Simultaneous Tether Extraction Contributes to Neutrophil Rolling Stabilization: A Model Study Biophys. J. 2007. 92:418-429.
[Abstract][Full Text][PDF]
Jans H. Alzate-Morales, Renato Contreras, Alejandro Soriano, Inaki Tunon, and Estanislao Silla
A Computational Study of the Protein-Ligand Interactions in CDK2 Inhibitors: Using Quantum Mechanics/Molecular Mechanics Interaction Energy as a Predictor of the Biological Activity Biophys. J. 2007. 92:430-439.
[Abstract][Full Text][PDF]
Sagar A. Pandit, George Khelashvili, Eric Jakobsson, Ananth Grama, and H. L. Scott
Lateral Organization in Lipid-Cholesterol Mixed Bilayers Biophys. J. 2007. 92:440-447.
[Abstract][Full Text][PDF]
Hideki Hayashi, Yohannes Shiferaw, Daisuke Sato, Motoki Nihei, Shien-Fong Lin, Peng-Sheng Chen, Alan Garfinkel, James N. Weiss, and Zhilin Qu
Dynamic Origin of Spatially Discordant Alternans in Cardiac Tissue Biophys. J. 2007. 92:448-460.
[Abstract][Full Text][PDF]
From Past Issues:
Patrick C. Stenger and Joseph A. Zasadzinski
Enhanced Surfactant Adsorption via Polymer Depletion Forces: A Simple Model for Reversing Surfactant Inhibition in Acute Respiratory Distress Syndrome Biophys. J. 2007. 92:3-9.
[Abstract][Full Text][PDF]
Maria Sammalkorpi and Themis Lazaridis
Modeling a Spin-Labeled Fusion Peptide in a Membrane: Implications for the Interpretation of EPR Experiments Biophys. J. 2007. 92:10-22.
[Abstract][Full Text][PDF]
A. Aird, J. Wrachtrup, K. Schulten, and C. Tietz
Possible Pathway for Ubiquinone Shuttling in Rhodospirillum rubrum Revealed by Molecular Dynamics Simulation Biophys. J. 2007. 92:23-33.
[Abstract][Full Text][PDF]
Austin Huang and Collin M. Stultz
Conformational Sampling with Implicit Solvent Models: Application to the PHF6 Peptide in Tau Protein Biophys. J. 2007. 92:34-45.
[Abstract][Full Text][PDF]
Hanning Chen, Boaz Ilan, Yujie Wu, Fangqiang Zhu, Klaus Schulten, and Gregory A. Voth
Charge Delocalization in Proton Channels, I: The Aquaporin Channels and Proton Blockage Biophys. J. 2007. 92:46-60.
[Abstract][Full Text][PDF]
Yujie Wu, Boaz Ilan, and Gregory A. Voth
Charge Delocalization in Proton Channels, II: The Synthetic LS2 Channel and Proton Selectivity Biophys. J. 2007. 92:61-69.
[Abstract][Full Text][PDF]
Laurent Bozec, Gert van der Heijden, and Michael Horton
Malkaram S. Achary, Aramati B. M. Reddy, Subhabrata Chakrabarti, Shirly G. Panicker, Anil K. Mandal, Niyaz Ahmed, Dorairajan Balasubramanian, Seyed E. Hasnain, and Hampapathalu A. Nagarajaram
Disease-Causing Mutations in Proteins: Structural Analysis of the CYP1b1 Mutations Causing Primary Congenital Glaucoma in Humans Biophys. J. 2006. 91:4329-4339.
[Abstract][Full Text][PDF]
Chrystel Faure, Frederic Nallet, Didier Roux, Scott T. Milner, Fabienne Gauffre, David Olea, and Olivier Lambert
Modeling Leakage Kinetics from Multilamellar Vesicles for Membrane Permeability Determination: Application to Glucose Biophys. J. 2006. 91:4340-4349.
[Abstract][Full Text][PDF]
Jeroen S. van Zon, Marco J. Morelli, Sorin Tanase-Nicola, and Pieter Rein ten Wolde
Diffusion of Transcription Factors Can Drastically Enhance the Noise in Gene Expression Biophys. J. 2006. 91:4350-4367.
[Abstract][Full Text][PDF]
Pontus Melke, Henrik Jonsson, Evangelia Pardali, Peter ten Dijke, and Carsten Peterson
A Rate Equation Approach to Elucidate the Kinetics and Robustness of the TGF-ß Pathway Biophys. J. 2006. 91:4368-4380.
[Abstract][Full Text][PDF]
Dynamic Studies of Scaffold-Dependent Mating Pathway in Yeast Biophys. J. 2006. 91:3986-4001.
[Abstract][Full Text][PDF]
Ganhui Lan and Sean X. Sun
Flexible Light-Chain and Helical Structure of F-Actin Explain the Movement and Step Size of Myosin-VI Biophys. J. 2006. 91:4002-4013.
[Abstract][Full Text][PDF]
Shi Zhong, Jeremy M. Moix, Stephen Quirk, and Rigoberto Hernandez
Dihedral-Angle Information Entropy as a Gauge of Secondary Structure Propensity Biophys. J. 2006. 91:4014-4023.
[Abstract][Full Text][PDF]
Heather J. Rose, Sheila Dargan, Jianwei Shuai, and Ian Parker
‘Trigger’ Events Precede Calcium Puffs in Xenopus Oocytes Biophys. J. 2006. 91:4024-4032.
[Abstract][Full Text][PDF]
Jianwei Shuai, Heather J. Rose, and Ian Parker
The Number and Spatial Distribution of IP3 Receptors Underlying Calcium Puffs in Xenopus Oocytes Biophys. J. 2006. 91:4033-4044.
[Abstract][Full Text][PDF]
Yajun Zhou and Xiaowei Zhuang
Robust Reconstruction of the Rate Constant Distribution Using the Phase Function Method Biophys. J. 2006. 91:4045-4053.
[Abstract][Full Text][PDF]
Igor M. Neelov, David B. Adolf, Tom C. B. McLeish, and Emanuele Paci
Molecular Dynamics Simulation of Dextran Extension by Constant Force in Single Molecule AFM Biophys. J. 2006. 91:3579-3588.
[Abstract][Full Text][PDF]
Burak Erman
The Gaussian Network Model: Precise Prediction of Residue Fluctuations and Application to Binding Problems Biophys. J. 2006. 91:3589-3599.
[Abstract][Full Text][PDF]
Lawrence C.-L. Lin, Jay T. Groves, and Frank L. H. Brown
Analysis of Shape, Fluctuations, and Dynamics in Intermembrane Junctions Biophys. J. 2006. 91:3600-3606.
[Abstract][Full Text][PDF]
Gerald S. Manning
The Persistence Length of DNA Is Reached from the Persistence Length of Its Null Isomer through an Internal Electrostatic Stretching Force Biophys. J. 2006. 91:3607-3616.
[Abstract][Full Text][PDF]
Ryan W. Benz, Hirsh Nanda, Francisco Castro-Roman, Stephen H. White, and Douglas J. Tobias
Diffraction-Based Density Restraints for Membrane and Membrane-Peptide Molecular Dynamics Simulations Biophys. J. 2006. 91:3617-3629.
[Abstract][Full Text][PDF]
Peter L. Freddolino, Markus Dittrich, and Klaus Schulten
Dynamic Switching Mechanisms in LOV1 and LOV2 Domains of Plant Phototropins Biophys. J. 2006. 91:3630-3639.
