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Articles by Wonpil Im
Identification of chemical features for improved outer membrane permeation in mycobacteria using machine learning
Abstract The ability of compounds to permeate and accumulate in bacterial cells is a critical determinant of antibiotic efficacy. Better therapeutics are urgently needed for the human pathogen Mycobacterium tuberculosis, yet the cell envelope, including the mycobacterial outer membrane, represents a significant barrier for drug entry, and the chemical features governing permeation remain poorly understood.
Conformational variability of HIV-1 Env trimer and viral vulnerability
eLife Assessment In this valuable study, the authors conducted an impressive amount of atomistic simulations with a glycosylated HIV-1 envelope glycoprotein (Env) trimer in a realistic asymmetric lipid bilayer. The aim was to probe how Env transmembrane domain, cytoplasmic tail, and membrane environment influence ectodomain orientation and antibody epitope exposure.
Dynamic architecture of mycobacterial outer membranes revealed by all-atom simulations
eLife Assessment In their study, Brown et. al. provide an important advance in understanding the architecture of the mycobacterial outer membrane. Using all-atom simulations of model mycomembranes, the work reports compelling structural insights into how α-mycolic acids and outer leaflet lipids (PDIM and PAT) shape membrane organisation.
Structural basis of fungal β-1,3-glucan synthase inhibition by caspofungin
Abstract Invasive fungal infections pose life-threatening risks to the increasing population of immunocompromised patients1,2. Treatment remains challenging due to limited antifungal drugs and increasing resistance. β-1,3-d-glucan synthase (GS), comprising the catalytic Fks1 and the regulatory small GTPase, Rho1 (refs. 3,4), is the target of clinically important echinocandin antifungals.
CHARMM-GUI Ligand Docker for Molecular Docking with Various Docking Programs Click to copy article link Article link copied!
Introduction Click to copy section linkSection link copied! Molecular docking has been one of the foundational techniques in computational drug discovery for more than three decades. (1) Its principal goal is to predict how a small molecule binds to a macromolecular target by exploring possible binding orientations, conformations, and positions of the ligand within the receptor’s binding pocket.
CHARMM-GUI Ligand Docker for Molecular Docking with Various Docking Programs Click to copy article link Article link copied!
Introduction Click to copy section linkSection link copied! Molecular docking has been one of the foundational techniques in computational drug discovery for more than three decades. (1) Its principal goal is to predict how a small molecule binds to a macromolecular target by exploring possible binding orientations, conformations, and positions of the ligand within the receptor’s binding pocket.
CHARMM-GUI Hybrid ML/MM Builder for Hybrid Machine Learning and Molecular Mechanical Modeling and Simulations Click to copy article link Article link copied!
In hybrid ML/MM simulations, the total potential energy of a system is expressed as V(r)=VMM(rMM)+VML(rML)+VMM/ML(rMM/ML) where V(r) denotes the potential energy of the whole system, VMM(rMM) corresponds to a classical MM potential acting on the MM region, VML(rML) represents an NNP describing the ML region, and VMM/ML(rMM/ML) accounts for nonbonded interactions between the MM and the ML regions.
Conformational Variability of HIV-1 Env Trimer and Viral Vulnerability
Abstract HIV-1 envelope glycoprotein (Env) is critical for viral fusion and entry into host cells and remains a primary target for vaccine and antiviral drug development. Advances in soluble gp140 trimer design have provided insight into the ectodomain structure and dynamics. However, the membrane-proximal external region (MPER) and transmembrane domain (TMD) are comparatively understudied, and knowledge of the cytoplasmic tail (CT) is virtually absent.
Click-based determination of accumulation of molecules in Escherichia coli - Nature Communications
Abstract Gram-negative bacterial pathogens pose a significant challenge in drug development because their outer membranes hinder the permeation of small molecules. The lack of widely adoptable methods for measuring the cytosolic accumulation of compounds in bacterial cells further hinders drug discovery efforts.
