BIOPHYSICAL THEORY AND MODELING:

Imre Derényi, Denis Bartolo, and Armand Ajdari

Effects of Intermediate Bound States in Dynamic Force Spectroscopy
Biophys. J. 2004 86: 1263-1269. [Abstract] [Full Text] [PDF]  

Xiao-jiang Feng and Herschel Rabitz

Optimal Identification of Biochemical Reaction Networks
Biophys. J. 2004 86: 1270-1281. [Abstract] [Full Text] [PDF]  

Moisés Santillán and Michael C. Mackey

Influence of Catabolite Repression and Inducer Exclusion on the Bistable Behavior of the lac Operon
Biophys. J. 2004 86: 1282-1292. [Abstract] [Full Text] [PDF]  

R. Hinch

A Mathematical Analysis of the Generation and Termination of Calcium Sparks
Biophys. J. 2004 86: 1293-1307. [Abstract] [Full Text] [PDF]  

Karen A. Selz, Arnold J. Mandell, Michael F. Shlesinger, Vani Arcuragi, and Michael J. Owens

Designing Human m₁ Muscarinic Receptor-Targeted Hydrophobic Eigenmode Matched Peptides as Functional Modulators
Biophys. J. 2004 86: 1308-1331. [Abstract] [Full Text] [PDF]  

Aleksij Aksimentiev, Ilya A. Balabin, Robert H. Fillingame, and Klaus Schulten

Insights into the Molecular Mechanism of Rotation in the F_o Sector of ATP Synthase
Biophys. J. 2004 86: 1332-1344. [Abstract] [Full Text] [PDF]  

Sagar A. Pandit, David Bostick, and Max L. Berkowitz

Complexation of Phosphatidylcholine Lipids with Cholesterol
Biophys. J. 2004 86: 1345-1356. [Abstract] [Full Text] [PDF]  

Jacek Puchalka and Andrzej M. Kierzek

Bridging the Gap between Stochastic and Deterministic Regimes in the Kinetic Simulations of the Biochemical Reaction Networks
Biophys. J. 2004 86: 1357-1372. [Abstract] [Full Text] [PDF] [Supplemental Materials]  

Sean X. Sun, Hongyun Wang, and George Oster

Asymmetry in the F₁-ATPase and Its Implications for the Rotational Cycle
Biophys. J. 2004 86: 1373-1384. [Abstract] [Full Text] [PDF]  

C. Nicolini, R. Ravindra, B. Ludolph, and R. Winter

Characterization of the Temperature- and Pressure-Induced Inverse and Reentrant Transition of the Minimum Elastin-Like Polypeptide GVG(VPGVG) by DSC, PPC, CD, and FT-IR Spectroscopy
Biophys. J. 2004 86: 1385-1392. [Abstract] [Full Text] [PDF]  

Roger Rousseau, Eduard Schreiner, Axel Kohlmeyer, and Dominik Marx

Temperature-Dependent Conformational Transitions and Hydrogen-Bond Dynamics of the Elastin-Like Octapeptide GVG(VPGVG): A Molecular-Dynamics Study
Biophys. J. 2004 86: 1393-1407. [Abstract] [Full Text] [PDF]  

Daniel Coombs, Micah Dembo, Carla Wofsy, and Byron Goldstein

Equilibrium Thermodynamics of Cell-Cell Adhesion Mediated by Multiple Ligand-Receptor Pairs
Biophys. J. 2004 86: 1408-1423. [Abstract] [Full Text] [PDF]  

CHANNELS, RECEPTORS, AND TRANSPORTERS:

Gabriel A. Cook, Om Prakash, Ke Zhang, Lalida P. Shank, Wade A. Takeguchi, Ashley Robbins, Yu-Xi Gong, Takeo Iwamoto, Bruce D. Schultz, and John M. Tomich

Activity and Structural Comparisons of Solution Associating and Monomeric Channel-Forming Peptides Derived from the Glycine Receptor M2 Segment
Biophys. J. 2004 86: 1424-1435. [Abstract] [Full Text] [PDF]  

Péter Szentesi, Henrietta Szappanos, Csaba Szegedi, Monika Gönczi, István Jona, Julianna Cseri, László Kovács, and László Csernoch

Altered Elementary Calcium Release Events and Enhanced Calcium Release by Thymol in Rat Skeletal Muscle
Biophys. J. 2004 86: 1436-1453. [Abstract] [Full Text] [PDF]  

