NEW AND NOTABLE:

Martin Oheim

A Deeper Look into Single-Secretory Vesicle Dynamics
Biophys. J. 2004 87: 1403-1405. [Full Text] [PDF]  

BIOPHYSICAL THEORY AND MODELING:

Thomas J. Lukas

A Signal Transduction Pathway Model Prototype I: From Agonist to Cellular Endpoint
Biophys. J. 2004 87: 1406-1416. [Abstract] [Full Text] [PDF]  

Thomas J. Lukas

A Signal Transduction Pathway Model Prototype II: Application to Ca²⁺-Calmodulin Signaling and Myosin Light Chain Phosphorylation
Biophys. J. 2004 87: 1417-1425. [Abstract] [Full Text] [PDF]  

Isabelle Navizet, Fabien Cailliez, and Richard Lavery

Probing Protein Mechanics: Residue-Level Properties and Their Use in Defining Domains
Biophys. J. 2004 87: 1426-1435. [Abstract] [Full Text] [PDF]  

Torsten Becker, Jennifer A. Hayward, John L. Finney, Roy M. Daniel, and Jeremy C. Smith

Neutron Frequency Windows and the Protein Dynamical Transition
Biophys. J. 2004 87: 1436-1444. [Abstract] [Full Text] [PDF]  

Rob B. M. Koehorst, Ruud B. Spruijt, Frank J. Vergeldt, and Marcus A. Hemminga

Lipid Bilayer Topology of the Transmembrane -Helix of M13 Major Coat Protein and Bilayer Polarity Profile by Site-Directed Fluorescence Spectroscopy
Biophys. J. 2004 87: 1445-1455. [Abstract] [Full Text] [PDF]  

Gwangrog Lee, Wieslaw Nowak, Justyna Jaroniec, Qingmin Zhang, and Piotr E. Marszalek

Molecular Dynamics Simulations of Forced Conformational Transitions in 1,6-Linked Polysaccharides
Biophys. J. 2004 87: 1456-1465. [Abstract] [Full Text] [PDF]  

Kevin Klapstein, Tom Chou, and Robijn Bruinsma

Physics of RecA-Mediated Homologous Recognition
Biophys. J. 2004 87: 1466-1477. [Abstract] [Full Text] [PDF]  

Ioan Andricioaei, Anita Goel, Dudley Herschbach, and Martin Karplus

Dependence of DNA Polymerase Replication Rate on External Forces: A Model Based on Molecular Dynamics Simulations
Biophys. J. 2004 87: 1478-1497. [Abstract] [Full Text] [PDF]  

Kosmas Kosmidis, Vangelis Karalis, Panos Argyrakis, and Panos Macheras

Michaelis-Menten Kinetics under Spatially Constrained Conditions: Application to Mibefradil Pharmacokinetics
Biophys. J. 2004 87: 1498-1506. [Abstract] [Full Text] [PDF]  

Vivek Iyer, Reza Mazhari, and Raimond L. Winslow

A Computational Model of the Human Left-Ventricular Epicardial Myocyte
Biophys. J. 2004 87: 1507-1525. [Abstract] [Full Text] [PDF]  

Denis B. Tikhonov and Boris S. Zhorov

In Silico Activation of KcsA K⁺ Channel by Lateral Forces Applied to the C-Termini of Inner Helices
Biophys. J. 2004 87: 1526-1536. [Abstract] [Full Text] [PDF]  

Noam Agmon

Coupling of Protein Relaxation to Ligand Binding and Migration in Myoglobin
Biophys. J. 2004 87: 1537-1543. [Abstract] [Full Text] [PDF]  

Alexander Rubinstein and Simon Sherman

Influence of the Solvent Structure on the Electrostatic Interactions in Proteins
Biophys. J. 2004 87: 1544-1557. [Abstract] [Full Text] [PDF]  