[Abstract][Full Text][PDF]
Yeshitila Gebremichael, Gary S. Ayton, and Gregory A. Voth
Mesoscopic Modeling of Bacterial Flagellar Microhydrodynamics Biophys. J. 2006. 91:3640-3652.
[Abstract][Full Text][PDF]
Leslie Chin, Pengtao Yue, James J. Feng, and Chun Y. Seow
Mathematical Simulation of Muscle Cross-Bridge Cycle and Force-Velocity Relationship Biophys. J. 2006. 91:3653-3663.
[Abstract][Full Text][PDF]
Chun Wu, Hongxing Lei, Zhixiang Wang, Wei Zhang, and Yong Duan
Phenol Red Interacts with the Protofibril-Like Oligomers of an Amyloidogenic Hexapeptide NFGAIL through Both Hydrophobic and Aromatic Contacts Biophys. J. 2006. 91:3664-3672.
[Abstract][Full Text][PDF]
Lorin S. Milescu, Ahmet Yildiz, Paul R. Selvin, and Frederick Sachs
Extracting Dwell Time Sequences from Processive Molecular Motor Data Biophys. J. 2006. 91:3135-3150.
[Abstract][Full Text][PDF]
Peter Carlsson, Sofia Burendahl, and Lennart Nilsson
Unbinding of Retinoic Acid from the Retinoic Acid Receptor by Random Expulsion Molecular Dynamics Biophys. J. 2006. 91:3151-3161.
[Abstract][Full Text][PDF]
Simone Furini, Francesco Zerbetto, and Silvio Cavalcanti
Application of the Poisson-Nernst-Planck Theory with Space-Dependent Diffusion Coefficients to KcsA Biophys. J. 2006. 91:3162-3169.
[Abstract][Full Text][PDF]
Huan-Xiang Zhou
Quantitative Relation between Intermolecular and Intramolecular Binding of Pro-Rich Peptides to SH3 Domains Biophys. J. 2006. 91:3170-3181.
[Abstract][Full Text][PDF]
Meredith C. Foley, Karunesh Arora, and Tamar Schlick
Sequential Side-Chain Residue Motions Transform the Binary into the Ternary State of DNA Polymerase Biophys. J. 2006. 91:3182-3195.
[Abstract][Full Text][PDF]
Jonathan Tomshine and Yiannis N. Kaznessis
Optimization of a Stochastically Simulated Gene Network Model via Simulated Annealing Biophys. J. 2006. 91:3196-3205.
[Abstract][Full Text][PDF]
K. Anton Feenstra, Karin Hofstetter, Rolien Bosch, Andreas Schmid, Jan N. M. Commandeur, and Nico P. E. Vermeulen
Enantioselective Substrate Binding in a Monooxygenase Protein Model by Molecular Dynamics and Docking Biophys. J. 2006. 91:3206-3216.
[Abstract][Full Text][PDF]
Ute F. Rohrig, Alessandro Laio, Nazario Tantalo, Michele Parrinello, and Roberto Petronzio
Stability and Structure of Oligomers of the Alzheimer Peptide Aß16–22: From the Dimer to the 32-Mer Biophys. J. 2006. 91:3217-3229.
[Abstract][Full Text][PDF]
Mark P. Brynildsen, Linh M. Tran, and James C. Liao
Versatility and Connectivity Efficiency of Bipartite Transcription Networks Biophys. J. 2006. 91:2749-2759.
[Abstract][Full Text][PDF]
Dmitry A. Kondrashov, Qiang Cui, and George N. Phillips Jr.
Optimization and Evaluation of a Coarse-Grained Model of Protein Motion Using X-Ray Crystal Data Biophys. J. 2006. 91:2760-2767.
[Abstract][Full Text][PDF]
G. Fiorin, A. Pastore, P. Carloni, and M. Parrinello
Using Metadynamics to Understand the Mechanism of Calmodulin/Target Recognition at Atomic Detail Biophys. J. 2006. 91:2768-2777.
[Abstract][Full Text][PDF]
Julia Adolphs and Thomas Renger
How Proteins Trigger Excitation Energy Transfer in the FMO Complex of Green Sulfur Bacteria Biophys. J. 2006. 91:2778-2797.
[Abstract][Full Text][PDF]
Jiyao Wang, Yuqing Deng, and Benoit Roux
Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials Biophys. J. 2006. 91:2798-2814.
[Abstract][Full Text][PDF]
Satyavani Vemparala, Leonor Saiz, Roderic G. Eckenhoff, and Michael L. Klein
Partitioning of Anesthetics into a Lipid Bilayer and their Interaction with Membrane-Bound Peptide Bundles Biophys. J. 2006. 91:2815-2825.
[Abstract][Full Text][PDF]
Michelle G. Botelho, Alex W. M. Rietveld, and Sergio T. Ferreira
Long-Lived Conformational Isomerism of Protein Dimers: The Role of the Free Energy of Subunit Association Biophys. J. 2006. 91:2826-2832.
[Abstract][Full Text][PDF]
M. J. A. van Hoek and P. Hogeweg
In Silico Evolved lac Operons Exhibit Bistability for Artificial Inducers, but Not for Lactose Biophys. J. 2006. 91:2833-2843.
[Abstract][Full Text][PDF]
Nir S. Gov
Modeling the Size Distribution of Focal Adhesions Biophys. J. 2006. 91:2844-2847.
[Abstract][Full Text][PDF]
Hyunbum Jang, Buyong Ma, Thomas B. Woolf, and Ruth Nussinov
Interaction of Protegrin-1 with Lipid Bilayers: Membrane Thinning Effect Biophys. J. 2006. 91:2848-2859.
[Abstract][Full Text][PDF]
Bernhard Windisch, Dennis Bray, and Thomas Duke
Balls and Chains—A Mesoscopic Approach to Tethered Protein Domains Biophys. J. 2006. 91:2383-2392.
[Abstract][Full Text][PDF]
Gernot Guigas and Matthias Weiss
Size-Dependent Diffusion of Membrane Inclusions Biophys. J. 2006. 91:2393-2398.
[Abstract][Full Text][PDF]
Lixin Zhan, Jeff Z. Y. Chen, and Wing-Ki Liu
Conformational Study of Met-Enkephalin Based on the ECEPP Force Fields Biophys. J. 2006. 91:2399-2404.
[Abstract][Full Text][PDF]
David Holcman and Antoine Triller
Modeling Synaptic Dynamics Driven by Receptor Lateral Diffusion Biophys. J. 2006. 91:2405-2415.
[Abstract][Full Text][PDF]
William H. Mather and Ronald F. Fox
Kinesin's Biased Stepping Mechanism: Amplification of Neck Linker Zippering Biophys. J. 2006. 91:2416-2426.
[Abstract][Full Text][PDF]
Jason K. Cheung, Pooja Shah, and Thomas M. Truskett
Heteropolymer Collapse Theory for Protein Folding in the Pressure-Temperature Plane Biophys. J. 2006. 91:2427-2435.
[Abstract][Full Text][PDF]
Assaf Ganoth, Ran Friedman, Esther Nachliel, and Menachem Gutman
A Molecular Dynamics Study and Free Energy Analysis of Complexes between the Mlc1p Protein and Two IQ Motif Peptides Biophys. J. 2006. 91:2436-2450.
[Abstract][Full Text][PDF]
Xiaoqin Huang and Huan-Xiang Zhou
Similarity and Difference in the Unfolding of Thermophilic and Mesophilic Cold Shock Proteins Studied by Molecular Dynamics Simulations Biophys. J. 2006. 91:2451-2463.
