Recently added articles from Biophysical Journal:

The Role of DNA Twist in the Packaging of Viral Genomes

Mar 01, 2008; Rollins, Geoffrey C; Petrov, Anton S; Harvey, Stephen C ... ABSTRACT We performed molecular dynamics simulations of the genome packaging of bacteriophage P4 using two coarse-grained models of DNA. The first model, 1DNA6 (one pseudo-atom per six DNA basepairs), represents DNA as a string of beads, for which DNA torsions are undefined. The second ...

Interleaflet Coupling Mechanisms in Bilayers of Lipids and Cholesterol

Mar 01, 2008; Collins, Marcus D ... ABSTRACT Whereas it appears to be generally believed that the leaflets of a phospholipid/cholesterol bilayer interact with each other in some way, the exact mechanism remains undetermined. Various suggestions have been invoked, including chain interdigitation and rapid translocation of ...

Translational Diffusion in Lipid Membranes beyond the Saffman-Delbrück Approximation

Mar 01, 2008; Petrov, Eugene P; Schwille, Petra ... ABSTRACT The Saffman-Delbrück approximation is commonly used in biophysics to relate the membrane inclusion size to its translational diffusion coefficient and membrane viscosity. However, this approximation has a restricted validity range, and its application to determination of ...

How Polymers Translocate Through Pores: Memory is Important

Mar 01, 2008; Kolomeisky, Anatoly B ... Many biological processes, such as DNA and RNA transport across nuclear pores, injections of viral DNA, gene swapping, and protein transport across cellular membranes, involve the motion of polymer molecules across narrow channels (1). Translocation through nanopores is also one of the most ...

Normal-Mode Flexible Fitting of High-Resolution Structure of Biological Molecules toward One-Dimensional Low-Resolution Data

Mar 01, 2008; Gorba, Christian; Miyashita, Osamu; Tama, Florence ... ABSTRACT We present a method for reconstructing a 3D structure from a pair distribution function by flexibly fitting known x-ray structures toward a conformation that agrees with the low-resolution data. This method uses a linear combination of low-frequency normal modes from ...

Fitting Low-Resolution Cryo-EM Maps of Proteins Using Constrained Geometric Simulations

Mar 01, 2008; Jolley, Craig C; Wells, Stephen A; Fromme, Petra; Thorpe, M F ... ABSTRACT Recent experimental advances in producing density maps from cryo-electron microscopy (cryo-EM) have challenged theorists to develop improved techniques to provide structural models that are consistent with the data and that preserve all the local stereochemistry associated with ...

Predicting the Folding Pathway of Engrailed Homeodomain with a Probabilistic Roadmap Enhanced Reaction-Path Algorithm

Mar 01, 2008; Li, Da-wei; Yang, Haijun; Han, Li; Huo, Shuanghong ... ABSTRACT To predict a protein-folding pathway, we present an alternative to the time-consuming dynamic simulation of atomistic models. We replace the actual dynamic simulation with variational optimization of a reaction path connecting known initial and final protein conformations in ...

Substrate Binding and Formation of an Occluded State in the Leucine Transporter

Mar 01, 2008; Celik, Leyla; Schiøtt, Birgit; Tajkhorshid, Emad ... ABSTRACT Translocation through the extracellular vestibule and binding of leucine in the leucine transporter (LeuT) have been studied with molecular dynamics simulations. More than 0.1 µs of all-atom molecular dynamics simulations have been performed on different combinations of LeuT, ...

In Silico Protein Fragmentation Reveals the Importance of Critical Nuclei on Domain Reassembly

Mar 01, 2008; Martínez, Lydia M Contreras; Quintana, Ernesto E Borrero; Escobedo, Fernando A; DeLisa, Matthew P ... ABSTRACT Protein complementation assays (PCAs) based on split protein fragments have become powerful tools that facilitate the study and engineering of intracellular protein-protein interactions. These assays are based on the observation that a given protein can be split into two ...

Microscopic Simulation of Membrane Molecule Diffusion on Corralled Membrane Surfaces

Mar 01, 2008; Niehaus, Anne Marie S; Vlachos, Dionisios G; Edwards, Jeremy S; Plechac, Petr; Tribe, Roger ... ABSTRACT The current understanding of how receptors diffuse and cluster in the plasma membrane is limited. Data from single-particle tracking and laser tweezer experiments have suggested that membrane molecule diffusion is affected by the presence of barriers dividing the membrane into ...

Role of Exchange and Dipolar Interactions in the Radical Pair Model of the Avian Magnetic Compass

Mar 01, 2008; Efimova, Olga; Hore, P J ... ABSTRACT It is not yet understood how migratory birds sense the Earth's magnetic field as a source of compass information. One suggestion is that the magnetoreceptor involves a photochemical reaction whose product yields are sensitive to external magnetic fields. Specifically, a ...

