Journal of Physical Chemistry B

Journal of Physical Chemistry B, Vol.121, No.15 Entire volume, number list

ISSN: 1520-6106 (Print)

In this Issue (65 articles)

3203 - 3205	Tribute to Klaus Schulten Tajkhorshid E, Chipot C
3206 - 3206	Biography of Klaus Schulten Amaro RE, Villa E, Luthey-Schulten Z
3228 - 3236	Protein Arrangement Effects on the Exciton Dynamics in the PE555 Complex Chandrasekaran S, Pothula KR, Kleinekathofer U
3237 - 3249	Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane van Eerden FJ, van den Berg T, Frederix PWJM, de Jong DH, Periole X, Marrink SJ
3250 - 3261	Primary Fibril Nucleation of Aggregation Prone Tau Fragments PHF6 and PHF6* Smit FX, Luiken JA, Bolhuis PG
3262 - 3275	Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations Gu RX, Ingolfsson HI, de Vries AH, Marrink SJ, Tieleman DP
3276 - 3284	Eliminating a Protein Folding Intermediate by Tuning a Local Hydrophobic Contact Kachlishvili K, Dave K, Gruebele M, Scheraga HA, Maisuradze GG
3285 - 3296	A Distal Disulfide Bridge in OXA-1 beta-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Omega Loop Simakov N, Leonard DA, Smith JC, Wymore T, Szarecka A
3297 - 3307	Predicted Structures of the Proton-Bound Membrane-Embedded Rotor Rings of the Saccharomyces cerevisiae and Escherichia coli ATP Synthases Zhou W, Leone V, Krah A, Faraldo-Gomez JD
3308 - 3317	Mutations at the Q(o) Site of the Cytochrome bc(1) Complex Strongly Affect Oxygen Binding Husen P, Solov'yov IA
3318 - 3330	Origin of pK(a) Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water Wu XW, Lee JY, Brooks BR
3331 - 3339	Dynamics of the Orientational Factor in Fluorescence Resonance Energy Transfer Hummer G, Szabo A
3340 - 3351	Does Proton Conduction in the Voltage-Gated H+ Channel hHv1 Involve Grotthuss-Like Hopping via Acidic Residues? van Keulen SC, Gianti E, Carnevale V, Klein ML, Rothlisberger U, Delemotte L
3352 - 3363	The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape Fajer M, Meng YL, Roux B
3364 - 3375	Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association Domanski J, Hedger G, Best RB, Stansfeld PJ, Sansom MSP
3376 - 3386	Finite Temperature String Method with Umbrella Sampling: Application on a Side Chain Flipping in Mhp1 Transporter Song HD, Zhu FQ
3387 - 3393	Molecular Dynamics Analysis of 4E-BP2 Protein Fold Stabilization Induced by Phosphorylation Bomblies R, Luitz MP, Zacharias M
3394 - 3402	Estimation of Nanodiamond Surface Charge Density from Zeta Potential and Molecular Dynamics Simulations Ge ZP, Wang Y
3403 - 3411	Classical and Quantum Shortcuts to Adiabaticity in a Tilted Piston Patra A, Jarzynski C
3412 - 3423	Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155-4 Yang M, Simon R, MacKerell AD
3424 - 3436	Direct Measurement of the Effect of Cholesterol and 6-Ketocholestanol on the Membrane Dipole Electric Field Using Vibrational Stark Effect Spectroscopy Coupled with Molecular Dynamics Simulations Shrestha R, Anderson CM, Cardenas AE, Elber R, Webb LJ
3437 - 3442	Dependence of the Enzymatic Velocity on the Substrate Dissociation Rate Berezhkovskii AM, Szabo A, Rotbart T, Urbakh M, Kolomeisky AB
3443 - 3457	Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbruck Model and Periodic Boundary Conditions Venable RM, Ingolfsson HI, Lerner MG, Perrin BS, Camley BA, Marrink SJ, Brown FLH, Pastor RW
3458 - 3472	Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies Gosink LJ, Overall CC, Reehl SM, Whitney PD, Mobley DL, Baker NA
3473 - 3482	Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for alpha/beta Proteins Chen MC, Lin XC, Lu W, Onuchic JN, Wolynes PG
3483 - 3492	Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details Massarczyk M, Rudack T, Schlitter J, Kuhne J, Kotting C, Gerwert K
3493 - 3501	A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen-Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A
3502 - 3514	Methodology for the Simulation of Molecular Motors at Different Scales Singharoy A, Chipot C
3515 - 3522	Ripping RNA by Force Using Gaussian Network Models Hyeon C, Thirumalai D
3523 - 3535	Structural Insights How PIP2 Imposes Preferred Binding Orientations of FAK at Lipid Membranes Herzog FA, Braun L, Schoen I, Vogel V
3536 - 3545	Redox-Driven Conformational Dynamics in a Photosystem-II-Inspired beta-Hairpin Maquette Determined through Spectroscopy and Simulation Hwang H, McCaslin TG, Hazel A, Pagba CV, Nevin CM, Paylova A, Barry BA, Gumbart JC
