BIOPHYSICAL THEORY AND MODELING:

Elena Olkhova, Michael C. Hutter, Markus A. Lill, Volkhard Helms, and Hartmut Michel

Dynamic Water Networks in Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Molecular Dynamics Simulations
Biophys. J. 2004 86: 1873-1889. [Abstract] [Full Text] [PDF]  

J. A. Tuszynski, S. Portet, J. M. Dixon, C. Luxford, and H. F. Cantiello

Ionic Wave Propagation along Actin Filaments
Biophys. J. 2004 86: 1890-1903. [Abstract] [Full Text] [PDF]  

Rene J. Trabanino, Spencer E. Hall, Nagarajan Vaidehi, Wely B. Floriano, Victor W. T. Kam, and William A. Goddard, 3rd

First Principles Predictions of the Structure and Function of G-Protein-Coupled Receptors: Validation for Bovine Rhodopsin
Biophys. J. 2004 86: 1904-1921. [Abstract] [Full Text] [PDF] [Supplemental Material]  

John Goutsias and Seungchan Kim

A Nonlinear Discrete Dynamical Model for Transcriptional Regulation: Construction and Properties
Biophys. J. 2004 86: 1922-1945. [Abstract] [Full Text] [PDF]  

Xiongwu Wu and Bernard R. Brooks

ß-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water
Biophys. J. 2004 86: 1946-1958. [Abstract] [Full Text] [PDF]  

Gertjan Veldhuis, Erwin P. P. Vos, Jaap Broos, Bert Poolman, and Ruud M. Scheek

Evaluation of the Flow-Dialysis Technique for Analysis of Protein-Ligand Interactions: An Experimental and a Monte Carlo Study
Biophys. J. 2004 86: 1959-1968. [Abstract] [Full Text] [PDF]  

Jiyao Wang, Alok Gambhir, Stuart McLaughlin, and Diana Murray

A Computational Model for the Electrostatic Sequestration of PI(4,5)P₂ by Membrane-Adsorbed Basic Peptides
Biophys. J. 2004 86: 1969-1986. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Markus Meuwly and Martin Karplus

Theoretical Investigations on Azotobacter vinelandii Ferredoxin I: Effects of Electron Transfer on Protein Dynamics
Biophys. J. 2004 86: 1987-2007. [Abstract] [Full Text] [PDF] [Supplemental Material]  

T. Kustanovich and Y. Rabin

Metastable Network Model of Protein Transport through Nuclear Pores
Biophys. J. 2004 86: 2008-2016. [Abstract] [Full Text] [PDF]  

Yuhua Song, Yongjie Zhang, Tongye Shen, Chandrajit L. Bajaj, J. Andrew McCammon, and Nathan A. Baker

Finite Element Solution of the Steady-State Smoluchowski Equation for Rate Constant Calculations
Biophys. J. 2004 86: 2017-2029. [Abstract] [Full Text] [PDF]  

Elizabeth A. Dolan, Robert B. Yelle, Brian W. Beck, Justin T. Fischer, and Toshiko Ichiye

Protein Control of Electron Transfer Rates via Polarization: Molecular Dynamics Studies of Rubredoxin
Biophys. J. 2004 86: 2030-2036. [Abstract] [Full Text] [PDF]  

Shelly Tzlil, Markus Deserno, William M. Gelbart, and Avinoam Ben-Shaul

A Statistical-Thermodynamic Model of Viral Budding
Biophys. J. 2004 86: 2037-2048. [Abstract] [Full Text] [PDF]  

Pierre Sens and Matthew S. Turner

Theoretical Model for the Formation of Caveolae and Similar Membrane Invaginations
Biophys. J. 2004 86: 2049-2057. [Abstract] [Full Text] [PDF]  

Johannes M. Nitsche, Hou-Chien Chang, Paul A. Weber, and Bruce J. Nicholson

A Transient Diffusion Model Yields Unitary Gap Junctional Permeabilities from Images of Cell-to-Cell Fluorescent Dye Transfer Between Xenopus Oocytes
Biophys. J. 2004 86: 2058-2077. [Abstract] [Full Text] [PDF]  

