted to a hexaloop fold, we present here a molecular dynamics study of an abasic hexaloop closed by an ...
Spatial Propagation and Localization of Blood Coagulation Are Regulated by Intrinsic and Protein C Pathways, Respectively
Mar 01, 2006; ... ABSTRACT Blood coagulation in vivo is a spatially nonuniform, multistage process: coagulation factors from plasma bind to tissue factor (TF)-expressing cells, become activated, dissociate, and diffuse into plasma to form enzymatic complexes on the membranes of activated platelets. We ...
Fatty Acid Binding Proteins: Same Structure but Different Binding Mechanisms? Molecular Dynamics Simulations of Intestinal Fatty Acid Binding Protein
Mar 01, 2006; ... ABSTRACT Fatty acid binding proteins (FABPs) carry fatty acids (FAs) and other lipids in the cellular environment, and are thus involved in processes such as FA uptake, transport, and oxidation. These proteins bind either one or two ligands in a binding site, which appears to be ...
Atomic-Level Simulations of Seeman DNA Nanostructures: The Paranemic Crossover in Salt Solution
Mar 01, 2006; ... ABSTRACT We use molecular dynamics (MD) simulations to understand the structure and stability of various paranemic crossover (PX) DNA molecules, synthesized recently by Seeman and co-workers at New York University. These studies include all atoms of the PX structures with an explicit ...
Modeling the VPAC^sub 2^-Activated cAMP/PKA Signaling Pathway: From Receptor to Circadian Clock Gene Induction
Mar 01, 2006; ... ABSTRACT Increasing evidence suggests an important role for VPAC^sub 2^-activated signal transduction pathways in maintaining a synchronized biological clock in the suprachiasmatic nucleus (SCN). Activation of the VPAC^sub 2^ signaling pathway induces per1 gene expression in the SCN and ...
A Sticky Chain Model of the Elongation and Unfolding of Escherichia coli P Pili under Stress
Mar 01, 2006; ... ABSTRACT A model of the elongation of P pili expressed by uropathogenic Escherichia coli exposed to stress is presented. The model is based upon the sticky chain concept, which is based upon Hooke's law for elongation of the layer-to-layer and head-to-tail bonds between neighboring units ...
The Intrinsic Flexibility of the Kv Voltage Sensor and Its Implications for Channel Gating
Mar 01, 2006; ... ABSTRACT Analysis of the crystal structures of the intact voltage-sensitive potassium channel KvAP (from Aeropyrum pernix) and Kv1.2 (from rat brain), along with the isolated voltage sensor (VS) domain from KvAP, raises the question of the exact nature of the voltage-sensing ...
Interaction of Zwitterionic Penicillins with the OmpF Channel Facilitates Their Translocation
Mar 01, 2006; ... ABSTRACT To study translocation of β-lactam antibiotics of different size and charge across the outer bacterial membrane, we combine an analysis of ion currents through single trimeric outer membrane protein F (OmpF) porins in planar lipid bilayers with molecular dynamics ...
Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations
Mar 01, 2006; ... ABSTRACT A coarse-grained (CG) procedure that incorporates the information obtained from all-atom molecular dynamics (MD) simulations is presented and applied to actin filaments (F-actin). This procedure matches the averaged values and fluctuations of the effective internal coordinates ...
Charge Translocation by the Na+/K+ Pump under Na+/Na+ Exchange Conditions: Intracellular Na+ Dependence
Mar 01, 2006; ... ABSTRACT The effect of intracellular (i) and extracellular (o) Na+ on pre-steady-state transient current associated with Na+/Na+ exchange by the Na+/K+ pump was investigated in the vegetal pole of Xenopus oocytes. Current records in response to 40-ms voltage pulses from -180 to +100 mV ...