3546 - 3554	Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods? Skolnick J, Zhou HY
3555 - 3564	Nonpolar Solvation Free Energy from Proximal Distribution Functions Ou SC, Drake JA, Pettitt BM
3565 - 3573	Understanding the Phosphorylation Mechanism by Using Quantum Chemical Calculations and Molecular Dynamics Simulations Han WW, Zhu JX, Wang S, Xu D
3574 - 3585	Toward Closing the Gap: Quantum Mechanical Calculations and Experimentally Measured Chemical Shifts of a Microcrystalline Lectin Fritz M, Quinn CM, Wang MZ, Hou GJ, Lu XG, Koharudin LMI, Polenova T, Gronenborn AM
3586 - 3596	Molecular Details of the PH Domain of ACAP1 (BAR-PH) Protein Binding to PIP-Containing Membrane Chan KC, Lu LY, Sun F, Fan J
3597 - 3606	SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding Votapka LW, Jagger BR, Heyneman AL, Amaro RE
3607 - 3619	Validity of the Electrodiffusion Model for Calculating Conductance of Simple Ion Channels Pohorille A, Wilson MA, Wei CY
3620 - 3625	Mechanical Stability of a High-Affinity Toxin Anchor from the Pathogen Clostridium perfringens Milles LF, Bayer EA, Nash MA, Gaub HE
3626 - 3635	Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite lambda Dynamics Hayes RL, Armacost KA, Vilseck JZ, Brooks CL
3636 - 3643	The Multiple Roles of Waters in Protein Solvation Hospital A, Candotti M, Gelpi JL, Orozco M
3644 - 3656	What Can and Cannot Be Learned from Molecular Dynamics Simulations of Bacterial Proton-Coupled Oligopeptide Transporter GkPOT? Immadisetty K, Hettige J, Moradi M
3657 - 3666	Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters Gur M, Cheng MH, Zomot E, Bahar I
3667 - 3675	Effects of Active Site Mutations on Specificity of Nucleobase Binding in Human DNA Polymerase eta Ucisik MN, Hammes-Schiffer S
3676 - 3685	Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method Lesage A, Lelievre T, Stoltz G, Henin J
3686 - 3700	Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations Ozgur B, Ozdemir ES, Gursoy A, Keskin O
3701 - 3717	The Q-Cycle Mechanism of the bc(1) Complex: A Biologist's Perspective on Atomistic Studies Crofts AR, Rose SW, Burton RL, Desai AV, Kenis PJA, Dikanov SA
3718 - 3723	CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments Qi YF, Lee JM, Singharoy A, McGreevy R, Schulten K, Im W
3724 - 3733	Modulation of Molecular Flux Using a Graphene Nanopore Capacitor Shankla M, Aksimentiev A
3734 - 3746	Equilibrium Denaturation and Preferential Interactions of an RNA Tetraloop with Urea Miner JC, Garcia AE
3747 - 3756	Quantitative Characterization of Domain Motions in Molecular Machines Maji S, Shahoei R, Schulten K, Frank J
3757 - 3763	Graphene Nanopores for Electronic Recognition of DNA Methylation Sarathy A, Qiu H, Leburton JP
3764 - 3776	Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents Vermaas JV, Pogorelov TV, Tajkhorshid E
3777 - 3786	Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation Chao E, Duan BG, Yu J
3787 - 3797	Determination of Cell Doubling Times from the Return-on-Investment Time of Photosynthetic Vesicles Based on Atomic Detail Structural Models Hitchcock A, Hunter CN, Sener M
3798 - 3803	Long-Range Dispersion Effects on the Water/Vapor Interface Simulated Using the Most Common Models Sega M, Dellago C
3804 - 3812	Atomistic Modeling of Ion Conduction through the Voltage-Sensing Domain of the Shaker K+ Ion Channel Wood ML, Freites JA, Tombola F, Tobias DJ
3813 - 3824	Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants Einav T, Phillips R
3825 - 3841	Relationship between Solvation Thermodynamics from IST and DFT Perspectives Levy RM, Cui D, Zhang BW, Matubayasi N
3842 - 3852	Photoactivation Intermediates of a G-Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation Kamiya M, Hayashi S
3853 - 3863	CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations Perilla JR, Zhao GP, Lu MM, Ning JY, Hou GJ, Byeon IJL, Gronenborn AM, Polenova T, Zhang PJ
3864 - 3870	1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations Dodda LS, Vilseck JZ, Tirado-Rives J, Jorgensen WL
3871 - 3881	Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations Earnest TM, Watanabe R, Stone JE, Mahamid J, Baumeister W, Villa E, Luthey-Schulten Z
3882 - 3894	Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion Bascom GD, Kim T, Schlick T
3895 - 3907	Determinants of Alanine Dipeptide Conformational Equilibria on Graphene and Hydroxylated Derivatives Poblete H, Miranda-Carvajal I, Comer J