BIOPHYSICAL THEORY AND MODELING:

Upinder S. Bhalla

Signaling in Small Subcellular Volumes. I. Stochastic and Diffusion Effects on Individual Pathways
Biophys. J. 2004 87: 733-744. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Upinder S. Bhalla

Signaling in Small Subcellular Volumes. II. Stochastic and Diffusion Effects on Synaptic Network Properties
Biophys. J. 2004 87: 745-753. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Rosemary Braun, Donald M. Engelman, and Klaus Schulten

Molecular Dynamics Simulations of Micelle Formation around Dimeric Glycophorin A Transmembrane Helices
Biophys. J. 2004 87: 754-763. [Abstract] [Full Text] [PDF]  

Gene Lamm and George R. Pack

Induced Coalescence of Cations through Low-Temperature Poisson-Boltzmann Calculations
Biophys. J. 2004 87: 764-767. [Abstract] [Full Text] [PDF]  

Idit Oren, Sarel J. Fleishman, Amit Kessel, and Nir Ben-Tal

Free Diffusion of Steroid Hormones Across Biomembranes: A Simplex Search with Implicit Solvent Model Calculations
Biophys. J. 2004 87: 768-779. [Abstract] [Full Text] [PDF]  

Craig M. Shepherd and Hans J. Vogel

A Molecular Dynamics Study of Ca²⁺-Calmodulin: Evidence of Interdomain Coupling and Structural Collapse on the Nanosecond Timescale
Biophys. J. 2004 87: 780-791. [Abstract] [Full Text] [PDF]  

Sanguk Kim, Aaron K. Chamberlain, and James U. Bowie

A Model of the Closed Form of the Nicotinic Acetylcholine Receptor M2 Channel Pore
Biophys. J. 2004 87: 792-799. [Abstract] [Full Text] [PDF]  

Manuel Rueda, Elena Cubero, Charles A. Laughton, and Modesto Orozco

Exploring the Counterion Atmosphere around DNA: What Can Be Learned from Molecular Dynamics Simulations?
Biophys. J. 2004 87: 800-811. [Abstract] [Full Text] [PDF]  

Lu Yang, Jonathan S. Dordick, and Shekhar Garde

Hydration of Enzyme in Nonaqueous Media Is Consistent with Solvent Dependence of Its Activity
Biophys. J. 2004 87: 812-821. [Abstract] [Full Text] [PDF]  

CHANNELS, RECEPTORS, AND TRANSPORTERS:

Ofer Yifrach

Hill Coefficient for Estimating the Magnitude of Cooperativity in Gating Transitions of Voltage-Dependent Ion Channels
Biophys. J. 2004 87: 822-830. [Abstract] [Full Text] [PDF]  

Satinder S. Rawat, Devaki A. Kelkar, and Amitabha Chattopadhyay

Monitoring Gramicidin Conformations in Membranes: A Fluorescence Approach
Biophys. J. 2004 87: 831-843. [Abstract] [Full Text] [PDF]  

Evgeny Kobrinsky, Klaus J. F. Kepplinger, Alexander Yu, Jo Beth Harry, Heike Kahr, Christoph Romanin, Darrell R. Abernethy, and Nikolai M. Soldatov

Voltage-Gated Rearrangements Associated with Differential ß-Subunit Modulation of the L-Type Ca²⁺ Channel Inactivation
Biophys. J. 2004 87: 844-857. [Abstract] [Full Text] [PDF]  

Ingo Dreyer, Fabien Porée, Antje Schneider, Jessica Mittelstädt, Adam Bertl, Hervé Sentenac, Jean-Baptiste Thibaud, and Bernd Mueller-Roeber

Assembly of Plant Shaker-Like K_out Channels Requires Two Distinct Sites of the Channel -Subunit
Biophys. J. 2004 87: 858-872. [Abstract] [Full Text] [PDF]  

Annette Scholle, Thomas Zimmer, Rolf Koopmann, Birgit Engeland, Olaf Pongs, and Klaus Benndorf