[Abstract][Full Text][PDF]
Daniel J. V. A. dos Santos and Leif A. Eriksson
Permeability of Psoralen Derivatives in Lipid Membranes Biophys. J. 2006. 91:2464-2474.
[Abstract][Full Text][PDF]
Karl I. Skau, Rebecca B. Hoyle, and Matthew S. Turner
A Kinetic Model Describing the Processivity of Myosin-V Biophys. J. 2006. 91:2475-2489.
[Abstract][Full Text][PDF]
Gen Kurosawa, Kazuyuki Aihara, and Yoh Iwasa
A Model for the Circadian Rhythm of Cyanobacteria that Maintains Oscillation without Gene Expression Biophys. J. 2006. 91:2015-2023.
[Abstract][Full Text][PDF]
Ivan Degtyarenko, Risto M. Nieminen, and Carme Rovira
Structure and Dynamics of Dioxygen Bound to Cobalt and Iron Heme Biophys. J. 2006. 91:2024-2034.
[Abstract][Full Text][PDF]
Vitor H. Teixeira, Antonio M. Baptista, and Claudio M. Soares
Pathways of H2 toward the Active Site of [NiFe]-Hydrogenase Biophys. J. 2006. 91:2035-2045.
[Abstract][Full Text][PDF]
Kristen E. Norman and Hugh Nymeyer
Indole Localization in Lipid Membranes Revealed by Molecular Simulation Biophys. J. 2006. 91:2046-2054.
[Abstract][Full Text][PDF]
Rhoda J. Hawkins and Tom C. B. McLeish
Coupling of Global and Local Vibrational Modes in Dynamic Allostery of Proteins Biophys. J. 2006. 91:2055-2062.
[Abstract][Full Text][PDF]
Marco Berrera, Antonino Cattaneo, and Paolo Carloni
Molecular Simulation of the Binding of Nerve Growth Factor Peptide Mimics to the Receptor Tyrosine Kinase A Biophys. J. 2006. 91:2063-2071.
[Abstract][Full Text][PDF]
Yoshihiro Morishita, Tetsuya J. Kobayashi, and Kazuyuki Aihara
An Optimal Number of Molecules for Signal Amplification and Discrimination in a Chemical Cascade Biophys. J. 2006. 91:2072-2081.
[Abstract][Full Text][PDF]
Craig S. Nunemaker, Richard Bertram, Arthur Sherman, Krasimira Tsaneva-Atanasova, Camille R. Daniel, and Leslie S. Satin
Glucose Modulates [Ca2+]i Oscillations in Pancreatic Islets via Ionic and Glycolytic Mechanisms Biophys. J. 2006. 91:2082-2096.
[Abstract][Full Text][PDF]
Jin Yu, Taekjip Ha, and Klaus Schulten
Structure-Based Model of the Stepping Motor of PcrA Helicase Biophys. J. 2006. 91:2097-2114.
[Abstract][Full Text][PDF]
Holger Gohlke and M. F. Thorpe
A Natural Coarse Graining for Simulating Large Biomolecular Motion Biophys. J. 2006. 91:2115-2120.
[Abstract][Full Text][PDF]
Anthony R. Geonnotti and David F. Katz
Dynamics of HIV Neutralization by a Microbicide Formulation Layer: Biophysical Fundamentals and Transport Theory Biophys. J. 2006. 91:2121-2130.
[Abstract][Full Text][PDF]
Rudiyanto Gunawan and Francis J. Doyle III
Isochron-Based Phase Response Analysis of Circadian Rhythms Biophys. J. 2006. 91:2131-2141.
[Abstract][Full Text][PDF]
Sergio Aragon and David K. Hahn
Precise Boundary Element Computation of Protein Transport Properties: Diffusion Tensors, Specific Volume, and Hydration Biophys. J. 2006. 91:1591-1603.
[Abstract][Full Text][PDF]
J. R. Wedagedera and N. J. Burroughs
T-Cell Activation: A Queuing Theory Analysis at Low Agonist Density Biophys. J. 2006. 91:1604-1618.
[Abstract][Full Text][PDF]
Nigel J. Burroughs, Zorana Lazic, and P. Anton van der Merwe
Ligand Detection and Discrimination by Spatial Relocalization: A Kinase-Phosphatase Segregation Model of TCR Activation Biophys. J. 2006. 91:1619-1629.
[Abstract][Full Text][PDF]
Grischa R. Meyer, Justin Gullingsrud, Klaus Schulten, and Boris Martinac
Molecular Dynamics Study of MscL Interactions with a Curved Lipid Bilayer Biophys. J. 2006. 91:1630-1637.
[Abstract][Full Text][PDF]
Guanghong Wei and Joan-Emma Shea
Effects of Solvent on the Structure of the Alzheimer Amyloid-ß(25–35) Peptide Biophys. J. 2006. 91:1638-1647.
[Abstract][Full Text][PDF]
Masood A. Machingal and S. V. Ramanan
A Steady-State Electrochemical Model of Vascular Smooth Muscle Cells Biophys. J. 2006. 91:1648-1662.
[Abstract][Full Text][PDF]
Michele Koenigsberger, Roger Sauser, Jean-Louis Beny, and Jean-Jacques Meister
Effects of Arterial Wall Stress on Vasomotion Biophys. J. 2006. 91:1663-1674.
[Abstract][Full Text][PDF]
Nathan W. Moore and Tonya L. Kuhl
The Role of Flexible Tethers in Multiple Ligand-Receptor Bond Formation between Curved Surfaces Biophys. J. 2006. 91:1675-1687.
[Abstract][Full Text][PDF]
Yanling Lu, Emma Longman, Kenneth G. Davis, Alvaro Ortega, J. Gunter Grossmann, Terje E. Michaelsen, Jose Garcia de la Torre, and Stephen E. Harding
Crystallohydrodynamics of Protein Assemblies: Combining Sedimentation, Viscometry, and X-Ray Scattering Biophys. J. 2006. 91:1688-1697.
[Abstract][Full Text][PDF]
S. Fernandez-Alberti, D. E. Bacelo, R. C. Binning Jr., J. Echave, M. Chergui, and J. Lopez-Garriga
Sulfide-Binding Hemoglobins: Effects of Mutations on Active-Site Flexibility Biophys. J. 2006. 91:1698-1709.
[Abstract][Full Text][PDF]
Jinming Zhang and Themis Lazaridis
Calculating the Free Energy of Association of Transmembrane Helices Biophys. J. 2006. 91:1710-1723.
[Abstract][Full Text][PDF]
Petras J. Kundrotas and Emil Alexov
Electrostatic Properties of Protein-Protein Complexes Biophys. J. 2006. 91:1724-1736.
[Abstract][Full Text][PDF]
Ellen F. Krasik, Ka Lai Yee, and Daniel A. Hammer
Adhesive Dynamics Simulation of Neutrophil Arrest with Deterministic Activation Biophys. J. 2006. 91:1145-1155.
[Abstract][Full Text][PDF]
Lorin S. Milescu, Ahmet Yildiz, Paul R. Selvin, and Frederick Sachs
Maximum Likelihood Estimation of Molecular Motor Kinetics from Staircase Dwell-Time Sequences Biophys. J. 2006. 91:1156-1168.
[Abstract][Full Text][PDF]
Brian L. Sprague, Florian Muller, Robert L. Pego, Peter M. Bungay, Diana A. Stavreva, and James G. McNally
Analysis of Binding at a Single Spatially Localized Cluster of Binding Sites by Fluorescence Recovery after Photobleaching Biophys. J. 2006. 91:1169-1191.
