Selected Publications of J. Andrew McCammon - The Journal of

Special Issue Preface pubs.acs.org/JPCB

Selected Publications of J. Andrew McCammon

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JOURNAL ARTICLES

1. McCammon, J.A., B.R. Gelin, M. Karplus, and P.G. Wolynes. The Hinge-Bending Mode in Lysozyme. Nature 262, 325−326 (1976). 2. McCammon, J.A., B.R. Gelin, and M. Karplus. Dynamics of Folded Proteins. Nature 267, 585−590 (1977). 3. McCammon, J.A., and M. Karplus. Internal Motions of Antibody Molecules. Nature 268, 765−766 (1977). 4. Ermak, D.L., and J.A. McCammon. Brownian Dynamics with Hydrodynamic Interactions. J. Chem. Phys. 69, 1352−1360 (1978). 5. McCammon, J.A., P.G. Wolynes, and M. Karplus. Picosecond Dynamics of Tyrosine Side Chains in Proteins. Biochemistry 18, 927−942 (1979). 6. McCammon, J.A., S.H. Northrup, M. Karplus, and R.M. Levy. Helix−Coil Transitions in a Simple Polypeptide Model. Biopolymers 19, 2033−2045 (1980). 7. McCammon, J.A., and S.H. Northrup. Gated Binding of Ligands to Proteins. Nature 293, 316−317 (1981). 8. Harvey, S.C., and J.A. McCammon. Intramolecular Flexibility in Phenylalanine Transfer RNA. Nature 294, 286−287 (1981). 9. Mao, B., M.R. Pear, J.A. McCammon, and F.A. Quiocho. Hinge-bending in L-Arabinose-binding Protein: The “Venus’s-Flytrap” Model. J. Biol. Chem. 257, 1131− 1133 (1982). 10. Szabo, A., D. Shoup, S.H. Northrup, and J.A. McCammon. Stochastically Gated Diffusion-Influenced Reactions. J. Chem. Phys. 77, 4484−4493 (1982). 11. Berkowitz, M., J.D. Morgan, and J.A. McCammon. Generalized Langevin Dynamics Simulations with Arbitrary Time-Dependent Memory Kernels. J. Chem. Phys. 78, 3256−3261 (1983). 12. McCammon, J.A., C.Y. Lee, and S.H. Northrup. SideChain Rotational Isomerization in Proteins: A Mechanism Involving Gating and Transient Packing Defects. J. Am. Chem. Soc. 105, 2232−2237 (1983). 13. Northrup, S.H., and J.A. McCammon. Saddle-Point Avoidance in Diffusional Reactions. J. Chem. Phys. 78, 987−989 (1983). 14. Berkowitz, M., J.D. Morgan, J.A. McCammon, and S.H. Northrup. Diffusion-Controlled Reactions: A Variational Formula for the Optimum Reaction Coordinate. J. Chem. Phys. 79, 5563−5565 (1983). 15. Harvey, S.C., M. Prabhakaran, B. Mao, and J.A. McCammon. Phenylalanine Transfer RNA: Molecular Dynamics Simulation. Science 223, 1189−1191 (1984). 16. Northrup, S.H., S.A. Allison, and J.A. McCammon. Brownian Dynamics of Diffusion-Influenced Bimolecular Reactions. J. Chem. Phys. 80, 1517−1524 (1984). 17. Lee, C.Y., J.A. McCammon, and P.J. Rossky. The Structure of Liquid Water at an Extended Hydrophobic Surface. J. Chem. Phys. 80, 4448−4455 (1984). 18. Berkowitz, M., O.A. Karim, J.A. McCammon, and P.J. Rossky. Sodium Chloride Ion Pair Interaction in Water: © 2016 J. Andrew McCammon