Effects of Kv1.2 Intracellular Regions on Activation of Kv2.1 Channels
Biophys. J. 2004 87: 873-882. [Abstract] [Full Text] [PDF]  

R. Daniel Peluffo

Effect of ADP on Na⁺-Na⁺ Exchange Reaction Kinetics of Na,K-ATPase
Biophys. J. 2004 87: 883-898. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Michela Ottolia, Kenneth D. Philipson, and Scott John

Conformational Changes of the Ca²⁺ Regulatory Site of the Na⁺-Ca²⁺ Exchanger Detected by FRET
Biophys. J. 2004 87: 899-906. [Abstract] [Full Text] [PDF]  

D. Eric Walters and Ronald S. Kaplan

Homology-Modeled Structure of the Yeast Mitochondrial Citrate Transport Protein
Biophys. J. 2004 87: 907-911. [Abstract] [Full Text] [PDF]  

Seunghoon Oh, Shira Rivkin, Qingxiu Tang, Vytas K. Verselis, and Thaddeus A. Bargiello

Determinants of Gating Polarity of a Connexin 32 Hemichannel
Biophys. J. 2004 87: 912-928. [Abstract] [Full Text] [PDF]  

David C. Sheridan, Weijun Cheng, Leah Carbonneau, Chris A. Ahern, and Roberto Coronado

Involvement of a Heptad Repeat in the Carboxyl Terminus of the Dihydropyridine Receptor ß1a Subunit in the Mechanism of Excitation-Contraction Coupling in Skeletal Muscle
Biophys. J. 2004 87: 929-942. [Abstract] [Full Text] [PDF]  

Antonio Alcaraz, Ekaterina M. Nestorovich, Marcel Aguilella-Arzo, Vicente M. Aguilella, and Sergey M. Bezrukov

Salting Out the Ionic Selectivity of a Wide Channel: The Asymmetry of OmpF
Biophys. J. 2004 87: 943-957. [Abstract] [Full Text] [PDF]  

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

The Permeability of Gap Junction Channels to Probes of Different Size Is Dependent on Connexin Composition and Permeant-Pore Affinities
Biophys. J. 2004 87: 958-973. [Abstract] [Full Text] [PDF]  

MEMBRANES:

T. Roopa, N. Kumar, S. Bhattacharya, and G. V. Shivashankar

Dynamics of Membrane Nanotubulation and DNA Self-Assembly
Biophys. J. 2004 87: 974-979. [Abstract] [Full Text] [PDF]  

Greger Orädd and Göran Lindblom

NMR Studies of Lipid Lateral Diffusion in the DMPC/Gramicidin D/Water System: Peptide Aggregation and Obstruction Effects
Biophys. J. 2004 87: 980-987. [Abstract] [Full Text] [PDF]  

Irene A. Chen and Jack W. Szostak

A Kinetic Study of the Growth of Fatty Acid Vesicles
Biophys. J. 2004 87: 988-998. [Abstract] [Full Text] [PDF]  

Yonathan Kozlovsky, Joshua Zimmerberg, and Michael M. Kozlov

Orientation and Interaction of Oblique Cylindrical Inclusions Embedded in a Lipid Monolayer: A Theoretical Model for Viral Fusion Peptides
Biophys. J. 2004 87: 999-1012. [Abstract] [Full Text] [PDF]  

Hung V. Ly and Marjorie L. Longo

The Influence of Short-Chain Alcohols on Interfacial Tension, Mechanical Properties, Area/Molecule, and Permeability of Fluid Lipid Bilayers
Biophys. J. 2004 87: 1013-1033. [Abstract] [Full Text] [PDF]  

Kirsten Bacia, Dag Scherfeld, Nicoletta Kahya, and Petra Schwille

Fluorescence Correlation Spectroscopy Relates Rafts in Model and Native Membranes
Biophys. J. 2004 87: 1034-1043. [Abstract] [Full Text] [PDF]  

