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Garisetti V, Dhanabalan AK, Dasararaju G. Orphan receptor GPR88 as a potential therapeutic target for CNS disorders - an in silico approach. J Biomol Struct Dyn 2024; 42:4745-4758. [PMID: 37306437 DOI: 10.1080/07391102.2023.2222820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
The G-protein-coupled receptors are a part of the largest and most physiologically relevant family of membrane proteins. One-third of the medications, now on the market, target the GPCR receptor family, which is one of the most important therapeutic targets for many disorders. In the reported work, we have focussed on orphan GPR88 receptor which is a part of the GPCR protein family and a potential target for central nervous system disorders. GPR88 is known to show the highest expression in the striatum, which is a key region in motor control and cognitive functions. Recent studies have reported that GPR88 is activated by two agonists, 2-PCCA and RTI-13951-33. In this study, we have predicted the three-dimensional protein structure for the orphan GPR88 using the homology modeling approach. We then used shape-based screening techniques based on known agonists and structure-based virtual screening methods employing docking to uncover novel GPR88 ligands. The screened GPR88-ligand complexes were further subjected to molecular dynamics simulation studies. The selected ligands could fasten the development of novel treatments for the vast list of movement and central nervous system disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vasavi Garisetti
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
| | - Anantha Krishnan Dhanabalan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
| | - Gayathri Dasararaju
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
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2
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Sharma P, Vaiwala R, Gopinath AK, Chockalingam R, Ayappa KG. Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7791-7811. [PMID: 38451026 DOI: 10.1021/acs.langmuir.3c03474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Bacteria have evolved over 3 billion years, shaping our intrinsic and symbiotic coexistence with these single-celled organisms. With rising populations of drug-resistant strains, the search for novel antimicrobials is an ongoing area of research. Advances in high-performance computing platforms have led to a variety of molecular dynamics simulation strategies to study the interactions of antimicrobial molecules with different compartments of the bacterial cell envelope of both Gram-positive and Gram-negative species. In this review, we begin with a detailed description of the structural aspects of the bacterial cell envelope. Simulations concerned with the transport and associated free energy of small molecules and ions through the outer membrane, peptidoglycan, inner membrane and outer membrane porins are discussed. Since surfactants are widely used as antimicrobials, a section is devoted to the interactions of surfactants with the cell wall and inner membranes. The review ends with a discussion on antimicrobial peptides and the insights gained from the molecular simulations on the free energy of translocation. Challenges involved in developing accurate molecular models and coarse-grained strategies that provide a trade-off between atomic details with a gain in sampling time are highlighted. The need for efficient sampling strategies to obtain accurate free energies of translocation is also discussed. Molecular dynamics simulations have evolved as a powerful tool that can potentially be used to design and develop novel antimicrobials and strategies to effectively treat bacterial infections.
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Affiliation(s)
- Pradyumn Sharma
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Rakesh Vaiwala
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Amar Krishna Gopinath
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Rajalakshmi Chockalingam
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
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3
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Fortea E, Lee S, Chadda R, Argyros Y, Sandal P, Mahoney-Kruszka R, Ciftci HD, Falzone ME, Huysmans G, Robertson JL, Boudker O, Accardi A. Structural basis of pH-dependent activation in a CLC transporter. Nat Struct Mol Biol 2024; 31:644-656. [PMID: 38279055 PMCID: PMC11262703 DOI: 10.1038/s41594-023-01210-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/22/2023] [Indexed: 01/28/2024]
Abstract
CLCs are dimeric chloride channels and anion/proton exchangers that regulate processes such as muscle contraction and endo-lysosome acidification. Common gating controls their activity; its closure simultaneously silences both protomers, and its opening allows them to independently transport ions. Mutations affecting common gating in human CLCs cause dominant genetic disorders. The structural rearrangements underlying common gating are unknown. Here, using single-particle cryo-electron microscopy, we show that the prototypical Escherichia coli CLC-ec1 undergoes large-scale rearrangements in activating conditions. The slow, pH-dependent remodeling of the dimer interface leads to the concerted opening of the intracellular H+ pathways and is required for transport. The more frequent formation of short water wires in the open H+ pathway enables Cl- pore openings. Mutations at disease-causing sites favor CLC-ec1 activation and accelerate common gate opening in the human CLC-7 exchanger. We suggest that the pH activation mechanism of CLC-ec1 is related to the common gating of CLC-7.