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Computer Simulation. Chem. Phys. Lett. 105, 577−580 (1984). Tembe, B.L., and J.A. McCammon. Ligand−Receptor Interactions. Comput. Chem. 8, 281−283 (1984). McCammon, J.A., S.H. Northrup, and S.A. Allison. Diffusional Dynamics of Ligand−Receptor Association. J. Phys. Chem. 90, 3901−3905 (1986). Lybrand, T.P., J.A. McCammon, and G. Wipff. Theoretical Calculation of Relative Binding Affinity in Host−Guest Systems. Proc. Natl. Acad. Sci. U.S.A. 83, 833−835 (1986). Karplus, M., and J.A. McCammon. Dynamics of Proteins. Scientific American 254, 42−51 (1986). Karim, O.A., and J.A. McCammon. Dynamics of a Sodium Chloride Ion Pair in Water. J. Am. Chem. Soc. 108, 1762−1766 (1986). Wong, C.F., and J.A. McCammon. Dynamics and Design of Enzymes and Inhibitors. J. Am. Chem. Soc. 108, 3830− 3832 (1986). Wong, C.F., and J.A. McCammon. Computer Simulation and the Design of New Biological Molecules. Isr. J. Chem. 27, 211−215 (1986). McCammon, J.A. Computer-Aided Molecular Design. Science 238, 486−491 (1987). Zheng, C., C.F. Wong, J.A. McCammon, and P.G. Wolynes. Quantum Simulation of Ferrocytochrome c. Nature 334, 726−728 (1988). Mazor, M.H., J.A. McCammon, and T.P. Lybrand. Molecular Recognition in Nonaqueous Solvents: Na+, K+, and 18-Crown-6 in Methanol. J. Am. Chem. Soc. 111, 55−56 (1989). Straatsma, T.P., and J.A. McCammon. Treatment of Rotational Isomers in Free Energy Evaluations. Analysis of the Evaluation of Free Energy Differences by Molecular Dynamics Simulations of Systems with Rotational Isomeric States. J. Chem. Phys. 90, 3300− 3304 (1989). Wong, C.F., C. Zheng, and J.A. McCammon. Glass Transition in SPC/E Water and in a Protein Solution: A Molecular Dynamics Simulation Study. Chem. Phys. Lett. 154, 151−154 (1989). Zheng, C., J.A. McCammon, and P.G. Wolynes. Quantum Simulation of Nuclear Rearrangement in Electron Transfer Reactions. Proc. Natl. Acad. Sci. U.S.A. 86, 6441−6444 (1989). Davis, M.E., and J.A. McCammon. Electrostatics in Biomolecular Structure and Dynamics. Chem. Rev. 90, 509−521 (1990). Straatsma, T.P., and J.A. McCammon. Free Energy Thermodynamic Integrations in Molecular Dynamics Simulations Using a Noniterative Method to Include

Special Issue: J. Andrew McCammon Festschrift Published: August 25, 2016 8065

DOI: 10.1021/acs.jpcb.6b07018 J. Phys. Chem. B 2016, 120, 8065−8070

The Journal of Physical Chemistry B

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Special Issue Preface

Electronic Polarization. Chem. Phys. Lett. 167, 252−254 (1990). Allison, S.A., J.A. McCammon, and J.J. Sines. Brownian Dynamics Simulations of Diffusion-Influenced Reactions: Inclusion of Intrinsic Reactivity and Gating. J. Phys. Chem. 94, 7133−7136 (1990). Straatsma, T.P., and J.A. McCammon. Free Energy Evaluation from Molecular Dynamics Simulations Using Force Fields Including Electronic Polarization. Chem. Phys. Lett. 177, 433−440 (1991). Straatsma, T.P., and J.A. McCammon. Computational Alchemy. Ann. Rev. Phys. Chem. 43, 407−435 (1992). Gilson, M.K., M.E. Davis, B.A. Luty, and J.A. McCammon. Computation of Electrostatic Forces on Solvated Molecules Using the Poisson−Boltzmann Equation. J. Phys. Chem. 97, 3591−3600 (1993). Zacharias, M., T.P. Straatsma, J.A. McCammon, and F.A. Quiocho. Inversion of Receptor Binding Preferences by Mutagenesis: Free Energy Thermodynamic Integration Studies on Sugar-Binding to L-Arabinose Binding Proteins. Biochemistry 32, 7428−7434 (1993). Luty, B.A., S. El Amrani, and J.A. McCammon. Simulation of the Bimolecular Reaction between Superoxide and Superoxide Dismutase: Synthesis of the Encounter and Reaction Steps. J. Am. Chem. Soc. 115, 11874−11877 (1993). Wade, R.C., B.A. Luty, E. Demchuk, J.D. Madura, M.E. Davis, J.M. Briggs, and J.A. McCammon. Simulation of Enzyme−Substrate Encounter with Gated Active Sites. Nat. Struct. Biol. 1, 65−69 (1994). Gilson, M.K., T.P. Straatsma, J.A. McCammon, D.R. Ripoll, C.H. Faerman, P.H. Axelsen, I. Silman, and J.L. Sussman. Open “Back Door” in a Molecular Dynamics Simulation of Acetylcholinesterase. Science 263, 1276− 1278 (1994). Cannon, W.R., J.M. Briggs, J. Shen, J.A. McCammon, and F.A. Quiocho. Conservative and Nonconservative Mutations in Proteins: Anomalous Mutations in a Transport Receptor Analyzed by Free Energy and Quantum Chemical Calculations. Protein Sci. 4, 387− 393 (1995). Gilson, M.K., J.A. McCammon, and J.D. Madura. Molecular Dynamics Simulation with a Continuum Electrostatic Model of the Solvent. J. Comput. Chem. 16, 1081−1095 (1995). Antosiewicz, J., J.A. McCammon, and M.K. Gilson. The Determinants of pKas in Proteins. Biochemistry 35, 7819−7833 (1996). Elcock, A.H., M.J. Potter, D.A. Matthews, D.R. Knighton, and J.A. McCammon. Electrostatic Channeling in the Bifunctional Enzyme Dihydrofolate Reductase−Thymidylate Synthase. J. Mol. Biol. 262, 370−374 (1996). Gilson, M.K., J.A. Given, B.L. Bush, and J.A. McCammon. The Statistical−Thermodynamic Basis for Computation of Binding Affinities: A Critical Review. Biophys. J. 72, 1047−1069 (1997). Radic, Z., P.D. Kirchhoff, D.M. Quinn, J.A. McCammon, and P. Taylor. Electrostatic Influence on the Kinetics of Ligand Binding to Acetylcholinesterase: Distinctions between Active Center Ligands and Fasciculin. J. Biol. Chem. 272, 23265−23277 (1997). Elcock, A.H., G.A. Huber, and J.A. McCammon. Electrostatic Channeling of Substrates between Enzyme

