Biophysical Journal back issues from July 2006:
Ground and Excited States of Retinal Schiff Base Chromophores by Multiconfigurational Perturbation Theory
Jul 01, 2006; ... ABSTRACT We have studied the wavelength dependence of retinal Schiff base absorbencies on the protonation state of the chromophore at the multiconfigurational level of theory using second order perturbation theory (CASPT2) within an atomic natural orbital basis set on MP2 optimized ...
Three-Dimensional Distribution of Ryanodine Receptor Clusters in Cardiac Myocytes
Jul 01, 2006; ... ABSTRACT The clustering of ryanodine receptors (RyR2) into functional Ca^sup 2+^ release units is central to current models for cardiac excitation-contraction (E-C) coupling. Using immunolabeling and confocal microscopy, we have analyzed the distribution of RyR2 clusters in rat and ...
Evidence for Lipid/Cholesterol Ordering in Model Lipid Membranes
Jul 01, 2006; ... ABSTRACT It has been postulated that for a binary mixture of phospholipid and cholesterol, phospholipid/cholesterol complexes are formed. Using grazing incidence x-ray diffraction, we have obtained evidence for lipid/cholesterol ordering in model membranes. Scattering features consistent ...
Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates
Jul 01, 2006; ... ABSTRACT Using distributed molecular dynamics simulations we located four distinct folding transitions for a 39-residue ββαβ protein fold. To characterize the nature of each room temperature transition, we calculated the probability of transmission for 500 points ...
A Model for the Pulsatile Secretion of Gonadotropin-Releasing Hormone from Synchronized Hypothalamic Neurons
Jul 01, 2006; ... ABSTRACT Cultured gonadotropin-releasing hormone (GnRH) neurons have been shown to express GnRH receptors. GnRH binding to its receptors activates three types of G-proteins at increasing doses. These G-proteins selectively activate or inhibit GnRH secretion by regulating the ...
Electrostatic Energy Calculation on the pH-Induced Conformational Change of Influenza Virus Hemagglutinin
Jul 01, 2006; ... ABSTRACT The pH-induced conformational change of influenza virus hemagglutinin (HA) has been investigated by calculating the change of electrostatic energy of the fragment of HA2 upon pH change. The average charge and electrostatic free energy are calculated as a function of pH for the ...
Langevin Dynamics Simulations of Genome Packing in Bacteriophage
Jul 01, 2006; ... ABSTRACT We use Langevin dynamics simulations to study the process by which a coarse-grained DNA chain is packaged within an icosahedral container. We focus our inquiry on three areas of interest in viral packing: the evolving structure of the packaged DNA condensate; the packing ...
Autologous Morphogen Gradients by Subtle Interstitial Flow and Matrix Interactions
Jul 01, 2006; ... ABSTRACT Cell response to extracellular cues is often driven by gradients of morphogenetic and chemotactic proteins, and therefore descriptions of how such gradients arise are critical to understanding and manipulating these processes. Many of these proteins are secreted in ...
Interplay of Ryanodine Receptor Distribution and Calcium Dynamics
Jul 01, 2006; ... ABSTRACT Spontaneously generated calcium (Ca^sup 2+^) waves can trigger arrhythmias in ventricular and atrial myocytes. Yet, Ca^sup 2+^ waves also serve the physiological function of mediating global Ca^sup 2+^ increase and muscle contraction in atrial myocytes. We examine the factors ...
Ensemble-Based Convergence Analysis of Biomolecular Trajectories
Jul 01, 2006; ... ABSTRACT Assessing the convergence of a biomolecular simulation is an essential part of any careful computational investigation, because many fundamental aspects of molecular behavior depend on the relative populations of different conformers. Here we present a physically intuitive ...