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Affiliation(s)
- Eva Fortea
- Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY, USA
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA
| | - Sangyun Lee
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA
| | - Rahul Chadda
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yiorgos Argyros
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medical School, New York, NY, USA
| | - Priyanka Sandal
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA, USA
| | - Robyn Mahoney-Kruszka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Hatice Didar Ciftci
- Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY, USA
- Tri-Institutional Training Program in Chemical Biology, New York, NY, USA
| | - Maria E Falzone
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medical School, New York, NY, USA
| | - Gerard Huysmans
- Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY, USA
- Erasmus University, Jette, Belgium
| | - Janice L Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Alessio Accardi
- Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY, USA.
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medical School, New York, NY, USA.
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4
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Harris J, Chipot C, Roux B. How is Membrane Permeation of Small Ionizable Molecules Affected by Protonation Kinetics? J Phys Chem B 2024; 128:795-811. [PMID: 38227958 DOI: 10.1021/acs.jpcb.3c06765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
According to the pH-partition hypothesis, the aqueous solution adjacent to a membrane is a mixture of the ionization states of the permeating molecule at fixed Henderson-Hasselbalch concentrations, such that each state passes through the membrane in parallel with its own specific permeability. An alternative view, based on the assumption that the rate of switching ionization states is instantaneous, represents the permeation of ionizable molecules via an effective Boltzmann-weighted average potential (BWAP). Such an assumption is used in constant-pH molecular dynamics simulations. The inhomogeneous solubility-diffusion framework can be used to compute the pH-dependent membrane permeability for each of these two limiting treatments. With biased WTM-eABF molecular dynamics simulations, we computed the potential of mean force and diffusivity of each ionization state of two weakly basic small molecules: nicotine, an addictive drug, and varenicline, a therapeutic for treating nicotine addiction. At pH = 7, the BWAP effective permeability is greater than that determined by pH-partitioning by a factor of 2.5 for nicotine and 5 for varenicline. To assess the importance of ionization kinetics, we present a Smoluchowski master equation that includes explicitly the protonation and deprotonation processes coupled with the diffusive motion across the membrane. At pH = 7, the increase in permeability due to the explicit ionization kinetics is negligible for both nicotine and varenicline. This finding is reaffirmed by combined Brownian dynamics and Markov state model simulations for estimating the permeability of nicotine while allowing changes in its ionization state. We conclude that for these molecules the pH-partition hypothesis correctly captures the physics of the permeation process. The small free energy barriers for the permeation of nicotine and varenicline in their deprotonated neutral forms play a crucial role in establishing the validity of the pH-partitioning mechanism. Essentially, BWAP fails because ionization kinetics are too slow on the time scale of membrane crossing to affect the permeation of small ionizable molecules such as nicotine and varenicline. For the singly protonated state of nicotine, the computational results agree well with experimental measurements (P1 = 1.29 × 10-7 cm/s), but the agreement for neutral (P0 = 6.12 cm/s) and doubly protonated nicotine (P2 = 3.70 × 10-13 cm/s) is slightly worse, likely due to factors associated with the aqueous boundary layer (neutral form) or leaks through paracellular pathways (doubly protonated form).