David L. Prole and Neil V. Marrion

Ionic Permeation and Conduction Properties of Neuronal KCNQ2/KCNQ3 Potassium Channels
Biophys. J. 2004 86: 1454-1469. [Abstract] [Full Text] [PDF]  

Gina M. Yanochko and Andrea J. Yool

Block by Extracellular Divalent Cations of Drosophila Big Brain Channels Expressed in Xenopus Oocytes
Biophys. J. 2004 86: 1470-1478. [Abstract] [Full Text] [PDF]  

Dirk Linke, Joachim Frank, Matthew S. Pope, Jürgen Soll, Iryna Ilkavets, Petra Fromme, Edward A. Burstein, Yana K. Reshetnyak, and Victor I. Emelyanenko

Folding Kinetics and Structure of OEP16
Biophys. J. 2004 86: 1479-1487. [Abstract] [Full Text] [PDF]  

Feng Qin

Restoration of Single-Channel Currents Using the Segmental k-Means Method Based on Hidden Markov Modeling
Biophys. J. 2004 86: 1488-1501. [Abstract] [Full Text] [PDF]  

Yang Qu and Gerhard Dahl

Accessibility of cx46 Hemichannels for Uncharged Molecules and Its Modulation by Voltage
Biophys. J. 2004 86: 1502-1509. [Abstract] [Full Text] [PDF]  

MEMBRANES:

Juha M. Holopainen, Antti J. Metso, Juha-Pekka Mattila, Arimatti Jutila, and Paavo K. J. Kinnunen

Evidence for the Lack of a Specific Interaction between Cholesterol and Sphingomyelin
Biophys. J. 2004 86: 1510-1520. [Abstract] [Full Text] [PDF]  

Zoltán Kóta, Tibor Páli, and Derek Marsh

Orientation and Lipid-Peptide Interactions of Gramicidin A in Lipid Membranes: Polarized Attenuated Total Reflection Infrared Spectroscopy and Spin-Label Electron Spin Resonance
Biophys. J. 2004 86: 1521-1531. [Abstract] [Full Text] [PDF]  

Amanda Parker, Keith Miles, Kwan Hon Cheng, and Juyang Huang

Lateral Distribution of Cholesterol in Dioleoylphosphatidylcholine Lipid Bilayers: Cholesterol-Phospholipid Interactions at High Cholesterol Limit
Biophys. J. 2004 86: 1532-1544. [Abstract] [Full Text] [PDF]  

Stephanie Künneke, Daniel Krüger, and Andreas Janshoff

Scrutiny of the Failure of Lipid Membranes as a Function of Headgroups, Chain Length, and Lamellarity Measured by Scanning Force Microscopy
Biophys. J. 2004 86: 1545-1553. [Abstract] [Full Text] [PDF]  

Elisabete Gonçalves, Robert J. Debs, and Timothy D. Heath

The Effect of Liposome Size on the Final Lipid/DNA Ratio of Cationic Lipoplexes
Biophys. J. 2004 86: 1554-1563. [Abstract] [Full Text] [PDF]  

Paresh C. Dave, Elvis K. Tiburu, Krishnan Damodaran, and Gary A. Lorigan

Investigating Structural Changes in the Lipid Bilayer upon Insertion of the Transmembrane Domain of the Membrane-Bound Protein Phospholamban Utilizing ³¹P and ²H Solid-State NMR Spectroscopy
Biophys. J. 2004 86: 1564-1573. [Abstract] [Full Text] [PDF]  

Horia I. Petrache, Stephanie Tristram-Nagle, Klaus Gawrisch, Daniel Harries, V. Adrian Parsegian, and John F. Nagle

Structure and Fluctuations of Charged Phosphatidylserine Bilayers in the Absence of Salt
Biophys. J. 2004 86: 1574-1586. [Abstract] [Full Text] [PDF]  

Isabelle Marcotte, Frances Separovic, Michèle Auger, and Stéphane M. Gagné

A Multidimensional ¹H NMR Investigation of the Conformation of Methionine-Enkephalin in Fast-Tumbling Bicelles
Biophys. J. 2004 86: 1587-1600. [Abstract] [Full Text] [PDF]  

Parag Mukhopadhyay, Luca Monticelli, and D. Peter Tieleman

Molecular Dynamics Simulation of a Palmitoyl-Oleoyl Phosphatidylserine Bilayer with Na⁺ Counterions and NaCl
Biophys. J. 2004 86: 1601-1609. [Abstract] [Full Text] [PDF]  