Solid-State NMR Investigation of the Membrane-Disrupting Mechanism of Antimicrobial Peptides MSI-78 and MSI-594 Derived from Magainin 2 and Melittin
Jul 01, 2006; ... ABSTRACT The mechanism of membrane interaction of two amphipathic antimicrobial peptides, MSI-78 and MSI-594, derived from magainin-2 and melittin, is presented. Both the peptides show excellent antimicrobial activity. The 8-anilinonaphthalene-1-sulfonic acid uptake experiment using ...
Clustering of Cyclic-Nucleotide-Gated Channels in Olfactory Cilia
Jul 01, 2006; ... ABSTRACT Olfactory cilia contain the known components of olfactory signal transduction, including a high density of cyclicnucleotide-gated (CNG) channels. CNG channels play an important role in mediating odor detection. The channels are activated by cAMP, which is formed by a ...
Mechanical Properties of Pore-Spanning Lipid Bilayers Probed by Atomic Force Microscopy
Jul 01, 2006; ... ABSTRACT We measure the elastic response of a free-standing lipid membrane to a local indentation by using an atomic force microscope. Starting point is a planar gold-coated alumina substrate with a chemisorbed 3-mercaptopropionic acid monolayer displaying circular pores of very well ...
Triggering and Visualizing the Aggregation and Fusion of Lipid Membranes in Microfluidic Chambers
Jul 01, 2006; ... ABSTRACT We present a method that makes it possible to trigger, observe, and quantify membrane aggregation and fusion of giant liposomes in microfluidic chambers. Using electroformation from spin-coated films of lipids on transparent indium tin oxide electrodes, we formed two-dimensional ...
First Steps of Retinal Photoisomerization in Proteorhodopsin
Jul 01, 2006; ... ABSTRACT The early steps (<1 ns) in the photocycle of the detergent solubilized proton pump proteorhodopsin are analyzed by ultrafast spectroscopic techniques. A comparison to the first primary events in reconstituted proteorhodopsin as well as to the well known archaeal proton pump ...
Controlling the Protein Dynamical Transition with Sugar-Based Bioprotectant Matrices: A Neutron Scattering Study
Jul 01, 2006; ... ABSTRACT Through elastic neutron scattering we measured the mean-square displacements of the hydrogen atoms of lysozyme embedded in a glucose-water glassy matrix as a function of the temperature and at various water contents. The elastic intensity of all the samples has been interpreted ...
Structural Comparison of the Two Alternative Transition States for Folding of TI I27
Jul 01, 2006; ... ABSTRACT TI I27, a β-sandwich domain from the human muscle protein titin, has been shown to fold via two alternative pathways, which correspond to a change in the folding mechanism. Under physiological conditions, TI I27 folds by a classical nucleation-condensation mechanism ...
Effects of Intracellular and Extracellular Concentrations of Ca^sup 2+^, K+, and Cl- on the Na+-Dependent Mg^sup 2+^ Efflux in Rat Ventricular Myocytes
Jul 01, 2006; ... ABSTRACT Intracellular Mg^sup 2+^ concentration ([Mg^sup 2+^]^sub i^) was measured in rat ventricular myocytes with the fluorescent indicator furaptra (25°C). After the myocytes were loaded with Mg^sup 2+^, the initial rate of decrease in [Mg^sup 2+^]^sub i^ (initial Δ[Mg^sup ...
Increasing the Net Charge and Decreasing the Hydrophobicity of Bovine Carbonic Anhydrase Decreases the Rate of Denaturation with Sodium Dodecyl Sulfate
Jul 01, 2006; ... ABSTRACT This study compares the rate of denaturation with sodium dodecyl sulfate (SDS) of the individual rungs of protein charge ladders generated by acylation of the lysine ε-NH^sup +^^sub 3^ groups of bovine carbonic anhydrase II (BCA). Each acylation decreases the number of ...
Effects of Denaturants on the Dynamics of Loop Formation in Polypeptides
Jul 01, 2006; ... ABSTRACT Quenching of the triplet state of tryptophan by close contact with cysteine has been used to measure the reaction-limited and diffusion-limited rates of loop formation in disordered polypeptides having the sequence cys-(ala-gly-gln)^sub j^-trp (j = 1-9). The decrease in the ...