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Active Sites: Comparison of Simulation and Experiment. Biochemistry 36, 16049−16058 (1997). Marrone, T.J., H. Resat, C.N. Hodge, C.-H. Chang, and J.A. McCammon. Solvation Studies of DMP323 and A76928 Bound to HIV Protease: Analysis of Water Sites Using Grand Canonical Monte Carlo Simulations. Protein Sci. 7, 573−579 (1998). McCammon, J.A. Theory of Biomolecular Recognition. Curr. Opin. Struct. Biol. 8, 245−249 (1998). Zhou, H.-X., S.T. Wlodek, and J.A. McCammon. Conformation Gating as a Mechanism for Enzyme Specificity. Proc. Natl. Acad. Sci. U.S.A. 95, 9280−9283 (1998). Wriggers, W., R.A. Milligan, K. Schulten, and J.A. McCammon. Self-Organizing Neural Networks Bridge the Biomolecular Resolution Gap. J. Mol. Biol. 284, 1247−1254 (1998). Hunenberger, P.H., and J.A. McCammon. Ewald Artifacts in Computer Simulations of Ionic Solvation and Ion−Ion Interaction: A Continuum Electrostatics Study. J. Chem. Phys. 110, 1856−1872 (1999). Weber, W., V. Helms, J.A. McCammon, and P.W. Langhoff. Shedding Light on the Dark and Weakly Fluorescent States of Green Fluorescent Proteins. Proc. Natl. Acad. Sci. U.S.A. 96, 6177−6182 (1999). Elcock, A.H., R.R. Gabdoulline, R.C. Wade, and J.A. McCammon. Computer Simulation of Protein−Protein Association Kinetics: Acetylcholinesterase−Fasciculin. J. Mol. Biol. 291, 149−162 (1999). Sept, D., A.H. Elcock, and J.A. McCammon. Computer Simulations of Actin Polymerization Can Explain the Barbed-Pointed End Asymmetry. J. Mol. Biol. 294, 1181− 1189 (1999). Carlson, H.A., and J.A. McCammon. Accommodating Protein Flexibility in Computational Drug Design. Mol. Pharmacol. 57, 213−218 (2000). Brown, F.L.H., D.M. Leitner, J.A. McCammon, and K.R. Wilson. Lateral Diffusion of Membrane Proteins in the Presence of Static and Dynamic Corrals: Suggestions for Appropriate Observables. Biophys. J. 78, 2257−2269 (2000). Sotriffer, C.A., H. Ni, and J.A. McCammon. Active Site Binding Modes of HIV-1 Integrase Inhibitors. J. Med. Chem. 43, 4109−4117 (2000). Elcock, A.H., D. Sept, and J.A. McCammon. Computer Simulation of Protein−protein Interactions. J. Phys. Chem. B 105, 1504−1518 (2001). Sept, D., and J.A. McCammon. Thermodynamics and Kinetics of Actin Filament Nucleation. Biophys. J. 81, 667−674 (2001). Baker, N.A., D. Sept, S. Joseph, M.J. Holst, and J.A. McCammon. Electrostatics of Nanosystems: Application to Microtubules and the Ribosome. Proc. Natl. Acad. Sci. U.S.A. 98, 10037−10041 (2001). Shen, T., K. Tai, R.H. Henchman, and J.A. McCammon. Molecular Dynamics of Acetylcholinesterase. Acc. Chem. Res. 35, 332−340 (2002). Lin, J.H., A. Perryman, J. Schames, and J.A. McCammon. Computational Drug Design Accommodating Receptor FlexibilityThe Relaxed Complex Scheme. J. Am. Chem. Soc. 124, 5632−5633 (2002). DOI: 10.1021/acs.jpcb.6b07018 J. Phys. Chem. B 2016, 120, 8065−8070



