Journal of Physical Chemistry B

Journal of Physical Chemistry B, Vol.120, No.33 Entire volume, number list

ISSN: 1520-6106 (Print)

In this Issue (62 articles)

8055 - 8056	Tribute to J. Andrew McCammon Amaro RE, Madura JD, Wong CF
8057 - 8060	Autobiography of J. Andrew McCammon McCammon JA
8071 - 8079	Electrophoretic Mobility of a Dilute, Highly Charged "Soft" Spherical Particle in a Charged Hydrogel Allison S, Li F, Le M
8080 - 8089	Reversible Stochastically Gated Diffusion-Influenced Reactions Gopich IV, Szabo A
8090 - 8101	Folding PDZ2 Domain Using the Molecular Transfer Model Liu ZX, Reddy G, Thirumalai D
8102 - 8114	Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water Yan XC, Tirado-Rives J, Jorgensen WL
8115 - 8126	Multi-Conformation Monte Carlo: A Method for Introducing Flexibility in Efficient Simulations of Many-Protein Systems Prytkova V, Heyden M, Khago D, Freites JA, Butts CT, Martin RW, Tobias DJ
8127 - 8136	Solvent Fluctuations Induce Non-Markovian Kinetics in Hydrophobic Pocket-Ligand Binding Weiss RG, Setny P, Dzubiella J
8137 - 8146	Recognition of Poly-Ubiquitins by the Proteasome through Protein Refolding Guided by Electrostatic and Hydrophobic Interactions Zhang Y, Vukovic L, Rudack T, Han W, Schulten K
8147 - 8153	Charged Substrate and Product Together Contribute Like a Nonreactive Species to the Overall Electrostatic Steering in Diffusion-Reaction Processes Xu JJ, Xie Y, Lu BZ, Zhang LB
8154 - 8163	Free Energy Landscape of Lipid Interactions with Regulatory Binding Sites on the Transmembrane Domain of the EGF Receptor Hedger G, Shorthouse D, Koldso H, Sansom MSP
8164 - 8174	Fast Method for Computing Chemical Potentials and Liquid Liquid Phase Equilibria of Macromolecular Solutions Qin SB, Zhou HX
8175 - 8185	HCN, Formamidic Acid, and Formamide in Aqueous Solution: A Free Energy Map Kua J, Thrush KL
8186 - 8192	Mechanism of pKID/KIX Association Studied by Molecular Dynamics Free Energy Simulations Bomblies R, Luitz MP, Zacharias M
8193 - 8207	Contribution of Electrostatics to the Kinetics of Electron Transfer from NADH-Cytochrome b(5) Reductase to Fe(III)-Cytochrome b(5) Kollipara S, Tatireddy S, Pathirathne T, Rathnayake LK, Northrup SH
8208 - 8216	Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning Cardenas AE, Elber R
8217 - 8229	Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization Miller MS, Lay WK, Elcock AH
8230 - 8237	Solute-Solvent Energetics Based on Proximal Distribution Functions Ou SC, Pettitt BM
8238 - 8253	Effects of Cardiac Troponin I Mutation P83S on Contractile Properties and the Modulation by PKA-Mediated Phosphorylation Cheng YH, Lindert S, Oxenford L, Tu AY, McCulloch AD, Regnier M
8254 - 8263	Mechanism of Inhibition of Cholesteryl Ester Transfer Protein by Small Molecule Inhibitors Chirasani VR, Sankar R, Senapati S
8264 - 8275	Molecular Effects of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation-An Integrated Multiscale Modeling Study Dewan S, McCabe KJ, Regnier M, McCulloch AD, Lindert S
8276 - 8288	Rapid Characterization of Allosteric Networks with Ensemble Normal Mode Analysis Yao XQ, Skjaerven L, Grant BJ
8289 - 8301	Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit Zhang BW, Dai W, Gallicchio E, He P, Xia JC, Tan ZQ, Levy RM
8302 - 8312	The "Lid" in the Streptococcus pneumoniae SrtC1 Sortase Adopts a Rigid Structure that Regulates Substrate Access to the Active Site Jacobitz AW, Naziga EB, Yi SW, McConnell SA, Peterson R, Jung ME, Clubb RT, Wereszczynski J
8313 - 8320	Picosecond to Millisecond Structural Dynamics in Human Ubiquitin Lindorff-Larsen K, Maragakis P, Piana S, Shaw DE
8321 - 8337	Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches Mills JD, Ben-Nun M, Rollin K, Bromley MWJ, Li JB, Hinde RJ, Winstead CL, Sheehy JA, Boatz JA, Langhoff PW
8338 - 8345	The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor Clark AK, Wilder JH, Grayson AW, Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen TY
8346 - 8353	Computational Modeling of Competitive Metabolism between omega 3-and omega 6-Polyunsaturated Fatty Acids in Inflammatory Macrophages Gupta S, Kihara Y, Maurya MR, Norris PC, Dennis EA, Subramanian S
8354 - 8360	Energy Minimization of Discrete Protein Titration State Models Using Graph Theory Purvine E, Monson K, Jurrus E, Star K, Baker NA
