Wonpil Im
Research Group
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REFEREED JOURNALS || BOOK CHAPTERS


2017
  • J. Lee, D.S. Patel, N.R. Kern, X. Cheng, S. Jo, J.B. Klauda, and W. Im
    CHARMM-GUI Glycolipid Modeler for Database and Structure Generation of Various Glycolipids.
    submitted
  • N.I. Nissen, K.R. Anderson, H. Wang, H.S. Lee, C. Garrison, S.A. Eichelberger, K. Ackerman, W. Im, and J.M. Miwa
    Augmenting the Antinociceptive Effects of Nicotinic Acetylcholine Receptor Activity through Lynx Modulation.
    submitted
  • A.H. Beaven, A.J. Sodt, R.W. Pastor, R.E. Koeppe II, O.S. Andersen, and W. Im
    Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes.
    J. Chem. Theory Comput. revision (2017)
  • K.A. Matthias, M.B Strader, H.F. Nawar, J. Lee, D.S. Patel, W. Im, M.C. Bash
    Heterogeneity in Non-Epitope Loop Sequence and Outer Membrane Protein Complexes Alters Antibody Binding to the Major Porin Protein PorB in Serogroup B Neisseria meningitidis.
    Mol. Microbiol. in press (2017)
  • P.C. Hsu, B. Bruininks, D. Jefferies, P.T. de Souza, J. Lee, D.S. Patel, S.J. Marrink, Y. Qi, S. Khalid, and W. Im
    CHARMM-GUI Martini Maker for Modeling and Simulation of Complex Bacterial Membranes with Lipopolysaccharides.
    J. Comput. Chem. in press (2017)
  • P. Morales, D.S. Patel, O. Engström, W. Im, and G. Widmalm
    Conformational Dynamics of the Lipopolysaccharide from Escherichia coli O91 Revealed by NMR Spectroscopy and Molecular Simulations.
    Biochemistry, in press (2017)
  • S-J. Park, J. Lee, D.S. Patel, H. Ma, H.S. Lee, S. Jo, and W. Im
    Glycan Reader is Improved to Recognize Most Sugar Types and Chemical Modifications in the Protein Data Bank.
    Bioinformatics, in press (2017)
  • H.S. Lee and W. Im
    Transmembrane Motions of PglB Induced by LLO are Coupled with EL5 Loop Conformational Changes Necessary for OST Activity.
    Glycobiology 27:734-742 (2017)
  • S. Kim, J. Lee, S. Jo, C.L. Brooks III, H.S. Lee, and W. Im
    CHARMM-GUI Ligand Reader and Modeler for CHARMM Force Field Generation of Small Molecules.
    J. Comput. Chem. 38:1879-1886 (2017)
  • J. Lee, Z. Ren, M. Zhou, and W. Im
    Molecular Simulation and Biochemical Studies Support an Elevator-Type Transport Mechanism in EIIC.
    Biophys. J. 112:2249-2252 (2017)
  • S. Jo, X. Cheng, J. Lee, S. Kim, S-J. Park, D.S. Patel, A.H. Beaven, K.I. Lee, H. Rui, S. Park, H.S. Lee, B. Roux, A.D. MacKerell Jr, J.B. Klauda, Y. Qi, and W. Im
    CHARMM-GUI 10 Years for Biomolecular Modeling and Simulation.
    J. Comput. Chem. 38:1114-1124 (2017)
  • Y. Qi, J. Lee, A. Singharoy, R. Mcgreevy, K. Schulten, and W. Im
    CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments.
    J. Phys. Chem. B. 121:3718-3723 (2017)
  • A.J. Sodt, A.H. Beaven, O.S. Andersen, W. Im, and R.W. Pastor
    Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model.
    Biophys. J. 112:1198-1213 (2017)
  • A.H. Beaven, A.M. Maer, A.J. Sodt, H. Rui, R.W. Pastor, O.S. Andersen, and W. Im
    Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation.
    Biophys. J. 112:1185-1197 (2017)
2016
  • D. Kong, H-C. Hu, E. Okuma, Y. Lee, H.S. Lee, S. Munemasa, D. Cho, L. Pedoeim, B. Rodriguez, C. Ju, W. Im, Y. Murara, Z-M. Pei, and J. M. Kwak
    L-Met Activates Arabidopsis GLR Ca2+ Channels Upstream of ROS and Regulates Stomatal Movement.
