Recently added articles from Biophysical Journal:
Packaging Double-Helical DNA into Viral Capsids: Structures, Forces, and Energetics
Jul 15, 2008; ... ABSTRACT Small, icosahedral double-stranded DNA bacteriophage pack their genomes tightly into preformed protein capsids using an ATP-driven motor. Coarse-grain molecular-mechanics models provide a detailed picture of DNA packaging in bacteriophage, revealing how conformation depends on ...
Synthetic Nanopores as a Test Case for Ion Channel Theories: The Anomalous Mole Fraction Effect without Single Filing
Jul 15, 2008; ... ABSTRACT The predictions of a theory for the anomalous mole fraction effect (AMFE) are tested experimentally with synthetic nanopores in plastic. The negatively charged synthetic nanopores under consideration are highly cation selective and 50 [Angstrom] in diameter at their smallest ...
Part I: An X-Ray Scattering Study of Cholera Toxin Penetration and Induced Phase Transformations in Lipid Membranes
Jul 15, 2008; ... ABSTRACT Cholera toxin is a highly efficient biotoxin, which is frequently used as a tool to investigate protein-membrane interactions and as a reporter for membrane rafts. Cholera toxin binds selectively to gangliosides with highest affinity to GM^sub 1^. However, the mechanism by which ...
Atomistic Simulations of the HIV-1 Protease Folding Inhibition
Jul 15, 2008; ... ABSTRACT Biochemical experiments have recently revealed that the p-S8 peptide, with an amino-acid sequence identical to the conserved fragment 83-93 (S8) of the HIV-1 protease, can inhibit catalytic activity of the enzyme by interfering with protease folding and dimerization. In this ...
Gating Mechanisms of Mechanosensitive Channels of Large Conductance, I: A Continuum Mechanics-Based Hierarchical Framework
Jul 15, 2008; ... ABSTRACT A hierarchical simulation framework that integrates information from molecular dynamics (MD) simulations into a continuum model is established to study the mechanical response of mechanosensitive channel of large-conductance (MscL) using the finite element method (FEM). The ...
Profiling the Thermodynamic Softness of Adenoviral Promoters
Jul 15, 2008; ... ABSTRACT We showed previously that enharmonic DNA dynamical features correlate with transcriptional activity in selected viral promoters, and hypothesized that areas of DNA softness may represent loci of functional significance. The nine known promoters from human adenovirus type 5 were ...
Gating Mechanisms of Mechanosensitive Channels of Large Conductance, II: Systematic Study of Conformational Transitions
Jul 15, 2008; ... ABSTRACT Part II of this study is based on the continuum mechanics-based molecular dynamics-decorated finite element method (MDeFEM) framework established in Part I. In Part II, the gating pathways of Escherichia coli-MscL channels under various basic deformation modes are simulated ....
Part II: Diffraction from Two-Dimensional Cholera Toxin Crystals Bound to Their Receptors in a Lipid Monolayer
Jul 15, 2008; ... ABSTRACT The structure of cholera toxin (CTAB^sub 5^) bound to its putative ganglioside receptor, galactosyl-N-acetylgalactosaminyl (N-acetyl-neuraminyl) galactosylglucosylceramide (GM^sub 1^), in a lipid monolayer at the air-water interface has been studied utilizing grazing incidence ...
Liquid-Liquid Domains in Bilayers Detected by Wide Angle X-Ray Scattering
Jul 15, 2008; ... ABSTRACT Wide angle x-ray scattering (WAXS) from oriented lipid multilayers is used to examine liquid-ordered (Lo)/liquid-disordered (Ld) phase coexistence in the system 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dipalmitoyl-sn-glycero-3-phosphocholine/cholesterol (DOPC/DPPC/Chol), ...
Influence of Lipid Saturation Grade and Headgroup Charge: A Refined Lung Surfactant Adsorption Model
Jul 15, 2008; ... ABSTRACT Rapid adsorption of surfactant material to the air/liquid interface of the lung is essential for maintaining normal lung function. The detailed mechanism of this process, however, remains unclear. In this study, we elucidate the influence of lipid saturation grade and headgroup ...
