Biophysical Journal back issues from January 2007:
Localized Functional Chemical Stimulation of TE 671 Cells Cultured on Nanoporous Membrane by Calcein and Acetylcholine
Jan 01, 2007; ... ABSTRACT Acetylcholine sensitive TE 671 cells were cultured on nanoporous membranes and chemically stimulated by localized application of i), calcein-AM and ii), acetylcholine, respectively, onto the bottom face of the membrane employing an ink jet print head. Stimulus correlated ...
Competitive Displacement of DNA during Surface Hybridization
Jan 01, 2007; ... ABSTRACT Using real-time dual-color fluorescence detection, we have experimentally tracked individual target species during competitive DNA surface hybridization in a two-component sample. Our experimental results demonstrate displacement of the lower affinity species by the higher ...
Facile Lipid Flip-Flop in a Phospholipid Bilayer Induced by Gramicidin A Measured by Sum-Frequency Vibrational Spectroscopy
Jan 01, 2007; ... ABSTRACT The first direct experimental evidence that gramicidin A (gA), a transmembrane peptide, facilitates the translocation of unlabeled lipids in a phospholipid bilayer was obtained with sum-frequency vibrational spectroscopy (SFVS). SFVS was used to investigate the effect of gA on ...
SGTx1, a Kv Channel Gating-Modifier Toxin, Binds to the Interfacial Region of Lipid Bilayers
Jan 01, 2007; ... ABSTRACT SGTx1 is a gating-modifier toxin that has been shown to inhibit the voltage-gated potassium channel Kv2.1. SGTx1 is thought to bind to the S3b-S4a region of the voltage-sensor, and is believed to alter the energetics of gating. Gating-modifier toxins such as SGTx1 are of ...
Anesthesia, Analgesia, and Euphoria
Jan 01, 2007; ... Seeking a unified theory of achieving the stale induced by anesthetics is deep in the Biophysicist's psyche. A search of the Biophysical Journal contents for titles containing "anesthetic" yields 84 hits. Both sleep and anesthesia uncouple functional connections between activities in hemispheres ...
Possible Pathway for Ubiquinone Shuttling in Rhodospirillum rubrum Revealed by Molecular Dynamics Simulation
Jan 01, 2007; ... ABSTRACT In the last decade, the structures of many components of the photosynthetic apparatus of purple bacteria, as well as the mutual organization of these components within the purple membrane, were resolved. One key question that emerged concerned the assembly of the core complex ...
Charge Delocalization in Proton Channels, I: The Aquaporin Channels and Proton Blockage
Jan 01, 2007; ... ABSTRACT The explicit contribution to the free energy barrier and proton conductance from the delocalized nature of the excess proton is examined in aquaporin channels using an accurate all-atom molecular dynamics computer simulation model. In particular, the channel permeation free ...
Modeling a Spin-Labeled Fusion Peptide in a Membrane: Implications for the Interpretation of EPR Experiments
Jan 01, 2007; ... ABSTRACT Site-directed spin-labeling and electron paramagnetic resonance are powerful tools for studying structure and conformational dynamics of proteins, especially in membranes. The position of the spin label is used as an indicator of the position of the site to which it is attached ....
Enhanced Surfactant Adsorption via Polymer Depletion Forces: A Simple Model for Reversing Surfactant Inhibition in Acute Respiratory Distress Syndrome
Jan 01, 2007; ... ABSTRACT Lung surfactant adsorption to an air-water interface is strongly inhibited by an energy barrier imposed by the competitive adsorption of albumin and other surface-active serum proteins that are present in the lung during acute respiratory distress syndrome. This reduction in ...
pH-dependent Formation of Membranous Cytoplasmic Body-Like Structure of Ganglioside G^sub M1^/Bis(Monoacylglycero)Phosphate Mixed Membranes
Jan 01, 2007; ... ABSTRACT Membrane structures of the mixtures of ganglioside G^sub M1^ and endosome specific lipid, bis (monoacylglycero) phosphate (BMP, also known as lysobisphosphatidic acid) were examined at various pH conditions by freeze-fracture electron microscopy and small-angle x-ray scattering ....