    Cell reports 17:2553-2561 (2016)
  • D.S. Patel, S. Park, E.L. Wu, M.S. Yeom, G. Widmalm, J.B. Klauda, and W. Im
    Influence of Ganglioside GM1 Concentration on Lipid Clustering and Membrane Properties and Curvature.
    Biophys. J. 111:1987-1999 (2016)
  • P.J. Fleming, D.S. Patel, E.L. Wu, Y. Qi, M.S. Yeom, M.C. Sousa, K.G. Fleming, and W. Im
    BamA POTRA Domain Interacts with a Native Lipid Membrane Surface.
    Biophys. J. 110:2698-2709 (2016)
  • J.G. McCoy, Z. Ren, V. Stanevich, J. Lee, S. Mitra, E.J. Levin, S. Poget, M. Quick, W. Im, and M. Zhou
    The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight Into the Elevator Mechanism of Membrane Transport.
    Structure 24:956-964 (2016)
  • R. Kumar, Y. Qi, H. Matsumura, S. Lovell, H. Yao, K.P. Battaile, W. Im, P. Moënne-Loccoz, and M Rivera
    Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonas aeruginosa Causes Closure of the H32 Loop in the Apo-Protein.
    Biochemistry 55:2622-2631 (2016)
  • H.S. Lee and W. Im
    G-LoSA: An Efficient Computational Tool for Local Structure-Centric Biological Studies and Drug Design.
    Protein Sci. 25:865-876 (2016)
  • D.S. Patel, S. Re, E.L. Wu, Y. Qi, P.E. Klebba, G. Widmalm, M.S. Yeom, Y. Sugita, and W. Im
    Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.
    Biophys. J. 110:930-938 (2016)
  • J. Lee, X. Cheng, J.M. Swails, M.S. Yeom, P. Eastman, J. Lemkul, S. Wei, J. Buckner, J.C. Jeong, Y. Qi, S. Jo, V.S. Pande, D.A. Case, C.L. Brooks III, A.D. MacKerell Jr, J.B. Klauda, and W. Im
    CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field.
    J. Chem. Theory Comput. 12:405-413 (2016)
  • J.H. Lee, M. Oh, H.S. Kim, H.S. Lee, W. Im, and H-S. Lim
    Converting One-Face α-Helix Mimetics into Amphiphilic α-Helix Mimetics as Potent Inhibitors of Protein-Protein Interactions.
    ACS Comb. Sci. 18:36-42 (2016)
  • S. Jo, Y. Qi, and W. Im
    Preferred Conformations of N-glycan Core Pentasaccharide in Solution and in Glycoproteins.
    Glycobiology 26:19-29 (2016)
2015
  • E.L. Wu, Y. Qi, S. Park, S.S. Mallajosyula, A.D. MacKerell, Jr., J.B. Klauda, and W. Im
    Insight into Early-stage Unfolding of GPI-anchored Human Prion Protein.
    Biophys. J. 109:2090-2100 (2015)
  • Y. Qi, X. Cheng, J. Lee, J.V. Vermaas, T.V. Pogorelov, E. Tajkhorshid, S. Park, J.B. Klauda, and W. Im
    CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model.
    Biophys. J. 109:2012-2022 (2015)
  • K. Knoblich, S. Park, M. Lutfi, L. van 't Hag, C.E. Conn, S.A. Seabrook, J. Newman, P.E. Czabotar, W. Im, M.E. Call and M.J. Call
    Transmembrane Complexes of DAP12 Crystallized in Lipid Membranes Provide Insights into Control of Oligomerization in Immunoreceptor Assembly.
    Cell reports 11:1184-1192 (2015)
  • X. Cheng, S. Jo, Y. Qi, F.M. Marassi, and W. Im
    Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes.
    Biophys. J. 108:1954-1962 (2015)
  • H.S. Lee, Y. Qi, and W. Im
    Effects of N-glycosylation on Protein Conformation and Dynamics: Protein Data Bank Analysis and Molecular Dynamics Simulation Study.
    Sci. Rep. 5:8926 (2015)
  • H. Yao, H. Rui, R. Kumar, K. Eshelman, S. Lovell, K.P. Battaile, W. Im, and M. Rivera
    Concerted Motions Networking Pores and Distant Ferroxidase Centers Enable Bacterioferritin Function and Iron Traffic.
    Biochemistry 54:1611-1627 (2015)
2014
  • W.S. Lee, H-J. Moon, M. Oh, H.S. Lee, J.H. Lee, W. Im, and H-S. Lim
    Design, Solid-Phase Synthesis, and Evaluation of a Phenyl-Piperazine-Triazine Scaffold as α-Helix Mimetics.