Thomas Huber, Ana V. Botelho, Klaus Beyer, and Michael F. Brown

Membrane Model for the G-Protein-Coupled Receptor Rhodopsin: Hydrophobic Interface and Dynamical Structure
Biophys. J. 2004 86: 2078-2100. [Abstract] [Full Text] [PDF]  

CHANNELS, RECEPTORS, AND TRANSPORTERS:

Peter Drain, Xuehui Geng, and Lehong Li

Concerted Gating Mechanism Underlying K_ATP Channel Inhibition by ATP
Biophys. J. 2004 86: 2101-2112. [Abstract] [Full Text] [PDF]  

Kenjiro Yoshimura, Takeshi Nomura, and Masahiro Sokabe

Loss-of-Function Mutations at the Rim of the Funnel of Mechanosensitive Channel MscL
Biophys. J. 2004 86: 2113-2120. [Abstract] [Full Text] [PDF]  

Inna Györke, Nichole Hester, Larry R. Jones, and Sandor Györke

The Role of Calsequestrin, Triadin, and Junctin in Conferring Cardiac Ryanodine Receptor Responsiveness to Luminal Calcium
Biophys. J. 2004 86: 2121-2128. [Abstract] [Full Text] [PDF]  

Kyu-Ho Park, Catherine Berrier, Boris Martinac, and Alexandre Ghazi

Purification and Functional Reconstitution of N- and C-Halves of the MscL Channel
Biophys. J. 2004 86: 2129-2136. [Abstract] [Full Text] [PDF]  

HoSook Choi and Lise Heginbotham

Functional Influence of the Pore Helix Glutamate in the KcsA K⁺ Channel
Biophys. J. 2004 86: 2137-2144. [Abstract] [Full Text] [PDF]  

H. Sackin, L.G. Palmer, and M. Krambis

Potassium-Dependent Slow Inactivation of Kir1.1 (ROMK) Channels
Biophys. J. 2004 86: 2145-2155. [Abstract] [Full Text] [PDF]  

MEMBRANES:

Hari Leontiadou, Alan E. Mark, and Siewert J. Marrink

Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers
Biophys. J. 2004 86: 2156-2164. [Abstract] [Full Text] [PDF]  

Emir Haleva, Nir Ben-Tal, and Haim Diamant

Increased Concentration of Polyvalent Phospholipids in the Adsorption Domain of a Charged Protein
Biophys. J. 2004 86: 2165-2178. [Abstract] [Full Text] [PDF]  

A. Viallat, J. Dalous, and M. Abkarian

Giant Lipid Vesicles Filled with a Gel: Shape Instability Induced by Osmotic Shrinkage
Biophys. J. 2004 86: 2179-2187. [Abstract] [Full Text] [PDF]  

Alok Gambhir, Gyöngyi Hangyás-Mihályné, Irina Zaitseva, David S. Cafiso, Jiyao Wang, Diana Murray, Srinivas N. Pentyala, Steven O. Smith, and Stuart McLaughlin

Electrostatic Sequestration of PIP₂ on Phospholipid Membranes by Basic/Aromatic Regions of Proteins
Biophys. J. 2004 86: 2188-2207. [Abstract] [Full Text] [PDF]  

Ying Feng, Dominique Rainteau, Claude Chachaty, Zhi-Wu Yu, Claude Wolf, and Peter J. Quinn

Characterization of a Quasicrystalline Phase in Codispersions of Phosphatidylethanolamine and Glucocerebroside
Biophys. J. 2004 86: 2208-2217. [Abstract] [Full Text] [PDF]  

Marie-Cécile Giocondi and Christian Le Grimellec

Temperature Dependence of the Surface Topography in Dimyristoylphosphatidylcholine/Distearoylphosphatidylcholine Multibilayers
Biophys. J. 2004 86: 2218-2230. [Abstract] [Full Text] [PDF]  

Silvia Micelli, Daniela Meleleo, Vittorio Picciarelli, and Enrico Gallucci

Effect of Sterols on ß-Amyloid Peptide (AßP 1–40) Channel Formation and their Properties in Planar Lipid Membranes
Biophys. J. 2004 86: 2231-2237. [Abstract] [Full Text] [PDF]  

Daniel C. H. Kwan, Cyrus Eduljee, Logan Lee, Shetuan Zhang, David Fedida, and Steven J. Kehl