Yuhua Song, Yongjie Zhang, Chandrajit L. Bajaj, and Nathan A. Baker

Continuum Diffusion Reaction Rate Calculations of Wild-Type and Mutant Mouse Acetylcholinesterase: Adaptive Finite Element Analysis
Biophys. J. 2004 87: 1558-1566. [Abstract] [Full Text] [PDF]  

Roosevelt Alves da Silva, Léo Degrève, and Antonio Caliri

LMProt: An Efficient Algorithm for Monte Carlo Sampling of Protein Conformational Space
Biophys. J. 2004 87: 1567-1577. [Abstract] [Full Text] [PDF]  

Bernardo A. Mello, Leah Shaw, and Yuhai Tu

Effects of Receptor Interaction in Bacterial Chemotaxis
Biophys. J. 2004 87: 1578-1595. [Abstract] [Full Text] [PDF]  

Marieke Kranenburg, Martin Vlaar, and Berend Smit

Simulating Induced Interdigitation in Membranes
Biophys. J. 2004 87: 1596-1605. [Abstract] [Full Text] [PDF]  

Jan Hrabe, Sabina Hrabetová, and Karel Segeth

A Model of Effective Diffusion and Tortuosity in the Extracellular Space of the Brain
Biophys. J. 2004 87: 1606-1617. [Abstract] [Full Text] [PDF]  

Ting Wang, Sanja Tomic, Razif R. Gabdoulline, and Rebecca C. Wade

How Optimal Are the Binding Energetics of Barnase and Barstar?
Biophys. J. 2004 87: 1618-1630. [Abstract] [Full Text] [PDF]  

Brian M. Baynes and Bernhardt L. Trout

Rational Design of Solution Additives for the Prevention of Protein Aggregation
Biophys. J. 2004 87: 1631-1639. [Abstract] [Full Text] [PDF]  

M. Coppey, O. Bénichou, R. Voituriez, and M. Moreau

Kinetics of Target Site Localization of a Protein on DNA: A Stochastic Approach
Biophys. J. 2004 87: 1640-1649. [Abstract] [Full Text] [PDF]  

Thomas Stockner, Walter L. Ash, Justin L. MacCallum, and D. Peter Tieleman

Direct Simulation of Transmembrane Helix Association: Role of Asparagines
Biophys. J. 2004 87: 1650-1656. [Abstract] [Full Text] [PDF]  

CHANNELS, RECEPTORS, AND ELECTRICAL SIGNALING:

Feng Qin and Ling Li

Model-Based Fitting of Single-Channel Dwell-Time Distributions
Biophys. J. 2004 87: 1657-1671. [Abstract] [Full Text] [PDF]  

Ravshan Z. Sabirov and Yasunobu Okada

Wide Nanoscopic Pore of Maxi-Anion Channel Suits its Function as an ATP-Conductive Pathway
Biophys. J. 2004 87: 1672-1685. [Abstract] [Full Text] [PDF]  

David L. Bostick and Max L. Berkowitz

Exterior Site Occupancy Infers Chloride-Induced Proton Gating in a Prokaryotic Homolog of the ClC Chloride Channel
Biophys. J. 2004 87: 1686-1696. [Abstract] [Full Text] [PDF]  

Viksita Vijayvergiya, Ryan Wilson, Adam Chorak, Philip Fei Gao, Timothy A. Cross, and David D. Busath

Proton Conductance of Influenza Virus M2 Protein in Planar Lipid Bilayers
Biophys. J. 2004 87: 1697-1704. [Abstract] [Full Text] [PDF]  

H. Duclohier, G. M. Alder, C. L. Bashford, H. Brückner, J. K. Chugh, and B. A. Wallace

Conductance Studies on Trichotoxin_A50E and Implications for Channel Structure
Biophys. J. 2004 87: 1705-1710. [Abstract] [Full Text] [PDF]  

MEMBRANES:

Fernanda F. Rossetti, Ilya Reviakine, Gábor Csúcs, Fabiano Assi, János Vörös, and Marcus Textor

