NEW AND NOTABLE:

Joachim Heberle

A Local Area Network of Protonated Water Molecules
Biophys. J. 2004 87: 2105-2106; Published ahead of print on August 17, 2004 as doi:10.1529/biophysj.104.050054. [Full Text] [PDF]  

BIOPHYSICAL THEORY AND MODELING:

Steve O. Nielsen, Carlos F. Lopez, Ivaylo Ivanov, Preston B. Moore, John C. Shelley, and Michael L. Klein

Transmembrane Peptide-Induced Lipid Sorting and Mechanism of L-to-Inverted Phase Transition Using Coarse-Grain Molecular Dynamics
Biophys. J. 2004 87: 2107-2115. [Abstract] [Full Text] [PDF]  

Stewart R. Durell, Indira H. Shrivastava, and H. Robert Guy

Models of the Structure and Voltage-Gating Mechanism of the Shaker K⁺ Channel
Biophys. J. 2004 87: 2116-2130. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Dirk R. Albrecht, Robert L. Sah, and Sangeeta N. Bhatia

Geometric and Material Determinants of Patterning Efficiency by Dielectrophoresis
Biophys. J. 2004 87: 2131-2147. [Abstract] [Full Text] [PDF]  

Jianhua Xing, Hongyun Wang, Christoph von Ballmoos, Peter Dimroth, and George Oster

Torque Generation by the F_o motor of the Sodium ATPase
Biophys. J. 2004 87: 2148-2163. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Jin Wang

The Complex Kinetics of Protein Folding in Wide Temperature Ranges
Biophys. J. 2004 87: 2164-2171. [Abstract] [Full Text] [PDF]  

Nathan D. Price, Jan Schellenberger, and Bernhard O. Palsson

Uniform Sampling of Steady-State Flux Spaces: Means to Design Experiments and to Interpret Enzymopathies
Biophys. J. 2004 87: 2172-2186. [Abstract] [Full Text] [PDF]  

Jin Wang, Weimin Huang, Hongyang Lu, and Erkang Wang

Downhill Kinetics of Biomolecular Interface Binding: Globally Connected Scenario
Biophys. J. 2004 87: 2187-2194. [Abstract] [Full Text] [PDF]  

Xiao-jiang Feng, Sara Hooshangi, David Chen, Genyuan Li, Ron Weiss, and Herschel Rabitz

Optimizing Genetic Circuits by Global Sensitivity Analysis
Biophys. J. 2004 87: 2195-2202. [Abstract] [Full Text] [PDF]  

Martin Zacharias and Sebastian Springer

Conformational Flexibility of the MHC Class I ₁-₂ Domain in Peptide Bound and Free States: A Molecular Dynamics Simulation Study
Biophys. J. 2004 87: 2203-2214. [Abstract] [Full Text] [PDF]  

Daniel Coombs and Byron Goldstein

Effects of the Geometry of the Immunological Synapse on the Delivery of Effector Molecules
Biophys. J. 2004 87: 2215-2220. [Abstract] [Full Text] [PDF]  

Sonja Braun-Sand, Marek Strajbl, and Arieh Warshel

Studies of Proton Translocations in Biological Systems: Simulating Proton Transport in Carbonic Anhydrase by EVB-Based Models
Biophys. J. 2004 87: 2221-2239. [Abstract] [Full Text] [PDF]  

Bojan Zagrovic and Vijay S. Pande

How Does Averaging Affect Protein Structure Comparison on the Ensemble Level?
Biophys. J. 2004 87: 2240-2246. [Abstract] [Full Text] [PDF]  

Fan-Guo Meng, Yuan-Kai Hong, Hua-Wei He, Arkadii E. Lyubarev, Boris I. Kurganov, Yong-Bin Yan, and Hai-Meng Zhou

Osmophobic Effect of Glycerol on Irreversible Thermal Denaturation of Rabbit Creatine Kinase
Biophys. J. 2004 87: 2247-2254. [Abstract] [Full Text] [PDF]  

Indira H. Shrivastava, Stewart R. Durell, and H. Robert Guy

A Model of Voltage Gating Developed Using the KvAP Channel Crystal Structure
Biophys. J. 2004 87: 2255-2270. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Takashi Ashihara and Natalia A. Trayanova

Asymmetry in Membrane Responses to Electric Shocks: Insights from Bidomain Simulations
Biophys. J. 2004 87: 2271-2282. [Abstract] [Full Text] [PDF]  