A. James Mason, Stephan L. Grage, Suzana K. Straus, Clemens Glaubitz, and Anthony Watts

Identifying Anisotropic Constraints in Multiply Labeled Bacteriorhodopsin by ¹⁵N MAOSS NMR: A General Approach to Structural Studies of Membrane Proteins
Biophys. J. 2004 86: 1610-1617. [Abstract] [Full Text] [PDF] [Supplemental Materials]  

MUSCLE AND CONTRACTILITY:

Anthony Cammarato, Victoria Hatch, Judith Saide, Roger Craig, John C. Sparrow, Larry S. Tobacman, and William Lehman

Drosophila Muscle Regulation Characterized by Electron Microscopy and Three-Dimensional Reconstruction of Thin Filament Mutants
Biophys. J. 2004 86: 1618-1624. [Abstract] [Full Text] [PDF]  

NUCLEIC ACIDS:

Haribabu Arthanari, Kristi Wojtuszewski, Ishita Mukerji, and Philip H. Bolton

Effects of HU Binding on the Equilibrium Cyclization of Mismatched, Curved, and Normal DNA
Biophys. J. 2004 86: 1625-1631. [Abstract] [Full Text] [PDF] [Supplemental Materials]  

Raymond W. Friddle, Jennifer E. Klare, Shelley S. Martin, Michelle Corzett, Rod Balhorn, Enoch P. Baldwin, Ronald J. Baskin, and Aleksandr Noy

Mechanism of DNA Compaction by Yeast Mitochondrial Protein Abf2p
Biophys. J. 2004 86: 1632-1639. [Abstract] [Full Text] [PDF] [Supplemental Material]  

Thomas T. Perkins, Hung-Wen Li, Ravindra V. Dalal, Jeff Gelles, and Steven M. Block

Forward and Reverse Motion of Single RecBCD Molecules on DNA
Biophys. J. 2004 86: 1640-1648. [Abstract] [Full Text] [PDF]  

PHOTOBIOPHYSICS:

B. Yu, F. Zeng, Y. Yang, Q. Xing, A. Chechin, X. Xin, I. Zeylikovich, and R.R. Alfano

Torsional Vibrational Modes of Tryptophan Studied by Terahertz Time-Domain Spectroscopy
Biophys. J. 2004 86: 1649-1654. [Abstract] [Full Text] [PDF]  

Zoltán Bálint, Melinda Lakatos, Constanta Ganea, Janos K. Lanyi, and György Váró

The Nitrate Transporting Photochemical Reaction Cycle of the Pharaonis Halorhodopsin
Biophys. J. 2004 86: 1655-1663. [Abstract] [Full Text] [PDF]  

M. Germano, C. C. Gradinaru, A. Ya. Shkuropatov, I. H. M. van Stokkum, V. A. Shuvalov, J. P. Dekker, R. van Grondelle, and H. J. van Gorkom

Energy and Electron Transfer in Photosystem II Reaction Centers with Modified Pheophytin Composition
Biophys. J. 2004 86: 1664-1672. [Abstract] [Full Text] [PDF]  

Hazime Saitô, Satoru Yamaguchi, Keiji Ogawa, Satoru Tuzi, Mercedes Márquez, Carolina Sanz, and Esteve Padrós

Glutamic Acid Residues of Bacteriorhodopsin at the Extracellular Surface as Determinants for Conformation and Dynamics as Revealed by Site-Directed Solid-State ¹³C NMR
Biophys. J. 2004 86: 1673-1681. [Abstract] [Full Text] [PDF]  

PROTEINS:

Yong-Bin Yan, Qi Wang, Hua-Wei He, and Hai-Meng Zhou

Protein Thermal Aggregation Involves Distinct Regions: Sequential Events in the Heat-Induced Unfolding and Aggregation of Hemoglobin
Biophys. J. 2004 86: 1682-1690. [Abstract] [Full Text] [PDF]  

G. Settanni, J. Gsponer, and A. Caflisch

Formation of the Folding Nucleus of an SH3 Domain Investigated by Loosely Coupled Molecular Dynamics Simulations
Biophys. J. 2004 86: 1691-1701. [Abstract] [Full Text] [PDF]  

Qiuying Chen, Peter G. Vekilov, Ronald L. Nagel, and Rhoda Elison Hirsch

Liquid-Liquid Phase Separation in Hemoglobins: Distinct Aggregation Mechanisms of the ß6 Mutants
Biophys. J. 2004 86: 1702-1712. [Abstract] [Full Text] [PDF]  

