BIOPHYSICAL THEORY AND MODELING:

D. Bemporad, C. Luttmann, and J. W. Essex

Computer Simulation of Small Molecule Permeation across a Lipid Bilayer: Dependence on Bilayer Properties and Solute Volume, Size, and Cross-Sectional Area
Biophys. J. 2004 87: 1-13. [Abstract] [Full Text] [PDF]  

Qiang Huang, Cheng-Lung Chen, and Andreas Herrmann

Bilayer Conformation of Fusion Peptide of Influenza Virus Hemagglutinin: A Molecular Dynamics Simulation Study
Biophys. J. 2004 87: 14-22. [Abstract] [Full Text] [PDF]  

Mihail Mihailescu and Michael K. Gilson

On the Theory of Noncovalent Binding
Biophys. J. 2004 87: 23-36. [Abstract] [Full Text] [PDF]  

Jason A. Papin and Bernhard O. Palsson

The JAK-STAT Signaling Network in the Human B-Cell: An Extreme Signaling Pathway Analysis
Biophys. J. 2004 87: 37-46. [Abstract] [Full Text] [PDF] [Supplemental Material]  

D. Moscovitch, O. Noivirt, A. Mezer, E. Nachliel, T. Mark, M. Gutman, and G. Fibich

Determination of a Unique Solution to Parallel Proton Transfer Reactions Using the Genetic Algorithm
Biophys. J. 2004 87: 47-57. [Abstract] [Full Text] [PDF]  

Matteo Ceccarelli, Christophe Danelon, Alessandro Laio, and Michele Parrinello

Microscopic Mechanism of Antibiotics Translocation through a Porin
Biophys. J. 2004 87: 58-64. [Abstract] [Full Text] [PDF]  

Dagmar Flöck and Volkhard Helms

A Brownian Dynamics Study: The Effect of a Membrane Environment on an Electron Transfer System
Biophys. J. 2004 87: 65-74. [Abstract] [Full Text] [PDF]  

Anna L. Lin, Bernward A. Mann, Gelsy Torres-Oviedo, Bryan Lincoln, Josef Käs, and Harry L. Swinney

Localization and Extinction of Bacterial Populations under Inhomogeneous Growth Conditions
Biophys. J. 2004 87: 75-80. [Abstract] [Full Text] [PDF]  

D. Holcman, Z. Schuss, and E. Korkotian

Calcium Dynamics in Dendritic Spines and Spine Motility
Biophys. J. 2004 87: 81-91. [Abstract] [Full Text] [PDF]  

Michèle Koenigsberger, Roger Sauser, Mathieu Lamboley, Jean-Louis Bény, and Jean-Jacques Meister

Ca²⁺ Dynamics in a Population of Smooth Muscle Cells: Modeling the Recruitment and Synchronization
Biophys. J. 2004 87: 92-104. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Yingliang Wu, Zhijian Cao, Hong Yi, Dahe Jiang, Xin Mao, Hui Liu, and Wenxin Li

Simulation of the Interaction Between ScyTx and Small Conductance Calcium-Activated Potassium Channel by Docking and MM-PBSA
Biophys. J. 2004 87: 105-112. [Abstract] [Full Text] [PDF]  

David C. Sullivan and Irwin D. Kuntz

Distributions in Protein Conformation Space: Implications for Structure Prediction and Entropy
Biophys. J. 2004 87: 113-120. [Abstract] [Full Text] [PDF]  

P.-L. Chau

Water Movement during Ligand Unbinding from Receptor Site
Biophys. J. 2004 87: 121-128. [Abstract] [Full Text] [PDF]  

Hyunbum Jang, Paul S. Crozier, Mark J. Stevens, and Thomas B. Woolf

How Environment Supports a State: Molecular Dynamics Simulations of Two States in Bacteriorhodopsin Suggest Lipid and Water Compensation
Biophys. J. 2004 87: 129-145. [Abstract] [Full Text] [PDF]  