Probabilistic Modeling of Rosette Formation
Jul 01, 2006; ... ABSTRACT Rosetting, or forming a cell aggregate between a single target nucleated cell and a number of red blood cells (RBCs), is a simple assay for cell adhesion mediated by specific receptor-ligand interaction. For example, rosette formation between sheep RBC and human lymphocytes has ...
Pulsed Laser Microbeam-Induced Cell Lysis: Time-Resolved Imaging and Analysis of Hydrodynamic Effects
Jul 01, 2006; ... ABSTRACT Time-resolved imaging was used to examine the use of pulsed laser microbeam irradiation to produce cell lysis. Lysis was accomplished through the delivery of 6 ns, λ = 532 nm laser pulses via a 40 × , 0.8 NA objective to a location 10 µm above confluent monolayers of ...
Diffusional Anisotropy in Collagenous Tissues: Fluorescence Imaging of Continuous Point Photobleaching
Jul 01, 2006; ... ABSTRACT Molecular transport in avascular collagenous tissues such as articular cartilage occurs primarily via diffusion. The presence of ordered structures in the extracellular matrix may influence the local transport of macromolecules, leading to anisotropic diffusion depending on the ...
In Vivo Quantitative Studies of Dynamic Intracellular Processes Using Fluorescence Correlation Spectroscopy
Jul 01, 2006; ... ABSTRACT It has been a significant challenge to quantitatively study the dynamic intracellular processes in live cells. These studies are essential for a thorough understanding of the underlying mechanisms regulating the signaling pathways and the transitions between cell cycle stages ....
Lateral Diffusion Anisotropy and Membrane Lipid/Skeleton Interaction in Outer Hair Cells
Jul 01, 2006; ... ABSTRACT The organization of the plasma membrane of cells in lipid domains affects the way the membrane interacts with the underlying protein skeleton, which in turn affects the lateral mobility of lipid and protein molecules in the membrane. Membrane fluidity properties can be monitored ...
A Computational Framework for the Topological Analysis and Targeted Disruption of Signal Transduction Networks
Jul 01, 2006; ... ABSTRACT In this article, optimization-based frameworks are introduced for elucidating the input-output structure of signaling networks and for pinpointing targeted disruptions leading to the silencing of undesirable outputs in therapeutic interventions. The frameworks are demonstrated ...
First-Principles Transversal DNA Conductance Deconstructed
Jul 01, 2006; ... ABSTRACT First-principles calculation of the transverse conductance across DNA fragments placed between gold nanoelectrodes reveals that such conductance describes electron tunneling that depends critically on geometrical rather than electronic-structure properties. By factoring the ...
Viscoelastic Study of the Mechanical Unfolding of a Protein by AFM
Jul 15, 2006; ... ABSTRACT We have applied a dynamic force modulation technique to the mechanical unfolding of a homopolymer of immunoglobulin (Ig) domains from titin, (C47S C63S I27)^sub 5^, [(I27)^sub 5^] to determine the viscoelastic response of single protein molecules as a function of extension. Both ...
Probing the Double Layer: Effect of Image Forces on AFM
Jul 15, 2006; ... ABSTRACT Force probes such as AFM tips or laser trap latex beads have a dielectric constant much less than that of the water that they displace. Thus when a probe approaches a charged surface under water it will be repelled simply based upon the image forces, and these can be of nN ...
Dynamics of DNA Ejection from Bacteriophage
Jul 15, 2006; ... ABSTRACT The ejection of DNA from a bacterial virus (i.e., phage) into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The simplest mechanism for this motion is diffusion, but in the case of phage ...
A Mechanism for Copper Inhibition of Infectious Prion Conversion
Jul 15, 2006; ... ABSTRACT We employ ab initio electronic structure calculations to obtain two structural models for copper bound in the strongest binding site of the noninfectious form of the prion protein. The models are compatible with available experimental constraints from electron spin resonance ...