Microfluidic Generation of Oxidized Phospholipid Gradients in Supported Lipid Bilayers to Examine Scavenger Receptor Interactions
Introduction Click to copy section linkSection link copied! Reactive oxygen species (ROS) originate from both endogenous and exogenous sources. Endogenous sources include mitochondrial respiration and enzymatic activity, while smoking and pollution are exogenous causes of ROS production. (1) The ROS can oxidize biological molecules like proteins, nucleic acids, and lipids.
Molecular basis of the urate transporter URAT1 inhibition by gout drugs - Nature Communications
Abstract Hyperuricemia is a condition when uric acid, a waste product of purine metabolism, accumulates in the blood. Untreated hyperuricemia can lead to crystal formation of monosodium urate in the joints, causing a painful inflammatory disease known as gout. These conditions are associated with many other diseases and affect a significant and increasing proportion of the population.
Dynamics and Interactions of OmpF Porin in an Asymmetric Bacterial Outer Membrane including LPS, ECA, and CPS
Introduction Click to copy section linkSection link copied! Outer membrane proteins (OMPs), exposed on the surface of Gram-negative bacteria, play vital roles in various cellular processes and interactions with the external environment. Among these, outer membrane protein F (OmpF) porin is one of the best-characterized major OMPs in terms of their structure and function in Escherichia coli.
Surface lipoprotein sorting by crosstalk between Lpt and Lol pathways in gram-negative bacteria - Nature Communications
Abstract Lipopolysaccharide (LPS) and lipoprotein, two essential components of the outer membrane (OM) in Gram-negative bacteria, play critical roles in bacterial physiology and pathogenicity. LPS translocation to the OM is mediated by LptDE, yet how lipoproteins sort to the cell surface remains elusive. Here, we identify candidate lipoproteins that may be transported to the cell surface via LptDE.
Substrates (Acyl‐CoA and Diacylglycerol) Entry and Products (CoA and Triacylglycerol) Egress Pathways in DGAT1
1 Introduction A proper storage of energy reserves is vital for the survival of all living organisms, serving as a preparation for potential future challenging conditions. Triacylglycerols (TAGs) represent the most efficient and commonly utilized form of energy storage, consisting of three acyl chains esterified to a glycerol backbone [1, 2].
Dynamics of a von Willebrand Factor A1 Autoinhibitory Module with O-Linked Glycans and Its Roles in Regulation of GPIbα Binding
The Journal of Physical Chemistry B Cite this: J. Phys. Chem. B 2025, XXXX, XXX Click to copy citationCitation copied! . This publication is licensed under CC-BY-NC-ND 4.0 . You are free to share (copy and redistribute) this article in any medium or format within the parameters below: Creative Commons (CC): This is a Creative Commons license. Attribution (BY): Credit must be given to the creator. Non-Commercial (NC): Only non-commercial uses of the work are permitted.
Dynamics of a von Willebrand Factor A1 Autoinhibitory Module with O-Linked Glycans and Its Roles in Regulation of GPIbα Binding
The Journal of Physical Chemistry B Cite this: J. Phys. Chem. B 2025, 129, 15 Click to copy citationCitation copied! . This publication is licensed under CC-BY-NC-ND 4.0 . You are free to share (copy and redistribute) this article in any medium or format within the parameters below: Creative Commons (CC): This is a Creative Commons license. Attribution (BY): Credit must be given to the creator. Non-Commercial (NC): Only non-commercial uses of the work are permitted.
Molecular basis of neurosteroid and anticonvulsant regulation of TRPM3 - Nature Structural & Molecular Biology
Abstract Transient receptor potential channel subfamily M member 3 (TRPM3) is a Ca2+-permeable cation channel activated by the neurosteroid pregnenolone sulfate (PregS) or heat, serving as a nociceptor in the peripheral sensory system. Recent discoveries of autosomal dominant neurodevelopmental disorders caused by gain-of-function mutations in TRPM3 highlight its role in the central nervous system.