S. A. Oprisan, A. A. Prinz, and C. C. Canavier

Phase Resetting and Phase Locking in Hybrid Circuits of One Model and One Biological Neuron
Biophys. J. 2004 87: 2283-2298. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Sergei Yu. Noskov, Wonpil Im, and Benoît Roux

Ion Permeation through the -Hemolysin Channel: Theoretical Studies Based on Brownian Dynamics and Poisson-Nernst-Plank Electrodiffusion Theory
Biophys. J. 2004 87: 2299-2309. [Abstract] [Full Text] [PDF]  

B. Urbanc, L. Cruz, F. Ding, D. Sammond, S. Khare, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan

Molecular Dynamics Simulation of Amyloid ß Dimer Formation
Biophys. J. 2004 87: 2310-2321. [Abstract] [Full Text] [PDF]  

L. Haider, P. Snabre, and M. Boynard

Rheology and Ultrasound Scattering from Aggregated Red Cell Suspensions in Shear Flow
Biophys. J. 2004 87: 2322-2334. [Abstract] [Full Text] [PDF]  

CHANNELS, RECEPTORS, AND ELECTRICAL SIGNALING:

William Welch, Shana Rheault, Duncan J. West, and Alan J. Williams

A Model of the Putative Pore Region of the Cardiac Ryanodine Receptor Channel
Biophys. J. 2004 87: 2335-2351. [Abstract] [Full Text] [PDF]  

Vahid Shahrezaei and Kerry R. Delaney

Consequences of Molecular-Level Ca²⁺ Channel and Synaptic Vesicle Colocalization for the Ca²⁺ Microdomain and Neurotransmitter Exocytosis: A Monte Carlo Study
Biophys. J. 2004 87: 2352-2364. [Abstract] [Full Text] [PDF]  

Werner Treptow, Bernard Maigret, Christophe Chipot, and Mounir Tarek

Coupled Motions between Pore and Voltage-Sensor Domains: A Model for Shaker B, a Voltage-Gated Potassium Channel
Biophys. J. 2004 87: 2365-2379. [Abstract] [Full Text] [PDF]  

Henry H. Jerng, Yan Qian, and Paul J. Pfaffinger

Modulation of Kv4.2 Channel Expression and Gating by Dipeptidyl Peptidase 10 (DPP10)
Biophys. J. 2004 87: 2380-2396. [Abstract] [Full Text] [PDF]  

Jun-Jie Tong, Xiaoqin Liu, Lixian Dong, and Lisa Ebihara

Exchange of Gating Properties Between Rat Cx46 and Chicken Cx45.6
Biophys. J. 2004 87: 2397-2406. [Abstract] [Full Text] [PDF]  

T. W. Claydon, S. Y. Makary, K. M. Dibb, and M. R. Boyett

K⁺ Activation of Kir3.1/Kir3.4 and Kv1.4 K⁺ Channels Is Regulated by Extracellular Charges
Biophys. J. 2004 87: 2407-2418. [Abstract] [Full Text] [PDF]  

MEMBRANES:

H. Raghuraman and Amitabha Chattopadhyay

Interaction of Melittin with Membrane Cholesterol: A Fluorescence Approach
Biophys. J. 2004 87: 2419-2432. [Abstract] [Full Text] [PDF]  

Jakob Wohlert and Olle Edholm

The Range and Shielding of Dipole-Dipole Interactions in Phospholipid Bilayers
Biophys. J. 2004 87: 2433-2445. [Abstract] [Full Text] [PDF]  

Ioana Pera, Rüdiger Stark, Michael Kappl, Hans-Jürgen Butt, and Fabio Benfenati

Using the Atomic Force Microscope to Study the Interaction between Two Solid Supported Lipid Bilayers and the Influence of Synapsin I
Biophys. J. 2004 87: 2446-2455. [Abstract] [Full Text] [PDF]  

Alexandre Arnold, Michaël Paris, and Michèle Auger

Anomalous Diffusion in a Gel-Fluid Lipid Environment: A Combined Solid-State NMR and Obstructed Random-Walk Perspective
Biophys. J. 2004 87: 2456-2469. [Abstract] [Full Text] [PDF]  

Feng Liu, Ruthven N. A. H. Lewis, Robert S. Hodges, and Ronald N. McElhaney

Effect of Variations in the Structure of a Polyleucine-Based -Helical Transmembrane Peptide on Its Interaction with Phosphatidylethanolamine Bilayers
Biophys. J. 2004 87: 2470-2482. [Abstract] [Full Text] [PDF]  

