Wonpil Im

University of Kansas, Lawrence, Kansas, United States

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Publications (166)688.99 Total impact

  • Sunhwan Jo · Yifei Qi · Wonpil Im
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    ABSTRACT: N-linked glycans are on protein surface and have direct and water/ion-mediated interactions with surrounding amino acids. Such contacts could restrict their conformational freedom of N-linked glycans compared to the same glycans free in solution. In this work, we have examined the conformational freedom of the N-glycan core pentasaccharide moiety in solution using standard molecular dynamics (MD) simulations as well as temperature replica-exchange MD simulations. Both simulations yield the comparable conformational variability of the pentasaccharide in solution, indicating the convergence of both simulations. The glycoprotein crystal structures are analyzed to compare the conformational freedom of the N-glycan on the protein surface with the simulation result. Surprisingly, the pentasaccharide free in solution shows more restricted conformational variability than the N-glycan on the protein surface. The interactions between the carbohydrate and the protein side chain appear to be responsible for the increased conformational diversity of the N-glycan on the protein surface. Finally, the transfer entropy analysis of the simulation trajectory also reveals an unexpected causality relationship between intramolecular hydrogen bonds and the conformational states in that the hydrogen bonds play a role in maintaining the conformational states rather than driving the change in glycosidic torsional states.
    Glycobiology 09/2015; DOI:10.1093/glycob/cwv083 · 3.15 Impact Factor
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    ABSTRACT: Difficulties in estimating the correct number of lipids in each leaflet of complex bilayer membrane simulation systems make it inevitable to introduce a mismatch in lipid packing (i.e., area per lipid) and thus alter the lateral pressure of each leaflet. To investigate potential effects of such mismatch on simulation results, we performed molecular dynamics simulations of saturated and monounsaturated lipid bilayers with and without gramicidin A or WALP23 at various mismatches by adjusting the number of lipids in the bottom leaflet from no mismatch to a 25% reduction compared to those in the upper leaflet. All simulations were stable under the constant pressure barostat, but the mismatch induces asymmetric lipid packing between the leaflets, so that the top leaflet becomes more ordered, and the bottom leaflet becomes less ordered. The mismatch effects on various bilayer properties are mild up to 5-10% mismatch, and bilayers with fully saturated chains appear to be more prone to these effects than those with unsaturated tails. The non-vanishing leaflet surface tensions and the free energy derivatives with respect to the bilayer curvature indicate that the bilayer would be energetically unstable in the presence of mismatch. We propose a quantitative criterion for allowable mismatch based on the energetics derived from a continuum elastic model, which grows as a square root of the number of the lipids in the system. Based on this criterion, we infer that the area per lipid mismatch up to 5% would be tolerable in various membrane simulations of reasonable all-atom system sizes (40-160 lipids per leaflet).
    Journal of Chemical Theory and Computation 07/2015; 11(7):3466-3477. DOI:10.1021/acs.jctc.5b00232 · 5.50 Impact Factor
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    ABSTRACT: The membrane-spanning α helices of single-pass receptors play crucial roles in stabilizing oligomeric structures and transducing biochemical signals across the membrane. Probing intermolecular transmembrane interactions in single-pass receptors presents unique challenges, reflected in a gross underrepresentation of their membrane-embedded domains in structural databases. Here, we present two high-resolution structures of transmembrane assemblies from a eukaryotic single-pass protein crystallized in a lipidic membrane environment. Trimeric and tetrameric structures of the immunoreceptor signaling module DAP12, determined to 1.77-Å and 2.14-Å resolution, respectively, are organized by the same polar surfaces that govern intramembrane assembly with client receptors. We demonstrate that, in addition to the well-studied dimeric form, these trimeric and tetrameric structures are made in cells, and their formation is competitive with receptor association in the ER. The polar transmembrane sequences therefore act as primary determinants of oligomerization specificity through interplay between charge shielding and sequestration of polar surfaces within helix interfaces.