Laura Rusu, Alok Gambhir, Stuart McLaughlin, and Joachim Rädler

Fluorescence Correlation Spectroscopy Studies of Peptide and Protein Binding to Phospholipid Vesicles
Biophys. J. 2004 87: 1044-1053. [Abstract] [Full Text] [PDF]  

Yury S. Tarahovsky, Rumiana Koynova, and Robert C. MacDonald

DNA Release from Lipoplexes by Anionic Lipids: Correlation with Lipid Mesomorphism, Interfacial Curvature, and Membrane Fusion
Biophys. J. 2004 87: 1054-1064. [Abstract] [Full Text] [PDF]  

Silvia Micelli, Daniela Meleleo, Vittorio Picciarelli, Maria G. Stoico, and Enrico Gallucci

Effect of Nanomolar Concentrations of Sodium Dodecyl Sulfate, a Catalytic Inductor of -Helices, on Human Calcitonin Incorporation and Channel Formation in Planar Lipid Membranes
Biophys. J. 2004 87: 1065-1075. [Abstract] [Full Text] [PDF]  

Emma Falck, Michael Patra, Mikko Karttunen, Marja T. Hyvönen, and Ilpo Vattulainen

Lessons of Slicing Membranes: Interplay of Packing, Free Area, and Lateral Diffusion in Phospholipid/Cholesterol Bilayers
Biophys. J. 2004 87: 1076-1091. [Abstract] [Full Text] [PDF]  

Sagar A. Pandit, S. Vasudevan, S. W. Chiu, R. Jay Mashl, Eric Jakobsson, and H. L. Scott

Sphingomyelin-Cholesterol Domains in Phospholipid Membranes: Atomistic Simulation
Biophys. J. 2004 87: 1092-1100. [Abstract] [Full Text] [PDF]  

MUSCLE AND CONTRACTILITY:

Marco Linari, Michael K. Reedy, Mary C. Reedy, Vincenzo Lombardi, and Gabriella Piazzesi

Ca-Activation and Stretch-Activation in Insect Flight Muscle
Biophys. J. 2004 87: 1101-1111. [Abstract] [Full Text] [PDF]  

Mark C. Leake, David Wilson, Mathias Gautel, and Robert M. Simmons

The Elasticity of Single Titin Molecules Using a Two-Bead Optical Tweezers Assay
Biophys. J. 2004 87: 1112-1135. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Dmitry S. Kudryashov, Martin Phillips, and Emil Reisler

Formation and Destabilization of Actin Filaments with Tetramethylrhodamine-Modified Actin
Biophys. J. 2004 87: 1136-1145. [Abstract] [Full Text] [PDF]  

Emöke Bódis, Giovanni B. Strambini, Margherita Gonnelli, András Málnási-Csizmadia, and Béla Somogyi

Characterization of F-Actin Tryptophan Phosphorescence in the Presence and Absence of Tryptophan-Free Myosin Motor Domain
Biophys. J. 2004 87: 1146-1154. [Abstract] [Full Text] [PDF]  

PHOTOBIOPHYSICS:

Irena Bronshtein, Michal Afri, Hana Weitman, Aryeh A. Frimer, Kevin M. Smith, and Benjamin Ehrenberg

Porphyrin Depth in Lipid Bilayers as Determined by Iodide and Parallax Fluorescence Quenching Methods and Its Effect on Photosensitizing Efficiency
Biophys. J. 2004 87: 1155-1164. [Abstract] [Full Text] [PDF]  

J. Psencík, T. P. Ikonen, P. Laurinmäki, M. C. Merckel, S. J. Butcher, R. E. Serimaa, and R. Tuma

Lamellar Organization of Pigments in Chlorosomes, the Light Harvesting Complexes of Green Photosynthetic Bacteria
Biophys. J. 2004 87: 1165-1172. [Abstract] [Full Text] [PDF]  

PROTEINS:

Angelika Krebs, Helmut Durchschlag, and Peter Zipper

Small Angle X-Ray Scattering Studies and Modeling of Eudistylia vancouverii Chlorocruorin and Macrobdella decora Hemoglobin
Biophys. J. 2004 87: 1173-1185. [Abstract] [Full Text] [PDF]  

Luca Tofani, Alessandro Feis, Roy E. Snoke, Debora Berti, Piero Baglioni, and Giulietta Smulevich

Spectroscopic and Interfacial Properties of Myoglobin/Surfactant Complexes
Biophys. J. 2004 87: 1186-1195. [Abstract] [Full Text] [PDF]  

Julien Uzan, Sylvia Dewilde, Thorsten Burmester, Thomas Hankeln, Luc Moens, Djemel Hamdane, Michael C. Marden, and Laurent Kiger

Neuroglobin and Other Hexacoordinated Hemoglobins Show a Weak Temperature Dependence of Oxygen Binding
Biophys. J. 2004 87: 1196-1204. [Abstract] [Full Text] [PDF]  

Emily E. Metcalfe, Jamillah Zamoon, David D. Thomas, and Gianluigi Veglia

¹H/¹⁵N Heteronuclear NMR Spectroscopy Shows Four Dynamic Domains for Phospholamban Reconstituted in Dodecylphosphocholine Micelles
Biophys. J. 2004 87: 1205-1214. [Abstract] [Full Text] [PDF]  

Marcin Golczak, Aneta Kirilenko, Joanna Bandorowicz-Pikula, Bernard Desbat, and Slawomir Pikula

Structure of Human Annexin A6 at the Air-Water Interface and in a Membrane-Bound State
Biophys. J. 2004 87: 1215-1226. [Abstract] [Full Text] [PDF]  

Giuseppe Nicastro, Paola Margiocco, Barbara Cardinali, Paola Stagnaro, Fabio Cauglia, Carla Cuniberti, Maddalena Collini, David Thomas, Annalisa Pastore, and Mattia Rocco

The Role of Unstructured Extensions in the Rotational Diffusion Properties of a Globular Protein: The Example of the Titin I27 Module
Biophys. J. 2004 87: 1227-1240. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Wei Li, Yang Zhang, and Jeffrey Skolnick

Application of Sparse NMR Restraints to Large-Scale Protein Structure Prediction
Biophys. J. 2004 87: 1241-1248. [Abstract] [Full Text] [PDF]  

SUPRAMOLECULAR ASSEMBLIES:

S. Jun, Y. Hong, H. Imamura, B.-Y. Ha, J. Bechhoefer, and P. Chen

Self-Assembly of the Ionic Peptide EAK16: The Effect of Charge Distributions on Self-Assembly
Biophys. J. 2004 87: 1249-1259. [Abstract] [Full Text] [PDF]  

SPECTROSCOPY, IMAGING, OTHER TECHNIQUES:

Qiaoqiao Ruan, Melanie A. Cheng, Moshe Levi, Enrico Gratton, and William W. Mantulin

Spatial-Temporal Studies of Membrane Dynamics: Scanning Fluorescence Correlation Spectroscopy (SFCS)
Biophys. J. 2004 87: 1260-1267. [Abstract] [Full Text] [PDF]  

Alena M. Lieto and Nancy L. Thompson

Total Internal Reflection with Fluorescence Correlation Spectroscopy: Nonfluorescent Competitors
Biophys. J. 2004 87: 1268-1278. [Abstract] [Full Text] [PDF]  

Rhonda Dzakpasu and Daniel Axelrod

Dynamic Light Scattering Microscopy. A Novel Optical Technique to Image Submicroscopic Motions. I: Theory
Biophys. J. 2004 87: 1279-1287. [Abstract] [Full Text] [PDF]  

Rhonda Dzakpasu and Daniel Axelrod

Dynamic Light Scattering Microscopy. A Novel Optical Technique to Image Submicroscopic Motions. II: Experimental Applications
Biophys. J. 2004 87: 1288-1297. [Abstract] [Full Text] [PDF]  