Yun-Wei Chiang, Yuhei Shimoyama, Gerald W. Feigenson, and Jack H. Freed

Dynamic Molecular Structure of DPPC-DLPC-Cholesterol Ternary Lipid System by Spin-Label Electron Spin Resonance
Biophys. J. 2004 87: 2483-2496. [Abstract] [Full Text] [PDF]  

Kaoru Nomura, Gerardo Corzo, Terumi Nakajima, and Takashi Iwashita

Orientation and Pore-Forming Mechanism of a Scorpion Pore-Forming Peptide Bound to Magnetically Oriented Lipid Bilayers
Biophys. J. 2004 87: 2497-2507; Published ahead of print on August 6, 2004 as doi:10.1529/biophysj.104.043513. [Abstract] [Full Text] [PDF]  

Yonathan Kozlovsky, Avishay Efrat, David A. Siegel, and Michael M. Kozlov

Stalk Phase Formation: Effects of Dehydration and Saddle Splay Modulus
Biophys. J. 2004 87: 2508-2521. [Abstract] [Full Text] [PDF]  

O. Enders, A. Ngezahayo, M. Wiechmann, F. Leisten, and H.-A. Kolb

Structural Calorimetry of Main Transition of Supported DMPC Bilayers by Temperature-Controlled AFM
Biophys. J. 2004 87: 2522-2531. [Abstract] [Full Text] [PDF]  

MUSCLE AND CONTRACTILITY:

Christina Karatzaferi, Marc K. Chinn, and Roger Cooke

The Force Exerted by a Muscle Cross-Bridge Depends Directly on the Strength of the Actomyosin Bond
Biophys. J. 2004 87: 2532-2544. [Abstract] [Full Text] [PDF]  

NUCLEIC ACIDS:

Congju Chen and Irina M. Russu

Sequence-Dependence of the Energetics of Opening of AT Basepairs in DNA
Biophys. J. 2004 87: 2545-2551. [Abstract] [Full Text] [PDF]  

Renaud Fulconis, Aurélien Bancaud, Jean-Francois Allemand, Vincent Croquette, Marie Dutreix, and Jean-Louis Viovy

Twisting and Untwisting a Single DNA Molecule Covered by RecA Protein
Biophys. J. 2004 87: 2552-2563. [Abstract] [Full Text] [PDF]  

Nina Y. Sidorova and Donald C. Rau

Differences between EcoRI Nonspecific and "Star" Sequence Complexes Revealed by Osmotic Stress
Biophys. J. 2004 87: 2564-2576. [Abstract] [Full Text] [PDF]  

PHOTOBIOPHYSICS:

Petra A. W. van den Berg, Arie van Hoek, and Antonie J. W. G. Visser

Evidence for a Novel Mechanism of Time-Resolved Flavin Fluorescence Depolarization in Glutathione Reductase
Biophys. J. 2004 87: 2577-2586. [Abstract] [Full Text] [PDF]  

Keiichi Inoue, Jun Sasaki, Masayo Morisaki, Fumio Tokunaga, and Masahide Terazima

Time-Resolved Detection of Sensory Rhodopsin II-Transducer Interaction
Biophys. J. 2004 87: 2587-2597. [Abstract] [Full Text] [PDF]  

Davey Loos, Mircea Cotlet, Frans De Schryver, Satoshi Habuchi, and Johan Hofkens

Single-Molecule Spectroscopy Selectively Probes Donor and Acceptor Chromophores in the Phycobiliprotein Allophycocyanin
Biophys. J. 2004 87: 2598-2608. [Abstract] [Full Text] [PDF]  

Melinda Noronha, João C. Lima, Margarida Bastos, Helena Santos, and António L. Maçanita

Unfolding of Ubiquitin Studied by Picosecond Time-Resolved Fluorescence of the Tyrosine Residue
Biophys. J. 2004 87: 2609-2620. [Abstract] [Full Text] [PDF]  

PROTEINS:

Angela R. Feeling-Taylor, S.-T. Yau, Dimiter N. Petsev, Ronald L. Nagel, Rhoda Elison Hirsch, and Peter G. Vekilov

Crystallization Mechanisms of Hemoglobin C in the R State
Biophys. J. 2004 87: 2621-2629. [Abstract] [Full Text] [PDF]  

Reinat Nevo, Vlad Brumfeld, Michael Elbaum, Peter Hinterdorfer, and Ziv Reich

Direct Discrimination between Models of Protein Activation by Single-Molecule Force Measurements
Biophys. J. 2004 87: 2630-2634. [Abstract] [Full Text] [PDF]  