Charge Delocalization in Proton Channels, II: The Synthetic LS2 Channel and Proton Selectivity
Jan 01, 2007; ... ABSTRACT In this study, the minimalist synthetic LS2 channel is used as a prototype to examine the selectivity of protons over other cations. The free-energy profiles along the transport pathway of LS2 are calculated for three cation species: a realistic delocalized proton (including ...
Conformational Sampling with Implicit Solvent Models: Application to the PHF6 Peptide in Tau Protein
Jan 01, 2007; ... ABSTRACT Implicit solvent models approximate the effects of solvent through a potential of mean force and therefore make solvated simulations computationally efficient. Yet despite their computational efficiency, the inherent approximations made by implicit solvent models can sometimes ...
Collagen Fibrils: Nanoscale Ropes
Jan 01, 2007; ... ABSTRACT The formation of collagen fibrils from staggered repeats of individual molecules has become "accepted" wisdom. However, for over thirty years now, such a model has failed to resolve several structural and functional questions. In a novel approach, it was found, using atomic ...
Role of Pairwise Interactions between M1 and M2 Domains of the Nicotinic Receptor in Channel Gating
Jan 01, 2007; ... ABSTRACT The adult form of the nicotinic acetytcholine receptor (AChR) consists of five submits (α2βεδ), each having four transmembrane domains (M1-M4). The atomic model of the nicotinic acetylcholine receptor shows that the pore-lining M2 domains make no extensive ...
A Structural Origin of Latency Relaxation in Frog Skeletal Muscle
Jan 01, 2007; ... ABSTRACT A time-resolved x-ray diffraction study at a time resolution of 0.53 ms was made to investigate the structural origin of latency relaxation (LR) in frog skeletal muscle. Intensity and spacing measurements were made on meridional reflections from the Ca-binding protein troponin ...
Novel Lipid Transfer Property of Two Mitochondrial Proteins that Bridge the Inner and Outer Membranes
Jan 01, 2007; ... ABSTRACT This study provides evidence of a novel function for mitochondrial creatine kinase (MtCK) and nucleoside diphosphate kinase (NDPK-D). Both are basic peripheral membrane proteins with symmetrical homo-oligomeric structure, which in the case of MtCK was already shown to allow ...
Cholesterol Sulfate and Ca^sup 2+^ Modulate the Mixing Properties of Lipids in Stratum Corneum Model Mixtures
Jan 01, 2007; ... ABSTRACT The influence of cholesterol sulfate (CS) and calcium on the phase behavior of lipid mixtures mimicking the stratum corneum (SC) lipids was examined using vibrational spectroscopy. Raman microspectrocopy showed that equimolar mixtures of ceramide, palmitic acid, and cholesterol ...
Growth Dynamics of Domains in Ternary Fluid Vesicles
Jan 01, 2007; ... ABSTRACT We have studied the growth dynamics of domains on ternary fluid vesicles composed of saturated (dipalmitoylphosphatidylcholine), unsaturated (dioleoylphosphatidylcholine) phosphatidylcholine lipids, and cholesterol using a fluorescence microscopy. The domain coarsening processes ...
Composition Effect on Peptide Interaction with Lipids and Bacteria: Variants of C3a Peptide CNY21
Jan 01, 2007; ... ABSTRACT The effect of peptide hydrophobicity and charge on peptide interaction with model lipid bilayers was investigated for the C3a-derived peptide CNY21 by fluorescence spectroscopy, circular dichroism, ellipsometry, z-potential, and photon correlation spectroscopy measurements. For ...
Mechanism of the Difference in the Binding Affinity of E. coli tRNA^sup Gln^ to Glutaminyl-tRNA Synthetase Caused by Noninterface Nucleotides in Variable Loop
Jan 01, 2007; ... ABSTRACT Aminoacyl-tRNA synthetases (ARSs) distinguish their cognate tRNAs from many other kinds of tRNAs, despite the very similar tertiary structures of tRNAs. Many researchers have supported the view that this recognition is achieved by intermolecular interactions between tRNA and ...