[Abstract][Full Text][PDF]
Giovanni Caruso, Paolo Bisegna, Lixin Shen, Daniele Andreucci, Heidi E. Hamm, and Emmanuele DiBenedetto
Modeling the Role of Incisures in Vertebrate Phototransduction Biophys. J. 2006. 91:1192-1212.
[Abstract][Full Text][PDF]
Yoshito Sawada and Shinya Honda
Structural Diversity of Protein Segments Follows a Power-Law Distribution Biophys. J. 2006. 91:1213-1223.
[Abstract][Full Text][PDF]
Phuong H. Nguyen, Roman D. Gorbunov, and Gerhard Stock
Photoinduced Conformational Dynamics of a Photoswitchable Peptide: A Nonequilibrium Molecular Dynamics Simulation Study Biophys. J. 2006. 91:1224-1234.
[Abstract][Full Text][PDF]
Reiko J. Tanaka, Hiroyuki Okano, and Hidenori Kimura
Mathematical Description of Gene Regulatory Units Biophys. J. 2006. 91:1235-1247.
[Abstract][Full Text][PDF]
Yuye Tang, Guoxin Cao, Xi Chen, Jejoong Yoo, Arun Yethiraj, and Qiang Cui
A Finite Element Framework for Studying the Mechanical Response of Macromolecules: Application to the Gating of the Mechanosensitive Channel MscL Biophys. J. 2006. 91:1248-1263.
[Abstract][Full Text][PDF]
Kalyan Vinnakota, Melissa L. Kemp, and Martin J. Kushmerick
Dynamics of Muscle Glycogenolysis Modeled with pH Time Course Computation and pH-Dependent Reaction Equilibria and Enzyme Kinetics Biophys. J. 2006. 91:1264-1287.
[Abstract][Full Text][PDF]
Glenn T. Lines, Jorn B. Sande, William E. Louch, Halvor K. Mork, Per Grottum, and Ole M. Sejersted
Contribution of the Na+/Ca2+ Exchanger to Rapid Ca2+ Release in Cardiomyocytes Biophys. J. 2006. 91:779-792.
[Abstract][Full Text][PDF]
Zhilin Qu, Alan Garfinkel, and James N. Weiss
Vulnerable Window for Conduction Block in a One-Dimensional Cable of Cardiac Cells, 1: Single Extrasystoles Biophys. J. 2006. 91:793-804.
[Abstract][Full Text][PDF]
Zhilin Qu, Alan Garfinkel, and James N. Weiss
Vulnerable Window for Conduction Block in a One-Dimensional Cable of Cardiac Cells, 2: Multiple Extrasystoles Biophys. J. 2006. 91:805-815.
[Abstract][Full Text][PDF]
Samuel L. C. Moors, Mario Hellings, Marc De Maeyer, Yves Engelborghs, and Arnout Ceulemans
Tryptophan Rotamers as Evidenced by X-Ray, Fluorescence Lifetimes, and Molecular Dynamics Modeling Biophys. J. 2006. 91:816-823.
[Abstract][Full Text][PDF]
Jie Zheng, Buyong Ma, Chung-Jung Tsai, and Ruth Nussinov
Structural Stability and Dynamics of an Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35 Biophys. J. 2006. 91:824-833.
[Abstract][Full Text][PDF]
Gerard Adriaan Vliegenthart and Gerhard Gompper
Mechanical Deformation of Spherical Viruses with Icosahedral Symmetry Biophys. J. 2006. 91:834-841.
[Abstract][Full Text][PDF]
Chemical Potential Derivatives and Preferential Interaction Parameters in Biological Systems from Kirkwood-Buff Theory Biophys. J. 2006. 91:849-856.
[Abstract][Full Text][PDF]
Philip W. Fowler and Peter V. Coveney
A Computational Protocol for the Integration of the Monotopic Protein Prostaglandin H2 Synthase into a Phospholipid Bilayer Biophys. J. 2006. 91:401-410.
[Abstract][Full Text][PDF]
Mandar M. Inamdar, William M. Gelbart, and Rob Phillips
Nigar Kantarci, Pemra Doruker, and Turkan Haliloglu
Cooperative Fluctuations Point to the Dimerization Interface of P53 Core Domain Biophys. J. 2006. 91:421-432.
[Abstract][Full Text][PDF]
Peter P. Jones, Hojjat Bazzazi, Gary J. Kargacin, and John Colyer
Inhibition of cAMP-Dependent Protein Kinase under Conditions Occurring in the Cardiac Dyad during a Ca2+ Transient Biophys. J. 2006. 91:433-443.
[Abstract][Full Text][PDF]
Yufang Hu, Kieche Meleson, and Jacob Israelachvili
Thermodynamic Equilibrium of Domains in a Two-Component Langmuir Monolayer Biophys. J. 2006. 91:444-453.
[Abstract][Full Text][PDF]
Petr V. Nazarov, Rob B. M. Koehorst, Werner L. Vos, Vladimir V. Apanasovich, and Marcus A. Hemminga
FRET Study of Membrane Proteins: Simulation-Based Fitting for Analysis of Membrane Protein Embedment and Association Biophys. J. 2006. 91:454-466.
[Abstract][Full Text][PDF]
German Pabon and L. Mario Amzel
Mechanism of Titin Unfolding by Force: Insight from Quasi-Equilibrium Molecular Dynamics Calculations Biophys. J. 2006. 91:467-472.
[Abstract][Full Text][PDF]
Norberto M. Grzywacz and Charles L. Zucker
Modeling Starburst Cells' GABAB Receptors and Their Putative Role in Motion Sensitivity Biophys. J. 2006. 91:473-486.
[Abstract][Full Text][PDF]
Ira R. Cooke and Markus Deserno
Coupling between Lipid Shape and Membrane Curvature Biophys. J. 2006. 91:487-495.
[Abstract][Full Text][PDF]
Lucy R. Forrest, Christopher L. Tang, and Barry Honig
On the Accuracy of Homology Modeling and Sequence Alignment Methods Applied to Membrane Proteins Biophys. J. 2006. 91:508-517.
[Abstract][Full Text][PDF]
Shawn Means, Alexander J. Smith, Jason Shepherd, John Shadid, John Fowler, Richard J. H. Wojcikiewicz, Tomas Mazel, Gregory D. Smith, and Bridget S. Wilson
Reaction Diffusion Modeling of Calcium Dynamics with Realistic ER Geometry Biophys. J. 2006. 91:537-557.
[Abstract][Full Text][PDF]
Loredana Vaccaro, Vassilis Koronakis, and Mark S. P. Sansom
Flexibility in a Drug Transport Accessory Protein: Molecular Dynamics Simulations of MexA Biophys. J. 2006. 91:558-564.
[Abstract][Full Text][PDF]
Ye Chen-Izu, Stacey L. McCulle, Chris W. Ward, Christian Soeller, Bryan M. Allen, Cal Rabang, Mark B. Cannell, C. William Balke, and Leighton T. Izu
Three-Dimensional Distribution of Ryanodine Receptor Clusters in Cardiac Myocytes Biophys. J. 2006. 91:1-13.
[Abstract][Full Text][PDF]
Christopher D. Snow, Young Min Rhee, and Vijay S. Pande
Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates Biophys. J. 2006. 91:14-24.
[Abstract][Full Text][PDF]
Christopher Forrey and M. Muthukumar
Langevin Dynamics Simulations of Genome Packing in Bacteriophage Biophys. J. 2006. 91:25-41.