    ACS Comb. Sci. 16:695-701 (2014)
  • K.I. Lee, W. Im, and R.W. Pastor
    Langevin Dynamics Simulations of Charged Model Phosphatidylinositol Lipids in the Presence of Diffusion Barriers: Toward an Atomic Level Understanding of Corralling of PIP2 by Protein Fences in Biological Membranes.
    BMC Biophys. 7:13 (2014)
  • N.R. Kern, H.S. Lee, E.L. Wu, S. Park, K. Vanommeslaeghe, A.D. MacKerell, Jr., J.B. Klauda, S. Jo, and W. Im
    Lipid-Linked Oligosaccharides in Membranes Sample Conformations that Facilitate Binding to Oligosaccharyltransferase.
    Biophys. J. 107:1885-1895 (2014)
  • S. Jo, X. Cheng, S.M. Islam, L. Huang, H. Rui, A. Zhu, H.S. Lee, Y. Qi, W. Han, K. Vanommeslaeghe, A.D. MacKerell, Jr., B. Roux, and W. Im
    CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues.
    Adv. Protein Chem. Struct. Biol. 96:235-265 (2014)
  • E.L. Wu, X. Cheng, S. Jo, H. Rui, K.C. Song, E.M. Dávila-Contreras, Y. Qi, J. Lee, V. Monje-Galvan, R.M. Venable, J.B. Klauda, and W. Im
    CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations.
    J. Comput. Chem. 35:1997-2004 (2014)  [cover]
  • M. Oh, J.H. Lee, W. Wang, H.S. Lee, W.S. Lee, C. Burlak, W. Im, Q.Q. Hoang, and H-S. Lim
    Potential Pharmacological Chaperones Targeting Cancer-associated MCL-1 and Parkinson's Disease-associated α-synuclein.
    Proc. Natl. Acad. Sci. USA 111, 11007-11012 (2014)
  • E.L. Wu, Y. Qi, K.C. Song, J.B. Klauda, and W. Im
    Preferred Orientations of Phosphoinositides in Bilayers and Their Implications in Protein Recognition Mechanisms.
    J. Phys. Chem. B. 118:4315-4325 (2014)
  • P-C. Li, N. Miyashita, W. Im, S. Ishido, and Y. Sugita
    Multidimensional Umbrella Sampling and Replica-Exchange Molecular Dynamics Simulations for Structure Prediction of Transmembrane Helix Dimers.
    J. Comput. Chem. 35:300-308 (2014)
2013
  • E.L. Wu, O. Engström, S. Jo, D. Stuhlsatz, M.S. Yeom, J.B. Klauda, G. Widmalm, and W. Im
    Molecular Dynamics Simulation and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics.
    Biophys. J. 105:1444-1455 (2013)
  • S. Jo, H.S. Lee, J. Skolnick, and W. Im
    Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling.
    PLoS Comput. Biol. 9:e1002946 (2013)
2012
  • H.S. Lee, S. Jo, H-S. Lim, and W. Im
    Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors.
    J. Chem. Inf. Model. 52:1821-1832 (2012)
  • T. Kim, K.I. Lee, P. Morris, R.W. Pastor, O.S. Andersen, and W. Im
    Influence of Hydrophobic Mismatch on Structures and Dynamics of Gramicidin A and Lipid Bilayers.
    Biophys. J. 102:1551-1560 (2012)
  • X. Cheng and W. Im
    NMR Observable-Based Structure Refinement of DAP12-NKG2C Activating Immunoreceptor Complex in Explicit Membranes.
    Biophys. J. 102:L27-L29 (2012)
  • K.I. Lee, S. Jo, H. Rui, B. Egwolf, B. Roux, R.W. Pastor, and W. Im
    Web Interface for Brownian Dynamics Simulation of Ion Transport and Its Applications to Beta-Barrel Pores.
    J. Comput. Chem. 33:331-339 (2012)  [cover]
2011
  • U. Golebiewska, J.G. Kay, T. Masters, S. Grinstein, W. Im, R.W. Pastor, S. Scarlata, and S. McLaughlin
    Evidence for a Fence/Corral that Impedes the Diffusion of Phosphatidylinositol 4,5-bisphosphate (PIP2) into and out of the Forming Phagosomes of Macrophages.