Neuronal SNAREs Do Not Trigger Fusion between Synthetic Membranes but Do Promote PEG-Mediated Membrane Fusion
Mar 01, 2006; ... ABSTRACT At low surface concentrations that permit formation of impermeable membranes, neuronal soluble N-ethyl maleimide sensitive factor attachment protein receptor (SNARE) proteins form a stable, parallel, trans complex when vesicles are brought into contact by a low concentration of ...
Flexural Rigidity of Individual Microtubules Measured by a Buckling Force with Optical Traps
Mar 01, 2006; ... ABSTRACT We used direct buckling force measurements with optical traps to determine the flexural rigidity of individual microtubules bound to polystyrene beads. To optimize the accuracy of the measurement, we used two optical traps and antibody-coated beads to manipulate each ...
Redox Regulation of CLIC1 by Cysteine Residues Associated with the Putative Channel Pore
Mar 01, 2006; ... ABSTRACT Chloride intracellular channels (CLICs) are putative pore-forming glutathione-S-transferase homologs that are thought to insert into cell membranes directly from the cytosol. We incorporated soluble, recombinant human CLIC1 into planar lipid bilayers to investigate the ...
Evaluating Tilt Angles of Membrane-Associated Helices: Comparison of Computational and NMR Techniques
Mar 01, 2006; ... ABSTRACT A computational method to calculate the orientation of membrane-associated α-helices with respect to a lipid bilayer has been developed. It is based on a previously derived implicit membrane representation, which was parameterized using the structures of 46 α-helical ...
Temperature Dependence and Thermodynamics of Klenow Polymerase Binding to Primed-Template DNA
Mar 01, 2006; ... ABSTRACT DNA binding of Klenow polymerase has been characterized with respect to temperature to delineate the thermodynamic driving forces involved in the interaction of this polymerase with primed-template DNA. The temperature dependence of the binding affinity exhibits distinct ...
Confinement Effects on the Thermodynamics of Protein Folding: Monte Carlo Simulations
Mar 01, 2006; ... ABSTRACT The effects of chaperonin-like cage-induced confinement on protein stability have been studied for molecules of varying sizes and topologies. Minimalist models based on Go-like interactions are employed for the proteins, and density-of-states-based Monte Carlo simulations are ...
Solid-State NMR Analysis of the PGLa Peptide Orientation in DMPC Bilayers: Structural Fidelity of ^sup 2^H-Labels versus High Sensitivity of ^sup 19^F-NMR
Mar 01, 2006; ... ABSTRACT The structure and alignment of the amphipathic α-helical antimicrobial peptide PGLa in a lipid membrane is determined with high accuracy by solid-state ^sup 2^H-NMR. Orientational constraints are derived from a series of eight alanine-3,3,3-d^sub 3^-labeled peptides, in ...
Conformation and Environment of Channel-Forming Peptides: A Simulation Study
Mar 15, 2006; ... ABSTRACT Ion channel-forming peptides enable us to study the conformational dynamics of a transmembrane helix as a function of sequence and environment. Molecular dynamics simulations are used to study the conformation and dynamics of three 22-residue peptides derived from the second ...
Stereochemistry and Position-Dependent Effects of Carcinogens on TATA/TBP Binding
Mar 15, 2006; ... ABSTRACT The TATA-box binding protein (TBP) is required by eukaryotic RNA polymerases to bind to the TATA box, an eight-basepair DNA promoter element, to initiate transcription. Carcinogen adducts that bind to the TATA box can hamper this important process. Benzo[a]pyrene (BP) is a ...
Dissecting the Contribution of Diffusion and Interactions to the Mobility of Nuclear Proteins
Mar 15, 2006; ... ABSTRACT Quantitative characterization of protein interactions under physiological conditions is vital for systems biology. Fluorescence photobleaching/activation experiments of GFP-tagged proteins are frequently used for this purpose, but robust analysis methods to extract ...
Nearly Neutral Secretory Vesicles in Drosophila Nerve Terminals
Mar 15, 2006; ... ABSTRACT The acidity of mammalian secretory vesicles drives concentration and processing of their contents. Here, pH-sensitive green fluorescent protein (GFP) variants show that the ≥30-fold (H+) difference between secretory vesicles (pH ≤ 5.7) and the cytoplasm (pH = 7.2) in ...