[Abstract][Full Text][PDF]
Electrostatic Energy Calculation on the pH-Induced Conformational Change of Influenza Virus Hemagglutinin Biophys. J. 2006. 91:55-60.
[Abstract][Full Text][PDF]
Alice Nicolas and Samuel. A. Safran
Limitation of Cell Adhesion by the Elasticity of the Extracellular Matrix Biophys. J. 2006. 91:61-73.
[Abstract][Full Text][PDF]
Anmar Khadra and Yue-Xian Li
A Model for the Pulsatile Secretion of Gonadotropin-Releasing Hormone from Synchronized Hypothalamic Neurons Biophys. J. 2006. 91:74-83.
[Abstract][Full Text][PDF]
Ting Lu, Jeff Hasty, and Peter G. Wolynes
Effective Temperature in Stochastic Kinetics and Gene Networks Biophys. J. 2006. 91:84-94.
[Abstract][Full Text][PDF]
Leighton T. Izu, Shawn A. Means, John N. Shadid, Ye Chen-Izu, and C. William Balke
Interplay of Ryanodine Receptor Distribution and Calcium Dynamics Biophys. J. 2006. 91:95-112.
[Abstract][Full Text][PDF]
Mark E. Fleury, Kendrick C. Boardman, and Melody A. Swartz
Autologous Morphogen Gradients by Subtle Interstitial Flow and Matrix Interactions Biophys. J. 2006. 91:113-121.
[Abstract][Full Text][PDF]
Evan T. Powers and David L. Powers
The Kinetics of Nucleated Polymerizations at High Concentrations: Amyloid Fibril Formation Near and Above the "Supercritical Concentration" Biophys. J. 2006. 91:122-132.
[Abstract][Full Text][PDF]
Gaurav Arya, Qing Zhang, and Tamar Schlick
Flexible Histone Tails in a New Mesoscopic Oligonucleosome Model Biophys. J. 2006. 91:133-150.
[Abstract][Full Text][PDF]
Erin R. Higgins, Mark B. Cannell, and James Sneyd
A Buffering SERCA Pump in Models of Calcium Dynamics Biophys. J. 2006. 91:151-163.
[Abstract][Full Text][PDF]
Edward Lyman and Daniel M. Zuckerman
Ensemble-Based Convergence Analysis of Biomolecular Trajectories Biophys. J. 2006. 91:164-172.
[Abstract][Full Text][PDF]
A. Schug and W. Wenzel
An Evolutionary Strategy for All-Atom Folding of the 60-Amino-Acid Bacterial Ribosomal Protein L20 Biophys. J. 2006. 90:4273-4280.
[Abstract][Full Text][PDF]
Jonathan L. Eide, Arup K. Chakraborty, and George F. Oster
Simple Models for Extracting Mechanical Work from the ATP Hydrolysis Cycle Biophys. J. 2006. 90:4281-4294.
[Abstract][Full Text][PDF]
Le Yang, David Sept, and A. E. Carlsson
Energetics and Dynamics of Constrained Actin Filament Bundling Biophys. J. 2006. 90:4295-4304.
[Abstract][Full Text][PDF]
Nikolay Korolev, Alexander P. Lyubartsev, and Lars Nordenskiold
Computer Modeling Demonstrates that Electrostatic Attraction of Nucleosomal DNA is Mediated by Histone Tails Biophys. J. 2006. 90:4305-4316.
[Abstract][Full Text][PDF]
Monica L. Skoge, Robert G. Endres, and Ned S. Wingreen
Receptor-Receptor Coupling in Bacterial Chemotaxis: Evidence for Strongly Coupled Clusters Biophys. J. 2006. 90:4317-4326.
[Abstract][Full Text][PDF]
Wenjun Zheng and Bernard R. Brooks
Modeling Protein Conformational Changes by Iterative Fitting of Distance Constraints Using Reoriented Normal Modes Biophys. J. 2006. 90:4327-4336.
[Abstract][Full Text][PDF]
Cristina S. Pereira, David Kony, Riccardo Baron, Martin Muller, Wilfred F. van Gunsteren, and Philippe H. Hunenberger
Conformational and Dynamical Properties of Disaccharides in Water: a Molecular Dynamics Study Biophys. J. 2006. 90:4337-4344.
[Abstract][Full Text][PDF]
Andrea Catte, James C. Patterson, Martin K. Jones, W. Gray Jerome, Denys Bashtovyy, Zhengchang Su, Feifei Gu, Jianguo Chen, Marcela P. Aliste, Stephen C. Harvey, Ling Li, Gilbert Weinstein, and Jere P. Segrest
Novel Changes in Discoidal High Density Lipoprotein Morphology: A Molecular Dynamics Study Biophys. J. 2006. 90:4345-4360.
[Abstract][Full Text][PDF]
Attila Csikasz-Nagy, Dorjsuren Battogtokh, Katherine C. Chen, Bela Novak, and John J. Tyson
Analysis of a Generic Model of Eukaryotic Cell-Cycle Regulation Biophys. J. 2006. 90:4361-4379.
[Abstract][Full Text][PDF]
Dehong Zeng, Aldo Ferrari, Jens Ulmer, Alexey Veligodskiy, Peter Fischer, Joachim Spatz, Yiannis Ventikos, Dimos Poulikakos, and Ruth Kroschewski
Three-Dimensional Modeling of Mechanical Forces in the Extracellular Matrix during Epithelial Lumen Formation Biophys. J. 2006. 90:4380-4391.
[Abstract][Full Text][PDF]
V. Barsegov, D. K. Klimov, and D. Thirumalai
Mapping the Energy Landscape of Biomolecules Using Single Molecule Force Correlation Spectroscopy: Theory and Applications Biophys. J. 2006. 90:3827-3841.
[Abstract][Full Text][PDF]
Elad Project, Ran Friedman, Esther Nachliel, and Menachem Gutman
A Molecular Dynamics Study of the Effect of Ca2+ Removal on Calmodulin Structure Biophys. J. 2006. 90:3842-3850.
[Abstract][Full Text][PDF]
M. Raible, M. Evstigneev, F. W. Bartels, R. Eckel, M. Nguyen-Duong, R. Merkel, R. Ros, D. Anselmetti, and P. Reimann
Theoretical Analysis of Single-Molecule Force Spectroscopy Experiments: Heterogeneity of Chemical Bonds Biophys. J. 2006. 90:3851-3864.
[Abstract][Full Text][PDF]
Nan-Jie Deng, Lisa Yan, Deepak Singh, and Piotr Cieplak
Molecular Basis for the Cu2+ Binding-Induced Destabilization of ß2-Microglobulin Revealed by Molecular Dynamics Simulation Biophys. J. 2006. 90:3865-3879.
[Abstract][Full Text][PDF]
Chia-En Chang, Tongye Shen, Joanna Trylska, Valentina Tozzini, and J. Andrew McCammon
Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model Biophys. J. 2006. 90:3880-3885.
[Abstract][Full Text][PDF]
Hiroshi Ishikita and Ernst-Walter Knapp
Function of Redox-Active Tyrosine in Photosystem II Biophys. J. 2006. 90:3886-3896.
[Abstract][Full Text][PDF]
Daniel Fraiman, Bernardo Pando, Sheila Dargan, Ian Parker, and Silvina Ponce Dawson
Analysis of Puff Dynamics in Oocytes: Interdependence of Puff Amplitude and Interpuff Interval Biophys. J. 2006. 90:3897-3907.