Ching-Ling Teng and Robert G. Bryant

Mapping Oxygen Accessibility to Ribonuclease A Using High-Resolution NMR Relaxation Spectroscopy
Biophys. J. 2004 86: 1713-1725. [Abstract] [Full Text] [PDF] [Supplemental Materials]  

SPECTROSCOPY, IMAGING, OTHER TECHNIQUES:

D. L. Wokosin, C. M. Loughrey, and G. L. Smith

Characterization of a Range of Fura Dyes with Two-Photon Excitation
Biophys. J. 2004 86: 1726-1738. [Abstract] [Full Text] [PDF]  

Hideki Shirakawa and Shunichi Miyazaki

Blind Spectral Decomposition of Single-Cell Fluorescence by Parallel Factor Analysis
Biophys. J. 2004 86: 1739-1752. [Abstract] [Full Text] [PDF]  

N. Almqvist, R. Bhatia, G. Primbs, N. Desai, S. Banerjee, and R. Lal

Elasticity and Adhesion Force Mapping Reveals Real-Time Clustering of Growth Factor Receptors and Associated Changes in Local Cellular Rheological Properties
Biophys. J. 2004 86: 1753-1762. [Abstract] [Full Text] [PDF]  

I. Burgess, M. Li, S. L. Horswell, G. Szymanski, J. Lipkowski, J. Majewski, and S. Satija

Electric Field-Driven Transformations of a Supported Model Biological Membrane—An Electrochemical and Neutron Reflectivity Study
Biophys. J. 2004 86: 1763-1776. [Abstract] [Full Text] [PDF]  

CELL BIOPHYSICS:

R. E. Mahaffy, S. Park, E. Gerde, J. Käs, and C. K. Shih

Quantitative Analysis of the Viscoelastic Properties of Thin Regions of Fibroblasts Using Atomic Force Microscopy
Biophys. J. 2004 86: 1777-1793. [Abstract] [Full Text] [PDF]  

Benjamin J. Dubin-Thaler, Gregory Giannone, Hans-Günther Döbereiner, and Michael P. Sheetz

Nanometer Analysis of Cell Spreading on Matrix-Coated Surfaces Reveals Two Distinct Cell States and STEPs
Biophys. J. 2004 86: 1794-1806. [Abstract] [Full Text] [PDF] [Supplement]  

BIOENERGETICS:

Bengt Svensson, David M. Tiede, David R. Nelson, and Bridgette A. Barry

Structural Studies of the Manganese Stabilizing Subunit in Photosystem II
Biophys. J. 2004 86: 1807-1812. [Abstract] [Full Text] [PDF]  

Ming-Liang Tan, Ilya Balabin, and José Nelson Onuchic

Dynamics of Electron Transfer Pathways in Cytochrome c Oxidase
Biophys. J. 2004 86: 1813-1819. [Abstract] [Full Text] [PDF]  

ELECTROPHYSIOLOGY:

Shigeyoshi Fujisawa, Maki K. Yamada, Nobuyoshi Nishiyama, Norio Matsuki, and Yuji Ikegaya

BDNF Boosts Spike Fidelity in Chaotic Neural Oscillations
Biophys. J. 2004 86: 1820-1828. [Abstract] [Full Text] [PDF]  

Claude Bédard, Helmut Kröger, and Alain Destexhe

Modeling Extracellular Field Potentials and the Frequency-Filtering Properties of Extracellular Space
Biophys. J. 2004 86: 1829-1842. [Abstract] [Full Text] [PDF]  

M. Tateyama, H. Liu, A-S. Yang, J. W. Cormier, and R. S. Kass

Structural Effects of an LQT-3 Mutation on Heart Na⁺ Channel Gating
Biophys. J. 2004 86: 1843-1851. [Abstract] [Full Text] [PDF]  

OTHER:

Daniela Russo, Greg Hura, and Teresa Head-Gordon

Hydration Dynamics Near a Model Protein Surface
Biophys. J. 2004 86: 1852-1862. [Abstract] [Full Text] [PDF]  

Nicholas Darnton, Linda Turner, Kenneth Breuer, and Howard C. Berg

Moving Fluid with Bacterial Carpets
Biophys. J. 2004 86: 1863-1870. [Abstract] [Full Text] [PDF]  

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