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Affiliation(s)
- Jonathan Harris
- Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n◦7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy Cedex, France
- Theoretical and Computational Biophysics Group, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry and Molecular Biology, Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
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Acharya A, Jana K, Gurvic D, Zachariae U, Kleinekathöfer U. Fast prediction of antibiotic permeability through membrane channels using Brownian dynamics. Biophys J 2023; 122:2996-3007. [PMID: 36992560 PMCID: PMC10398345 DOI: 10.1016/j.bpj.2023.03.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 03/02/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
The efficient permeation across the Gram-negative bacterial membrane is an important step in the overall process of antibacterial action of a molecule and the one that has posed a significant hurdle on the way toward approved antibiotics. Predicting the permeability for a large library of molecules and assessing the effect of different molecular transformations on permeation rates of a given molecule is critical to the development of effective antibiotics. We present a computational approach for obtaining estimates of molecular permeability through a porin channel in a matter of hours using a Brownian dynamics approach. The fast sampling using a temperature acceleration scheme enables the approximate estimation of permeability using the inhomogeneous solubility diffusion model. Although the method is a significant approximation to similar all-atom approaches tested previously, we show that the present approach predicts permeabilities that correlate fairly well with the respective experimental permeation rates from liposome swelling experiments and accumulation rates from antibiotic accumulation assays, and is significantly, i.e., about 14 times, faster compared with a previously reported approach. The possible applications of the scheme in high-throughput screening for fast permeators are discussed.
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Affiliation(s)
| | | | - Dominik Gurvic
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ulrich Zachariae
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
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6
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Donoghue A, Winterhalter M, Gutsmann T. Influence of Membrane Asymmetry on OmpF Insertion, Orientation and Function. MEMBRANES 2023; 13:membranes13050517. [PMID: 37233578 DOI: 10.3390/membranes13050517] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/29/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
The effect of asymmetric membranes containing lipopolysaccharides (LPS) on the outer membrane protein F (OmpF) reconstitution, channel orientation, and antibiotic permeation across the outer membrane was investigated. After forming an asymmetric planar lipid bilayer composed of LPS on one and phospholipids on the other side, the membrane channel OmpF was added. The ion current recordings demonstrate that LPS has a strong influence on the OmpF membrane insertion, orientation, and gating. Enrofloxacin was used as an example of an antibiotic interacting with the asymmetric membrane and with OmpF. The enrofloxacin caused the blockage of the ion current through the OmpF, depending on the side of addition, the transmembrane voltage applied, and the composition of the buffer. Furthermore, the enrofloxacin changed the phase behavior of the LPS-containing membranes, demonstrating that its membrane activity influences the function of OmpF and potentially the membrane permeability.
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Affiliation(s)
- Annemarie Donoghue
- Research Center Borstel, Leibniz Lung Center, Parkallee 10, 23845 Borstel, Germany
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | | | - Thomas Gutsmann
- Research Center Borstel, Leibniz Lung Center, Parkallee 10, 23845 Borstel, Germany
- Center for Structural Systems Biology, Notkestraße 85, Building 15, 22607 Hamburg, Germany
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7
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Acharya A, Ghai I, Piselli C, Prajapati JD, Benz R, Winterhalter M, Kleinekathöfer U. Conformational Dynamics of Loop L3 in OmpF: Implications toward Antibiotic Translocation and Voltage Gating. J Chem Inf Model 2023; 63:910-927. [PMID: 36525563 DOI: 10.1021/acs.jcim.2c01108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the present work, we delineate the molecular mechanism of a bulky antibiotic permeating through a bacterial channel and uncover the role of conformational dynamics of the constriction loop in this process. Using the temperature accelerated sliced sampling approach, we shed light onto the dynamics of the L3 loop, in particular the F118 to S125 segment, at the constriction regions of the OmpF porin. We complement the findings with single channel electrophysiology experiments and applied-field simulations, and we demonstrate the role of hydrogen-bond stabilization in the conformational dynamics of the L3 loop. A molecular mechanism of permeation is put forward wherein charged antibiotics perturb the network of stabilizing hydrogen-bond interactions and induce conformational changes in the L3 segment, thereby aiding the accommodation and permeation of bulky antibiotic molecules across the constriction region. We complement the findings with single channel electrophysiology experiments and demonstrate the importance of the hydrogen-bond stabilization in the conformational dynamics of the L3 loop. The generality of the present observations and experimental results regarding the L3 dynamics enables us to identify this L3 segment as the source of gating. We propose a mechanism of OmpF gating that is in agreement with previous experimental data that showed the noninfluence of cysteine double mutants that tethered the L3 tip to the barrel wall on the OmpF gating behavior. The presence of similar loop stabilization networks in porins of other clinically relevant pathogens suggests that the conformational dynamics of the constriction loop is possibly of general importance in the context of antibiotic permeation through porins.