Conformation of a Peptide Encompassing the Proton Translocation Channel of Vacuolar H^sup +^-ATPase
Jan 01, 2007; ... ABSTRACT The structural properties of a crucial transmembrane helix for proton translocation in vacuolar ATPase are studied using double site-directed spin-labeling combined with electron spin resonance (ESR) (or electron paramagnetic resonance) and circular dichroism spectroscopy in ...
A Molecular View of Melting in Anhydrous Phospholipidic Membranes
Jan 01, 2007; ... ABSTRACT A high-flux backscattering spectrometer and a time-of-flight disk chopper spectrometer are used to probe the molecular mobility of model freeze-dried phospholipid liposomes at a range of temperatures surrounding the main melting transition. Using specific deuteration, ...
Dynamics of the Nucleotide Pocket of Myosin Measured by Spin-Labeled Nucleotides
Jan 01, 2007; ... ABSTRACT We have used electron paramagnetic probes attached to the ribose of ATP (SL-ATP) to monitor conformational changes in the nucleotide pocket of myosin. Spectra for analogs bound to myosin in the absence of actin showed a high degree of immobilization, indicating a closed ...
The Gas-Phase Absorption Spectrum of a Neutral GFP Model Chromophore
Jan 01, 2007; ... ABSTRACT We have studied the gas-phase absorption properties of the green fluorescent protein (GFP) chromophore in its neutral (protonated) charge state in a heavy-ion storage ring. To accomplish this we synthesized a new molecular chromophore with a charged NH^sub 3^ group attached to a ...
Attributes of Glycosylation in the Establishment of the Unfolding Pathway of Soybean Agglutinin
Jan 01, 2007; ... ABSTRACT Soybean agglutinin (gSBA) is a tetrameric legume lectin, each of whose subunits are glycosylated. Earlier studies have shown that this protein shows exceptionally high stability in terms of free energy of unfolding when compared to other proteins from the same family. This ...
Protein Crystallography under Xenon and Nitrous Oxide Pressure: Comparison with In Vivo Pharmacology Studies and Implications for the Mechanism of Inhaled Anesthetic Action
Jan 01, 2007; ... ABSTRACT In contrast with most inhalational anesthetics, the anesthetic gases xenon (Xe) and nitrous oxide (N^sub 2^O) act by blocking the N-methyl-D-aspartate (NMDA) receptor. Using x-ray crystallography, we examined the binding characteristics of these two gases on two soluble proteins ...
Contour Length and Refolding Rate of a Small Protein Controlled by Engineered Disulfide Bonds
Jan 01, 2007; ... ABSTRACT The introduction of disulfide bonds into proteins creates additional mechanical barriers and limits the unfolded contour length (i.e., the maximal extension) measured by single-molecule force spectroscopy. Here, we engineer single disulfide bonds into four different locations of ...
pK^sub a^ Values for Side-Chain Carboxyl Groups of a PGB1 Variant Explain Salt and pH-Dependent Stability
Jan 01, 2007; ... ABSTRACT Determination of pK^sub a^ values of titrating residues in proteins provides a direct means of studying electrostatic coupling as well as pH-dependent stability. The B1 domain of protein G provides an excellent model system for such investigations. In this work, we analyze the ...
A Mesoporous Pattern Created by Nature in Spicules from Thetya aurantium Sponge
Jan 01, 2007; ... ABSTRACT Siliceous or carbonate spicules provide support and defense to marine sponges. The inorganic envelope usually embodies a protein core. Our SAXS study of the siliceous spicules from the demosponge Thetya aurantium proves the very ordered structure assumed by the protein core ...
pH-Dependent Self-Assembly of Polyalanine Peptides
Jan 01, 2007; ... ABSTRACT Polyalanine expansions in the nuclear RNA-binding protein PABP2 induce misfolding and aggregation of the protein into insoluble inclusions in muscle tissues and cell nuclei, leading to the disease oculopharyngeal muscular dystrophy (OPMD). We have explored the effect of solvent ...