8361 - 8368	Structure and Dynamics Study of LeuT Using the Markov State Model and Perturbation Response Scanning Reveals Distinct Ion Induced Conformational States Asciutto EK, Gedeon PC, General IJ, Madura JD
8369 - 8378	Scanning of 16S Ribosomal RNA for Peptide Nucleic Acid Targets Gorska A, Markowska-Zagrajek A, Rownicki M, Trylska J
8379 - 8388	Secondary Interaction Interfaces with PCNA Control Conformational Switching of DNA Polymerase PoIB from Polymerization to Editing Xu XJ, Yan CL, Kossmann BR, Ivanov I
8389 - 8404	Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II Taraphder S, Maupin CM, Swanson JMJ, Voth GA
8405 - 8415	Coupled Dynamics and Entropic Contribution to the Allosteric Mechanism of Pin1 Barman A, Hamelberg D
8416 - 8423	Electrostatic Steering Accelerates C3d:CR2 Association Mohan RR, Huber GA, Morikis D
8424 - 8437	Ionic Hydrogen Bonds and Lipid Packing Defects Determine the Binding Orientation and Insertion Depth of RecA on Multicomponent Lipid Bilayers Zhang LL, Rajendram M, Weibel DB, Yethiraj A, Cui Q
8438 - 8448	Behavior of Bilayer Leaflets in Asymmetric Model Membranes: Atomistic Simulation Studies Tian JH, Nickels J, Katsaras J, Cheng XL
8449 - 8456	Transitions of Double-Stranded DNA Between the A- and B-Forms Waters JT, Lu XJ, Galindo-Murillo R, Gumbart JC, Kim HD, Cheatham TE, Harvey SC
8457 - 8472	A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes Ovchinnikov V, Nam K, Karplus M
8473 - 8484	Spatial Heat Maps from Fast Information Matching of Fast and Slow Degrees of Freedom: Application to Molecular Dynamics Simulations Kovacs JA, Wriggers W
8485 - 8517	Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity-Basity Scale Revisited Reif MM, Hunenberger PH
8518 - 8531	Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations Roberts CC, Chang CEA
8532 - 8538	PEST Control of Molecular Stripping of NF kappa B from DNA Transcription Sites Potoyan DA, Zheng WH, Ferreiro DU, Wolynes PG, Komives EA
8539 - 8546	Exploring Electrostatic Effects on the Hydrogen Bond Network of Liquid Water through Many-Body Molecular Dynamics Straight SC, Paesani F
8547 - 8556	Computational Equilibrium Thermodynamic and Kinetic Analysis of K-Ras Dimerization through an Effector Binding Surface Suggests Limited Functional Role Sayyed-Ahmad A, Cho KJ, Hancock JF, Gorfe AA
8557 - 8565	Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model Chen MC, Lin XC, Zheng WH, Onuchic JN, Wolynes PG
8566 - 8570	Parameter-Free Hydrogen-Bond Definition to Classify Protein Secondary Structure Haghighi H, Higham J, Henchman RH
8571 - 8579	Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models Mereghetti P, Maccari G, Spampinato GLB, Tozzini V
8580 - 8589	Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen Subramanian SR, Singam ERA, Berinski M, Subramanian V, Wade RC
8590 - 8599	Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants Durrant JD, Bush RM, Amaro RE
8600 - 8605	Reaction Coordinate-Free Approach to Recovering Kinetics from Potential-Scaled Simulations: Application of Kramers' Rate Theory Frank AT, Andricioaei I
8606 - 8616	Two Relations to Estimate Membrane Permeability Using Milestoning Votapka LW, Lee CT, Amaro RE
8617 - 8630	Understanding Ion Binding Affinity and Selectivity in beta-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory Kucharski AN, Scott CE, Davis JP, Kekenes-Huskey PM
8631 - 8641	Behavior of P85 and P188 Poloxamer Molecules: Computer Simulations Using United-Atom Force-Field Goliaei A, Lau EY, Adhikari U, Schwegler E, Berkowitz ML
8642 - 8653	Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements Bascom GD, Sanbonmatsu KY, Schlick T
8654 - 8667	Claws, Disorder, and Conformational Dynamics of the C-Terminal Region of Human Desmoplakin McAnany CE, Mura C
8668 - 8684	Evaluation of Representations and Response Models for Polarizable Force Fields Li A, Voronin A, Fenley AT, Gilson MK
8685 - 8695	Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems Ghanakota P, Carlson HA
8696 - 8706	Quantifying the Influence of the Crowded Cytoplasm on Small Molecule Diffusion Kekenes-Huskey PM, Scott CE, Atalay S
8707 - 8721	Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions Xiao L, Wang CH, Ye X, Luo R
8722 - 8732	Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes Vogele M, Hummer G
8733 - 8742	Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations Jo S, Suh D, He ZW, Chipot C, Roux B