Tatiana Krouglova, Jo Vercammen, and Yves Engelborghs

Correct Diffusion Coefficients of Proteins in Fluorescence Correlation Spectroscopy. Application to Tubulin Oligomers Induced by Mg²⁺ and Paclitaxel
Biophys. J. 2004 87: 2635-2646. [Abstract] [Full Text] [PDF]  

Yang Zhang and Jeffrey Skolnick

Tertiary Structure Predictions on a Comprehensive Benchmark of Medium to Large Size Proteins
Biophys. J. 2004 87: 2647-2655. [Abstract] [Full Text] [PDF]  

Rajesh Kumar, N. Prakash Prabhu, M. Yadaiah, and Abani K. Bhuyan

Protein Stiffening and Entropic Stabilization in the Subdenaturing Limit of Guanidine Hydrochloride
Biophys. J. 2004 87: 2656-2662. [Abstract] [Full Text] [PDF]  

Shinpei Nishida, Tomokazu Nada, and Masahide Terazima

Kinetics of Intermolecular Interaction during Protein Folding of Reduced Cytochrome c
Biophys. J. 2004 87: 2663-2675. [Abstract] [Full Text] [PDF]  

Florian Garczarek, Jianping Wang, Mostafa A. El-Sayed, and Klaus Gerwert

The Assignment of the Different Infrared Continuum Absorbance Changes Observed in the 3000–1800-cm^–1 Region during the Bacteriorhodopsin Photocycle
Biophys. J. 2004 87: 2676-2682; Published ahead of print on August 6, 2004 as doi:10.1529/biophysj.104.046433. [Abstract] [Full Text] [PDF]  

F. Kühner, L. T. Costa, P. M. Bisch, S. Thalhammer, W. M. Heckl, and H. E. Gaub

LexA-DNA Bond Strength by Single Molecule Force Spectroscopy
Biophys. J. 2004 87: 2683-2690. [Abstract] [Full Text] [PDF]  

Daniella Ishimaru, Luis M. T. R. Lima, Lenize F. Maia, Priscila M. Lopez, Ana P. Ano Bom, Ana P. Valente, and Jerson L. Silva

Reversible Aggregation Plays a Crucial Role on the Folding Landscape of p53 Core Domain
Biophys. J. 2004 87: 2691-2700; Published ahead of print on August 6, 2004 as doi:10.1529/biophysj.104.044685. [Abstract] [Full Text] [PDF]  

Mark J. Waner, Irina Navrotskaya, Amanda Bain, Edward Davis Oldham, and David P. Mascotti

Thermal and Sodium Dodecylsulfate Induced Transitions of Streptavidin
Biophys. J. 2004 87: 2701-2713; Published ahead of print on August 6, 2004 as doi:10.1529/biophysj.104.047266. [Abstract] [Full Text] [PDF] [Supplemental Material]  

SUPRAMOLECULAR ASSEMBLIES:

Chang-Shung Tung and Kevin Y. Sanbonmatsu

Atomic Model of the Thermus thermophilus 70S Ribosome Developed in Silico
Biophys. J. 2004 87: 2714-2722. [Abstract] [Full Text] [PDF]  

Marcel E. Janson and Marileen Dogterom

A Bending Mode Analysis for Growing Microtubules: Evidence for a Velocity-Dependent Rigidity
Biophys. J. 2004 87: 2723-2736. [Abstract] [Full Text] [PDF]  

Marina Casselyn, Annette Tardieu, Hervé Delacroix, and Stéphanie Finet

Birth and Growth Kinetics of Brome Mosaïc Virus Microcrystals
Biophys. J. 2004 87: 2737-2748. [Abstract] [Full Text] [PDF]  

SPECTROSCOPY, IMAGING, OTHER TECHNIQUES:

Hazen P. Babcock, Chen Chen, and Xiaowei Zhuang

Using Single-Particle Tracking to Study Nuclear Trafficking of Viral Genes
Biophys. J. 2004 87: 2749-2758. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Gonzalo Cosa, Elizabeth J. Harbron, Yining Zeng, Hsiao-Wei Liu, Donald B. O'Connor, Chie Eta-Hosokawa, Karin Musier-Forsyth, and Paul F. Barbara

Secondary Structure and Secondary Structure Dynamics of DNA Hairpins Complexed with HIV-1 NC Protein
Biophys. J. 2004 87: 2759-2767. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Brett Shoelson, Emilios K. Dimitriadis, Hongxue Cai, Bechara Kachar, and Richard S. Chadwick

