BIOPHYSICAL THEORY AND MODELING:

Kay-Eberhard Gottschalk, Misha Soskine, Shimon Schuldiner, and Horst Kessler

A Structural Model of EmrE, a Multi-Drug Transporter from Escherichia coli
Biophys. J. 2004 86: 3335-3348. [Abstract] [Full Text] [PDF]  

Chi Zhang, Song Liu, Hongyi Zhou, and Yaoqi Zhou

The Dependence of All-Atom Statistical Potentials on Structural Training Database
Biophys. J. 2004 86: 3349-3358. [Abstract] [Full Text] [PDF]  

Thomas J. English and Daniel A. Hammer

Brownian Adhesive Dynamics (BRAD) for Simulating the Receptor-Mediated Binding of Viruses
Biophys. J. 2004 86: 3359-3372. [Abstract] [Full Text] [PDF]  

Yariv Kafri, David K. Lubensky, and David R. Nelson

Dynamics of Molecular Motors and Polymer Translocation with Sequence Heterogeneity
Biophys. J. 2004 86: 3373-3391. [Abstract] [Full Text] [PDF]  

Linjing Yang, William A. Beard, Samuel H. Wilson, Suse Broyde, and Tamar Schlick

Highly Organized but Pliant Active Site of DNA Polymerase ß: Compensatory Mechanisms in Mutant Enzymes Revealed by Dynamics Simulations and Energy Analyses
Biophys. J. 2004 86: 3392-3408. [Abstract] [Full Text] [PDF]  

Kevin McHale, Andrew J. Berglund, and Hideo Mabuchi

Bayesian Estimation for Species Identification in Single-Molecule Fluorescence Microscopy
Biophys. J. 2004 86: 3409-3422. [Abstract] [Full Text] [PDF]  

Andrea Cavalli, Andrea E. Prota, Thilo Stehle, Terence S. Dermody, Maurizio Recanatini, Gerd Folkers, and Leonardo Scapozza

A Molecular Dynamics Study of Reovirus Attachment Protein 1 Reveals Conformational Changes in 1 Structure
Biophys. J. 2004 86: 3423-3431. [Abstract] [Full Text] [PDF]  

Ling Yang, W. Robb MacLellan, Zhangang Han, James N. Weiss, and Zhilin Qu

Multisite Phosphorylation and Network Dynamics of Cyclin-Dependent Kinase Signaling in the Eukaryotic Cell Cycle
Biophys. J. 2004 86: 3432-3443. [Abstract] [Full Text] [PDF]  

Markus Zweckstetter, Gerhard Hummer, and Ad Bax

Prediction of Charge-Induced Molecular Alignment of Biomolecules Dissolved in Dilute Liquid-Crystalline Phases
Biophys. J. 2004 86: 3444-3460. [Abstract] [Full Text] [PDF]  

Andrey A. Gurtovenko, Michael Patra, Mikko Karttunen, and Ilpo Vattulainen

Cationic DMPC/DMTAP Lipid Bilayers: Molecular Dynamics Study
Biophys. J. 2004 86: 3461-3472. [Abstract] [Full Text] [PDF]  

Brian L. Sprague, Robert L. Pego, Diana A. Stavreva, and James G. McNally

Analysis of Binding Reactions by Fluorescence Recovery after Photobleaching
Biophys. J. 2004 86: 3473-3495. [Abstract] [Full Text] [PDF]  

Justin Gullingsrud and Klaus Schulten

Lipid Bilayer Pressure Profiles and Mechanosensitive Channel Gating
Biophys. J. 2004 86: 3496-3509. [Abstract] [Full Text] [PDF]  

David Colquhoun, Kathryn A. Dowsland, Marco Beato, and Andrew J. R. Plested

How to Impose Microscopic Reversibility in Complex Reaction Mechanisms
Biophys. J. 2004 86: 3510-3518. [Abstract] [Full Text] [PDF]  

Niranjan Deo and Karl Grosh

Two-State Model for Outer Hair Cell Stiffness and Motility
Biophys. J. 2004 86: 3519-3528. [Abstract] [Full Text] [PDF]  

Vladimir L. Dorman and Peter C. Jordan

Ionic Permeation Free Energy in Gramicidin: A Semimicroscopic Perspective
Biophys. J. 2004 86: 3529-3541. [Abstract] [Full Text] [PDF]  