Tunable Blinking Kinetics of Cy5 for Precise DNA Quantification and Single-Nucleotide Difference Detection
Jul 15, 2008; ... ABSTRACT Fluorescence correlation spectroscopy (FCS) can resolve the intrinsic fast-blinking kinetics (FBKs) of fluorescent molecules that occur on the order of microseconds. These FBKs can be heavily influenced by the microenvironments in which the fluorescent molecules are contained ....
Equinatoxin II Permeabilizing Activity Depends on the Presence of Sphingomyelin and Lipid Phase Coexistence
Jul 15, 2008; ... ABSTRACT Equinatoxin II is a pore-forming protein of the actinoporin family. After membrane binding, it inserts its N-terminal α-helix and forms a protein/lipid pore. Equinatoxin II activity depends on the presence of sphingomyelin in the target membrane; however, the role of this ...
Order Parameters and Areas in Fluid-Phase Oriented Lipid Membranes Using Wide Angle X-Ray Scattering
Jul 15, 2008; ... ABSTRACT We used wide angle x-ray scattering (WAXS) from stacks of oriented lipid bilayers to measure chain orientational order parameters and lipid areas in model membranes consisting of mixtures of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)/cholesterol and ...
Darcy Permeability of Agarose-Glycosaminoglycan Gels Analyzed Using Fiber-Mixture and Donnan Models
Jul 15, 2008; ... ABSTRACT Agarose-glycosaminoglycan (GAG) membranes were synthesized to provide a model system in which the factors controlling the Darcy (or hydraulic) permeability could be assessed in composite gels of biological relevance. The membranes contained a GAG (chondroitin sulfate) that was ...
Asymmetric Structural Features in Single Supported Lipid Bilayers Containing Cholesterol and G^sub M1^ Resolved with Synchrotron X-Ray Reflectivity
Jul 15, 2008; ... ABSTRACT The cell membrane comprises numerous protein and lipid molecules capable of asymmetric organization between leaflets and liquid-liquid phase separation. We use single supported lipid bilayers (SLBs) to model cell membranes, and study how cholesterol and asymmetrically oriented ...
Temperature Dependence of the Rotation and Hydrolysis Activities of F^sub 1^-ATPase
Jul 15, 2008; ... ABSTRACT F^sub 1^-ATPase, a water-soluble portion of the enzyme ATP synthase, is a rotary molecular motor driven by ATP hydrolysis. To learn how the kinetics of rotation are regulated, we have investigated the rotational characteristics of a thermophilic F^sub 1^-ATPase over the ...
A Long-Lived M-Like State of Phoborhodopsin that Mimics the Active State
Jul 15, 2008; ... ABSTRACT Pharaonis phoborhodopsin (ppR, also called pharaonis sensory rhodopsin II) is a seven transmembrane helical retinal protein. ppR forms a signaling complex with pharaonis Halobacterial transducer II (pHtrII) in the membrane that transmits a light signal to the sensory system in ...
Cavity-Creating Mutations in Pseudomonas aeruginosa Azurin: Effects on Protein Dynamics and Stability
Jul 15, 2008; ... ABSTRACT Changes in flexibility and structural stability of Pseudomonas aeruginosa azurin in response to cavity-creating mutations were probed by the phosphorescence emission of Trp-48, which was deeply buried in the compact hydrophobic core of the macromolecule, and by measurements of ...
Mechanism of Signal Propagation upon Retinal Isomerization: Insights from Molecular Dynamics Simulations of Rhodopsin Restrained by Normal Modes
Jul 15, 2008; ... ABSTRACT As one of the best studied members of the pharmaceutically relevant family of G-protein-coupled receptors, rhodopsin serves as a prototype for understanding the mechanism of G-protein-coupled receptor activation. Here, we aim at exploring functionally relevant conformational ...
Direct Observation of Markovian Behavior of the Mechanical Unfolding of Individual Proteins
Jul 15, 2008; ... ABSTRACT Single-molecule force-clamp spectroscopy is a valuable tool to analyze unfolding kinetics of proteins. Previous force-clamp spectroscopy experiments have demonstrated that the mechanical unfolding of ubiquitin deviates from the generally assumed Markovian behavior and involves ...