Statistical-Mechanical Theory of DNA Looping
Mar 15, 2006; ... ABSTRACT The lack of a rigorous analytical theory for DNA looping has caused many DNA-loop-mediated phenomena to be interpreted using theories describing the related process of DNA cyclization. However, distinctions in the mechanics of DNA looping versus cyclization can have profound ...
Diffusional Encounter of Barnase and Barstar
Mar 15, 2006; ... ABSTRACT We present an analysis of trajectories from Brownian dynamics simulations of diffusional protein-protein encounter for the well-studied system of barnase and barstar. This analysis reveals details about the optimal association pathways, the regions of the encounter complex, ...
Coarse-Grained Strategy for Modeling Protein Stability in Concentrated Solutions. II: Phase Behavior
Mar 15, 2006; ... ABSTRACT We use highly efficient transition-matrix Monte Carlo simulations to determine equilibrium unfolding curves and fluid phase boundaries for solutions of coarse-grained globular proteins. The model we analyze derives the intrinsic stability of the native state and protein-protein ...
Bidirectional Modulation of Neuronal Responses by Depolarizing GABAergic Inputs
Mar 15, 2006; ... ABSTRACT The reversal potential of GABA^sub A^ receptor channels is known to be less negative than the resting membrane potential under some cases. Recent electrophysiological experiments revealed that a GABAergic unitary conductance with such a depolarized reversal potential could not ...
Role of the Met^sup 3534^-Ala^sup 4271^ Region of the Ryanodine Receptor in the Regulation of Ca^sup 2+^ Release Induced by Calmodulin Binding Domain Peptide
Mar 15, 2006; ... ABSTRACT CaMBP, a peptide corresponding to the 3614-3643 calmodulin (CaM) binding region of the ryanodine receptor (RyR1), is known to activate RyR1 Ca^sup 2+^ channel. To analyze the mechanism of channel regulation by the CaMBP-RyR1 interaction, we investigated a), CaMBP binding to ...
Unbinding Pathways of an Agonist and an Antagonist from the 5-HT^sub 3^ Receptor
Mar 15, 2006; ... ABSTRACT The binding sites of 5-HT^sub 3^ and other Cys-loop receptors have been extensively studied, but there are no data on the entry and exit routes of ligands for these sites. Here we have used molecular dynamics simulations to predict the pathway for agonists and antagonists ...
Syntillas Release Ca^sup 2+^ at a Site Different from the Microdomain Where Exocytosis Occurs in Mouse Chromaffin Cells
Mar 15, 2006; ... ABSTRACT Spontaneous, short-lived, focal cytosolic Ca^sup 2+^ transients were found for the first time and characterized in freshly dissociated chromaffin cells from mouse. Produced by release of Ca^sup 2+^ from intracellular stores and mediated by type 2 and perhaps type 3 ryanodine ...
C-Terminal Charged Cluster of MscL, RKKEE, Functions as a pH Sensor
Mar 15, 2006; ... ABSTRACT The RKKEE cluster of charged residues located within the cytoplasmic helix of the bacterial mechanosensitive channel, MscL, is essential for the channel function. The structure of MscL determined by x-ray crystallography and electron paramagnetic resonance spectroscopy has ...
A 3D Monte Carlo Analysis of the Role of Dyadic Space Geometry in Spark Generation
Mar 15, 2006; ... ABSTRACT In multiple biological systems, vital intracellular signaling processes occur locally in minute periplasmic subspaces often referred to as signaling microdomains. The number of signaling molecules in these microdomains is small enough to render the notion of continuous ...
Bistability, Stochasticity, and Oscillations in the Mitogen-Activated Protein Kinase Cascade
Mar 15, 2006; ... ABSTRACT Signaling pathways respond to stimuli in a variety of ways, depending on the magnitude of the input and the physiological status of the cell. For instance, yeast can respond to pheromone stimulation in either a binary or graded fashion. Here we present single cell transcription ...