    Cell Reports 05/2015; 11(8):1184-1192. DOI:10.1016/j.celrep.2015.04.045 · 8.36 Impact Factor
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    ABSTRACT: Solid-state NMR has been used to determine the structures of membrane proteins in native-like lipid bilayer environments. Most structure calculations based on solid-state NMR observables are performed using simulated annealing with restrained molecular dynamics and an energy function, where all nonbonded interactions are represented by a single, purely repulsive term with no contributions from van der Waals attractive, electrostatic, or solvation energy. To our knowledge, this is the first application of an ensemble dynamics technique performed in explicit membranes that uses experimental solid-state NMR observables to obtain the refined structure of a membrane protein together with information about its dynamics and its interactions with lipids. Using the membrane-bound form of the fd coat protein as a model membrane protein and its experimental solid-state NMR data, we performed restrained ensemble dynamics simulations with different ensemble sizes in explicit membranes. For comparison, a molecular dynamics simulation of fd coat protein was also performed without any restraints. The average orientation of each protein helix is similar to a structure determined by traditional single-conformer approaches. However, their variations are limited in the resulting ensemble of structures with one or two replicas, as they are under the strong influence of solid-state NMR restraints. Although highly consistent with all solid-state NMR observables, the ensembles of more than two replicas show larger orientational variations similar to those observed in the molecular dynamics simulation without restraints. In particular, in these explicit membrane simulations, Lys(40), residing at the C-terminal side of the transmembrane helix, is observed to cause local membrane curvature. Therefore, compared to traditional single-conformer approaches in implicit environments, solid-state NMR restrained ensemble simulations in explicit membranes readily characterize not only protein dynamics but also protein-lipid interactions in detail. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.
    Biophysical Journal 04/2015; 108(8):1954-62. DOI:10.1016/j.bpj.2015.03.012 · 3.97 Impact Factor
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    ABSTRACT: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner. A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the PDB N-linked glycan library and PDB homologous/non-homologous N-glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility. wonpil@ku.edu Availability: http://www.glycanstructure.org/gsalign. Supplementary data are available at Bioinformatics online. © The Author (2015). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
    Bioinformatics 04/2015; 31(16). DOI:10.1093/bioinformatics/btv202 · 4.98 Impact Factor
  • Hui Sun Lee · Chaok Seok · Wonpil Im
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    ABSTRACT: G protein-coupled receptors (GPCRs) play fundamental roles in physiological processes by modulating diverse signaling pathways and thus have been one of the most important drug targets. Based on the fact that GPCR-mediated signaling is modulated in a ligand-specific manner such as agonist, inverse agonist, and neutral antagonist, termed efficacy, quantitative characterization of the ligand efficacy is essential for rational design of selective modulators for GPCR targets. As experimental approaches for this purpose are time-, cost-, and labor-intensive, computational tools that can systematically predict GPCR ligand efficacy can have a big impact on GPCR drug design. Here, we have performed free energy perturbation molecular dynamics simulations to calculate absolute binding free energy of an inverse agonist, a neutral antagonist, and an agonist to β2-adrenergic receptor (β2-AR) active and inactive states, respectively, in explicit lipid bilayers. Relatively short alchemical free energy calculations reveal that both the time-series of the total binding free energy and decomposed energy contributions can be used as relevant physical properties to discriminate β2-AR ligand efficacy. This study illustrates a merit of the current approach over simple, fast docking calculations and highly expensive millisecond-timescale simulations.
    Journal of Chemical Theory and Computation 03/2015; 11(3):1255-1266. DOI:10.1021/ct5008907 · 5.50 Impact Factor
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    ABSTRACT: Molecular dynamics simulations are an effective tool to study the structure, dynamics, and thermodynamics of carbohydrates and proteins. However, the simulations of heterogeneous glycoprotein systems have been limited due to the lack of appropriate molecular force field parameters describing the linkage between the carbohydrate and the protein regions as well as the tools to prepare these systems for modeling studies. In this work we outline the recent developments in the CHARMM carbohydrate force field to treat glycoproteins and describe in detail the step-by-step procedures involved in building glycoprotein geometries using CHARMM-GUI Glycan Reader.
    Methods in molecular biology (Clifton, N.J.) 03/2015; 1273:407-29. DOI:10.1007/978-1-4939-2343-4_25 · 1.29 Impact Factor
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    ABSTRACT: While membrane simulations are widely employed to study the structure and dynamics of various lipid bilayers and membrane proteins in the bilayers, simulations of lipopolysaccharides (LPS) in membrane environments have been limited due to their structural complexity, difficulties in building LPS-membrane systems, and lack of the appropriate molecular force fields. In this work, as a first step to extend CHARMM-GUI Membrane Builder to incorporate LPS molecules and to explore their structures and dynamics in membrane environments using molecular dynamics simulations, we describe step-by-step procedures to build LPS bilayer systems using CHARMM and the recently developed CHARMM carbohydrate and lipid force fields. Such procedures are illustrated by building various bilayers of Escherichia coli R1.O6 LPS and the presentation of preliminary simulation results in terms of per-LPS area and density distributions of various components along the membrane normal.