[Abstract][Full Text][PDF]
Thomas Hirschberger, Martina Stork, Bernhard Schropp, Konstanze F. Winklhofer, Jorg Tatzelt, and Paul Tavan
Structural Instability of the Prion Protein upon M205S/R Mutations Revealed by Molecular Dynamics Simulations Biophys. J. 2006. 90:3908-3918.
[Abstract][Full Text][PDF]
Nathan D. Price, Ines Thiele, and Bernhard O. Palsson
Candidate States of Helicobacter pylori's Genome-Scale Metabolic Network upon Application of "Loop Law" Thermodynamic Constraints Biophys. J. 2006. 90:3919-3928.
[Abstract][Full Text][PDF]
Indira H. Shrivastava and Ivet Bahar
Common Mechanism of Pore Opening Shared by Five Different Potassium Channels Biophys. J. 2006. 90:3929-3940.
[Abstract][Full Text][PDF]
Turgut Bastug and Serdar Kuyucak
Energetics of Ion Permeation, Rejection, Binding, and Block in Gramicidin A from Free Energy Simulations Biophys. J. 2006. 90:3941-3950.
[Abstract][Full Text][PDF]
Sukit Leekumjorn and Amadeu K. Sum
Molecular Simulation Study of Structural and Dynamic Properties of Mixed DPPC/DPPE Bilayers Biophys. J. 2006. 90:3951-3965.
[Abstract][Full Text][PDF]
G. Civelekoglu-Scholey, D. J. Sharp, A. Mogilner, and J. M. Scholey
Model of Chromosome Motility in Drosophila Embryos: Adaptation of a General Mechanism for Rapid Mitosis Biophys. J. 2006. 90:3966-3982.
[Abstract][Full Text][PDF]
Yuguang Mu, Lars Nordenskiold, and James P. Tam
Folding, Misfolding, and Amyloid Protofibril Formation of WW Domain FBP28 Biophys. J. 2006. 90:3983-3992.
[Abstract][Full Text][PDF]
Harish Shankaran, H. Steven Wiley, and Haluk Resat
Modeling the Effects of HER/ErbB1-3 Coexpression on Receptor Dimerization and Biological Response Biophys. J. 2006. 90:3993-4009.
[Abstract][Full Text][PDF]
Y. Dehouck, D. Gilis, and M. Rooman
A New Generation of Statistical Potentials for Proteins Biophys. J. 2006. 90:4010-4017.
[Abstract][Full Text][PDF]
Buyong Ma and Ruth Nussinov
The Stability of Monomeric Intermediates Controls Amyloid Formation: Aß25–35 and its N27Q Mutant Biophys. J. 2006. 90:3365-3374.
[Abstract][Full Text][PDF]
Ivan Coluzza, Saskia M. van der Vies, and Daan Frenkel
Translocation Boost Protein-Folding Efficiency of Double-Barreled Chaperonins Biophys. J. 2006. 90:3375-3381.
[Abstract][Full Text][PDF]
Dengming Ming and Rafael Bruschweiler
Reorientational Contact-Weighted Elastic Network Model for the Prediction of Protein Dynamics: Comparison with NMR Relaxation Biophys. J. 2006. 90:3382-3388.
[Abstract][Full Text][PDF]
David E. Prosser, YuDing Guo, Zongchao Jia, and Glenville Jones
Structural Motif-Based Homology Modeling of CYP27A1 and Site-Directed Mutational Analyses Affecting Vitamin D Hydroxylation Biophys. J. 2006. 90:3389-3409.
[Abstract][Full Text][PDF]
Changbong Hyeon and D. Thirumalai
Forced-Unfolding and Force-Quench Refolding of RNA Hairpins Biophys. J. 2006. 90:3410-3427.
[Abstract][Full Text][PDF]
Marco Berrera, Sergio Pantano, and Paolo Carloni
cAMP Modulation of the Cytoplasmic Domain in the HCN2 Channel Investigated by Molecular Simulations Biophys. J. 2006. 90:3428-3433.
[Abstract][Full Text][PDF]
Krasimira Tsaneva-Atanasova, Charles L. Zimliki, Richard Bertram, and Arthur Sherman
Diffusion of Calcium and Metabolites in Pancreatic Islets: Killing Oscillations with a Pitchfork Biophys. J. 2006. 90:3434-3446.
[Abstract][Full Text][PDF]
Toby W. Allen, Olaf S. Andersen, and Benoit Roux
Ion Permeation through a Narrow Channel: Using Gramicidin to Ascertain All-Atom Molecular Dynamics Potential of Mean Force Methodology and Biomolecular Force Fields Biophys. J. 2006. 90:3447-3468.
[Abstract][Full Text][PDF]
Achim Besser and Samuel A. Safran
Force-Induced Adsorption and Anisotropic Growth of Focal Adhesions Biophys. J. 2006. 90:3469-3484.
[Abstract][Full Text][PDF]
Ghanim Ullah and Peter Jung
Modeling the Statistics of Elementary Calcium Release Events Biophys. J. 2006. 90:3485-3495.
[Abstract][Full Text][PDF]
Marcos Sotomayor, Trudy A. van der Straaten, Umberto Ravaioli, and Klaus Schulten
Electrostatic Properties of the Mechanosensitive Channel of Small Conductance MscS Biophys. J. 2006. 90:3496-3510.
[Abstract][Full Text][PDF]
Martin Hemberg, Sophia N. Yaliraki, and Mauricio Barahona
Stochastic Kinetics of Viral Capsid Assembly Based on Detailed Protein Structures Biophys. J. 2006. 90:3029-3042.
[Abstract][Full Text][PDF]
Chigusa Kobayashi and Shoji Takada
Protein Grabs a Ligand by Extending Anchor Residues: Molecular Simulation for Ca2+ Binding to Calmodulin Loop Biophys. J. 2006. 90:3043-3051.
[Abstract][Full Text][PDF]
Alfonso De Simone, Roberta Spadaccini, Piero A. Temussi, and Franca Fraternali
Toward the Understanding of MNEI Sweetness from Hydration Map Surfaces Biophys. J. 2006. 90:3052-3061.
[Abstract][Full Text][PDF]
Sergej Vasil'ev and Doug Bruce
A Protein Dynamics Study of Photosystem II: The Effects of Protein Conformation on Reaction Center Function Biophys. J. 2006. 90:3062-3073.
[Abstract][Full Text][PDF]
Edmund J. Crampin and Nicolas P. Smith
A Dynamic Model of Excitation-Contraction Coupling during Acidosis in Cardiac Ventricular Myocytes Biophys. J. 2006. 90:3074-3090.
[Abstract][Full Text][PDF]
Andrew Krueger, Ekaterina Protozanova, and Maxim D. Frank-Kamenetskii
Sequence-Dependent Basepair Opening in DNA Double Helix Biophys. J. 2006. 90:3091-3099.
[Abstract][Full Text][PDF]
C. Weber, A. Stasiak, P. De Los Rios, and G. Dietler
Numerical Simulation of Gel Electrophoresis of DNA Knots in Weak and Strong Electric Fields Biophys. J. 2006. 90:3100-3105.
[Abstract][Full Text][PDF]
Li Zhang and Dimitrios Morikis
Immunophysical Properties and Prediction of Activities for Vaccinia Virus Complement Control Protein and Smallpox Inhibitor of Complement Enzymes Using Molecular Dynamics and Electrostatics Biophys. J. 2006. 90:3106-3119.
[Abstract][Full Text][PDF]
Antonio Politi, Lawrence D. Gaspers, Andrew P. Thomas, and Thomas Hofer
Models of IP3 and Ca2+ Oscillations: Frequency Encoding and Identification of Underlying Feedbacks Biophys. J. 2006. 90:3120-3133.