A Computational Protocol for the Integration of the Monotopic Protein Prostaglandin H2 Synthase into a Phospholipid Bilayer
Jul 15, 2006; ... ABSTRACT Prostaglandin H2 synthase (PGHS) synthesizes PGH^sub 2^, a prostaglandin precursor, from arachidonic acid and was the first monotopic enzyme to have its structure experimentally determined. Both isozymes of PGHS are inhibited by nonsteroidal antiinflammatory drugs, an important ...
Inhibition of cAMP-Dependent Protein Kinase under Conditions Occurring in the Cardiac Dyad during a Ca^sup 2+^ Transient
Jul 15, 2006; ... ABSTRACT The space between the t-tubule invagination and the sarcoplasmic reticulum (SR) membrane, the dyad, in ventricular myocytes has been predicted to experience very high [Ca^sup 2+^] for short periods of time during a Ca^sup 2+^ transient. The dyadic space accommodates many protein ...
Modeling Starburst Cells' GABA^sub B^ Receptors and Their Putative Role in Motion Sensitivity
Jul 15, 2006; ... ABSTRACT Neal and Cunningham (Neal, M. J., and J. R. Cunningham. 1995. J. Physiol. (Lond.). 482:363-372) showed that GABA^sub B^ agonists and glycinergic antagonists enhance the light-evoked release of retinal acetylcholine. They proposed that glycinergic cells inhibit the cholinergic ...
Thermodynamic Equilibrium of Domains in a Two-Component Langmuir Monolayer
Jul 15, 2006; ... ABSTRACT This paper article outlines the results from a combined experimental and theoretical study on the properties of circular domains in a mixed Langmuir monolayer at thermodynamic equilibrium. The mixed monolayer consisted of a binary mixture of dimyristoyl-phosphatidyl-choline and ...
Dissociation of Biological Catch-Bond by Periodic Perturbation
Jul 15, 2006; ... ABSTRACT The analysis of the P-selectin/PSGL-1 catch-slip bond that is periodically driven by a detaching force predicts that in the frequency range on the order of 1 s^sup -1^ the bond lifetime undergoes significant changes with respect to both frequency and amplitude of the force. The ...
Mechanism of Titin Unfolding by Force: Insight from Quasi-Equilibrium Molecular Dynamics Calculations
Jul 15, 2006; ... ABSTRACT We have studied the unfolding by force of one of the immunoglobulin domains of the muscle protein titin using molecular dynamics simulations at 300 K. Previous studies, done at constant pulling rates, showed that under the effect of the force two strands connected to each other ...
Flexibility in a Drug Transport Accessory Protein: Molecular Dynamics Simulations of MexA
Jul 15, 2006; ... ABSTRACT Drug resistance in Gram-negative bacteria may be conferred via efflux through a tripartite complex of an inner membrane pump, an outer membrane pore, and a periplasmic adaptor protein. These are AcrB, TolC, and AcrA, respectively, in Escherichia coli. In Pseudomonas aerugonisa, ...
Modeling Hsp70-Mediated Protein Folding
Jul 15, 2006; ... ABSTRACT The Hsp70 chaperone system is the major molecular chaperone system that assists protein-folding processes in all cells. To understand these processes, we analyzed the kinetic characteristics of the Escherichia coli homologs of this chaperone system during folding of a denatured ...
On the Accuracy of Homology Modeling and Sequence Alignment Methods Applied to Membrane Proteins
Jul 15, 2006; ... ABSTRACT In this study, we investigate the extent to which techniques for homology modeling that were developed for water-soluble proteins are appropriate for membrane proteins as well. To this end we present an assessment of current strategies for homology modeling of membrane proteins ...
Cooperative Fluctuations Point to the Dimerization Interface of P53 Core Domain
Jul 15, 2006; ... ABSTRACT Elastic network models are used for investigation of the p53 core domain functional dynamics. Global modes of motion indicate high positive correlations for residue fluctuations across the A-B interface, which are not observed at the B-C interface. Major hinge formation is ...