Dakota Watson, Norbert Hagen, Jonathan Diver, Philippe Marchand, and Mirianas Chachisvilis

Elastic Light Scattering from Single Cells: Orientational Dynamics in Optical Trap
Biophys. J. 2004 87: 1298-1306. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Dimitri Ivanov, Nicolas Dubreuil, Vincent Raussens, Jean-Marie Ruysschaert, and Erik Goormaghtigh

Evaluation of the Ordering of Membranes in Multilayer Stacks Built on an ATR-FTIR Germanium Crystal with Atomic Force Microscopy: The Case of the H⁺,K⁺-ATPase-containing Gastric Tubulovesicle Membranes
Biophys. J. 2004 87: 1307-1315. [Abstract] [Full Text] [PDF]  

Marisa Martin-Fernandez, Samantha V. Longshaw, Ian Kirby, George Santis, Mark J. Tobin, David T. Clarke, and Gareth R. Jones

Adenovirus Type-5 Entry and Disassembly Followed in Living Cells by FRET, Fluorescence Anisotropy, and FLIM
Biophys. J. 2004 87: 1316-1327. [Abstract] [Full Text] [PDF]  

Sungchul Hohng, Chirlmin Joo, and Taekjip Ha

Single-Molecule Three-Color FRET
Biophys. J. 2004 87: 1328-1337. [Abstract] [Full Text] [PDF]  

CELL BIOPHYSICS:

Wolfgang Feneberg, Martin Aepfelbacher, and Erich Sackmann

Microviscoelasticity of the Apical Cell Surface of Human Umbilical Vein Endothelial Cells (HUVEC) within Confluent Monolayers
Biophys. J. 2004 87: 1338-1350. [Abstract] [Full Text] [PDF]  

Dieter Braun and Peter Fromherz

Imaging Neuronal Seal Resistance on Silicon Chip using Fluorescent Voltage-Sensitive Dye
Biophys. J. 2004 87: 1351-1359. [Abstract] [Full Text] [PDF]  

Sanda Despa, Jens Kockskämper, Lothar A. Blatter, and Donald M. Bers

Na/K Pump-Induced [Na]_i Gradients in Rat Ventricular Myocytes Measured with Two-Photon Microscopy
Biophys. J. 2004 87: 1360-1368. [Abstract] [Full Text] [PDF] [Supplemental Material]  

BIOENERGETICS:

Jie-Lou Liao and David N. Beratan

How Does Protein Architecture Facilitate the Transduction of ATP Chemical-Bond Energy into Mechanical Work? The Cases of Nitrogenase and ATP Binding-Cassette Proteins
Biophys. J. 2004 87: 1369-1377. [Abstract] [Full Text] [PDF]  

OTHER:

Marc P. Scherer and Anthony W. Gummer

Impedance Analysis of the Organ of Corti with Magnetically Actuated Probes
Biophys. J. 2004 87: 1378-1391. [Abstract] [Full Text] [PDF]  

LETTERS TO THE EDITOR:

Roee Amit, Amos B. Oppenheim, and Joel Stavans

Single Molecule Elasticity Measurements: A Biophysical Approach to Bacterial Nucleoid Organization
Biophys. J. 2004 87: 1392-1393. [Full Text] [PDF]  

Jerome Baudry, Emad Tajkhorshid, and Klaus Schulten

Complementarities and Convergence of Results in Bacteriorhodopsin Trimer Simulations
Biophys. J. 2004 87: 1394-1395. [Full Text] [PDF]  

Christian Kandt, Juergen Schlitter, and Klaus Gerwert

Reply to "Complementarities and Convergence of Results in Bacteriorhodopsin Trimer Simulations"
Biophys. J. 2004 87: 1396(2) [Full Text] [PDF]  

CORRECTIONS:

Correction
Biophys. J. 2004 87: 1397(2) [Full Text] [PDF]  

Correction
Biophys. J. 2004 87: 1398(2) [Full Text] [PDF]  

Correction
Biophys. J. 2004 87: 1399(2) [Full Text] [PDF]  

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