Three-Color Alternating-Laser Excitation of Single Molecules: Monitoring Multiple Interactions and Distances
Jan 01, 2007; ... ABSTRACT We introduce three-color alternating-laser excitation (3c-ALEX), a fluorescence resonance energy transfer (FRET) method that measures up to three intramolecular distances and complex interaction stoichiometries of single molecules in solution. This tool extends substantially the ...
Multiple Diffusion Mechanisms Due to Nanostructuring in Crowded Environments
Jan 01, 2007; ... ABSTRACT One of the key questions regarding intracellular diffusion is how the environment affects molecular mobility. Mostly, intracellular diffusion has been described as hindered, and the physical reasons for this behavior are: immobile barriers, molecular crowding, and binding ...
Membrane Order and Molecular Dynamics Associated with IgE Receptor Cross-Linking in Mast Cells
Jan 01, 2007; ... ABSTRACT Cholesterol-rich microdomains (or "lipid rafts") within the plasma membrane have been hypothesized to exist in a liquid-ordered phase and play functionally important roles in cell signaling; however, these microdomains defy detection using conventional imaging. To visualize ...
A Mathematical Model of Glioblastoma Tumor Spheroid Invasion in a Three-Dimensional In Vitro Experiment
Jan 01, 2007; ... ABSTRACT Glioblastoma, the most malignant form of brain cancer, is responsible for 23% of primary brain tumors and has extremely poor outcome. Confounding the clinical management of glioblastomas is the extreme local invasiveness of these cancer cells. The mechanisms that govern invasion ...
Membrane Simulations of OpcA: Gating in the Loops?
Jan 15, 2007; ... ABSTRACT Mobility of extracellular loops may play an important role in the function of outer membrane proteins from Gram-negative bacteria. Molecular dynamics simulations of OpcA from Neisseria meningitidis, embedded in a lipid bilayer, have been used to explore the relationship between ...
Conformational Effects in Enzyme Catalysis: Reaction via a High Energy Conformation in Fatty Acid Amide Hydrolase
Jan 15, 2007; ... ABSTRACT Quantum mechanics/molecular mechanics and molecular dynamics simulations of fatty acid amide hydrolase show that reaction (amide hydrolysis) occurs via a distinct, high energy conformation. This unusual finding has important implications for fatty acid amide hydrolase, a key ...
Understanding the Molecular Basis for Differential Binding of Integrins to Collagen and Gelatin
Jan 15, 2007; ... ABSTRACT Integrin-mediated cell adhesion plays a central role in cell migration and signaling. Overexpression of integrins is also associated with cancer invasion and metastasis. Although a number of problems in integrin-matrix interactions have been studied in detail, the molecular ...
Downhill All the Way: H+ Gradients within Cardiac Myocytes
Jan 15, 2007; ... It has been known since at least 1880 that acidosis decreases the strength of contraction of the heart (1). Since then it has become clear that acidosis alters almost all aspects of cardiac cell fund inn, including electrical activity, ion handling, intracellular signaling, and the ability of ...
The Origin of Long-Range Attraction between Hydrophobes in Water
Jan 15, 2007; ... ABSTRACT When water-coated hydrophobic surfaces meet, direct contacts form between the surfaces, driving water out. However, long-range attractive forces first bring those surfaces close. This analysis reveals the source and strength of the long-range attraction between water-coated ...
Microtubule Stability Studied by Three-Dimensional Molecular Theory of Solvation
Jan 15, 2007; ... ABSTRACT We study microtubular supramolecular architectures of tubulin dimers self-assembling into linear protofilaments, in turn forming a closed tube, which is an important component of the cytoskeleton. We identify the protofilament arrangements with the lowest free energy using ...