81. Lu, B., X. Cheng, J. Huang, and J.A. McCammon. An order N Algorithm for Computation of Electrostatic Interactions in Biomolecular Systems. Proc. Natl. Acad. Sci. U.S.A. 103, 19314−19319 (2006). 82. Tozzini, V., J. Trylska, C. Chang, and J.A. McCammon. Flap Opening Dynamics in HIV-1 Protease Explored with a Coarse-Grained Model. J. Struct. Biol. 157, 606− 615 (2007). 83. Ivanov, I., J.A. Tainer, and J.A. McCammon. Unraveling the Three-Metal-Ion Catalytic Mechanism of the DNA Repair Enzyme Endonuclease IV. Proc. Natl. Acad. Sci. U.S.A. 104, 1465−1470 (2007). 84. Amaro, R.E., D.D.L. Minh, L.S. Cheng, W.M. Lindstrom, Jr., A.J. Olson, J.-H. Lin, W.W. Li, and J.A. McCammon. Remarkable Loop Flexibility in Avian Influenza N1 and its Implications for Antiviral Drug Design. J. Am. Chem. Soc. 129, 7764−7765 (2007). 85. Cheng, L.-T., J. Dzubiella, J.A. McCammon, and B. Li. Application of the Level-Set Method to the Implicit Solvation of Nonpolar Molecules. J. Chem. Phys. 127, article 084503 (2007). 86. Hamelberg, D., T. Shen, and J.A. McCammon. A Proposed Signaling Motif for Nuclear Import in mRNA Processing via the Formation of “Arginine Claw”. Proc. Natl. Acad. Sci. U.S.A. 104, 14947−14951 (2007). 87. Minh, D.D.L., and J.A. McCammon. Springs and Speeds in Free Energy Reconstruction from Irreversible SingleMolecule Pulling Experiments. J. Phys. Chem. B (A. Szabo Festschrift) 112, 5892−5897 (2008). 88. Zhou, Y.C., B. Lu, G.A. Huber, M.J. Holst, and J.A. McCammon. Continuum Simulations of Acetylcholine Consumption by Acetylcholinesterase: A Poisson− Nernst−Planck Approach. J. Phys. Chem. B (Casey Hynes Festschrift) 112, 270−275 (2008). 89. Amaro, R.E., R. Baron, and J.A. McCammon. An Improved Relaxed Complex Scheme for Receptor Flexibility in Computer-Aided Drug Design. J. Comput.Aided Mol. Des. 22, 693−705 (2008). 90. Fajer, M., D. Hamelberg, and J.A. McCammon. ReplicaExchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. J. Chem. Theory Comput. 4, 1565−1569 (2008). 91. Cheng, Y., C.A. Chang, Z. Yu, Y. Zhang, M. Sun, T.S. Leyh, M.J. Holst, and J.A. McCammon. Diffusional Channeling in the Sulfate Activating Complex: Combined Continuum Modeling and Coarse-grained Brownian Dynamics Studies. Biophys. J. 95, 4659−4667 (2008). 92. Amaro, R.E., A. Schnaufer, H. Interthal, W. Hol, K.D. Stuart, and J.A. McCammon. Discovery of Drug-like Inhibitors of an Essential RNA-Editing Ligase in Trypanosoma brucei. Proc. Natl. Acad. Sci. U.S.A. 106, 17278−17283 (2008). 93. Swift, R.V., J. Durrant, R.E. Amaro, and J.A. McCammon. Toward Understanding the Conformational Dynamics of RNA Ligation. Biochemistry 48, 709−719 (2009). 94. Grant, B.J., A.A. Gorfe, and J.A. McCammon. Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics. PLoS Comput. Biol. 5, article e1000325 (2009). 95. Fajer, M., R.V. Swift, and J.A. McCammon. Using Multistate Free Energy Techniques to Improve the