    Mol. Biol. Cell 22:3498-3507 (2011)
  • S. Jo, K.C. Song, H. Desaire, A.D. MacKerell, Jr., and W. Im
    Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins.
    J. Comput. Chem. 32:3135-3141 (2011)  [cover]
  • H. Rui, R. Kumar, and W. Im
    Membrane Tension, Lipid Adaptation, Conformational Changes, and Energetics in MscL Gating.
    Biophys. J. 101:671-679 (2011)
  • H. Park, W. Im, and C. Seok
    Transmembrane Signaling of Chemotaxis Receptor Tar: Insights from Molecular Dynamics Simulation Studies.
    Biophys. J. 100:2955-2963 (2011)
  • S. Jo and W. Im
    Transmembrane Helix Orientation and Dynamics: Insights from Ensemble Dynamics with Solid-State NMR Observables.
    Biophys. J. 100:2913-2921 (2011)
  • K.C. Song, P.W. Livanec, J.B. Klauda, K. Kuczera, R.C. Dunn, and W. Im
    Orientation of Fluorescent Lipid Analog BODIPY-PC to Probe Lipid Membrane Properties: Insights from Molecular Dynamics Simulations.
    J. Phys. Chem. B. 115:6157–6165 (2011)
  • J.H. Lee, Q. Zhang, S. Jo, S.C. Chai, M. Oh, W. Im, H. Lu, and H-S. Lim
    Novel Pyrrolopyrimidine-Based α-Helix Mimetics: Cell-Permeable Inhibitors of Protein-Protein Interactions.
    J. Am. Chem. Soc. 133:676-679 (2011)
2010
  • H. Rui and W. Im
    Protegrin-1 Orientation and Physicochemical Properties in Membrane Bilayers Studied by Potential of Mean Force Calculations.
    J. Comput. Chem. 31:2859-2867 (2010)
  • G. Jepkorir, J.C. Rodriguez, H. Rui, W. Im, S. Lovell, K.P. Battaile, A.Y. Alontaga, E. Yukl, P. Moenne-Loccoz, and M. Rivera
    Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa.
    J. Am. Chem. Soc. 132:9857–9872 (2010)
  • T. Kim and W. Im
    Revisiting Hydrophobic Mismatch with Free Energy Simulation Studies of Transmembrane Helix Tilt and Rotation.
    Biophys. J. 99:175-183 (2010)
  • K.H. Lim, P. Nagchowdhuri, T. Rathinavelan, and W. Im
    NMR Characterization of Hydrophobic Collapses in Amyloidogenic Partially Folded States and Their Implications for Protein Misfolding and Amyloid Formation.
    Biochem. Biophys. Res. Commun. 396:800-805 (2010)
  • T. Rathinavelan, L. Zhang, W.L. Picking, D.D. Weis, R.N. De Guzman, and W. Im
    A Repulsive Electrostatic Mechanism for Protein Export through the Type III Secretion Apparatus.
    Biophys. J. 98:452-461 (2010)  [cover]
2009
  • H. Rui, J. Lee, and W. Im
    Comparative Molecular Dynamics Simulation Studies of Protegrin-1 Monomer and Dimer in Different Lipid Bilayers.
    Biophys. J. 97:787-795 (2009)
  • S. Jo, J.B. Lim, J.B. Klauda, and W. Im
    CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes.
    Biophys. J. 97:50-58 (2009)
  • W. Im, J. Lee, T. Kim, and H. Rui
    Novel Free Energy Calculations to Explore Mechanisms and Energetics of Membrane Protein Structure and Function.
    J. Comput. Chem. 30:1622-1633 (2009)
  • B.R. Brooks, C.L. Brooks III, A.D. MacKerell, Jr., L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A.R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R.W. Pastor, C.B. Post, J.Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D.M. York, and M. Karplus
    CHARMM: The Biomolecular Simulation Program.
    J. Comput. Chem. 30:1545-1614 (2009)
  • J. Lee, S. Ham, and W. Im
    Beta-Hairpin Restraint Potentials for Calculations of Potentials of Mean Force as a Function of Beta-Hairpin Tilt, Rotation, and Distance.
    J. Comput. Chem. 30:1334-1343 (2009)
  • T. Kim, J. Lee, and W. Im
    Molecular Dynamics Studies on Structure and Dynamics of Phospholamban Monomer and Pentamer in Membranes.
    Proteins 76:86-98 (2009)
2008
  • J. Lee, J. Chen, C.L. Brooks III, and W. Im
    Application of Solid-state NMR Restraint Potentials in Membrane Protein Modeling.