The External K⁺ Concentration and Mutations in the Outer Pore Mouth Affect the Inhibition of Kv1.5 Current by Ni²⁺
Biophys. J. 2004 86: 2238-2250. [Abstract] [Full Text] [PDF]  

Rebekah S. Vest, Laurie J. Gonzales, Seth A. Permann, Emily Spencer, Lee D. Hansen, Allan M. Judd, and John D. Bell

Divalent Cations Increase Lipid Order in Erythrocytes and Susceptibility to Secretory Phospholipase A₂
Biophys. J. 2004 86: 2251-2260. [Abstract] [Full Text] [PDF]  

Rodrigo F. M. de Almeida, Luís M. S. Loura, Manuel Prieto, Anthony Watts, Aleksandre Fedorov, and Francisco J. Barrantes

Cholesterol Modulates the Organization of the M4 Transmembrane Domain of the Muscle Nicotinic Acetylcholine Receptor
Biophys. J. 2004 86: 2261-2272. [Abstract] [Full Text] [PDF]  

Cristina S. Pereira, Roberto D. Lins, Indira Chandrasekhar, Luiz Carlos G. Freitas, and Philippe H. Hünenberger

Interaction of the Disaccharide Trehalose with a Phospholipid Bilayer: A Molecular Dynamics Study
Biophys. J. 2004 86: 2273-2285. [Abstract] [Full Text] [PDF]  

MUSCLE AND CONTRACTILITY:

Naoto Yagi, Juichiro Shimizu, Satoshi Mohri, Jun'ichi Araki, Kazufumi Nakamura, Hiroshi Okuyama, Hiroko Toyota, Taro Morimoto, Yuki Morizane, Mie Kurusu, Tatsushi Miura, Katsushi Hashimoto, Katsuhiko Tsujioka, Hiroyuki Suga, and Fumihiko Kajiya

X-ray Diffraction from a Left Ventricular Wall of Rat Heart
Biophys. J. 2004 86: 2286-2294. [Abstract] [Full Text] [PDF]  

Corrado Bacchiocchi, Philip Graceffa, and Sherwin S. Lehrer

Myosin-Induced Movement of , ß, and ßß Smooth Muscle Tropomyosin on Actin Observed by Multisite FRET
Biophys. J. 2004 86: 2295-2307. [Abstract] [Full Text] [PDF]  

J. Borejdo, A. Shepard, D. Dumka, I. Akopova, J. Talent, A. Malka, and T. P. Burghardt

Changes in Orientation of Actin during Contraction of Muscle
Biophys. J. 2004 86: 2308-2317. [Abstract] [Full Text] [PDF]  

Alexander S. Khromov, Martin R. Webb, Michael A. Ferenczi, David R. Trentham, Andrew P. Somlyo, and Avril V. Somlyo

Myosin Regulatory Light Chain Phosphorylation and Strain Modulate Adenosine Diphosphate Release from Smooth Muscle Myosin
Biophys. J. 2004 86: 2318-2328. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Andrew S. Brack, Birgit D. Brandmeier, Roisean E. Ferguson, Susan Criddle, Robert E. Dale, and Malcolm Irving

Bifunctional Rhodamine Probes of Myosin Regulatory Light Chain Orientation in Relaxed Skeletal Muscle Fibers
Biophys. J. 2004 86: 2329-2341. [Abstract] [Full Text] [PDF]  

PHOTOBIOPHYSICS:

Elena G. Govorunova, Kwang-Hwan Jung, Oleg A. Sineshchekov, and John L. Spudich

Chlamydomonas Sensory Rhodopsins A and B: Cellular Content and Role in Photophobic Responses
Biophys. J. 2004 86: 2342-2349. [Abstract] [Full Text] [PDF]  

J. Wachtveitl, S. Spörlein, H. Satzger, B. Fonrobert, C. Renner, R. Behrendt, D. Oesterhelt, L. Moroder, and W. Zinth

Ultrafast Conformational Dynamics in Cyclic Azobenzene Peptides of Increased Flexibility
Biophys. J. 2004 86: 2350-2362. [Abstract] [Full Text] [PDF]  