Sphingomyelin Structure Influences the Lateral Diffusion and Raft Formation in Lipid Bilayers
Mar 15, 2006; ... ABSTRACT Liquid-disordered/liquid-ordered two-phase coexistence regions in hydrated bilayers have been investigated for sphingomyelins (SMs) of three different origins: egg, brain, and milk with the pulsed-field gradient NMR technique for lateral diffusion measurement. It is found that ...
Complex Folding Kinetics of a Multidomain Protein
Mar 15, 2006; ... ABSTRACT Spectrin domains are three-helix bundles, commonly found in large tandem arrays. Equilibrium studies have shown that spectrin domains are significantly stabilized by their neighbors. In this work we show that domain:domain interactions can also have profound effects on their ...
Characterization of the Liquid-Ordered State by Proton MAS NMR
Mar 15, 2006; ... ABSTRACT We investigated if magic angle spinning (MAS) ^sup 1^H NMR can be used as a tool for detection of liquid-ordered domains (rafts) in membranes. In experiments with the lipids SOPC, DOPC, DPPC, and cholesterol we demonstrated that ^sup 1^H MAS NMR spectra of liquid-ordered domains ...
Differential Stiffness and Lipid Mobility in the Leaflets of Purple Membranes
Mar 15, 2006; ... ABSTRACT Purple membranes (PM) are two-dimensional crystals formed by bacteriorhodopsin and a variety of lipids. The lipid composition and density in the cytoplasmic (CP) leaflet differ from those of the extracellular (EC) leaflet. A new way of differentiating the two sides of such ...
SNARE-Mediated Lipid Mixing Depends on the Physical State of the Vesicles
Mar 15, 2006; ... ABSTRACT Reconstitution experiments have suggested that N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) proteins constitute a minimal membrane fusion machinery but have yielded contradictory results, and it is unclear whether the mechanism of membrane merger is ...
SARS Coronavirus E Protein in Phospholipid Bilayers: An X-Ray Study
Mar 15, 2006; ... ABSTRACT We investigated the structure of the hydrophobic domain of the severe acute respiratory syndrome E protein in model lipid membranes by x-ray reflectivity and x-ray scattering. In particular, we used x-ray reflectivity to study the location of an iodine-labeled residue within the ...
A Conformational Two-State Peptide Model System Containing an Ultrafast but Soft Light Switch
Mar 15, 2006; ... ABSTRACT Combining an azobenzene chromophore with the bis-cysteinyl active-site sequence of the protein disulfide isomerase (PDI) we constructed a simple but promising model for allosteric conformational rearrangements. Paralleling cellular signaling events, an external trigger, here ...
Rates and Equilibrium of Cu^sub A^ to Heme a Electron Transfer in Paracoccus denitrificans Cytochrome c Oxidase
Mar 15, 2006; ... ABSTRACT Intramolecular electron transfer between Cu^sub A^ and heme a in solubilized bacterial (Paracoccus denitrificans) cytochrome c oxidase was investigated by pulse radiolysis. Cu^sub A^, the initial electron acceptor, was reduced by 1-methylnicotinamide radicals in a ...
Mechanism and Dynamics of Breakage of Fluorescent Microtubules
Mar 15, 2006; ... ABSTRACT The breakage of fluorescence-labeled microtubules under irradiation of excitation light is found in our experiments. Its mechanism is studied. The results indicate that free radicals are the main reason for the photosensitive breakage. Furthermore, the mechanical properties of ...
Dehydration of Ribonucleotides Catalyzed by Ribonucleotide Reductase: The Role of the Enzyme
Mar 15, 2006; ... ABSTRACT This article focuses on the second step of the catalytic mechanism for the reduction of ribonucleotides catalyzed by the enzyme Ribonucleotide Reductase (RNR). This step corresponds to the protonation/elimination of the substrate's C-2' hydroxyl group. Protonation is ...