Proton Transfer in Gramicidin Water Wires in Phospholipid Bilayers: Attenuation by Phosphoethanolamine
Jul 15, 2006; ... ABSTRACT The transfer of protons in water wires was studied in native gramicidin A (gA), and in the SS- and RR-diastereoisomers of dioxolane-linked gA channels (SS and RR channels). These peptides were incorporated into membranes comprised of distinct combinations of phospholipid ...
Influence of Thermally Driven Surface Undulations on Tethers Formed from Bilayer Membranes
Jul 15, 2006; ... ABSTRACT Tether formation is a powerful method to study the mechanical properties of soft lipid bilayer membranes. The force required to maintain a tether at a given length depends upon both membrane elastic properties and tension. In this report, we develop a theoretical analysis that ...
Membrane-Bound Basic Peptides Sequester Multivalent (PIP^sub 2^), but Not Monovalent (PS), Acidic Lipids
Jul 15, 2006; ... ABSTRACT Several biologically important peripheral (e.g., myristoylated alanine-rich C kinase substrate) and integral (e.g., the epidermal growth factor receptor) membrane proteins contain clusters of basic residues that interact with acidic lipids in the plasma membrane. Previous ...
Reaction Diffusion Modeling of Calcium Dynamics with Realistic ER Geometry
Jul 15, 2006; ... ABSTRACT We describe a finite-element model of mast cell calcium dynamics that incorporates the endoplasmic reticulum's complex geometry. The model is built upon a three-dimensional reconstruction of the endoplasmic reticulum (ER) from an electron tomographic tilt series. Tetrahedral ...
Kinetic Measurement of Transient Dimerization and Dissociation Reactions of Arabidopsis Phototropin 1 LOV2 Domain
Jul 15, 2006; ... ABSTRACT Photochemical reaction of a plant blue-light photoreceptor, Arabidopsis phototropin 1-LOV (light-oxygen-voltage sensing) domain 2, was studied with a view to the diffusion coefficients (D) using the pulsed-laser-induced transient grating method. Although the reaction dynamics ...
DNA Diffusion in Mucus: Effect of Size, Topology of DNAs, and Transfection Reagents
Jul 15, 2006; ... ABSTRACT DNA represents a promising therapeutic and prophylactic macromolecule in treating genetic diseases, infectious diseases and cancers. The therapeutic potential of DNA is directly related to how DNA transports within the targeted tissue. In this study, fluorescence photobleaching ...
Dynamic Protein Domains: Identification, Interdependence, and Stability
Jul 15, 2006; ... ABSTRACT Existing methods of domain identification in proteins usually provide no information about the degree of domain independence and stability. However, this information is vital for many areas of protein research. The recently developed hierarchical clustering of correlation ...
Coupling between Lipid Shape and Membrane Curvature
Jul 15, 2006; ... ABSTRACT Using molecular dynamics simulations, we examine the behavior of lipids whose preferred curvature can be systematically varied. This curvature is imposed by controlling the headgroup size of a coarse-grained lipid model recently developed by us. To validate this approach, we ...
Characterization of the Structure of RAMP1 by Mutagenesis and Molecular Modeling
Jul 15, 2006; ... ABSTRACT Receptor activity modifying proteins (RAMPs) are a family of single-pass transmembrane proteins that dimerize with G-protein-coupled receptors. They may alter the ligand recognition properties of the receptors (particularly for the calcitonin receptor-like receptor, CLR). Very ...
Method of X-Ray Anomalous Diffraction for Lipid Structures
Jul 15, 2006; ... ABSTRACT The structures of the unit cells of lipid phases that exhibit long-range crystalline order but short-range liquid-like disorder are of biological interests. In particular, the recently discovered rhombohedral phase has a unit cell containing either the structure of a membrane ...