Atherosclerotic Oxidized Lipids Affect Formation and Biophysical Properties of Supported Lipid Bilayers and Simulated Membranes
The Journal of Physical Chemistry B Cite this: J. Phys. Chem. B 2024, XXXX, XXX Click to copy citationCitation copied! . This publication is licensed under CC-BY-NC-ND 4.0 . You are free to share (copy and redistribute) this article in any medium or format within the parameters below: Creative Commons (CC): This is a Creative Commons license. Attribution (BY): Credit must be given to the creator. Non-Commercial (NC): Only non-commercial uses of the work are permitted.
Conformational Rearrangements in the Sensory RcsF/OMP Complex Mediate Signal Transduction Across the Bacterial Cell Envelope
Home > UTHealth > McGovern Medical School > Journal Articles > 1312 Bacterial Outer Membrane Proteins, Cell Membrane, Escherichia coli, Escherichia coli Proteins, Signal Transduction DOWNLOADS Included in Medical Genetics Commons, Medical Microbiology Commons, Medical Molecular Biology Commons COinS
Neuroprotective amyloid β N‐terminal peptides differentially alter human α7‐ and α7β2‐nicotinic acetylcholine (nACh) receptor single‐channel properties - Roberts - British Journal of Pharmacology - Wiley Online Library
oAβ1–42 oligomeric amyloid β1–42 N-Aβ fragment N-terminal fragment of amyloid β1-15 N-Aβcore N-terminal amyloid β core hexapeptide PAM positive allosteric modulator What is already known Oligomeric amyloid β1–42 (oAβ1–42) induces neuronal instability via activation of α7-containing nACh receptors. What does this study add Neuroprotective forms of amyloid β N-terminal peptides activate and differentially alter single-channel properties between α7-nACh and α7β2-receptors.
Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Chem. Inf. Model. 2024, XXXX, XXX RETURN TO ARTICLES ASAPPREVComputational Bioche...Computational BiochemistryNEXT Han Zhang Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States and * Cite this: J. Chem. Inf. Model. 2024, XXXX, XXX research-article ACS Publications.
CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods
RETURN TO ARTICLES ASAPPREVBiomolecular SystemsNEXT Donghyuk Suh Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States , Abdul Raafik Arattu Thodika Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019-9800, United States , Seonghoon Kim Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering,...
Antiviral drug recognition and elevator-type transport motions of CNT3 - Nature Chemical Biology
Abstract Nucleoside analogs have broad clinical utility as antiviral drugs. Key to their systemic distribution and cellular entry are human nucleoside transporters. Here, we establish that the human concentrative nucleoside transporter 3 (CNT3) interacts with antiviral drugs used in the treatment of coronavirus infections.
Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family - Nature Communications
Abstract Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of OR51E2 bound to propionate provided molecular insight into odorant recognition, but the lack of an inactive OR structure limited understanding of the activation mechanism of ORs upon odorant binding.
Spontaneous curvature generation by peptides in asymmetric bilayers
Supporting Information Filename Description jcc27261-sup-0001-Supinfo.pdfPDF document, 2.1 MB Data S1: Supporting information. REFERENCES 1, , , Nat. Chem. Biol. 2020, 16, 1321. 2, , , , Data Brief. 2021, 35, 106927. 3, , Biophys. J. 2019, 117, 1037. 4, , , Membranes 2023, 13, 629. 5, , , , , , , Symmetry 2021, 13, 1356. 6, , Biophys. J. 2014, 106, 1958. 7, , J. Chem. Phys. 2015, 142, 54101. 8, , , , , , , , Nat. Chem. Biol. 2020, 16, 644. 9, , , Biophys. J. 2021, 120, 5041. 10, , , , , , , , Nat. Commun. 2022, 13, 7336.
CHARMM-GUI Multicomponent Assembler for Modeling and Simulation of Complex Multicomponent Systems
Abstract Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation.
TRPV4-Rho GTPase complex structures reveal mechanisms of gating and disease - Nature Communications
Abstract Crosstalk between ion channels and small GTPases is critical during homeostasis and disease, but little is known about the structural underpinnings of these interactions. TRPV4 is a polymodal, calcium-permeable cation channel that has emerged as a potential therapeutic target in multiple conditions. Gain-of-function mutations also cause hereditary neuromuscular disease.