Differential Roles of S6 Domain Hinges in the Gating of KCNQ Potassium Channels
Mar 15, 2006; ... ABSTRACT Voltage-gated K+ channel activation is proposed to result from simultaneous bending of all S6 segments away from the central axis, enlarging the aperture of the pore sufficiently to permit diffusion of K+ into the water-filled central cavity. The hinge position for the bending ...
A FRET-Based Calcium Biosensor with Fast Signal Kinetics and High Fluorescence Change
Mar 01, 2006; ... ABSTRACT Genetically encoded calcium biosensors have become valuable tools in cell biology and neuroscience, but some aspects such as signal strength and response kinetics still need improvement. Here we report the generation of a FRET-based calcium biosensor employing troponin C as ...
Structure, Surface Interactions, and Compressibility of Bacterial S-Layers through Scanning Force Microscopy and the Surface Force Apparatus
Mar 01, 2006; ... ABSTRACT Two-dimensional crystalline bacterial surface layers (S-layers) are found in a broad range of bacteria and archaea as the outermost cell envelope component. The self-assembling properties of the S-layers permit them to recrystallize on solid substrates. Beyond their biological ...
Temperature Dependence of the Volumetric Parameters of Drug Binding to Poly[d(A-T)]*Poly[d(A-T)] and Poly(dA)*Poly(dT)
Mar 01, 2006; ... ABSTRACT We report the temperature and salt dependence of the volume change (ΔV^sub b^) associated with the binding of ethidium bromide and netropsin with poly(dA)*poly(dT) and poly[d(A-T)]*poly[d(A-T)]. The ΔV^sub b^ of binding of ethidium with poly(dA)*poly(dT) was much more ...
Structural Characterization and pH-Induced Conformational Transition of Full-Length KcsA
Mar 01, 2006; ... ABSTRACT The bacterial K+ channel KcsA from Streptomyces lividans was analyzed by neutron and x-ray small-angle solution scattering. The C-terminally truncated version of KcsA, amenable to crystallographic studies, was compared with the full-length channel. Analyzing the scattering data ...
Subcellular In Vivo ^sup 1^H MR Spectroscopy of Xenopus laevis Oocytes
Mar 01, 2006; ... ABSTRACT In vivo magnetic resonance (MR) spectra are typically obtained from voxels whose spatial dimensions far exceed those of the cells they contain. This study was designed to evaluate the potential of localized MR spectroscopy to investigate subcellular phenomena. Using a high ...
Structure of Core Domain of Fibril-Forming PHF/Tau Fragments
Mar 01, 2006; ... ABSTRACT Short peptide sequences within the microtubule binding domain of the protein Tau are proposed to be core nucleation sites for formation of amyloid fibrils displaying the paired helical filament (PHF) morphology characteristic of neurofibrillary tangles. To study the structure of ...
Weak Force Stalls Protrusion at the Leading Edge of the Lamellipodium
Mar 01, 2006; ... ABSTRACT Protrusion, the first step of cell migration, is driven by actin polymerization coupled to adhesion at the cell's leading edge. Polymerization and adhesive forces have been estimated, but the net protrusion force has not been measured accurately. We arrest the leading edge of a ...
The Amplitude Distribution of Release Events through a Fusion Pore
Mar 01, 2006; ... ABSTRACT Neurotransmitters, hormones, or dyes may be released from vesicles via a fusion pore, rather than by full fusion of the vesicle with the plasma membrane. If the lifetime of the fusion pore is comparable to the time required for the substance to exit the vesicle, only a fraction ...
Rigidity Sensing at the Leading Edge through [alpha]^sub v^[beta]^sub 3^ Integrins and RPTP[alpha]
Mar 01, 2006; ... ABSTRACT Cells require optimal substrate stiffness for normal function and differentiation. The mechanisms for sensing matrix rigidity and durotaxis, however, are not clear. Here we showed that control, Shp2^sup -/-^, integrin β1^sup -/-^, and talin1^sup -/-^ cell lines all spread ...