Mechanical Properties of Murine Leukemia Virus Particles: Effect of Maturation
Jul 15, 2006; ... ABSTRACT After budding from the host cell, retroviruses undergo a process of internal reorganization called maturation, which is prerequisite to infectivity. Viral maturation is accompanied by dramatic morphological changes, which are poorly understood in physical/mechanistic terms ....
Nonperturbative Chemical Imaging of Organelle Transport in Living Cells with Coherent Anti-Stokes Raman Scattering Microscopy
Jul 15, 2006; ... ABSTRACT Nonperturbative monitoring of intracellular organelle transport in unstained living cells was achieved with coherent anti-Stokes Raman scattering (CARS) microscopy. To avoid possible interference with the organelle transport introduced by laser radiation, we first examined ...
Ion-Mediated Nucleic Acid Helix-Helix Interactions
Jul 15, 2006; ... ABSTRACT Salt ions are essential for the folding of nucleic acids. We use the tightly bound ion (TBI) model, which can account for the correlations and fluctuations for the ions bound to the nucleic acids, to investigate the electrostatic free-energy landscape for two parallel nucleic ...
Corrections
Jul 15, 2006; ... Matthew J. German, Azzedine Hammiche, Narasimhan Ragavan, Mark J. Tobin, Nigel J. Fullwood, Shyam S. Matanhelia, Andrew C. Hindley, Caroline M. Nicholson, Hubert M. Pollock, and Francis L. Martin. 2006. Infrared spectroscopy with inultivariate analysis potentially facilitates the segregation of ...
Gap-Junctional Single-Channel Permeability for Fluorescent Tracers in Mammalian Cell Cultures
Jul 15, 2006; ... ABSTRACT We have developed a simple dye transfer method that allows quantification of the gap-junction permeability of small cultured cells. Fluorescent dyes (calcein and Lucifer yellow) were perfused into one cell of an isolated cell pair using a patch-type micropipette in the ...
Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme
Jul 15, 2006; ... ABSTRACT The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location ...
Tetramer Formation Kinetics in the Signaling State of AppA Monitored by Time-Resolved Diffusion
Jul 15, 2006; ... ABSTRACT The photoreaction kinetics of the BLUF domain of AppA^sub 5-125^ was studied by monitoring time-dependence of an apparent diffusion coefficient (D) using the pulsed laser-induced transient grating technique. It was found that D of the photoproduct is time-dependent. From the ...
Assisting the Reactivation of Guanidine Hydrochloride-Denatured Aminoacylase by Hydroxypropyl Cyclodextrins
Jul 15, 2006; ... ABSTRACT Cyclodextrin is a water-soluble circular oligosaccharide with a cylinder shape characterized by exterior hydrophilic rims and an interior hydrophobic cavity, which makes it an ideal additive to prevent proteins from aggregating during refolding. In this research, three ...
Simultaneous Multicolor Fluorescence Cross-Correlation Spectroscopy to Detect Higher Order Molecular Interactions Using Single Wavelength Laser Excitation
Jul 15, 2006; ... ABSTRACT Fluorescence cross-correlation spectroscopy is a powerful method for the study of molecular interactions and dynamics in solution and even in living cells. Usually, in the optical setup, either two laser beams have to be superimposed in their respective confocal volumes or ...
Single Molecule Mechanical Probing of the SNARE Protein Interactions
Jul 15, 2006; ... ABSTRACT Exocytotic release of neurotransmitters is mediated by the ternary soluble N-ethyl maleimide-sensitive fusion protein attachment protein receptors (SNAREs) complex, comprised of syntaxin (Sx), synaptosome-associated protein of 25 kDa (SNAP25), and synaptobrevin 2 (Sb2). Since ...
The Net Orientation of Nicotinic Receptor Transmembrane [alpha]-Helices in the Resting and Desensitized States
Jul 15, 2006; ... ABSTRACT The net orientation of nicotinic acetylcholine receptor transmembrane α-helices has been probed in both the activatable resting and nonactivatable desensitized states using linear dichroism Fourier-transform infrared spectroscopy. Infrared spectra recorded from ...