Axel Schubert, Anna Stenstam, Wichard J. D. Beenken, Jennifer L. Herek, Richard Cogdell, Tõnu Pullerits, and Villy Sundström

In Vitro Self-Assembly of the Light Harvesting Pigment-Protein LH2 Revealed by Ultrafast Spectroscopy and Electron Microscopy
Biophys. J. 2004 86: 2363-2373. [Abstract] [Full Text] [PDF]  

Duohai Pan, Andrew Philip, Wouter D. Hoff, and Richard A. Mathies

Time-Resolved Resonance Raman Structural Studies of the pB' Intermediate in the Photocycle of Photoactive Yellow Protein
Biophys. J. 2004 86: 2374-2382. [Abstract] [Full Text] [PDF] [Supplemental Material]  

PROTEINS:

Antonello Merlino, Luigi Vitagliano, Marc Antoine Ceruso, and Lelio Mazzarella

Dynamic Properties of the N-Terminal Swapped Dimer of Ribonuclease A
Biophys. J. 2004 86: 2383-2391. [Abstract] [Full Text] [PDF]  

Maria Isabel Viseu, Teresa Isabel Carvalho, and Sílvia M. B. Costa

Conformational Transitions in ß-Lactoglobulin Induced by Cationic Amphiphiles: Equilibrium Studies
Biophys. J. 2004 86: 2392-2402. [Abstract] [Full Text] [PDF]  

Salvador Casares, Mourad Sadqi, Obdulio López-Mayorga, Francisco Conejero-Lara, and Nico A. J. van Nuland

Detection and Characterization of Partially Unfolded Oligomers of the SH3 Domain of -Spectrin
Biophys. J. 2004 86: 2403-2413. [Abstract] [Full Text] [PDF]  

Raul Perez-Jimenez, Raquel Godoy-Ruiz, Beatriz Ibarra-Molero, and Jose M. Sanchez-Ruiz

The Efficiency of Different Salts to Screen Charge Interactions in Proteins: A Hofmeister Effect?
Biophys. J. 2004 86: 2414-2429. [Abstract] [Full Text] [PDF]  

Timothy V. Ratto, Kevin C. Langry, Robert E. Rudd, Rodney L. Balhorn, Michael J. Allen, and Michael W. McElfresh

Force Spectroscopy of the Double-Tethered Concanavalin-A Mannose Bond
Biophys. J. 2004 86: 2430-2437. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Constantinos Koutsoupakis, Tewfik Soulimane, and Constantinos Varotsis

Probing the Q-Proton Pathway of ba₃-Cytochrome c Oxidase by Time-Resolved Fourier Transform Infrared Spectroscopy
Biophys. J. 2004 86: 2438-2444. [Abstract] [Full Text] [PDF]  

Y. Ling, M. Ascano, P. Robinson, and S. K. Gregurick

Experimental and Computational Studies of the Desensitization Process in the Bovine Rhodopsin-Arrestin Complex
Biophys. J. 2004 86: 2445-2454. [Abstract] [Full Text] [PDF]  

Ricardo A. García and Hilary Arnold Godwin

High Metal Concentrations Are Required for Self-Association of Synaptotagmin II
Biophys. J. 2004 86: 2455-2466. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Marsia Gustiananda, John R. Liggins, Peter L. Cummins, and Jill E. Gready

Conformation of Prion Protein Repeat Peptides Probed by FRET Measurements and Molecular Dynamics Simulations
Biophys. J. 2004 86: 2467-2483. [Abstract] [Full Text] [PDF]  

SUPRAMOLECULAR ASSEMBLIES:

C. Valéry, F. Artzner, B. Robert, T. Gulick, G. Keller, C. Grabielle-Madelmont, M.-L. Torres, R. Cherif-Cheikh, and M. Paternostre

Self-Association Process of a Peptide in Solution: From ß-Sheet Filaments to Large Embedded Nanotubes
Biophys. J. 2004 86: 2484-2501. [Abstract] [Full Text] [PDF]  

SPECTROSCOPY, IMAGING, OTHER TECHNIQUES:

Itamar Kass, Eyal Arbely, and Isaiah T. Arkin

Modeling Sample Disorder in Site-Specific Dichroism Studies of Uniaxial Systems
Biophys. J. 2004 86: 2502-2507. [Abstract] [Full Text] [PDF]  