Interaction of Poly(L-Lysine)-g-Poly(Ethylene Glycol) with Supported Phospholipid Bilayers
Biophys. J. 2004 87: 1711-1721. [Abstract] [Full Text] [PDF]  

Howard L. Brockman, Maureen M. Momsen, Rhoderick E. Brown, Linli He, Jiong Chun, Hoe-Sup Byun, and Robert Bittman

The 4,5-Double Bond of Ceramide Regulates Its Dipole Potential, Elastic Properties, and Packing Behavior
Biophys. J. 2004 87: 1722-1731. [Abstract] [Full Text] [PDF]  

Canay Ege and Ka Yee C. Lee

Insertion of Alzheimer's Aß40 Peptide into Lipid Monolayers
Biophys. J. 2004 87: 1732-1740. [Abstract] [Full Text] [PDF]  

Ivan V. Polozov and Klaus Gawrisch

Domains in Binary SOPC/POPE Lipid Mixtures Studied by Pulsed Field Gradient ¹H MAS NMR
Biophys. J. 2004 87: 1741-1751. [Abstract] [Full Text] [PDF]  

Saame Raza Shaikh, Alfred C. Dumaual, Alicia Castillo, Daniel LoCascio, Rafat A. Siddiqui, William Stillwell, and Stephen R. Wassall

Oleic and Docosahexaenoic Acid Differentially Phase Separate from Lipid Raft Molecules: A Comparative NMR, DSC, AFM, and Detergent Extraction Study
Biophys. J. 2004 87: 1752-1766. [Abstract] [Full Text] [PDF]  

MUSCLE AND CONTRACTILITY:

Marilyn van Duffelen, Lynn R. Chrin, and Christopher L. Berger

Nucleotide Dependent Intrinsic Fluorescence Changes of W29 and W36 in Smooth Muscle Myosin
Biophys. J. 2004 87: 1767-1775. [Abstract] [Full Text] [PDF]  

Gregory E. Snyder, Takeshi Sakamoto, John A. Hammer, III, James R. Sellers, and Paul R. Selvin

Nanometer Localization of Single Green Fluorescent Proteins: Evidence that Myosin V Walks Hand-Over-Hand via Telemark Configuration
Biophys. J. 2004 87: 1776-1783. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Bishow B. Adhikari, Michael Regnier, Anthony J. Rivera, Kareen L. Kreutziger, and Donald A. Martyn

Cardiac Length Dependence of Force and Force Redevelopment Kinetics with Altered Cross-Bridge Cycling
Biophys. J. 2004 87: 1784-1794. [Abstract] [Full Text] [PDF]  

Yangrong Zhang and William O. Hancock

The Two Motor Domains of KIF3A/B Coordinate for Processive Motility and Move at Different Speeds
Biophys. J. 2004 87: 1795-1804. [Abstract] [Full Text] [PDF]  

Douglas M. Swank, William A. Kronert, Sanford I. Bernstein, and David W. Maughan

Alternative N-Terminal Regions of Drosophila Myosin Heavy Chain Tune Muscle Kinetics for Optimal Power Output
Biophys. J. 2004 87: 1805-1814. [Abstract] [Full Text] [PDF]  

M. Regnier, H. Martin, R. J. Barsotti, A. J. Rivera, D. A. Martyn, and E. Clemmens

Cross-Bridge versus Thin Filament Contributions to the Level and Rate of Force Development in Cardiac Muscle
Biophys. J. 2004 87: 1815-1824. [Abstract] [Full Text] [PDF]  

Boris Gafurov, Yi-Der Chen, and Joseph M. Chalovich

Ca²⁺ and Ionic Strength Dependencies of S1-ADP Binding to Actin-Tropomyosin-Troponin: Regulatory Implications
Biophys. J. 2004 87: 1825-1835. [Abstract] [Full Text] [PDF]  

Edwin D. Moore, Tilman Voigt, Yvonne M. Kobayashi, Gerrit Isenberg, Fred S. Fay, Maria F. Gallitelli, and Clara Franzini-Armstrong