Interaction between the Cytoplasmic and Transmembrane Domains of the Mechanosensitive Channel MscS

Mar 01, 2008; Nomura, Takeshi; Sokabe, Masahiro; Yoshimura, Kenjiro ... ABSTRACT The bacterial mechanosensitive channel MscS protects the bacteria from rupture on hypoosmotic shock. MscS is composed of a transmembrane domain with an ion permeation pore and a large cytoplasmic vestibule that undergoes significant conformational changes on gating. In this ...

Spatial Distribution of Maxi-Anion Channel on Cardiomyocytes Detected by Smart-Patch Technique

Mar 01, 2008; Dutta, Amal K; Korchev, Yuri E; Shevchuk, Andrew I; Hayashi, Seiji; Okada, Yasunobu; Sabirov, Ravshan Z ... ABSTRACT Spatial distribution of maxi-anion channels in rat cardiomyocytes were studied by applying the recently developed patch clamp technique under scanning ion conductance microscopy, called the "smart-patch" technique. In primary-cultured neonatal cells, the channel was found to be ...

Effect of Metabolic Inhibition on Couplon Behavior in Rabbit Ventricular Myocytes

Mar 01, 2008; Chantawansri, Chana; Huynh, Nhi; Yamanaka, Jun; Garfinkel, Alan; Lamp, Scott T; Inoue, Masashi; Bridge, John H B; Goldhaber, Joshua I ... ABSTRACT We investigated the effect of combined inhibition of oxidative and glycolytic metabolism on L-type Ca^sup 2+^ channels (LCCs) and Ca^sup 2+^ spikes in isolated patch-clamped rabbit ventricular myocytes. Metabolic inhibition (MI) reduced LCC open probability, increased null ...

Calculation of Free Energy Barriers to the Fusion of Small Vesicles

Mar 01, 2008; Lee, J Y; Schick, M ... ABSTRACT The fusion of small vesicles, either with a planar bilayer or with one another, is studied using a microscopic model in which the bilayers are composed of hexagonal- and lamellar-forming amphiphiles. The free energy of the system is obtained within the self-consistent field ...

Binding of Anionic Lipids to at Least Three Nonannular Sites on the Potassium Channel KcsA is Required for Channel Opening

Mar 01, 2008; Marius, Phedra; Zagnoni, Michele; Sandison, Mairi E; East, J Malcolm; Morgan, Hywel; Lee, Anthony G ... ABSTRACT In addition to the annular or boundary lipids that surround the transmembrane surface of the potassium channel KcsA from Streptomyces lividans, x-ray crystallographic studies have detected one anionic lipid molecule bound at each protein-protein interface in the homotetrameric ...

The Structure of Isolated Cardiac Myosin Thick Filaments from Cardiac Myosin Binding Protein-C Knockout Mice

Mar 01, 2008; Kensler, Robert W; Harris, Samantha P ... ABSTRACT Mutations in the thick filament associated protein cardiac myosin binding protein-C (cMyBP-C) are a major cause of familial hypertrophic cardiomyopathy. Although cMyBP-C is thought to play both a structural and a regulatory role in the contraction of cardiac muscle, detailed ...

Surface Rheology and Adsorption Kinetics Reveal the Relative Amphiphilicity, Interfacial Activity, and Stability of Human Exchangeable Apolipoproteins

Mar 01, 2008; Bolanos-Garcia, Victor Martin; Renault, Anne; Beaufils, Sylvie ... ABSTRACT Exchangeable apolipoproteins are located in the surface of lipoprotein particles and regulate lipid metabolism through direct protein-protein and protein-lipid interactions. These proteins are characterized by the presence of tandem repeats of amphiphatic α-helix segments ...

A Quantitative Model for the All-or-None Permeabilization of Phospholipid Vesicles by the Antimicrobial Peptide Cecropin A

Mar 01, 2008; Gregory, Sonia M; Cavenaugh, Allison; Journigan, Velvet; Pokorny, Antje; Almeida, Paulo F F ... ABSTRACT The mechanism of the all-or-none release of the contents of phospholipid vesicles induced by the antimicrobial peptide cecropin A was investigated. A detailed experimental study of the kinetics of dye release showed that the rate of release increases with the ratio of peptide ...

Defects in Vesicle Core Induced by Escherichia coli Dihydroorotate Dehydrogenase

Mar 01, 2008; Couto, Sheila G; Nonato, M Cristina; Costa-Filho, Antonio J ... ABSTRACT Dihydroorotate dehydrogenase (DHODH) catalyzes the oxidation of dihydroorotate to orotate during the fourth step of the de novo pyrimidine synthesis pathway. In rapidly proliferating mammalian cells, pyrimidine salvage pathway is insufficient to overcome deficiencies in that ...