    Methods in molecular biology (Clifton, N.J.) 03/2015; 1273:391-406. DOI:10.1007/978-1-4939-2343-4_24 · 1.29 Impact Factor
  • Hui Sun Lee · Yifei Qi · Wonpil Im
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    ABSTRACT: N-linked glycosylation is one of the most important, chemically complex, and ubiquitous post-translational modifications in all eukaryotes. The N-glycans that are covalently linked to proteins are involved in numerous biological processes. There is considerable interest in developments of general approaches to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in protein design with advantageous properties. In this study, the impacts of N-glycans on protein structure and dynamics are systematically investigated using an integrated computational approach of the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated and deglycosylated proteins. Our study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein stability. Overall, these results suggest not only a common role of glycosylation in proteins, but also a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.
    Scientific Reports 03/2015; 5:8926. DOI:10.1038/srep08926 · 5.58 Impact Factor
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    ABSTRACT: X-ray crystallography, molecular dynamics (MD) simulations and biochemistry were utilized to investigate the effect of introducing hydrophobic interactions in the 4-fold (N148L and Q151L) and B-pores (D34F) of Pseudomonas aeruginosa bacterioferritin B (BfrB) on BfrB function. The structures show only local structural perturbations and confirm the anticipated hydrophobic interactions. Surprisingly, structures obtained after soaking crystals in Fe2+-containing crystallization solution revealed that although iron loads into the ferroxidase centers of the mutants, the side chains of ferroxidase ligands E51 and H130 do not reorganize to bind the iron ions, as is seen in the wt BfrB structures. Similar experiments with a double mutant (C89S/K96C) prepared to introduce changes outside the pores show competent ferroxidase centers that function akin to those in wt BfrB. MD simulations comparing wt BfrB with the D34F and N148L mutants show that the mutants exhibit significantly reduced flexibility, and reveal a network of concerted motions linking ferroxidase centers and 4-fold and B-pores, which are important for imparting ferroxidase centers in BfrB with the required flexibility to function efficiently. In agreement, the efficiency of Fe2+ oxidation and uptake of the 4-fold and B-pore mutants in solution is significantly compromised relative to wt or C89S/K96C BfrB. Finally, our structures show a large number of previously unknown iron binding sites in the interior cavity and B-pores of BfrB, which reveal in unprecedented detail conduits followed by iron and phosphate ions across the BfrB shell, as well as paths in the interior cavity that may facilitate nucleation of the iron phosphate mineral.
    Biochemistry 01/2015; 54(8). DOI:10.1021/bi501255r · 3.02 Impact Factor
  • Jumin Lee · Wonpil Im
    Biophysical Journal 01/2015; 108(2):467a. DOI:10.1016/j.bpj.2014.11.2552 · 3.97 Impact Factor
  • Biophysical Journal 01/2015; 108(2):209a. DOI:10.1016/j.bpj.2014.11.1155 · 3.97 Impact Factor
  • Soohyung Park · Wonpil Im
    Biophysical Journal 01/2015; 108(2):467a. DOI:10.1016/j.bpj.2014.11.2553 · 3.97 Impact Factor
  • Xi Cheng · Yifei Qi · Jumin Lee · Sunhwan Jo · Wonpil Im
    Biophysical Journal 01/2015; 108(2):159a. DOI:10.1016/j.bpj.2014.11.877 · 3.97 Impact Factor
  • Biophysical Journal 01/2015; 108(2):249a. DOI:10.1016/j.bpj.2014.11.1377 · 3.97 Impact Factor
  • Hui Sun Lee · Wonpil Im
    Biophysical Journal 01/2015; 108(2):473a. DOI:10.1016/j.bpj.2014.11.2584 · 3.97 Impact Factor
  • Yifei Qi · Xi Cheng · Wonpil Im
    Biophysical Journal 01/2015; 108(2):161a. DOI:10.1016/j.bpj.2014.11.888 · 3.97 Impact Factor
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    ABSTRACT: CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since it is originally developed in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations including free energy calculation and large-scale coarse-grained representation. Here, we describe functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator, such as ligand force field generation, incorporation of methanethiosulfonate spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids. These new features are expected to be useful in advanced biomolecular modeling and simulation of proteins. © 2014 Elsevier Inc. All rights reserved.