Organization of Ca²⁺ Release Units in Excitable Smooth Muscle of the Guinea-Pig Urinary Bladder
Biophys. J. 2004 87: 1836-1847. [Abstract] [Full Text] [PDF]  

PHOTOBIOPHYSICS:

Mikas Vengris, Michael A. van der Horst, Goran Zgrablic, Ivo H. M. van Stokkum, Stefan Haacke, Majed Chergui, Klaas J. Hellingwerf, Rienk van Grondelle, and Delmar S. Larsen

Contrasting the Excited-State Dynamics of the Photoactive Yellow Protein Chromophore: Protein versus Solvent Environments
Biophys. J. 2004 87: 1848-1857. [Abstract] [Full Text] [PDF]  

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

Incoherent Manipulation of the Photoactive Yellow Protein Photocycle with Dispersed Pump-Dump-Probe Spectroscopy
Biophys. J. 2004 87: 1858-1872. [Abstract] [Full Text] [PDF]  

Lymari Fuentes, Jessica Oyola, Mónica Fernández, and Edwin Quiñones

Conformational Changes in Azurin from Pseudomona aeruginosa Induced through Chemical and Physical Protocols
Biophys. J. 2004 87: 1873-1880. [Abstract] [Full Text] [PDF]  

Jan Helbing, Luigi Bonacina, Ruth Pietri, Jens Bredenbeck, Peter Hamm, Frank van Mourik, Frédéric Chaussard, Alejandro Gonzalez-Gonzalez, Majed Chergui, Cacimar Ramos-Alvarez, Carlos Ruiz, and Juan López-Garriga

Time-Resolved Visible and Infrared Study of the Cyano Complexes of Myoglobin and of Hemoglobin I from Lucina pectinata
Biophys. J. 2004 87: 1881-1891. [Abstract] [Full Text] [PDF]  

PROTEINS:

Kenneth D. Osborn, Asma Zaidi, Abhijit Mandal, Ramona J. Bieber Urbauer, and Carey K. Johnson

Single-Molecule Dynamics of the Calcium-Dependent Activation of Plasma-Membrane Ca²⁺-ATPase by Calmodulin
Biophys. J. 2004 87: 1892-1899. [Abstract] [Full Text] [PDF] [Supplemental Material]  

John M. Finke, Margaret S. Cheung, and José N. Onuchic

A Structural Model of Polyglutamine Determined from a Host-Guest Method Combining Experiments and Landscape Theory
Biophys. J. 2004 87: 1900-1918. [Abstract] [Full Text] [PDF]  

X. Wang, H. P. Permentier, R. Rink, J. A. W. Kruijtzer, R. M. J. Liskamp, H. A. B. Wösten, B. Poolman, and G. T. Robillard

Probing the Self-Assembly and the Accompanying Structural Changes of Hydrophobin SC3 on a Hydrophobic Surface by Mass Spectrometry
Biophys. J. 2004 87: 1919-1928. [Abstract] [Full Text] [PDF]  

Ingemar André, Tõnu Kesvatera, Bo Jönsson, Karin S. Åkerfeldt, and Sara Linse

The Role of Electrostatic Interactions in Calmodulin-Peptide Complex Formation
Biophys. J. 2004 87: 1929-1938. [Abstract] [Full Text] [PDF]  

François J. M. Chartier and Manon Couture

Stability of the Heme Environment of the Nitric Oxide Synthase from Staphylococcus aureus in the Absence of Pterin Cofactor
Biophys. J. 2004 87: 1939-1950. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Jun Yang, Mary Prorok, Francis J. Castellino, and David P. Weliky

Oligomeric ß-Structure of the Membrane-Bound HIV-1 Fusion Peptide Formed from Soluble Monomers
Biophys. J. 2004 87: 1951-1963. [Abstract] [Full Text] [PDF]  

SPECTROSCOPY, IMAGING, OTHER TECHNIQUES:

H. Wang, R. Bash, J. G. Yodh, G. Hager, S. M. Lindsay, and D. Lohr

Using Atomic Force Microscopy to Study Nucleosome Remodeling on Individual Nucleosomal Arrays in Situ
Biophys. J. 2004 87: 1964-1971. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Rajalakshmi Nambiar, Arivalagan Gajraj, and Jens-Christian Meiners

All-Optical Constant-Force Laser Tweezers
Biophys. J. 2004 87: 1972-1980. [Abstract] [Full Text] [PDF]  

Cordula M. Stroh, Andreas Ebner, Manfred Geretschläger, Günter Freudenthaler, Ferry Kienberger, A. S. M. Kamruzzahan, Sandra J. Smith-Gill, Hermann J. Gruber, and Peter Hinterdorfer

Simultaneous Topography and Recognition Imaging Using Force Microscopy
Biophys. J. 2004 87: 1981-1990. [Abstract] [Full Text] [PDF]  

Dongdong Li, Jun Xiong, Anlian Qu, and Tao Xu

Three-Dimensional Tracking of Single Secretory Granules in Live PC12 Cells
Biophys. J. 2004 87: 1991-2001. [Abstract] [Full Text] [PDF]  

Rachel Marrington, Timothy R. Dafforn, David J. Halsall, and Alison Rodger

Micro-Volume Couette Flow Sample Orientation for Absorbance and Fluorescence Linear Dichroism
Biophys. J. 2004 87: 2002-2012. [Abstract] [Full Text] [PDF]  

CELL BIOPHYSICS:

Guido Böse, Petra Schwille, and Tilman Lamparter

The Mobility of Phytochrome within Protonemal Tip Cells of the Moss Ceratodon purpureus, Monitored by Fluorescence Correlation Spectroscopy
Biophys. J. 2004 87: 2013-2021. [Abstract] [Full Text] [PDF]  

Nathan R. Brady, Steven P. Elmore, Johannes J. H. G. M. van Beek, Klaas Krab, Pierre J. Courtoy, Louis Hue, and Hans V. Westerhoff

Coordinated Behavior of Mitochondria in Both Space and Time: A Reactive Oxygen Species-Activated Wave of Mitochondrial Depolarization
Biophys. J. 2004 87: 2022-2034. [Abstract] [Full Text] [PDF] [Supplemental]  

Mark F. Coughlin and Geert W. Schmid-Schönbein

Pseudopod Projection and Cell Spreading of Passive Leukocytes in Response to Fluid Shear Stress
Biophys. J. 2004 87: 2035-2042. [Abstract] [Full Text] [PDF]  

BIOENERGETICS:

Elizabeth L. Gross

A Brownian Dynamics Study of the Interaction of Phormidium laminosum Plastocyanin with Phormidium laminosum Cytochrome f
Biophys. J. 2004 87: 2043-2059. [Abstract] [Full Text] [PDF]  

Sonia Cortassa, Miguel A. Aon, Raimond L. Winslow, and Brian O'Rourke

A Mitochondrial Oscillator Dependent on Reactive Oxygen Species
Biophys. J. 2004 87: 2060-2073. [Abstract] [Full Text] [PDF]  

OTHER:

Hiroshi Watanabe, Seiryo Sugiura, Hidenobu Kafuku, and Toshiaki Hisada

Multiphysics Simulation of Left Ventricular Filling Dynamics Using Fluid-Structure Interaction Finite Element Method
Biophys. J. 2004 87: 2074-2085. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Aleksij Aksimentiev, Jiunn B. Heng, Gregory Timp, and Klaus Schulten

Microscopic Kinetics of DNA Translocation through Synthetic Nanopores
Biophys. J. 2004 87: 2086-2097. [Abstract] [Full Text] [PDF] [Supplemental Material]  

CORRECTIONS:

Correction
Biophys. J. 2004 87: 2098(3) [Full Text] [PDF]  

Correction
Biophys. J. 2004 87: 2099(3) [Full Text] [PDF]  

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