TOAC Spin Labels in the Backbone of Alamethicin: EPR Studies in Lipid Membranes
Jan 15, 2007; ... ABSTRACT Alamethicin is a 19-amino-acid residue hydrophobic peptide that produces voltage-dependent ion channels in membranes. Analogues of the Glu(OMe)^sup 7,18,19^ variant of alamethicin F50/5 that are rigidly spin-labeled in the peptide backbone have been synthesized by replacing ...
Effect of Surfactant Protein A on the Physical Properties and Surface Activity of KL^sub 4^-Surfactant
Jan 15, 2007; ... ABSTRACT SP-A, the major protein component of pulmonary surfactant, is absent in exogenous surfactants currently used in clinical practice. However, it is thought that therapeutic properties of natural surfactants improve after enrichment with SP-A. The objective of this study was to ...
Differential Effects of Lysophosphatidylcholine on the Adsorption of Phospholipids to an Air/Water Interface
Jan 15, 2007; ... ABSTRACT To determine how the hydrophobia surfactant proteins promote insertion of the surfactant lipids into an air/water interface, we measured the effect of lysophosphatidylcholine (LPC) on adsorption. Existing models contend that the proteins function either by disordering the lipids ...
Ceramide-Domain Formation and Collapse in Lipid Rafts: Membrane Reorganization by an Apoptotic Lipid
Jan 15, 2007; ... ABSTRACT The effect of physiologically relevant ceramide concentrations (≤4 mol %) in raft model membranes with a lipid composition resembling that of cell membranes, i.e., composed of different molar ratios of an unsaturated glycerophospholipid, sphingomyelin, and cholesterol ...
Cooperative Effects of Rigor and Cycling Cross-Bridges on Calcium Binding to Troponin C
Jan 15, 2007; ... ABSTRACT The effects of rigor and cycling cross-bridges on distributions of calcium (Ca) bound within sarcomeres of rabbit psoas muscle fibers were compared using electron probe x-ray microanalysis. Calcium in the overlap region of rigor fibers, after correction for that bound to thick ...
Activity of a Two-Domain Antifreeze Protein Is Not Dependent on Linker Sequence
Jan 15, 2007; ... ABSTRACT The reported NMR structure of RD3, a naturally occurring two-domain antifreeze protein, suggests that the two nearly identical domains are oriented to allow simultaneous binding of their active regions to the ice surface. It is implied that the nine residues linking the two ...
Refolding upon Force Quench and Pathways of Mechanical and Thermal Unfolding of Ubiquitin
Jan 15, 2007; ... ABSTRACT The refolding from stretched initial conformations of ubiquitin (PDB ID: 1 ubq) under the quenched force is studied using the C^sub α^-Go model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. The force-quench ...
Spectrin Domains Lose Cooperativity in Forced Unfolding
Jan 15, 2007; ... ABSTRACT Spectrin is a multidomain cytoskeletal protein, the component three-helix bundle domains are expected to experience mechanical force in vivo. In thermodynamic and kinetic studies, neighboring domains of chicken brain α-spectrin R16 and R17 have been shown to behave ...
Dissecting the Pretransitional Conformational Changes in Aminoacylase I Thermal Denaturation
Jan 15, 2007; ... ABSTRACT Aminoacylase I (ACYI) catalyzes the stereospecific hydrolysis of L-acylamino acids and is generally assumed to be involved in the final step of the degradation of intracellular N-acetylated proteins. Apart from its crucial functions in intracellular amino acid metabolism, ACYI ...
Haemophilus influenzae Outer Membrane Protein P5 Is Associated with Inorganic Polyphosphate and Polyhydroxybutyrate
Jan 15, 2007; ... ABSTRACT Outer membrane protein P5 of nontypeable (acapsulate) Haemophilus influenzae (NTHi P5) forms large pores in planar lipid bilayers between symmetric solutions that unpredictably display a nonzero reversal potential. Moreover, NTHi P5 has a high theoretical isoelectric point, ...
Quantitative Characterization of Biological Liquids for Third-Harmonic Generation Microscopy
Jan 15, 2007; ... ABSTRACT Third-harmonic generation (THG) microscopy provides images of unstained biological samples based on spatial variations in third-order nonlinear susceptibility, refractive index, and dispersion. In this study, we establish quantitative values for the third-order nonlinear ...