Zdzislaw Salamon and Gordon Tollin

Graphical Analysis of Mass and Anisotropy Changes Observed by Plasmon-Waveguide Resonance Spectroscopy Can Provide Useful Insights into Membrane Protein Function
Biophys. J. 2004 86: 2508-2516. [Abstract] [Full Text] [PDF]  

Jacco van Rheenen, Michiel Langeslag, and Kees Jalink

Correcting Confocal Acquisition to Optimize Imaging of Fluorescence Resonance Energy Transfer by Sensitized Emission
Biophys. J. 2004 86: 2517-2529. [Abstract] [Full Text] [PDF]  

M.C. Murphy, Ivan Rasnik, Wei Cheng, Timothy M. Lohman, and Taekjip Ha

Probing Single-Stranded DNA Conformational Flexibility Using Fluorescence Spectroscopy
Biophys. J. 2004 86: 2530-2537. [Abstract] [Full Text] [PDF]  

Delmar S. Larsen, Mikas Vengris, Ivo H. M. van Stokkum, Michael A. van der Horst, Frank L. de Weerd, Klaas J. Hellingwerf, and Rienk van Grondelle

Photoisomerization and Photoionization of the Photoactive Yellow Protein Chromophore in Solution
Biophys. J. 2004 86: 2538-2550. [Abstract] [Full Text] [PDF]  

Gunnar Jeschke, Christoph Wegener, Monika Nietschke, Heinrich Jung, and Heinz-Jürgen Steinhoff

Interresidual Distance Determination by Four-Pulse Double Electron-Electron Resonance in an Integral Membrane Protein: The Na⁺/Proline Transporter PutP of Escherichia coli
Biophys. J. 2004 86: 2551-2557. [Abstract] [Full Text] [PDF]  

CELL BIOPHYSICS:

Yan-Ting Shiu, Song Li, William A. Marganski, Shunichi Usami, Martin A. Schwartz, Yu-Li Wang, Micah Dembo, and Shu Chien

Rho Mediates the Shear-Enhancement of Endothelial Cell Migration and Traction Force Generation
Biophys. J. 2004 86: 2558-2565. [Abstract] [Full Text] [PDF]  

David Holcman and Juan I. Korenbrot

Longitudinal Diffusion in Retinal Rod and Cone Outer Segment Cytoplasm: The Consequence of Cell Structure
Biophys. J. 2004 86: 2566-2582. [Abstract] [Full Text] [PDF]  

Etienne Roux and Marko Marhl

Role of Sarcoplasmic Reticulum and Mitochondria in Ca²⁺ Removal in Airway Myocytes
Biophys. J. 2004 86: 2583-2595. [Abstract] [Full Text] [PDF]  

ELECTROPHYSIOLOGY:

Victor A. Maltsev, Tatiana M. Vinogradova, Konstantin Y. Bogdanov, Edward G. Lakatta, and Michael D. Stern

Diastolic Calcium Release Controls the Beating Rate of Rabbit Sinoatrial Node Cells: Numerical Modeling of the Coupling Process
Biophys. J. 2004 86: 2596-2605. [Abstract] [Full Text] [PDF]  

Colleen E. Clancy and Robert S. Kass

Theoretical Investigation of the Neuronal Na⁺ Channel SCN1A: Abnormal Gating and Epilepsy
Biophys. J. 2004 86: 2606-2614. [Abstract] [Full Text] [PDF]  

OTHER:

M.-P. Nieh, T. A. Harroun, V. A. Raghunathan, C. J. Glinka, and J. Katsaras

Spontaneously Formed Monodisperse Biomimetic Unilamellar Vesicles: The Effect of Charge, Dilution, and Time
Biophys. J. 2004 86: 2615-2629. [Abstract] [Full Text] [PDF]  

LETTERS TO THE EDITOR:

Derek Marsh

Scaling and Mean-Field Theories Applied to Polymer Brushes
Biophys. J. 2004 86: 2630-2633. [Full Text] [PDF]  

CORRECTIONS:

Erratum
Biophys. J. 2004 86: 2634-2635. [Full Text] [PDF]  

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