[Abstract][Full Text][PDF]
Jeroen van Gestel and Simon W. de Leeuw
A Statistical-Mechanical Theory of Fibril Formation in Dilute Protein Solutions Biophys. J. 2006. 90:3134-3145.
[Abstract][Full Text][PDF]
Marcin Imielinski, Calin Belta, Harvey Rubin, and Adam Halasz
Systematic Analysis of Conservation Relations in Escherichia coli Genome-Scale Metabolic Network Reveals Novel Growth Media Biophys. J. 2006. 90:2659-2672.
[Abstract][Full Text][PDF]
Evgeny B. Stukalin and Anatoly B. Kolomeisky
ATP Hydrolysis Stimulates Large Length Fluctuations in Single Actin Filaments Biophys. J. 2006. 90:2673-2685.
[Abstract][Full Text][PDF]
Helene Karcher, Seung E. Lee, Mohammad R. Kaazempur-Mofrad, and Roger D. Kamm
A Coarse-Grained Model for Force-Induced Protein Deformation and Kinetics Biophys. J. 2006. 90:2686-2697.
[Abstract][Full Text][PDF]
Eunice Ramirez, Alberto Santana, Anthony Cruz, Ines Plasencia, and Gustavo E. Lopez
Molecular Dynamics of Surfactant Protein C: From Single Molecule to Heptameric Aggregates Biophys. J. 2006. 90:2698-2705.
[Abstract][Full Text][PDF]
Sophie Sacquin-Mora and Richard Lavery
Investigating the Local Flexibility of Functional Residues in Hemoproteins Biophys. J. 2006. 90:2706-2717.
[Abstract][Full Text][PDF]
Pu Tian and Ioan Andricioaei
Size, Motion, and Function of the SecY Translocon Revealed by Molecular Dynamics Simulations with Virtual Probes Biophys. J. 2006. 90:2718-2730.
[Abstract][Full Text][PDF]
Tao Hu, A. Yu. Grosberg, and B. I. Shklovskii
How Proteins Search for Their Specific Sites on DNA: The Role of DNA Conformation Biophys. J. 2006. 90:2731-2744.
[Abstract][Full Text][PDF]
Patrick F. J. Fuchs, Alexandre M. J. J. Bonvin, Brigida Bochicchio, Antonietta Pepe, Alain J. P. Alix, and Antonio M. Tamburro
Kinetics and Thermodynamics of Type VIII ß-Turn Formation: A CD, NMR, and Microsecond Explicit Molecular Dynamics Study of the GDNP Tetrapeptide Biophys. J. 2006. 90:2745-2759.
[Abstract][Full Text][PDF]
Paul Smolen, Douglas A. Baxter, and John H. Byrne
A Model of the Roles of Essential Kinases in the Induction and Expression of Late Long-Term Potentiation Biophys. J. 2006. 90:2760-2775.
[Abstract][Full Text][PDF]
Mikko Heikela, Ilpo Vattulainen, and Marja T. Hyvonen
Atomistic Simulation Studies of Cholesteryl Oleates: Model for the Core of Lipoprotein Particles Biophys. J. 2006. 90:2247-2257.
[Abstract][Full Text][PDF]
Radostin D. Simitev and Vadim N. Biktashev
Conditions for Propagation and Block of Excitation in an Asymptotic Model of Atrial Tissue Biophys. J. 2006. 90:2258-2269.
[Abstract][Full Text][PDF]
Morten O. Jensen and Ole G. Mouritsen
Single-Channel Water Permeabilities of Escherichia coli Aquaporins AqpZ and GlpF Biophys. J. 2006. 90:2270-2284.
[Abstract][Full Text][PDF]
Turgut Bastug, Angus Gray-Weale, Swarna M. Patra, and Serdar Kuyucak
Role of Protein Flexibility in Ion Permeation: A Case Study in Gramicidin A Biophys. J. 2006. 90:2285-2296.
[Abstract][Full Text][PDF]
Jason M. Haugh
Deterministic Model of Dermal Wound Invasion Incorporating Receptor-Mediated Signal Transduction and Spatial Gradient Sensing Biophys. J. 2006. 90:2297-2308.
[Abstract][Full Text][PDF]
Hao Song, Paul Smolen, Evyatar Av-Ron, Douglas A. Baxter, and John H. Byrne
Bifurcation and Singularity Analysis of a Molecular Network for the Induction of Long-Term Memory Biophys. J. 2006. 90:2309-2325.
[Abstract][Full Text][PDF]
Senthil K. Kandasamy and Ronald G. Larson
Molecular Dynamics Simulations of Model Trans-Membrane Peptides in Lipid Bilayers: A Systematic Investigation of Hydrophobic Mismatch Biophys. J. 2006. 90:2326-2343.
[Abstract][Full Text][PDF]
Zhirong Liu, E. Lynn Zechiedrich, and Hue Sun Chan
Inferring Global Topology from Local Juxtaposition Geometry: Interlinking Polymer Rings and Ramifications for Topoisomerase Action Biophys. J. 2006. 90:2344-2355.
[Abstract][Full Text][PDF]
Jennifer M. Johnston, Gabriel A. Cook, John M. Tomich, and Mark S. P. Sansom
Conformation and Environment of Channel-Forming Peptides: A Simulation Study Biophys. J. 2006. 90:1855-1864.
[Abstract][Full Text][PDF]
Qing Zhang and Tamar Schlick
Stereochemistry and Position-Dependent Effects of Carcinogens on TATA/TBP Binding Biophys. J. 2006. 90:1865-1877.
[Abstract][Full Text][PDF]
Joel Beaudouin, Felipe Mora-Bermudez, Thorsten Klee, Nathalie Daigle, and Jan Ellenberg
Dissecting the Contribution of Diffusion and Interactions to the Mobility of Nuclear Proteins Biophys. J. 2006. 90:1878-1894.
[Abstract][Full Text][PDF]
Vincent K. Shen, Jason K. Cheung, Jeffrey R. Errington, and Thomas M. Truskett
Coarse-Grained Strategy for Modeling Protein Stability in Concentrated Solutions. II: Phase Behavior Biophys. J. 2006. 90:1949-1960.
[Abstract][Full Text][PDF]
Xiao Wang, Nan Hao, Henrik G. Dohlman, and Timothy C. Elston
Bistability, Stochasticity, and Oscillations in the Mitogen-Activated Protein Kinase Cascade Biophys. J. 2006. 90:1961-1978.
[Abstract][Full Text][PDF]
Prabal K. Maiti, Tod A. Pascal, Nagarajan Vaidehi, Jiyoung Heo, and William A. Goddard III
Atomic-Level Simulations of Seeman DNA Nanostructures: The Paranemic Crossover in Salt Solution Biophys. J. 2006. 90:1463-1479.
[Abstract][Full Text][PDF]
Flore Joli, Edith Hantz, and Brigitte Hartmann
Structure and Dynamics of Phosphate Linkages and Sugars in an Abasic Hexaloop RNA Hairpin Biophys. J. 2006. 90:1480-1488.
[Abstract][Full Text][PDF]
Mikhail A. Panteleev, Mikhail V. Ovanesov, Dmitrii A. Kireev, Aleksei M. Shibeko, Elena I. Sinauridze, Natalya M. Ananyeva, Andrey A. Butylin, Evgueni L. Saenko, and Fazoil I. Ataullakhanov
Spatial Propagation and Localization of Blood Coagulation Are Regulated by Intrinsic and Protein C Pathways, Respectively Biophys. J. 2006. 90:1489-1500.