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Affiliation(s)
- Abhishek Acharya
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen 28759, Germany
| | - Ishan Ghai
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | - Claudio Piselli
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | | | - Roland Benz
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen 28759, Germany
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8
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Interaction of Tryptophan- and Arginine-Rich Antimicrobial Peptide with E. coli Outer Membrane-A Molecular Simulation Approach. Int J Mol Sci 2023; 24:ijms24032005. [PMID: 36768325 PMCID: PMC9916935 DOI: 10.3390/ijms24032005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
A short antimicrobial peptide (AMP), rich in tryptophan and arginine (P6-HRWWRWWRR-NH2), was used in molecular dynamics (MD) simulations to investigate the interaction between AMPs and lipopolysaccharides (LPS) from two E. coli outer membrane (OM) membrane models. The OM of Gram-negative bacteria is an asymmetric bilayer, with the outer layer consisting exclusively of lipopolysaccharide molecules and the lower leaflet made up of phospholipids. The mechanisms by which short AMPs permeate the OM of Gram-negative bacteria are not well understood at the moment. For this study, two types of E. coli OM membrane models were built with (i) smooth LPS composed of lipid A, K12 core and O21 O-antigen, and (ii) rough type LPS composed of lipid A and R1 core. An OmpF monomer from E. coli was embedded in both membrane models. MD trajectories revealed that AMP insertion in the LPS layer was facilitated by the OmpF-created gap and allowed AMPs to form hydrogen bonds with the phosphate groups of inner core oligosaccharides. OM proteins such as OmpF may be essential for the permeation of short AMPs such as P6 by exposing the LPS binding site or even by direct translocation of AMPs across the OM.
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9
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You X, Cao L, Liu Y, Wu H, Li R, Xiao Q, Yuan J, Zhang R, Fan C, Wang X, Yang P, Yang X, Ma Y, Jiang Z. Charged Nanochannels in Covalent Organic Framework Membranes Enabling Efficient Ion Exclusion. ACS NANO 2022; 16:11781-11791. [PMID: 35771947 DOI: 10.1021/acsnano.2c04767] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Controllable ion transport through nanochannels is crucial for biological and artificial membrane systems. Covalent organic frameworks (COFs) with regular and tunable nanochannels are emerging as an ideal material platform to develop synthetic membranes for ion transport. However, ion exclusion by COF membranes remains challenging because most COF materials have large-sized nanochannels leading to nonselective transport of small ions. Here we develop ionic COF membranes (iCOFMs) to control ion transport through charged framework nanochannels, the interior surfaces of which are covered with arrayed sulfonate groups to render superior charge density. The overlap of an electrical double layer in charged nanochannels blocks the entry of co-ions, narrows their passageways, and concomitantly restrains the permeation of counterions via the charge balance. These highly charged large-sized nanochannels within the iCOFM enable ion exclusion while maintaining intrinsically high water permeability. Our results reveal possibilities for controllable ion transport based on COF membranes for water purification, ionic separation, sensing, and energy conversion.