Molecular basis of polyspecific drug and xenobiotic recognition by OCT1 and OCT2 - Nature Structural & Molecular Biology
Author notes These authors contributed equally: Yang Suo, Nicholas J. Wright. Authors and Affiliations Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA Yang Suo, Nicholas J. Wright, Justin G.
Molecular architecture of the Gαi-bound TRPC5 ion channel - Nature Communications
Abstract G-protein coupled receptors (GPCRs) and ion channels serve as key molecular switches through which extracellular stimuli are transformed into intracellular effects, and it has long been postulated that ion channels are direct effector molecules of the alpha subunit of G-proteins (Gα). However, no complete structural evidence supporting the direct interaction between Gα and ion channels is available.
Anillin Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study
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Conformational rearrangements in the sensory RcsF/OMP complex mediate signal transduction across the bacterial cell envelope
Characterization of RcsF variants defective in signaling from the OM Many more mutants were found to be depleted during growth on lactose, and they were indistinguishable from the nonsense rcsF mutants (Fig 2C). As expected, these included mutants defective in signaling to IgaA identified from the LOF[IM] screen (Fig 2C).
All-atom molecular dynamics simulations of Synaptotagmin-SNARE-complexin complexes bridging a vesicle and a flat lipid bilayer
Abstract Synaptic vesicles are primed into a state that is ready for fast neurotransmitter release upon Ca2+-binding to Synaptotagmin-1. This state likely includes trans-SNARE complexes between the vesicle and plasma membranes that are bound to Synaptotagmin-1 and complexins. However, the nature of this state and the steps leading to membrane fusion are unclear, in part because of the difficulty of studying this dynamic process experimentally.
Developing Initial Conditions for Simulations of Asymmetric Membranes: A Practical Recommendation
ABSTRACT It has been proposed that the surface tension difference between leaflets (or differential stress) in asymmetric bilayers is generally non-vanishing. This implies that there is no unique approach to generate initial conditions for simulations of asymmetric bilayers in the absence of experimentally derived constraints. Current generation methods include individual area per lipid (APL)-based, leaflet surface area (SA) matching, and zero leaflet tension-based (0-DS).
Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard-Jones potentials
Abstract The earlier integration of validated Lennard–Jones (LJ) potentials for 8 fcc metals into materials and biomolecular force fields has advanced multiple research fields, for example, metal–electrolyte interfaces, recognition of biomolecules, colloidal assembly of metal nanostructures, alloys, and catalysis.
Insight into Elongation Stages of Peptidoglycan Processing in Bacterial Cytoplasmic Membranes
Isolated lipid II, lipid VI, and lipid XII in a Gram-negative Bacterial Cytoplasmic Membrane To characterize the conformational dynamics of isolated lipid II, VI, and XII (Fig. 2B–D) embedded in a Gram-negative cytoplasmic membrane composition (POPE:POPG = 3:1), we performed 1-μs simulation for each system (Fig. S1; Table S1; see Methods for details).
Molecular Simulation and Biochemical Studies Support an Elevator-Type Transport Mechanism in EIIC
Enzyme IIC (EIIC) is a membrane-embedded sugar transport protein that is part of the phosphoenolpyruvate-dependent phosphotransferases. Crystal structures of two members of the glucose EIIC superfamily, bcChbC in the inward-facing conformation and bcMalT in the outward-facing conformation, were previously solved.
Scientists model outer membrane of 12 bacterial species to speed new drugs for 'bad bugs'
Information could be the key to winning the race against antibiotic resistance. If we lose, a UK-funded analysis predicts a frightening future where drug resistant bacterial infections kill more people worldwide than cancer. The lack of progress in creating "new drugs for bad bugs" (a term coined by the European Commission's Innovative Medicines Initiative) is due, in part, to a lack of information--especially in one particular area known as translocation.
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