[Abstract][Full Text][PDF]
Grace Brannigan and Frank L. H. Brown
A Consistent Model for Thermal Fluctuations and Protein-Induced Deformations in Lipid Bilayers Biophys. J. 2006. 90:1501-1520.
[Abstract][Full Text][PDF]
Magnus Andersson, Erik Fallman, Bernt Eric Uhlin, and Ove Axner
A Sticky Chain Model of the Elongation and Unfolding of Escherichia coli P Pili under Stress Biophys. J. 2006. 90:1521-1534.
[Abstract][Full Text][PDF]
Ran Friedman, Esther Nachliel, and Menachem Gutman
Fatty Acid Binding Proteins: Same Structure but Different Binding Mechanisms? Molecular Dynamics Simulations of Intestinal Fatty Acid Binding Protein Biophys. J. 2006. 90:1535-1545.
[Abstract][Full Text][PDF]
E. Z. Bagci, Y. Vodovotz, T. R. Billiar, G. B. Ermentrout, and I. Bahar
Bistability in Apoptosis: Roles of Bax, Bcl-2, and Mitochondrial Permeability Transition Pores Biophys. J. 2006. 90:1546-1559.
[Abstract][Full Text][PDF]
Haiping Hao, Daniel E. Zak, Thomas Sauter, James Schwaber, and Babatunde A. Ogunnaike
Modeling the VPAC2-Activated cAMP/PKA Signaling Pathway: From Receptor to Circadian Clock Gene Induction Biophys. J. 2006. 90:1560-1571.
[Abstract][Full Text][PDF]
Jhih-Wei Chu and Gregory A. Voth
Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations Biophys. J. 2006. 90:1572-1582.
[Abstract][Full Text][PDF]
Paula Petrone and Vijay S. Pande
Can Conformational Change Be Described by Only a Few Normal Modes? Biophys. J. 2006. 90:1583-1593.
[Abstract][Full Text][PDF]
Alexander Vologodskii
Brownian Dynamics Simulation of Knot Diffusion along a Stretched DNA Molecule Biophys. J. 2006. 90:1594-1597.
[Abstract][Full Text][PDF]
Michael Patra, Emppu Salonen, Emma Terama, Ilpo Vattulainen, Roland Faller, Bryan W. Lee, Juha Holopainen, and Mikko Karttunen
Under the Influence of Alcohol: The Effect of Ethanol and Methanol on Lipid Bilayers Biophys. J. 2006. 90:1121-1135.
[Abstract][Full Text][PDF]
Amit Mehra and Vassily Hatzimanikatis
An Algorithmic Framework for Genome-Wide Modeling and Analysis of Translation Networks Biophys. J. 2006. 90:1136-1146.
[Abstract][Full Text][PDF]
J. Reidl, P. Borowski, A. Sensse, J. Starke, M. Zapotocky, and M. Eiswirth
Model of Calcium Oscillations Due to Negative Feedback in Olfactory Cilia Biophys. J. 2006. 90:1147-1155.
[Abstract][Full Text][PDF]
Jonathan Bronson, One-Sun Lee, and Jeffery G. Saven
Molecular Dynamics Simulation of WSK-3, a Computationally Designed, Water-Soluble Variant of the Integral Membrane Protein KcsA Biophys. J. 2006. 90:1156-1163.
[Abstract][Full Text][PDF]
Hao Cheng, Kai Zhang, Joseph A. Libera, Monica Olvera de la Cruz, and Michael J. Bedzyk
Polynucleotide Adsorption to Negatively Charged Surfaces in Divalent Salt Solutions Biophys. J. 2006. 90:1164-1174.
[Abstract][Full Text][PDF]
Zhi-Jie Tan and Shi-Jie Chen
Nucleic Acid Helix Stability: Effects of Salt Concentration, Cation Valence and Size, and Chain Length Biophys. J. 2006. 90:1175-1190.
[Abstract][Full Text][PDF]
David R. Nutt and Markus Meuwly
Studying Reactive Processes with Classical Dynamics: Rebinding Dynamics in MbNO Biophys. J. 2006. 90:1191-1201.
[Abstract][Full Text][PDF]
Gang Cheng, Belgacem B. Youssef, Pauline Markenscoff, and Kyriacos Zygourakis
Cell Population Dynamics Modulate the Rates of Tissue Growth Processes Biophys. J. 2006. 90:713-724.
[Abstract][Full Text][PDF]
Tomasz Lipniacki, Pawel Paszek, Allan R. Brasier, Bruce A. Luxon, and Marek Kimmel
Chemical and Structural Disorder in Eumelanins: A Possible Explanation for Broadband Absorbance Biophys. J. 2006. 90:743-752.
[Abstract][Full Text][PDF]
Wendy Thomas, Manu Forero, Olga Yakovenko, Lina Nilsson, Paolo Vicini, Evgeni Sokurenko, and Viola Vogel
Catch-Bond Model Derived from Allostery Explains Force-Activated Bacterial Adhesion Biophys. J. 2006. 90:753-764.
[Abstract][Full Text][PDF]
Wenbing Zhang and Shi-Jie Chen
Exploring the Complex Folding Kinetics of RNA Hairpins: I. General Folding Kinetics Analysis Biophys. J. 2006. 90:765-777.
[Abstract][Full Text][PDF]
Wenbing Zhang and Shi-Jie Chen
Exploring the Complex Folding Kinetics of RNA Hairpins: II. Effect of Sequence, Length, and Misfolded States Biophys. J. 2006. 90:778-787.
[Abstract][Full Text][PDF]
Albertas Janulevicius, Jaap van Pelt, and Arjen van Ooyen
Compartment Volume Influences Microtubule Dynamic Instability: A Model Study Biophys. J. 2006. 90:788-798.
[Abstract][Full Text][PDF]
Ben Corry
An Energy-Efficient Gating Mechanism in the Acetylcholine Receptor Channel Suggested by Molecular and Brownian Dynamics Biophys. J. 2006. 90:799-810.
[Abstract][Full Text][PDF]
Yi Qin Gao
A Simple Theoretical Model Explains Dynein's Response to Load Biophys. J. 2006. 90:811-821.
[Abstract][Full Text][PDF]
Sundeep S. Deol, Carmen Domene, Peter J. Bond, and Mark S. P. Sansom
Anionic Phospholipid Interactions with the Potassium Channel KcsA: Simulation Studies Biophys. J. 2006. 90:822-830.
[Abstract][Full Text][PDF]
J. Bishop, S. Blair, and A. M. Chagovetz
A Competitive Kinetic Model of Nucleic Acid Surface Hybridization in the Presence of Point Mutants Biophys. J. 2006. 90:831-840.
[Abstract][Full Text][PDF]
Peter Monecke, Thorsten Borosch, Jurgen Brickmann, and Stefan M. Kast
Determination of the Interfacial Water Content in Protein-Protein Complexes from Free Energy Simulations Biophys. J. 2006. 90:841-850.
[Abstract][Full Text][PDF]
Perttu S. Niemela, Marja T. Hyvonen, and Ilpo Vattulainen
Influence of Chain Length and Unsaturation on Sphingomyelin Bilayers Biophys. J. 2006. 90:851-863.
[Abstract][Full Text][PDF]
Michael S. Lee and Mark A. Olson
Calculation of Absolute Protein-Ligand Binding Affinity Using Path and Endpoint Approaches Biophys. J. 2006. 90:864-877.