65. Karplus, M., and J.A. McCammon. Molecular Dynamics Simulations of Macromolecules: A Perspective. Nat. Struct. Biol. 9, 646−652 (2002). 66. Shen, T., L.S. Canino, and J.A. McCammon. Unfolding Proteins under External Forces: A Solvable Model under the Self-consistent Pair Contact Probability Approximation. Phys. Rev. Lett. 89, article 068103 (2002). 67. Zhang, Y., J. Kua, and J.A. McCammon. Role of the Catalytic Triad and Oxyanion Hole in Acetylcholinesterase Catalysis: An Ab Initio QM/MM Study. J. Am. Chem. Soc. 124, 10572−10577 (2002). 68. Morikis, D., A.H. Elcock, P.A. Jennings, and J.A. McCammon. The pH Dependence of Stability of the Activation Helix and the Catalytic Site of GART. Biophys. Chem. 105, 279−291 (2003). 69. Tai, K., SD. Bond, H.R. MacMillan, N.A. Baker, M.J. Holst, and J.A. McCammon. Finite Element Simulations of Acetylcholine Diffusion in Neuromuscular Junctions. Biophys. J. 84, 2234−2241 (2003). 70. Sept, D., N.A. Baker, and J.A. McCammon. The Physical Basis of Microtubule Structure and Stability. Protein Sci. 12, 2257−2261 (2003). 71. Schames, J., R.H. Henchman, J.S. Siegel, C.A. Sotriffer, H. Ni, and J.A. McCammon. Discovery of a Novel Binding Trench in HIV Integrase. J. Med. Chem. 47, 1879−1881 (2004). 72. Hamelberg, D., J. Mongan, and J.A. McCammon. Accelerated Molecular Dynamics: A Promising and Efficient Simulation Method for Biomolecules. J. Chem. Phys. 120, 11919−11929 (2004). 73. Sims, P.A., C.F. Wong, and J.A. McCammon. Charge Optimization of the Interface between Protein Kinases and their Ligands. J. Comput. Chem. 25, 1416−1429 (2004). 74. Mongan, J., D.A. Case, and J.A. McCammon. Constant pH Molecular Dynamics in Generalized Born Implicit Solvent. J. Comput. Chem. 25, 2038−2048 (2004). 75. Cheng, Y., Y. Zhang, and J.A. McCammon. How does the cAMP-Dependent Protein Kinase Catalyze the Phosphorylation Reaction: An ab initio QM/MM Study. J. Am. Chem. Soc. 127, 1553−1562 (2005). 76. Law, R., R.H. Henchman, and J.A. McCammon. A Gating Mechanism Proposed From a 15 ns Simulation of a Complete Human Alpha7 Nicotinic Acetylcholine Receptor Model. Proc. Natl. Acad. Sci. U.S.A. 102, 6813− 6818 (2005). 77. Gullingsrud, J., C. Kim, S.S. Taylor, and J.A. McCammon. Dynamic Binding of PKA Regulatory Subunit RIα. Structure 14, 141−149 (2006). 78. Dzubiella, J., J.M.J. Swanson, and J.A. McCammon. Coupling Hydrophobic, Dispersion, and Electrostatic Contributions in Continuum Solvent Models. Phys. Rev. Lett. 96, article 087802 (2006). 79. Chang, C., T. Shen, J. Trylska, V. Tozzini, and J.A. McCammon. Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a CoarseGrained Model. Biophys. J. 90, 3880−3885 (2006). 80. Bui, J.M., and J.A. McCammon. Protein Complex Formation by Acetylcholinesterase and the Neurotoxin Fasciculin-2 Appears to Involve an Induced Fit Mechanism. Proc. Natl. Acad. Sci. U.S.A. 103, 15451− 15456 (2006). 8067