Hui-Hsu Tsai, David Zanuy, Nurit Haspel, Kannan Gunasekaran, Buyong Ma, Chung-Jung Tsai, and Ruth Nussinov

The Stability and Dynamics of the Human Calcitonin Amyloid Peptide DFNKF
Biophys. J. 2004 87: 146-158. [Abstract] [Full Text] [PDF]  

Denis B. Tikhonov, Ian R. Mellor, and Peter N. R. Usherwood

Modeling Noncompetitive Antagonism of a Nicotinic Acetylcholine Receptor
Biophys. J. 2004 87: 159-170. [Abstract] [Full Text] [PDF]  

Yves Dehouck, Dimitri Gilis, and Marianne Rooman

Database-Derived Potentials Dependent on Protein Size for In Silico Folding and Design
Biophys. J. 2004 87: 171-181. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Frank Y. Jiang, Yann Bouret, and James T. Kindt

Molecular Dynamics Simulations of the Lipid Bilayer Edge
Biophys. J. 2004 87: 182-192. [Abstract] [Full Text] [PDF]  

Charles L. Zimliki, David Mears, and Arthur Sherman

Three Roads to Islet Bursting: Emergent Oscillations in Coupled Phantom Bursters
Biophys. J. 2004 87: 193-206. [Abstract] [Full Text] [PDF]  

Taras V. Pogorelov and Zaida Luthey-Schulten

Variations in the Fast Folding Rates of the -Repressor: A Hybrid Molecular Dynamics Study
Biophys. J. 2004 87: 207-214. [Abstract] [Full Text] [PDF]  

Roumen A. Dimitrov and Michael Zuker

Prediction of Hybridization and Melting for Double-Stranded Nucleic Acids
Biophys. J. 2004 87: 215-226. [Abstract] [Full Text] [PDF]  

Eva Fadrná, Nad'a Spacková, Richard Stefl, Jaroslav Koca, Thomas E. Cheatham, 3rd, and Jirí Sponer

Molecular Dynamics Simulations of Guanine Quadruplex Loops: Advances and Force Field Limitations
Biophys. J. 2004 87: 227-242. [Abstract] [Full Text] [PDF] [Supplemental Material]  

CHANNELS, RECEPTORS, AND TRANSPORTERS:

Chiu Shuen Hui, Henry R. Besch, Jr., and Keshore R. Bidasee

Effects of Ryanoids on Spontaneous and Depolarization-Evoked Calcium Release Events in Frog Muscle
Biophys. J. 2004 87: 243-255. [Abstract] [Full Text] [PDF]  

Carmen Domene, Alessandro Grottesi, and Mark S. P. Sansom

Filter Flexibility and Distortion in a Bacterial Inward Rectifier K⁺ Channel: Simulation Studies of KirBac1.1
Biophys. J. 2004 87: 256-267. [Abstract] [Full Text] [PDF]  

Claude Collet and Jianjie Ma

Calcium-Dependent Facilitation and Graded Deactivation of Store-Operated Calcium Entry in Fetal Skeletal Muscle
Biophys. J. 2004 87: 268-275. [Abstract] [Full Text] [PDF]  

James J. Celentano and Alan G. Hawkes

Use of the Covariance Matrix in Directly Fitting Kinetic Parameters: Application to GABA_A Receptors
Biophys. J. 2004 87: 276-294. [Abstract] [Full Text] [PDF]  

Steven A. Huntley, Daniel Krofchick, and Mel Silverman

Position 170 of Rabbit Na⁺/Glucose Cotransporter (rSGLT1) Lies in the Na⁺ Pathway; Modulation of Polarity/Charge at this Site Regulates Charge Transfer and Carrier Turnover
Biophys. J. 2004 87: 295-310. [Abstract] [Full Text] [PDF]  

Travis Hughes, Bradley Strongin, Fei Philip Gao, Viksita Vijayvergiya, David D. Busath, and Robert C. Davis

AFM Visualization of Mobile Influenza A M2 Molecules in Planar Bilayers
Biophys. J. 2004 87: 311-322. [Abstract] [Full Text] [PDF]  