Evidence and Implications of Inhomogeneity in Tectorial Membrane Elasticity
Biophys. J. 2004 87: 2768-2777. [Abstract] [Full Text] [PDF]  

Aikaterini Zoumi, Xiao Lu, Ghassan S. Kassab, and Bruce J. Tromberg

Imaging Coronary Artery Microstructure Using Second-Harmonic and Two-Photon Fluorescence Microscopy
Biophys. J. 2004 87: 2778-2786. [Abstract] [Full Text] [PDF]  

Alexa L. Mattheyses, Adam D. Hoppe, and Daniel Axelrod

Polarized Fluorescence Resonance Energy Transfer Microscopy
Biophys. J. 2004 87: 2787-2797. [Abstract] [Full Text] [PDF]  

Burak Okumus, Timothy J. Wilson, David M. J. Lilley, and Taekjip Ha

Vesicle Encapsulation Studies Reveal that Single Molecule Ribozyme Heterogeneities Are Intrinsic
Biophys. J. 2004 87: 2798-2806. [Abstract] [Full Text] [PDF]  

S. Pelet, M. J. R. Previte, L. H. Laiho, and P. T. C. So

A Fast Global Fitting Algorithm for Fluorescence Lifetime Imaging Microscopy Based on Image Segmentation
Biophys. J. 2004 87: 2807-2817. [Abstract] [Full Text] [PDF]  

CELL BIOPHYSICS:

Padmavathy Rajagopalan, William A. Marganski, Xin Q. Brown, and Joyce Y. Wong

Direct Comparison of the Spread Area, Contractility, and Migration of balb/c 3T3 Fibroblasts Adhered to Fibronectin- and RGD-Modified Substrata
Biophys. J. 2004 87: 2818-2827. [Abstract] [Full Text] [PDF]  

C. Ross Ethier, A. Thomas Read, and Darren Chan

Biomechanics of Schlemm's Canal Endothelial Cells: Influence on F-Actin Architecture
Biophys. J. 2004 87: 2828-2837. [Abstract] [Full Text] [PDF]  

Richard B. Dickinson, Luzelena Caro, and Daniel L. Purich

Force Generation by Cytoskeletal Filament End-Tracking Proteins
Biophys. J. 2004 87: 2838-2854. [Abstract] [Full Text] [PDF]  

Sébastien Pierrat, Françoise Brochard-Wyart, and Pierre Nassoy

Enforced Detachment of Red Blood Cells Adhering to Surfaces: Statics and Dynamics
Biophys. J. 2004 87: 2855-2869. [Abstract] [Full Text] [PDF]  

Guillaume T. Charras, Beatrice A. Williams, Stephen M. Sims, and Mike A. Horton

Estimating the Sensitivity of Mechanosensitive Ion Channels to Membrane Strain and Tension
Biophys. J. 2004 87: 2870-2884. [Abstract] [Full Text] [PDF]  

BIOENERGETICS:

Alice Haddy, K. V. Lakshmi, Gary W. Brudvig, and Harry A. Frank

Q-Band EPR of the S₂ State of Photosystem II Confirms an S = 5/2 Origin of the X-Band g = 4.1 Signal
Biophys. J. 2004 87: 2885-2896. [Abstract] [Full Text] [PDF]  

OTHER:

Isabelle Morfin, Ferenc Horkay, Peter J. Basser, Françoise Bley, Anne-Marie Hecht, Cyrille Rochas, and Erik Geissler

Adsorption of Divalent Cations on DNA
Biophys. J. 2004 87: 2897-2904. [Abstract] [Full Text] [PDF]  

Jiunn B. Heng, Chuen Ho, Taekyung Kim, Rolf Timp, Aleksij Aksimentiev, Yelena V. Grinkova, Stephen Sligar, Klaus Schulten, and Gregory Timp

Sizing DNA Using a Nanometer-Diameter Pore
Biophys. J. 2004 87: 2905-2911; Published ahead of print on August 23, 2004 as doi:10.1529/biophysj.104.041814. [Abstract] [Full Text] [PDF] [Supplemental]  

CORRECTIONS:

Correction
Biophys. J. 2004 87: 2912(4) [Full Text] [PDF]  

Correction
Biophys. J. 2004 87: 2913(4) [Full Text] [PDF]  

Correction
Biophys. J. 2004 87: 2914(4) [Full Text] [PDF]  

Correction
Biophys. J. 2004 87: 2915(4) [Full Text] [PDF]  

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