Interplay between Shear Stress and Adhesion on Neutrophil Locomotion
Jan 15, 2007; ... ABSTRACT Leukocyte locomotion over the lumen of inflamed endothelial cells is a critical step, following firm adhesion, in the inflammatory response. Once firmly adherent, the cell will spread and will either undergo diapedesis through individual vascular endothelial cells or will ...
pH-Dependence of Extrinsic and Intrinsic H+-Ion Mobility in the Rat Ventricular Myocyte, Investigated Using Flash Photolysis of a Caged-H+ Compound
Jan 15, 2007; ... ABSTRACT Passive H^sup +^-ion mobility within eukaryotic cells is low, due to H^sup +^-ion binding to cytoplasmic buffers. A localized intracellular acidosis can therefore persist for seconds or even minutes. Because H^sup +^-ions modulate so many biological processes, spatial ...
Time-Dependent DNA Condensation Induced by Amyloid [beta]-Peptide
Jan 01, 2007; ... ABSTRACT The major protein component of the amyloid deposition in Alzheimer's disease is a 39-43 residue peptide, amyloid β (Aβ). Aβ is toxic to neurons, although the mechanism of neurodegeneration is uncertain. Evidence exists for non-B DNA conformation in the hippocampus ...
Transient Directed Motions of GABA^sub A^ Receptors in Growth Cones Detected by a Speed Correlation Index
Jan 15, 2007; ... ABSTRACT Single-molecule tracking of membrane proteins has become an important tool for investigating dynamic processes in live cells, such as cell signaling, membrane compartmentation or trafficking. The extraction of relevant parameters, such as interaction times between molecular ...
Magnetic Optimization in a Multicellular Magnetotactic Organism
Jan 15, 2007; ... ABSTRACT Unicellular magnetotactic prokaryotes, which typically carry a natural remanent magnetic moment equal to the saturation magnetic moment, are the prime example of magnetically optimized organisms. We here report magnetic measurements on a multicellular magnetotactic prokaryote ...
Protein-Cofactor Interactions in Bacterial Reaction Centers from Rhodobacter sphaeroides R-26: II. Geometry of the Hydrogen Bonds to the Primary Quinone Q^sup . -^^sub A^ by ^sup 1^H and ^sup 2^H ENDOR Spectroscopy
Jan 15, 2007; ... ABSTRACT The geometry of the hydrogen bonds to the two carbonyl oxygens of the semiquinone Q^sup .-^^sub A^ in the reaction center (RC) from the photosynthetic purple bacterium Rhodobacter sphaeroides R-26 were determined by fitting a spin Hamiltonian to the data derived from ^sup 1^H ...
Phase Resetting Curves and Oscillatory Stability in Interneurons of Rat Somatosensory Cortex
Jan 15, 2007; ... ABSTRACT Synchronous oscillations in neural activity are found over wide areas of the cortex. Specific populations of interneurons are believed to play a significant role in generating these synchronized oscillations through mutual synaptic and gap-junctional interactions. Little is ...
Structural Features of Parathyroid Hormone Receptor Coupled to G[alpha]^sub s^-Protein
Jan 15, 2007; ... ABSTRACT The molecular basis of the activation of G-proteins by the G-protein coupled receptor for parathyroid hormone (PTH) is unknown. Employing a combination of NMR methods and computer-based structural refinement, structural features involved in the activation of Gα^sub s^ by ...
Molecular Alignment within [beta]-Sheets in A[beta]^sub 14-23^ Fibrils: Solid-State NMR Experiments and Theoretical Predictions
Jan 15, 2007; ... ABSTRACT We report investigations of the molecular structure of amyloid fibrils formed by residues 14-23 of the β-amyloid peptide associated with Alzheimer's disease (Aβ^sub 14-23^), using solid-state nuclear magnetic resonance (NMR) techniques in conjunction with electron ...