MEMBRANES:

Charlene C. Ng, Yu-Ling Cheng, and Peter S. Pennefather

Properties of a Self-Assembled Phospholipid Membrane Supported on Lipobeads
Biophys. J. 2004 87: 323-331. [Abstract] [Full Text] [PDF]  

Hans Binder and Göran Lindblom

A Molecular View on the Interaction of the Trojan Peptide Penetratin with the Polar Interface of Lipid Bilayers
Biophys. J. 2004 87: 332-343. [Abstract] [Full Text] [PDF]  

Fábio Fernandes, Luís M. S. Loura, Rob Koehorst, Ruud B. Spruijt, Marcus A. Hemminga, Alexander Fedorov, and Manuel Prieto

Quantification of Protein-Lipid Selectivity using FRET: Application to the M13 Major Coat Protein
Biophys. J. 2004 87: 344-352. [Abstract] [Full Text] [PDF]  

Magda S. C. Abreu, Maria Joao Moreno, and Winchil L. C. Vaz

Kinetics and Thermodynamics of Association of a Phospholipid Derivative with Lipid Bilayers in Liquid-Disordered and Liquid-Ordered Phases
Biophys. J. 2004 87: 353-365. [Abstract] [Full Text] [PDF]  

D. P. Siegel and M. M. Kozlov

The Gaussian Curvature Elastic Modulus of N-Monomethylated Dioleoylphosphatidylethanolamine: Relevance to Membrane Fusion and Lipid Phase Behavior
Biophys. J. 2004 87: 366-374. [Abstract] [Full Text] [PDF]  

Tomohiro Kimura, Emiko Okamura, Nobuyuki Matubayasi, Koji Asami, and Masaru Nakahara

NMR Study on the Binding of Neuropeptide Achatin-I to Phospholipid Bilayer: The Equilibrium, Location, and Peptide Conformation
Biophys. J. 2004 87: 375-385. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Kerstin Wagner, Nicole Van Mau, Sylvie Boichot, Andrey V. Kajava, Ulrike Krauss, Christian Le Grimellec, Annette Beck-Sickinger, and Frédéric Heitz

Interactions of the Human Calcitonin Fragment 9–32 with Phospholipids: A Monolayer Study
Biophys. J. 2004 87: 386-395. [Abstract] [Full Text] [PDF]  

Alexander Spaar, Christian Münster, and Tim Salditt

Conformation of Peptides in Lipid Membranes Studied by X-Ray Grazing Incidence Scattering
Biophys. J. 2004 87: 396-407. [Abstract] [Full Text] [PDF]  

Chad Leidy, Ole G. Mouritsen, Kent Jørgensen, and Günther H. Peters

Evolution of a Rippled Membrane during Phospholipase A₂ Hydrolysis Studied by Time-Resolved AFM
Biophys. J. 2004 87: 408-418. [Abstract] [Full Text] [PDF]  

Philippe Girard, Jacques Pécréaux, Guillaume Lenoir, Pierre Falson, Jean-Louis Rigaud, and Patricia Bassereau

A New Method for the Reconstitution of Membrane Proteins into Giant Unilamellar Vesicles
Biophys. J. 2004 87: 419-429. [Abstract] [Full Text] [PDF]  

MUSCLE AND CONTRACTILITY:

Jun'ichi Wakayama, Takumi Tamura, Naoto Yagi, and Hiroyuki Iwamoto

Structural Transients of Contractile Proteins upon Sudden ATP Liberation in Skeletal Muscle Fibers
Biophys. J. 2004 87: 430-441. [Abstract] [Full Text] [PDF]  

David A. Smith and John Sleep

Mechanokinetics of Rapid Tension Recovery in Muscle: The Myosin Working Stroke Is Followed by a Slower Release of Phosphate
Biophys. J. 2004 87: 442-456. [Abstract] [Full Text] [PDF]  

NUCLEIC ACIDS:

Goran Pljevaljcic, David P. Millar, and Ashok A. Deniz

Freely Diffusing Single Hairpin Ribozymes Provide Insights into the Role of Secondary Structure and Partially Folded States in RNA Folding
Biophys. J. 2004 87: 457-467. [Abstract] [Full Text] [PDF]  

Sean Ferree and Harvey W. Blanch

The Hydrodynamics of DNA Electrophoretic Stretch and Relaxation in a Polymer Solution
Biophys. J. 2004 87: 468-475. [Abstract] [Full Text] [PDF]  

PHOTOBIOPHYSICS:

C. Benda, C. Scheufler, N. Tandeau de Marsac, and W. Gärtner

Crystal Structures of Two Cyanobacterial Response Regulators in Apo- and Phosphorylated Form Reveal a Novel Dimerization Motif of Phytochrome-Associated Response Regulators
Biophys. J. 2004 87: 476-487. [Abstract] [Full Text] [PDF]  

Robert C. Jennings, Giuseppe Zucchelli, Enrico Engelmann, and Flavio M. Garlaschi

The Long-Wavelength Chlorophyll States of Plant LHCI at Room Temperature: A Comparison with PSI-LHCI
Biophys. J. 2004 87: 488-497. [Abstract] [Full Text] [PDF]  

PROTEINS:

Andrea Giachetti, Giovanni La Penna, Angelo Perico, and Lucia Banci

Modeling the Backbone Dynamics of Reduced and Oxidized Solvated Rat Microsomal Cytochrome b₅
Biophys. J. 2004 87: 498-512. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Francesc Sepulcre, M. Grazia Proietti, Maurizio Benfatto, Stefano Della Longa, Joaquin García, and Esteve Padrós

A Quantitative XANES Analysis of the Calcium High-Affinity Binding Site of the Purple Membrane
Biophys. J. 2004 87: 513-520. [Abstract] [Full Text] [PDF]  

Jose M. Borreguero, Feng Ding, Sergey V. Buldyrev, H. Eugene Stanley, and Nikolay V. Dokholyan

Multiple Folding Pathways of the SH3 Domain
Biophys. J. 2004 87: 521-533. [Abstract] [Full Text] [PDF]  

William Braunlin, Qiuwei Xu, Patrick Hook, Richard Fitzpatrick, Jeffrey D. Klinger, Robert Burrier, and Caroline B. Kurtz

Toxin Binding of Tolevamer, a Polyanionic Drug that Protects against Antibiotic-Associated Diarrhea
Biophys. J. 2004 87: 534-539. [Abstract] [Full Text] [PDF]  

Alexandra S. Solovyova, Marcelo Nöllmann, Timothy J. Mitchell, and Olwyn Byron

The Solution Structure and Oligomerization Behavior of Two Bacterial Toxins: Pneumolysin and Perfringolysin O
Biophys. J. 2004 87: 540-552. [Abstract] [Full Text] [PDF]  

Janos Vörös

The Density and Refractive Index of Adsorbing Protein Layers
Biophys. J. 2004 87: 553-561. [Abstract] [Full Text] [PDF]  

Arjan van der Vaart, Jianpeng Ma, and Martin Karplus

The Unfolding Action of GroEL on a Protein Substrate
Biophys. J. 2004 87: 562-573. [Abstract] [Full Text] [PDF]  

Paul L. Sorgen, Heather S. Duffy, David C. Spray, and Mario Delmar

pH-Dependent Dimerization of the Carboxyl Terminal Domain of Cx43
Biophys. J. 2004 87: 574-581. [Abstract] [Full Text] [PDF]  

Dimitri A. Svistunenko and Chris E. Cooper

A New Method of Identifying the Site of Tyrosyl Radicals in Proteins
Biophys. J. 2004 87: 582-595. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Wei Yuan Yang and Martin Gruebele

Folding -Repressor at Its Speed Limit
Biophys. J. 2004 87: 596-608. [Abstract] [Full Text] [PDF]  

SUPRAMOLECULAR ASSEMBLIES:

Sarah Weisman, Danielle Hirsch-Lerner, Yechezkel Barenholz, and Yeshayahu Talmon

Nanostructure of Cationic Lipid-Oligonucleotide Complexes
Biophys. J. 2004 87: 609-614. [Abstract] [Full Text] [PDF]  

Jonathan Nakane, Matthew Wiggin, and Andre Marziali

A Nanosensor for Transmembrane Capture and Identification of Single Nucleic Acid Molecules
Biophys. J. 2004 87: 615-621. [Abstract] [Full Text] [PDF]  

SPECTROSCOPY, IMAGING, OTHER TECHNIQUES:

Ganesh Shanmugam and Prasad L. Polavarapu

Structure of Aß(25–35) Peptide in Different Environments
Biophys. J. 2004 87: 622-630. [Abstract] [Full Text] [PDF]  

Bernd Kuhn, Peter Fromherz, and Winfried Denk

High Sensitivity of Stark-Shift Voltage-Sensing Dyes by One- or Two-Photon Excitation Near the Red Spectral Edge
Biophys. J. 2004 87: 631-639. [Abstract] [Full Text] [PDF]  

L. Kreplak, J. Doucet, P. Dumas, and F. Briki

New Aspects of the -Helix to ß-Sheet Transition in Stretched Hard -Keratin Fibers
Biophys. J. 2004 87: 640-647. [Abstract] [Full Text] [PDF]  

Oksana Kostyuk and Robert A. Brown

Novel Spectroscopic Technique for In Situ Monitoring of Collagen Fibril Alignment in Gels
Biophys. J. 2004 87: 648-655. [Abstract] [Full Text] [PDF]  

Dehong Hu and H. Peter Lu

Placing Single-Molecule T4 Lysozyme Enzymes on a Bacterial Cell Surface: Toward Probing Single-Molecule Enzymatic Reaction in Living Cells
Biophys. J. 2004 87: 656-661. [Abstract] [Full Text] [PDF]  

Orsolya Toke, W. Lee Maloy, Sung Joon Kim, Jack Blazyk, and Jacob Schaefer

Secondary Structure and Lipid Contact of a Peptide Antibiotic in Phospholipid Bilayers by REDOR
Biophys. J. 2004 87: 662-674. [Abstract] [Full Text] [PDF]  

Orsolya Toke, R. D. O'Connor, Thomas K. Weldeghiorghis, W. Lee Maloy, Ralf W. Glaser, Anne S. Ulrich, and Jacob Schaefer

Structure of (KIAGKIA)₃ Aggregates in Phospholipid Bilayers by Solid-State NMR
Biophys. J. 2004 87: 675-687. [Abstract] [Full Text] [PDF]  

CELL BIOPHYSICS:

Doncho V. Zhelev, Abdullatif M. Alteraifi, and David Chodniewicz

Controlled Pseudopod Extension of Human Neutrophils Stimulated with Different Chemoattractants
Biophys. J. 2004 87: 688-695. [Abstract] [Full Text] [PDF]  

BIOENERGETICS:

Marko Vendelin, Maris Lemba, and Valdur A. Saks

Analysis of Functional Coupling: Mitochondrial Creatine Kinase and Adenine Nucleotide Translocase
Biophys. J. 2004 87: 696-713. [Abstract] [Full Text] [PDF]  

ELECTROPHYSIOLOGY:

Joseph Santos-Sacchi

Determination of Cell Capacitance Using the Exact Empirical Solution of Y/C_m and Its Phase Angle
Biophys. J. 2004 87: 714-727. [Abstract] [Full Text] [PDF]  

LETTERS TO THE EDITOR:

Joanna Masel and Vincent A. A. Jansen

Prion Kinetics
Biophys. J. 2004 87: 728(1) [Full Text] [PDF]  

Thorsten Pöschel, Nikolai V. Brilliantov, and Cornelius Frömmel

Reply to "Prion Kinetics"
Biophys. J. 2004 87: 729(1) [Full Text] [PDF]  

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