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Affiliation(s)
- Xinda You
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Li Cao
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Yawei Liu
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Hong Wu
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, China
| | - Runlai Li
- Department of Chemistry, National University of Singapore, Singapore 117549, Singapore
| | - Qianxiang Xiao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Jinqiu Yuan
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Runnan Zhang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Chunyang Fan
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Xiaoyao Wang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Pengfei Yang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Xiaoyu Yang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Yu Ma
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Zhongyi Jiang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang 315201, China
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10
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Role of internal loop dynamics in antibiotic permeability of outer membrane porins. Proc Natl Acad Sci U S A 2022; 119:2117009119. [PMID: 35193963 PMCID: PMC8872756 DOI: 10.1073/pnas.2117009119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2022] [Indexed: 12/26/2022] Open
Abstract
Antibiotic resistance in Gram-negative pathogens has been identified as an urgent threat to human health by the World Health Organization. The major challenge with treating infections by these pathogens is developing antibiotics that can traverse the dense bacterial outer membrane (OM) formed by a mesh of lipopolysaccharides. Effective antibiotics permeate through OM porins, which have evolved for nutrient diffusion; however, the conformational states of these porins regulating permeation are still unclear. Here, we used molecular dynamics simulations, free energy calculations, Markov-state modeling, and whole-cell accumulation assays to provide mechanistic insight on how a porin shifts between open and closed states. We provide a mechanism of how Gram-negative bacteria confer resistance to antibiotics. Gram-negative bacteria pose a serious public health concern due to resistance to many antibiotics, caused by the low permeability of their outer membrane (OM). Effective antibiotics use porins in the OM to reach the interior of the cell; thus, understanding permeation properties of OM porins is instrumental to rationally develop broad-spectrum antibiotics. A functionally important feature of OM porins is undergoing open–closed transitions that modulate their transport properties. To characterize the molecular basis of these transitions, we performed an extensive set of molecular dynamics (MD) simulations of Escherichia coli OM porin OmpF. Markov-state analysis revealed that large-scale motion of an internal loop, L3, underlies the transition between energetically stable open and closed states. The conformation of L3 is controlled by H bonds between highly conserved acidic residues on the loop and basic residues on the OmpF β-barrel. Mutation of key residues important for the loop’s conformation shifts the equilibrium between open and closed states and regulates translocation of permeants (ions and antibiotics), as observed in the simulations and validated by our whole-cell accumulation assay. Notably, one mutant system G119D, which we find to favor the closed state, has been reported in clinically resistant bacterial strains. Overall, our accumulated ∼200 µs of simulation data (the wild type and mutants) along with experimental assays suggest the involvement of internal loop dynamics in permeability of OM porins and antibiotic resistance in Gram-negative bacteria.
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11
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Haloi N, Vasan AK, Geddes EJ, Prasanna A, Wen PC, Metcalf WW, Hergenrother PJ, Tajkhorshid E. Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge. Chem Sci 2021; 12:15028-15044. [PMID: 34909143 PMCID: PMC8612397 DOI: 10.1039/d1sc04445a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/13/2021] [Indexed: 11/28/2022] Open
Abstract
Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Recently, we disclosed the eNTRy rules, a key lesson of which is that the introduction of a primary amine enhances OM permeation in certain contexts. To understand the molecular basis for this finding, we perform an extensive set of molecular dynamics (MD) simulations and free energy calculations comparing the permeation of aminated and amine-free antibiotic derivatives through the most abundant OM porin of E. coli, OmpF. To improve sampling of conformationally flexible drugs in MD simulations, we developed a novel, Monte Carlo and graph theory based algorithm to probe more efficiently the rotational and translational degrees of freedom visited during the permeation of the antibiotic molecule through OmpF. The resulting pathways were then used for free-energy calculations, revealing a lower barrier against the permeation of the aminated compound, substantiating its greater OM permeability. Further analysis revealed that the amine facilitates permeation by enabling the antibiotic to align its dipole to the luminal electric field of the porin and form favorable electrostatic interactions with specific, highly-conserved charged residues. The importance of these interactions in permeation was further validated with experimental mutagenesis and whole cell accumulation assays. Overall, this study provides insights on the importance of the primary amine for antibiotic permeation into Gram-negative pathogens that could help the design of future antibiotics. We also offer a new computational approach for calculating free-energy of processes where relevant molecular conformations cannot be efficiently captured.