    Advances in Protein Chemistry and Structural Biology 12/2014; 96:235-65. DOI:10.1016/bs.apcsb.2014.06.002 · 3.04 Impact Factor
  • Source
    Kyu Il Lee · Wonpil Im · Richard W Pastor
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    ABSTRACT: The polyvalent acidic lipid phosphatidylinositol, 4,5-bisphosphate (PIP2) is important for many cellular functions. It has been suggested that different pools of PIP2 exist in the cytoplasmic leaflet of the plasma membrane, and that such pooling could play a role in the regulation of PIP2. The mechanism of fencing, however, is not understood. This study presents the results of Langevin dynamics simulations of PIP2 to elucidate some of the molecular level considerations that must be applied to models for fencing. For each simulation, a pool of PIP2 (modeled as charged spheres) was placed in containments with boundaries modeled as a single row of rods (steric or electrostatic) or rigid protein filaments. It is shown that even a small gap (20 Å, which is 1.85 times larger than the diameter of a PIP2 sphere) leads to poor steric blocking, and that electrostatic blockage is only effective at very high charge density. Filaments of human septin, yeast septin, and actin also failed to provide adequate blockage when placed on the membrane surface. The two septins do provide high blockage consistent with experiment and with phenomenological considerations of permeability when they are buried 9 Å and 12 Å below the membrane surface, respectively. In contrast, burial does not improve blockage by the "arch-shaped" actin filaments. Free energy estimates using implicit membrane-solvent models indicate that burial of the septins to about 10 Å can be achieved without penetration of charged residues into the hydrophobic region of the membrane. These results imply that a functioning fence assembled from protein filaments must either be buried well below the membrane surface, have more than a single row, or contain additional components that fill small gaps in the filaments.
    BMC Biophysics 11/2014; 7(1):13. DOI:10.1186/s13628-014-0013-3 · 2.89 Impact Factor
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    ABSTRACT: α-Helices play a critical role in mediating many protein-protein interactions (PPIs) as recognition motifs. Therefore, there is a considerable interest in developing small molecules that can mimic helical peptide segments to modulate α-helix-mediated PPIs. Due to the relatively low aqueous solubility and synthetic difficulty of most current α-helix mimetic small molecules, one important goal in this area is to develop small molecules with favorable physicochemical properties and ease of synthesis. Here we designed phenyl-piperazine-triazine-based α-helix mimetics that possess improved water solubility and excellent synthetic accessibility. We developed a facile solid-phase synthetic route that allows for rapid creation of a large, diverse combinatorial library of α-helix mimetics. Further we identified a selective inhibitor of the Mcl-1/BH3 interaction by screening a focused library of phenyl-piperazine-triazines, demonstrating that the scaffold is able to serve as functional mimetics of α-helical peptides. We believe that our phenyl-piperazine-triazine-based α-helix mimetics, along with the facile and divergent solid-phase synthetic method, have great potential as powerful tools for discovering potent inhibitors of given α-helix-mediated PPIs.
    ACS Combinatorial Science 10/2014; 16(12). DOI:10.1021/co500114f · 3.03 Impact Factor

Publication Stats

7k Citations
688.99 Total Impact Points


  • 2006–2015
    • University of Kansas
      • • Department of Molecular Biosciences
      • • Department of Chemistry
      Lawrence, Kansas, United States
  • 2013
    • Stockholm University
      • Department of Organic Chemistry
      Tukholma, Stockholm, Sweden
  • 2011
    • University of Maryland, College Park
      • Department of Chemical and Biomolecular Engineering
      CGS, Maryland, United States
  • 2009
    • National Heart, Lung, and Blood Institute
      베서스다, Maryland, United States
  • 2003–2007
    • The Scripps Research Institute
      • Department of Cell and Molecular Biology
      La Jolla, CA, United States
  • 2000–2004
    • Weill Cornell Medical College
      • Department of Biochemistry
      New York, New York, United States
    • Université de Montréal
      Montréal, Quebec, Canada
  • 2002
    • Cornell University
      • Department of Biochemistry
      Ithaca, New York, United States