Kunqian Yu, Wei Fu, Hong Liu, Xiaomin Luo, Kai Xian Chen, Jianping Ding, Jianhua Shen, and Hualiang Jiang

Computational Simulations of Interactions of Scorpion Toxins with the Voltage-Gated Potassium Ion Channel
Biophys. J. 2004 86: 3542-3555. [Abstract] [Full Text] [PDF]  

Morten Ø. Jensen, Ole G. Mouritsen, and Günther H. Peters

Simulations of a Membrane-Anchored Peptide: Structure, Dynamics, and Influence on Bilayer Properties
Biophys. J. 2004 86: 3556-3575. [Abstract] [Full Text] [PDF] [Supplemental Material]  

O. Flomenbom and J. Klafter

Translocation of a Single-Stranded DNA Through a Conformationally Changing Nanopore
Biophys. J. 2004 86: 3576-3584. [Abstract] [Full Text] [PDF]  

David L. Mobley, Daniel L. Cox, Rajiv R. P. Singh, Michael W. Maddox, and Marjorie L. Longo

Modeling Amyloid ß-Peptide Insertion into Lipid Bilayers
Biophys. J. 2004 86: 3585-3597. [Abstract] [Full Text] [PDF]  

Edelmira Valero, Ramón Varón, and Francisco García-Carmona

Kinetic Analysis of a Model for Double Substrate Cycling: Highly Amplified ADP (and/or ATP) Quantification
Biophys. J. 2004 86: 3598-3606. [Abstract] [Full Text] [PDF]  

Assaf Zemel, Avinoam Ben-Shaul, and Sylvio May

Membrane Perturbation Induced by Interfacially Adsorbed Peptides
Biophys. J. 2004 86: 3607-3619. [Abstract] [Full Text] [PDF]  

CHANNELS, RECEPTORS, AND TRANSPORTERS:

Chunbo Yuan, Robert J. O'Connell, Paula L. Feinberg-Zadek, Linda J. Johnston, and Steven N. Treistman

Bilayer Thickness Modulates the Conductance of the BK Channel in Model Membranes
Biophys. J. 2004 86: 3620-3633. [Abstract] [Full Text] [PDF]  

Sonal Srikanth, Zhengnan Wang, Huiping Tu, Shalima Nair, M. K. Mathew, Gaiti Hasan, and Ilya Bezprozvanny

Functional Properties of the Drosophila melanogaster Inositol 1,4,5-Trisphosphate Receptor Mutants
Biophys. J. 2004 86: 3634-3646. [Abstract] [Full Text] [PDF]  

Karim Shariff, Sandip Ghosal, and Andreas Matouschek

The Force Exerted by the Membrane Potential during Protein Import into the Mitochondrial Matrix
Biophys. J. 2004 86: 3647-3652. [Abstract] [Full Text] [PDF]  

Petri Ala-Laurila, Kristian Donner, and Ari Koskelainen

Thermal Activation and Photoactivation of Visual Pigments
Biophys. J. 2004 86: 3653-3662. [Abstract] [Full Text] [PDF]  

Lise Heginbotham and Esin Kutluay

Revisiting Voltage-Dependent Relief of Block in Ion Channels: A Mechanism Independent of Punchthrough
Biophys. J. 2004 86: 3663-3670. [Abstract] [Full Text] [PDF]  

Francesco Tadini Buoninsegni, Gianluca Bartolommei, Maria Rosa Moncelli, Giuseppe Inesi, and Rolando Guidelli

Time-Resolved Charge Translocation by Sarcoplasmic Reticulum Ca-ATPase Measured on a Solid Supported Membrane
Biophys. J. 2004 86: 3671-3686. [Abstract] [Full Text] [PDF]  

Z. O. Shenkarev, T. A. Balashova, Z. A. Yakimenko, T. V. Ovchinnikova, and A. S. Arseniev

Peptaibol Zervamicin IIB Structure and Dynamics Refinement from Transhydrogen Bond J Couplings
Biophys. J. 2004 86: 3687-3699. [Abstract] [Full Text] [PDF]  

MEMBRANES:

C. E. Miller, J. Majewski, R. Faller, S. Satija, and T. L. Kuhl

Cholera Toxin Assault on Lipid Monolayers Containing Ganglioside GM₁
Biophys. J. 2004 86: 3700-3708. [Abstract] [Full Text] [PDF]  

Erik Strandberg, Suat Özdirekcan, Dirk T. S. Rijkers, Patrick C. A. van der Wel, Roger E. Koeppe, II, Rob M. J. Liskamp, and J. Antoinette Killian

Tilt Angles of Transmembrane Model Peptides in Oriented and Non-Oriented Lipid Bilayers as Determined by ²H Solid-State NMR
Biophys. J. 2004 86: 3709-3721. [Abstract] [Full Text] [PDF]  

K. A. Riske, L. Q. Amaral, H.-G. Döbereiner, and M. T. Lamy

Mesoscopic Structure in the Chain-Melting Regime of Anionic Phospholipid Vesicles: DMPG
Biophys. J. 2004 86: 3722-3733. [Abstract] [Full Text] [PDF]  

Vincent Schram and Stephen B. Hall

SP-B and SP-C Alter Diffusion in Bilayers of Pulmonary Surfactant
Biophys. J. 2004 86: 3734-3743. [Abstract] [Full Text] [PDF]  

Peter M. Kasson and Vijay S. Pande

Molecular Dynamics Simulation of Lipid Reorientation at Bilayer Edges
Biophys. J. 2004 86: 3744-3749. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Andreas Kerth, Andreas Erbe, Margitta Dathe, and Alfred Blume

Infrared Reflection Absorption Spectroscopy of Amphipathic Model Peptides at the Air/Water Interface
Biophys. J. 2004 86: 3750-3758. [Abstract] [Full Text] [PDF]  

Jihong Tong and Thomas J. McIntosh

Structure of Supported Bilayers Composed of Lipopolysaccharides and Bacterial Phospholipids: Raft Formation and Implications for Bacterial Resistance
Biophys. J. 2004 86: 3759-3771. [Abstract] [Full Text] [PDF]  

Jonathan N. Sachs, Hirsh Nanda, Horia I. Petrache, and Thomas B. Woolf

Changes in Phosphatidylcholine Headgroup Tilt and Water Order Induced by Monovalent Salts: Molecular Dynamics Simulations
Biophys. J. 2004 86: 3772-3782. [Abstract] [Full Text] [PDF]  

Z. V. Leonenko, E. Finot, H. Ma, T. E. S. Dahms, and D. T. Cramb

Investigation of Temperature-Induced Phase Transitions in DOPC and DPPC Phospholipid Bilayers Using Temperature-Controlled Scanning Force Microscopy
Biophys. J. 2004 86: 3783-3793. [Abstract] [Full Text] [PDF]  

MUSCLE AND CONTRACTILITY:

J. David Lawson, Edward Pate, Ivan Rayment, and Ralph G. Yount

Molecular Dynamics Analysis of Structural Factors Influencing Back Door P_i Release in Myosin
Biophys. J. 2004 86: 3794-3803. [Abstract] [Full Text] [PDF]  

M. Yusuf Ali, Kazuaki Homma, Atsuko Hikikoshi Iwane, Kengo Adachi, Hiroyasu Itoh, Kazuhiko Kinosita, Jr., Toshio Yanagida, and Mitsuo Ikebe

Unconstrained Steps of Myosin VI Appear Longest among Known Molecular Motors
Biophys. J. 2004 86: 3804-3810. [Abstract] [Full Text] [PDF] [Supplemental Material]  

NUCLEIC ACIDS:

Nicola H. Green, Philip M. Williams, Omar Wahab, Martyn C. Davies, Clive J. Roberts, Saul J. B. Tendler, and Stephanie Allen

Single-Molecule Investigations of RNA Dissociation
Biophys. J. 2004 86: 3811-3821. [Abstract] [Full Text] [PDF]  

M. Bastos, V. Castro, G. Mrevlishvili, and J. Teixeira

Hydration of ds-DNA and ss-DNA by Neutron Quasielastic Scattering
Biophys. J. 2004 86: 3822-3827. [Abstract] [Full Text] [PDF]  

PHOTOBIOPHYSICS:

Chia-Pin Pan and Mary D. Barkley

Conformational Effects on Tryptophan Fluorescence in Cyclic Hexapeptides
Biophys. J. 2004 86: 3828-3835. [Abstract] [Full Text] [PDF] [Supplemental Material]  

PROTEINS:

Marcus T. Cicerone and Christopher L. Soles

Fast Dynamics and Stabilization of Proteins: Binary Glasses of Trehalose and Glycerol
Biophys. J. 2004 86: 3836-3845. [Abstract] [Full Text] [PDF]  

Sibsankar Kundu and Robert L. Jernigan

Molecular Mechanism of Domain Swapping in Proteins: An Analysis of Slower Motions
Biophys. J. 2004 86: 3846-3854. [Abstract] [Full Text] [PDF]  

Cecilia Bossa, Massimiliano Anselmi, Danilo Roccatano, Andrea Amadei, Beatrice Vallone, Maurizio Brunori, and Alfredo Di Nola

Extended Molecular Dynamics Simulation of the Carbon Monoxide Migration in Sperm Whale Myoglobin
Biophys. J. 2004 86: 3855-3862. [Abstract] [Full Text] [PDF]  

Sophie Bernad, Silke Oellerich, Tewfik Soulimane, Sylvie Noinville, Marie-Hélène Baron, Maité Paternostre, and Sophie Lecomte

Interaction of Horse Heart and Thermus thermophilus Type c Cytochromes with Phospholipid Vesicles and Hydrophobic Surfaces
Biophys. J. 2004 86: 3863-3872. [Abstract] [Full Text] [PDF]  

Le Zhang, René Buchet, and Gérard Azzar

Phosphate Binding in the Active Site of Alkaline Phosphatase and the Interactions of 2-Nitrosoacetophenone with Alkaline Phosphatase-Induced Small Structural Changes
Biophys. J. 2004 86: 3873-3881. [Abstract] [Full Text] [PDF]  

Paola D'Angelo, Debora Lucarelli, Stefano della Longa, Maurizio Benfatto, Jean Louis Hazemann, Alessandro Feis, Giulietta Smulevich, Andrea Ilari, Alessandra Bonamore, and Alberto Boffi

Unusual Heme Iron-Lipid Acyl Chain Coordination in Escherichia coli Flavohemoglobin
Biophys. J. 2004 86: 3882-3892. [Abstract] [Full Text] [PDF]  

SUPRAMOLECULAR ASSEMBLIES:

Mériem Er Rafik, Jean Doucet, and Fatma Briki

The Intermediate Filament Architecture as Determined by X-Ray Diffraction Modeling of Hard -Keratin
Biophys. J. 2004 86: 3893-3904. [Abstract] [Full Text] [PDF]  

Willem K. Kegel and Paul van der Schoot

Competing Hydrophobic and Screened-Coulomb Interactions in Hepatitis B Virus Capsid Assembly
Biophys. J. 2004 86: 3905-3913. [Abstract] [Full Text] [PDF]  

SPECTROSCOPY, IMAGING, OTHER TECHNIQUES:

Shi-Wei Chu, Szu-Yu Chen, Gia-Wei Chern, Tsung-Han Tsai, Yung-Chih Chen, Bai-Ling Lin, and Chi-Kuang Sun

Studies of ⁽²⁾/⁽³⁾ Tensors in Submicron-Scaled Bio-Tissues by Polarization Harmonics Optical Microscopy
Biophys. J. 2004 86: 3914-3922. [Abstract] [Full Text] [PDF]  

Tomasz Zal and Nicholas R. J. Gascoigne

Photobleaching-Corrected FRET Efficiency Imaging of Live Cells
Biophys. J. 2004 86: 3923-3939. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Eric J. Hustedt and Albert H. Beth

High Field/High Frequency Saturation Transfer Electron Paramagnetic Resonance Spectroscopy: Increased Sensitivity to Very Slow Rotational Motions
Biophys. J. 2004 86: 3940-3950. [Abstract] [Full Text] [PDF]  

Ibon Iloro, Rosana Chehín, Félix M. Goñi, María A. Pajares, and José-Luis R. Arrondo

Methionine Adenosyltransferase -Helix Structure Unfolds at Lower Temperatures than ß-Sheet: A 2D-IR Study
Biophys. J. 2004 86: 3951-3958. [Abstract] [Full Text] [PDF]  

Thommey P. Thomas, Mon Thiri Myaing, Jing Yong Ye, Kimberly Candido, Alina Kotlyar, James Beals, Peter Cao, Balazs Keszler, Anil K. Patri, Theodore B. Norris, and James R. Baker, Jr.