Low-Threshold Exocytosis Induced by cAMP-Recruited Ca^sub V^3.2 ([alpha]^sub 1H^) Channels in Rat Chromaffin Cells
Mar 01, 2006; ... ABSTRACT We have studied the functional role of Ca^sub V^3 channels in triggering fast exocytosis in rat chromaffin cells (RCCs). Ca^sub V^3 T-type channels were selectively recruited by chronic exposures to cAMP (3 days) via an exchange protein directly activated by cAMP (Epac)-mediated ...
An X-Ray Diffraction Study on Mouse Cardiac Cross-Bridge Function In Vivo: Effects of Adrenergic [beta]-Stimulation
Mar 01, 2006; ... ABSTRACT To investigate how β-stimulation affects the contractility of cardiac muscle, x-ray diffraction from cardiac muscle in the left ventricular free wall of a mouse heart was recorded in vivo. To our knowledge, this is the first x-ray diffraction study on a heart in a living ...
Local Induction of Acetylcholine Receptor Clustering in Myotube Cultures Using Microfluidic Application of Agrin
Mar 15, 2006; ... ABSTRACT During neuromuscular synaptogenesis, the exchange of spatially localized signals between nerve and muscle initiates the coordinated focal accumulation of the acetylcholine (ACh) release machinery and the ACh receptors (AChRs). One of the key first steps is the release of the ...
Rapid Quantitative Characterization of Protein Interactions by Composition Gradient Static Light Scattering
Mar 15, 2006; ... ABSTRACT Two new applications of the recently developed technique of composition gradient static light scattering (CG-SLS) are presented. 1), The method is demonstrated to be capable of detecting and quantitatively characterizing reversible association of chymotrypsin and bovine ...
Redesigning Channel-Forming Peptides: Amino Acid Substitutions that Enhance Rates of Supramolecular Self-Assembly and Raise Ion Transport Activity
Mar 15, 2006; ... ABSTRACT Three series of 22-residue peptides derived from the transmembrane M2 segment of the glycine receptor α1-subunit (M2GlyR) have been designed, synthesized, and tested to determine the plasticity of a channel-forming sequence and to define whether channel pores with enhanced ...
Correlated Fluorescence-Atomic Force Microscopy of Membrane Domains: Structure of Fluorescence Probes Determines Lipid Localization
Mar 15, 2006; ... ABSTRACT Coupling atomic force microscopy (AFM) with high-resolution fluorescence microscopy is an attractive means of identifying membrane domains by both physical topography and fluorescence. We have used this approach to study the ability of a suite of fluorescent molecules to probe ...
Substrate Rigidity Regulates the Formation and Maintenance of Tissues
Mar 15, 2006; ... ABSTRACT The ability of cells to form tissues represents one of the most fundamental issues in biology. However, it is unclear what triggers cells to adhere to one another in tissues and to migrate once a piece of tissue is planted on culture surfaces. Using substrates of identical ...
Filamin-A and Rheological Properties of Cultured Melanoma Cells
Mar 15, 2006; ... ABSTRACT Here we report the rheological properties of cultured hsFLNa (filamin-A)-expressing (FIL+) and hsFLNa-deficient (FIL-) melanoma cells. Using magnetic twisting cytometry over a wide range of probing frequencies, and targeting either cortical or deeper cytoskeletal structures, we ...
Biomechanics of P-Selectin PSGL-1 Bonds: Shear Threshold and Integrin-Independent Cell Adhesion
Mar 15, 2006; ... ABSTRACT Platelet-leukocyte adhesion may contribute to thrombosis and inflammation. We examined the heterotypic interaction between unactivated neutrophils and either thrombin receptor activating peptide (TRAP)-stimulated platelets or P-selectin-bearing beads (Ps-beads) in suspension ....