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Affiliation(s)
- Nandan Haloi
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Archit Kumar Vasan
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emily J Geddes
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Arjun Prasanna
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Department of Microbiology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Po-Chao Wen
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - William W Metcalf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Department of Microbiology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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12
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Prajapati JD, Kleinekathöfer U, Winterhalter M. How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics. Chem Rev 2021; 121:5158-5192. [PMID: 33724823 DOI: 10.1021/acs.chemrev.0c01213] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite tremendous successes in the field of antibiotic discovery seen in the previous century, infectious diseases have remained a leading cause of death. More specifically, pathogenic Gram-negative bacteria have become a global threat due to their extraordinary ability to acquire resistance against any clinically available antibiotic, thus urging for the discovery of novel antibacterial agents. One major challenge is to design new antibiotics molecules able to rapidly penetrate Gram-negative bacteria in order to achieve a lethal intracellular drug accumulation. Protein channels in the outer membrane are known to form an entry route for many antibiotics into bacterial cells. Up until today, there has been a lack of simple experimental techniques to measure the antibiotic uptake and the local concentration in subcellular compartments. Hence, rules for translocation directly into the various Gram-negative bacteria via the outer membrane or via channels have remained elusive, hindering the design of new or the improvement of existing antibiotics. In this review, we will discuss the recent progress, both experimentally as well as computationally, in understanding the structure-function relationship of outer-membrane channels of Gram-negative pathogens, mainly focusing on the transport of antibiotics.
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Affiliation(s)
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
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13
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Queralt-Martín M, Perini DA, Alcaraz A. Specific adsorption of trivalent cations in biological nanopores determines conductance dynamics and reverses ionic selectivity. Phys Chem Chem Phys 2021; 23:1352-1362. [PMID: 33367433 DOI: 10.1039/d0cp04486e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Adsorption processes are central to ionic transport in industrial and biological membrane systems. Multivalent cations modulate the conductive properties of nanofluidic devices through interactions with charged surfaces that depend principally on the ion charge number. Considering that ion channels are specialized valves that demand a sharp specificity in ion discrimination, we investigate the adsorption dynamics of trace amounts of different salts of trivalent cations in biological nanopores. We consider here OmpF from Escherichia coli, an archetypical protein nanopore, to probe the specificity of biological nanopores to multivalent cations. We systematically compare the effect of three trivalent electrolytes on OmpF current-voltage relationships and characterize the degree of rectification induced by each ion. We also analyze the open channel current noise to determine the existence of equilibrium/non-equilibrium mechanisms of ion adsorption and evaluate the extent of charge inversion through selectivity measurements. We show that the interaction of trivalent electrolytes with biological nanopores occurs via ion-specific adsorption yielding differential modulation of ion conduction and selectivity inversion. We also demonstrate the existence of non-equilibrium fluctuations likely related to ion-dependent trapping-detrapping processes. Our study provides fundamental information relevant to different biological and electrochemical systems where transport phenomena involve ion adsorption in charged surfaces under nanoscale confinement.
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Affiliation(s)
- María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain.
| | - D Aurora Perini
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain.
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain.