    J. Magn. Reson. 193:68-76 (2008)
  • S.H. Park, C. Cheong, J. Idoyaga, J.Y. Kim, J-H Choi, Y. Do, H. Lee, J.H. Jo, Y-S Oh, W. Im, R.M. Steinman, and C.G. Park
    Generation and Application of New Rat Monoclonal Antibodies against Synthetic Tags for Improved Immunodetection.
    J. Immunol. Methods 331:27-38 (2008)
2007
  • S. Jo, T. Kim, and W. Im
    Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations.
    PLoS ONE 2:e880 (2007)
  • Y. Wang, A.N. Ouellette, C.W. Egan, T. Rathinavelan, W. Im and R.N. De Guzman
    Differences in the Electrostatic Surfaces of the Type III Secretion Needle Proteins.
    J. Mol. Biol. 371:1304-1314 (2007)
  • T. Rathinavelan and W. Im
    Explicit Treatment of Force Contribution from Alignment Tensor using Overdetermined Linear Equations and Its Application in NMR Structure Determination.
    J. Comput. Chem. 28:1858-1864 (2007)
  • L. Bu, W. Im, and C.L. Brooks III
    Membrane Assembly of Simple Helix Homo-oligomers Studied via Molecular Dynamics Simulations.
    Biophys. J. 92:854-863 (2007)
2006
  • Y. Liu, M. Scolari, W. Im, and H.J. Woo
    Protein-Protein Interactions in Actin-Myosin Binding and Structural Effects of R405Q Mutation: A Molecular Dynamics Study.
    Proteins 64:156-166 (2006)
  • W. Im, J. Chen, and C.L. Brooks III
    Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models.
    Adv. Protein Chem. 72: 173-198 (2006)
2005
  • J. Chen, H. Won, W. Im, H.J. Dyson and C.L. Brooks III
    Generation of Native-like Models from Limited NMR Data, Modern Force Fields and Advanced Conformational Sampling.
    J. Biomol. NMR 31:59-64 (2005)
2004
  • S.Y. Noskov, W. Im, and B. Roux
    Ion Permeation through the α-Hemolysin Channel: Theoretical Studies based on Brownian Dynamics and Poisson-Nernst-Plank Electrodiffusion Theory.
    Biophys. J. 87:2299-2309 (2004)
  • W. Im and C.L. Brooks III
    De Novo Folding of Membrane Proteins: An Exploration of the Structure and NMR Properties of the fd Coat Protein.
    J. Mol. Biol. 337:513-519 (2004)
  • M. Feig, A. Onufriev, M.S. Lee, W. Im, D.A. Case, and C.L. Brooks III
    Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures.
    J. Comput. Chem. 25:265-284 (2004)
2003
  • W. Im, M. Feig, and C.L. Brooks III
    An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins.
    Biophys. J. 85:2900-2918 (2003)
2002
  • W. Im and B. Roux
    Ion Permeation and Selectivity of OmpF Porin: A Theoretical Study Based on Molecular Dynamics, Brownian Dynamics, and Continuum Electrodiffusion Theory.
    J. Mol. Biol. 322:851-869 (2002)
  • W. Im and B. Roux
    Ions and Counterions in a Biological Channel: A Molecular Dynamics Simulation of OmpF Porin from Escherichia coli in an Explicit Membrane with 1 M KCl Aqueous Salt Solution.
    J. Mol. Biol. 319:1177-1197 (2002)
  • A. Philippsen, W. Im, A. Engel, T. Schirmer, B. Roux, and D.J. Muller
    Imaging the Electrostatic Potential of Transmembrane Channels: Atomic Probe Microscopy of OmpF Porin.
    Biophys. J. 82:1667-1676 (2002)
2001
  • W. Im and B. Roux
    Brownian Dynamics Simulations of Ions Channels: A General Treatment of the Electrostatic Reaction Field for Molecular Pores of Arbitrary Geometry.
    J. Chem. Phys. 115:4850-4861 (2001)
2000
  • W. Im, S. Seefeld and B. Roux
    Grand Canonical Monte Carlo - Brownian Dynamics Algorithm for Simulating Ion Channels.
    Biophys. J. 79:788-801 (2000)
Before 2000
  • W. Im, D. Beglov, and B. Roux
    Continuum Solvation Model: Computation of Electrostatic Forces from Numerical Solutions to the Poisson-Boltzmann Equation.
    Comput. Phys. Comm. 111:59-75 (1998)