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Efficiency of Replica Exchange Accelerated Molecular Dynamics. J. Comput. Chem. 30, 1719−1725 (2009). McCammon, J.A. Darwinian Biophysics: Electrostatics and Evolution in the Kinetics of Molecular Binding. Proc. Natl. Acad. Sci. U.S.A. 106, 7683−7684 (2009). Baron, R., C. Riley, P. Chenprakhon, K. Thotsaporn, R. Winter, A. Alfieri, F. Forneris, W. van Berkel, P. Chaiyen, M. Fraaije, A. Mattevi, and J.A. McCammon. Multiple Pathways Guide Oxygen Diffusion into Flavoenzyme Active Sites. Proc. Natl. Acad. Sci. U.S.A. 106, 10603− 10608 (2009). Setny, P., Z. Wang, L.T. Cheng, B. Li, J. A. McCammon, and J. Dzubiella. Dewetting-Controlled Binding of Ligands to Hydrophobic Pockets. Phys. Rev. Lett. 103, article 187801 (2009). Zhou, H.X., and J.A. McCammon. The Gates of Ion Channels and Enzymes. Trends Biochem. Sci. 35, 179− 185 (2010). Durrant, J., R.E. Amaro, L. Xie, M.D. Urbaniak, M.A.J. Ferguson, A. Haapalainen, Z. Chen, A.M. Di Guilmi, F. Wunder, P.E. Bourne, and J.A. McCammon. A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Comput. Biol. 6, article e1000648 (2010). Markwick, P., C. Cervantes, B. Abel, E. Komives, M. Blackledge, and J.A. McCammon. Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins. J. Am. Chem. Soc. 132, 1220−1221 (2010). Grant, B.J., A.A. Gorfe, and J.A. McCammon. Large Conformational Changes in Proteins: Signaling and Other Functions. Curr. Opin. Struct. Biol. 20, 142−147 (2010). Baron, R., P. Setny, and J.A. McCammon. Water in Cavity-Ligand Recognition. J. Am. Chem. Soc. 132, 12091−12097 (2010). Lawrenz, M., R. Baron, Y, Wang, and J.A. McCammon. Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies. J. Chem. Theory Comput. 7, 2224−2232 (2011). Durrant, J.D., and J.A. McCammon. Molecular Dynamics Simulations and Drug Discovery. BMC Biol. 9, article 71 (2011). Grant, B.J., D. Gheorghe, W. Zheng, M. Alonsoc, G. Huber, M. Dlugosz, J.A. McCammon, and R.A. Cross. Electrostatically Biased Binding of Kinesin to Microtubules. PLoS Biol. 9, article e1001207 (2011). Bucher, D., B.J. Grant, and J.A. McCammon. Induced-Fit or Conformational Selection? The Role of the Semiclosed State in the Maltose Binding Protein. Biochemistry 50, 10530−10539 (2011). Wereszczynski, J., and J.A. McCammon. Statistical Mechanics and Molecular Dynamics in Evaluating Thermodynamic Properties of Biomolecular Recognition. Q. Rev. Biophys. 45, 1−25 (2012). Hake, J.E., A.G. Edwards, Z. Yu, P. Kekenes-Huskey, A.P. Michailova, J.A. McCammon, M.J. Holst, M. Hoshijima, and A.D. McCulloch. Modeling Cardiac Calcium Sparks in a Three-Dimensional Reconstruction of a Calcium Release Unit. J. Physiol. 590, 4403−4422 (2012). Wereszczynski, J., and J.A. McCammon. The Nucleotide Dependent Mechanism of Get3 as Elucidated from Free

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Energy Calculations. Proc. Natl. Acad. Sci. U.S.A. 109, 7759−7764 (2012). Pierce, L.C.T., R. Salomon-Ferrer, C.A.F. de Oliveira, J.A. McCammon, and R.C. Walker. Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J. Chem. Theory Comput. 8, 2997−3002 (2012). Lindert, S., P.M. Kekenes-Huskey, and J.A. McCammon. Long-time scale Molecular Dynamics Simulations Elucidate the Dynamics and Kinetics of Exposure of the Hydrophobic Patch in Troponin C. Biophys. J. 103, 1784−1789 (2012). Gasper, P., B. Fuglestad, E. Komives, P. Markwick, and J.A. McCammon. Allosteric Networks in Thrombin Distinguish Procoagulant vs Anticoagulant Activities. Proc. Natl. Acad. Sci. U.S.A. 109, 21216−21222 (2012). Baron, R., and J.A. McCammon. Molecular Recognition and Ligand Association. Ann. Rev. Phys. Chem. 64, 151− 175 (2013). Rogers, K., J.M. Ortiz Sánchez, R. Baron, M. Fajer, C.A.F. de Oliveira, and J.A. McCammon. On the Role of Dewetting Transitions in Host−Guest Binding Free Energy Calculations. J. Chem. Theory Comput. 9, 46−53 (2013). Zhu, W., Y. Zhang, W. Sinko, M. Hensler, J. Olson, K.J. Molohon, S. Lindert, R. Cao, K. Li, K. Wang, Y. Wang, Y.L. Liu, A. Sankovsky, C.A.F. de Oliveira, D.A. Mitchell, V. Nizet, J.A. McCammon, and E. Oldfield. Antibacterial Drug Leads Targeting Isoprenoid Biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 110, 123−128 (2013). Arrar, M., M. Fajer, W. Sinko, C. de Oliveira, and J.A. McCammon. w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations. J. Chem. Theory Comput. 9, 18−23 (2013). Setny, P., R. Baron, P. Kekenes-Huskey, J.A. McCammon, and J. Dzubiella. Solvent Fluctuations in Hydrophobic Cavity-Ligand Binding Kinetics. Proc. Natl. Acad. Sci. U.S.A. 110, 1197−1202 (2013). Fuglestad, B., P.M. Gasper, K.N. Stearns, J.A. McCammon, P.R.L. Markwick, and E.A. Komives. Correlated Motions and Residual Frustration in Thrombin. J. Phys. Chem. B (Peter Wolynes Festschrift) 117, 12857−12863 (2013). Miao, Y., S.E. Nichols, P.M. Gasper, V.T. Metzger, and J.A. McCammon. Activation and Dynamic Network of the M2Muscarinic Receptor. Proc. Natl. Acad. Sci. U.S.A. 110, 10982−10987 (2013). Zhou, S., K.E. Rogers, C.A.F. de Oliveira, R. Baron, L.T. Cheng, J. Dzubiella, B. Li, and J.A. McCammon. Variational Implicit-Solvent Modeling of Host−Guest Binding: A Case Study on Cucurbit[7]uril. J. Chem. Theory Comput. 8, 4195−4204 (2013). Kekenes-Huskey, P., T. Liao, A. Gillette, J. Hake, Y. Zhang, A. Michailova, A. McCulloch, and J.A. McCammon. Molecular and Subcellular-Scale Modeling of Nucleotide Diffusion in the Cardiac Myofilament Lattice. Biophys. J. 105, 2130−2140 (2013). Nguyen, C., R.W. Haushalter, D.J. Lee, P.R.L. Markwick, J. Bruegger, G. Caldara-Festin, K. Finzel, D.R. Jackson, F. Ishikawa, B.A. O’Dowd, J.A. McCammon, S.J. Opella, S.C. Tsai, and M.D. Burkart. Trapping the Dynamic Acyl DOI: 10.1021/acs.jpcb.6b07018 J. Phys. Chem. B 2016, 120, 8065−8070