Detection and Analysis of Tumor Fluorescence Using a Two-Photon Optical Fiber Probe
Biophys. J. 2004 86: 3959-3965. [Abstract] [Full Text] [PDF]  

Rikard Blunck, Dorine M. Starace, Ana M. Correa, and Francisco Bezanilla

Detecting Rearrangements of Shaker and NaChBac in Real-Time with Fluorescence Spectroscopy in Patch-Clamped Mammalian Cells
Biophys. J. 2004 86: 3966-3980. [Abstract] [Full Text] [PDF]  

Joachim D. Müller

Cumulant Analysis in Fluorescence Fluctuation Spectroscopy
Biophys. J. 2004 86: 3981-3992. [Abstract] [Full Text] [PDF]  

Sylvain V. Costes, Dirk Daelemans, Edward H. Cho, Zachary Dobbin, George Pavlakis, and Stephen Lockett

Automatic and Quantitative Measurement of Protein-Protein Colocalization in Live Cells
Biophys. J. 2004 86: 3993-4003. [Abstract] [Full Text] [PDF] [Supplemental Material]  

M. T. Valentine, Z. E. Perlman, M. L. Gardel, J. H. Shin, P. Matsudaira, T. J. Mitchison, and D. A. Weitz

Colloid Surface Chemistry Critically Affects Multiple Particle Tracking Measurements of Biomaterials
Biophys. J. 2004 86: 4004-4014. [Abstract] [Full Text] [PDF]  

Lucas P. Watkins and Haw Yang

Information Bounds and Optimal Analysis of Dynamic Single Molecule Measurements
Biophys. J. 2004 86: 4015-4029. [Abstract] [Full Text] [PDF]  

CELL BIOPHYSICS:

K. E. Kadash, M. B. Lawrence, and S. L. Diamond

Neutrophil String Formation: Hydrodynamic Thresholding and Cellular Deformation during Cell Collisions
Biophys. J. 2004 86: 4030-4039. [Abstract] [Full Text] [PDF]  

P. Thomas Vernier, Yinghua Sun, Laura Marcu, Cheryl M. Craft, and Martin A. Gundersen

Nanoelectropulse-Induced Phosphatidylserine Translocation
Biophys. J. 2004 86: 4040-4048. [Abstract] [Full Text] [PDF]  

Shahid Khan, Sanjay Jain, Gordon P. Reid, and David R. Trentham

The Fast Tumble Signal in Bacterial Chemotaxis
Biophys. J. 2004 86: 4049-4058. [Abstract] [Full Text] [PDF]  

Joana Vitte, Anne-Marie Benoliel, Philippe Eymeric, Pierre Bongrand, and Anne Pierres

ß-1 Integrin-Mediated Adhesion May Be Initiated by Multiple Incomplete Bonds, Thus Accounting for the Functional Importance of Receptor Clustering
Biophys. J. 2004 86: 4059-4074. [Abstract] [Full Text] [PDF]  

Kotono Murase, Takahiro Fujiwara, Yasuhiro Umemura, Kenichi Suzuki, Ryota Iino, Hidetoshi Yamashita, Mihoko Saito, Hideji Murakoshi, Ken Ritchie, and Akihiro Kusumi

Ultrafine Membrane Compartments for Molecular Diffusion as Revealed by Single Molecule Techniques
Biophys. J. 2004 86: 4075-4093. [Abstract] [Full Text] [PDF]  

BIOENERGETICS:

Boris A. Feniouk, Maria A. Kozlova, Dmitry A. Knorre, Dmitry A. Cherepanov, Armen Y. Mulkidjanian, and Wolfgang Junge

The Proton-Driven Rotor of ATP Synthase: Ohmic Conductance (10 fS), and Absence of Voltage Gating
Biophys. J. 2004 86: 4094-4109. [Abstract] [Full Text] [PDF]  

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