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Carrier Protein in Fatty Acid Biosynthesis. Nature 505, 427−431 (2014). Miao, Y., S.E. Nichols, and J.A. McCammon. Free Energy Landscape of G-Protein Coupled Receptors, Explored by Accelerated Molecular Dynamics. Phys. Chem. Chem. Phys. 16, 6398−6406 (2014). Ivetac, A., S.E. Swift, P.L. Boyer, A. Diaz, J. Naughton, J.A.T. Young, S.H. Hughes, and J.A. McCammon. Discovery of Novel Inhibitors of HIV-1 Reverse Transcriptase through Virtual Screening of Experimental and Theoretical Ensembles. Chem. Biol. Drug Des. 83, 521−531 (2014). Zhou, S., L.-T. Cheng, J. Dzubiella, B. Li, and J.A. McCammon. Variational Implicit Solvation with Poisson−Boltzmann Theory. J. Chem. Theory Comput. 10, 1454−1467 (2014). Kekenes-Huskey, P.M., A.K. Gillette, and J.A. McCammon. Predicting the Influence of Long-Range Molecular Interactions on Macroscopic-Scale Diffusion by Homogenization of the Smoluchowski Equation. J. Chem. Phys. 140, article 174106 (2014). Miao, Y., W. Sinko, L. Pierce, D. Bucher, R.C. Walker, and J.A. McCammon. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. J. Chem. Theory Comput. 10, 2677− 2689 (2014). Sinko, W., Y. Wang, W. Zhu, Y. Zhang, F. Feixas, C. Cox, D. Mitchell, E. Oldfield, and J.A. McCammon. Undecaprenyl Diphosphate Synthase Inhibitors: Antibacterial Drug Leads. J. Med. Chem. 57, 5693−701 (2014). Liu, Y.L., S. Lindert, W. Zhu, K. Wang, J.A. McCammon, and E. Oldfield. Taxodione and Arenarone Inhibit Farnesyl Diphosphate Synthase by Binding to the Isopentenyl Diphosphate Site. Proc. Natl. Acad. Sci. U.S.A. 111, E2530−E2539 (2014). Boechi, L., L. Pierce, E.A. Komives, and J.A. McCammon. Trypsinogen Activation as Observed in Accelerated Molecular Dynamics Simulations. Protein Sci. 23, 1550−1558 (2014). Lindert, S., M.X. Li, B. Sykes, and J.A. McCammon. Computer-Aided Drug Discovery Approach Finds Calcium Sensitizer of the Cardiac Troponin Complex. Chem. Biol. Drug Des. 85, 99−106 (2015). Kim, M.O., P.G. Blachly, J. Kaus, and J.A. McCammon. Protocols Utilizing Constant pH Molecular Dynamics Simulations to Compute pH-Dependent Binding Free Energies. J. Phys. Chem. B 119, 861−872 (2015). Kim, M.O., X. Feng, F. Feixas, Z. Wei, S. Lindert, S. Bogue, W. Sinko, C. Oliveira, G. Rao, E. Oldfield, and J.A. McCammon. A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility, and Implications for Computer-Aided Drug Discovery. Chem. Biol. Drug Des. 85, 756−769 (2015). Lindert, S., Y. Cheng, P. Kekenes-Huskey, M. Regnier, and J.A. McCammon. Effects of HCM cTnI Mutation R145G on Troponin Structure and Modulation by PKA Phosphorylation elucidated by Molecular Dynamics Simulations. Biophys. J. 108, 395−407 (2015). Mouchlis, V.D., D. Bucher, J.A. McCammon, and E.A. Dennis. Membranes Serve as Allosteric Activators of Phospholipase A2 Enabling it to Extract, Bind, and

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Hydrolyze Phospholipid Substrates. Proc. Natl. Acad. Sci. U.S.A. 112, E516−E525 (2015). Caliman, A.D., S.E. Swift, Y. Wang, Y. Miao, and J.A. McCammon. Investigation of the Conformational Dynamics of the apo A2A Adenosine Receptor. Protein Sci. 24, 1004−1012 (2015). Kappel, K., Y. Miao, and J.A. McCammon. Accelerated Molecular Dynamics Simulations of Ligand Binding to a Muscarinic G-protein Coupled Receptor. Q. Rev. Biophys. 48, 479−487 (2015). Kim, M.O., P.G. Blachly, and J.A. McCammon. Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. PLoS Comput. Biol. 11, article e1004341 (2015). Miao, Y., V. Feher, and J.A. McCammon. Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J. Chem. Theory Comput. 11, 3584−3595 (2015). Kekenes-Huskey, P.M., C. Eun, and J.A. McCammon. Enzyme Localization, Crowding and Buffers Collectively Modulate Diffusion Influenced Signal Transduction: Insights from Continuum Diffusion Modeling. J. Chem. Phys. 143, article 094103 (2015). Sun, H., J. Wen, Y. Zhao, B. Li, and J.A. McCammon. A Self-Consistent Phase-Field Approach to Implicit Solvation of Charged Molecules with Poisson−Boltzmann Electrostatics. J. Chem. Phys. 143, article 243110 (2015). Feng, X., W. Zhu, L.A. Schurig-Briccio, S. Lindert, C. Shoen, R. Hitchings, J. Li, Y. Wang, N. Baig, T. Zhou, B.K. Kim, D.C. Crick, M. Cynamon, J.A. McCammon, R.B. Gennis, and E. Oldfield. Anti-Infectives Targeting Enzymes, and the Proton Motive Force. Proc. Natl. Acad. Sci. U.S.A. 112 E7073−E7082 (2015). Wang, N., and J.A. McCammon. Substrate Channeling Between the Human Dihydrofolate Reductase and Thymidylate Synthase. Protein Sci. 25, 79−86 (2016). Huber, G.A., Y. Miao, S. Zhou, B. Li, and J.A. McCammon. Hybrid Finite Element and Brownian Dynamics Method for Charged Particles. J. Chem. Phys. 144, article 164107 (2016). Mouchlis, V.D., D. Limnios, M.G. Kokotou, G. Kokotos, J.A. McCammon, and E.A. Dennis. Development of Potent and Selective Inhibitors for Group VIA CalciumIndependent Phospholipase A2 Guided by Molecular Dynamics and Structure−Activity Relationships. J. Med. Chem. 59, 4403−4414 (2016).

BOOKS AND EDITED VOLUMES

147. McCammon, J.A., and S.C. Harvey. “Dynamics of Proteins and Nucleic Acids”, Cambridge University Press, Cambridge (1987). 148. McCammon, J.A., and G.L. Wilcox (Eds.). “Supercomputing in Biology”, ESCOM Science Publishers, Leiden, The Netherlands (1988). Special Issue of Journal of Computer-Aided Molecular Design. 149. Doolittle, R., J.A. McCammon, and P.G. Wolynes (Eds.). “Computational Biomolecular Science”, National Academy Press, Washington, DC (1998). 150. McCammon, J.A., and P.G. Wolynes (Eds.). “Current Opinion in Structural Biology”, Current Biology Press, London (2002).

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151. McCammon, J.A., and R.C. Wade (Eds.). “Current Opinion in Structural Biology”, Current Biology Press, London (2005). 152. Wade, R.C., P. Mereghetti, and J.A. McCammon (Eds.). “Biological Diffusion and Brownian Dynamics”, Special thematic series inaugurating volume 4 of BMC Biophysics (2011). 153. Clementi, E., J.M. André, and J.A. McCammon (Eds.). “Theory and Applications of Computational Chemistry: The First Decade of the Second Millennium”, American Institute of Physics (2012). 154. McCammon, J.A., B. Roux, G. Voth, and W. Yang (Guest Eds.). Special Issue on Free Energy, J. Chem. Theory Comput. 10, 2631−2880 (2014). 155. McCammon, J.A. (Ed.). Special Issue on ComputerAided Drug Discovery, Biopolymers (2016).

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Selected Publications of J. Andrew McCammon - The Journal of

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