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14
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Golla VK, Prajapati JD, Kleinekathöfer U. Millisecond-Long Simulations of Antibiotics Transport through Outer Membrane Channels. J Chem Theory Comput 2021; 17:549-559. [PMID: 33378186 DOI: 10.1021/acs.jctc.0c01088] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To reach their target site inside Gram-negative bacteria, almost all antibiotics need to cross the outer membrane. Computational modeling of such processes can be numerically demanding due to the size of the systems and especially due to the timescales involved. Recently, a hybrid Brownian and molecular dynamics approach, i.e., Brownian dynamics including explicit atoms (BRODEA), has been developed and evaluated for studying the transport of monoatomic ions through membrane channels. Later on, this numerically efficient scheme has been applied to determine the free energy surfaces of the ciprofloxacin and enrofloxacin translocation through the porin OmpC using temperature-accelerated simulations. To improve the usability and accuracy of the approach, schemes to approximate the position-dependent diffusion constant of the molecule while traversing the pore had to be established. To this end, we have studied the translocation of the charged phosphonic acid antibiotic fosfomycin through the porin OmpF from Escherichia coli devising and benchmarking several diffusion models. To test the efficiency and sensitivity of these models, the effect of OmpF mutations on the permeation of fosfomycin was analyzed. Permeation events have been recorded over millisecond-long biased and unbiased simulations, from which thermodynamics and kinetics quantities of the translocation processes were determined. As a result, the use of the BRODEA approach, together with the appropriate diffusion model, was seen to accurately reproduce the findings observed in electrophysiology experiments and all-atom molecular dynamics simulations. These results suggest that the BRODEA approach can become a valuable tool for screening numerous compounds to evaluate their outer membrane permeability, a property important in the development of new antibiotics.
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Affiliation(s)
- Vinaya Kumar Golla
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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15
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Winterhalter M. Antibiotic uptake through porins located in the outer membrane of Gram-negative bacteria. Expert Opin Drug Deliv 2020; 18:449-457. [PMID: 33161750 DOI: 10.1080/17425247.2021.1847080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Introduction: Making selective inhibitors of novel Gram-negative targets is not a substantial challenge - getting them into Gram-negative bacteria to reach their lethal target is the bottleneck. Poor permeability of the antibiotic requires high concentration causing off target activity. The lack of simple experimental techniques to measure antibiotic uptake as well as the local concentration at the target site creates a particular bottleneck in understanding and in improving the antibiotic activity.Areas covered: Here we recall current approaches to quantify the uptake. For a few antibiotics with known evidence for channel-limited permeation, the flux across a single OmpF or OmpC channel has been measured. For a typical concentration gradient of 1 µM of antibiotics the uptake varies between one up to few hundred molecules per second and per channel.Expert opinion: The current research effort is on quantifying the flux for a larger list of compounds on a cellular (mass spectra, fluorescence) or at single channel level (electrophysiology). A larger dataset of single channel permeabilities under various condition will be a powerful tool for understanding and improving the activity of antibiotics.
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16
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A constricted opening in Kir channels does not impede potassium conduction. Nat Commun 2020; 11:3024. [PMID: 32541684 PMCID: PMC7295778 DOI: 10.1038/s41467-020-16842-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/28/2020] [Indexed: 01/07/2023] Open
Abstract
The canonical mechanistic model explaining potassium channel gating is of a conformational change that alternately dilates and constricts a collar-like intracellular entrance to the pore. It is based on the premise that K+ ions maintain a complete hydration shell while passing between the transmembrane cavity and cytosol, which must be accommodated. To put the canonical model to the test, we locked the conformation of a Kir K+ channel to prevent widening of the narrow collar. Unexpectedly, conduction was unimpaired in the locked channels. In parallel, we employed all-atom molecular dynamics to simulate K+ ions moving along the conduction pathway between the lower cavity and cytosol. During simulations, the constriction did not significantly widen. Instead, transient loss of some water molecules facilitated K+ permeation through the collar. The low free energy barrier to partial dehydration in the absence of conformational change indicates Kir channels are not gated by the canonical mechanism.
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17
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Breaching the Barrier: Quantifying Antibiotic Permeability across Gram-negative Bacterial Membranes. J Mol Biol 2019; 431:3531-3546. [DOI: 10.1016/j.jmb.2019.03.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/29/2019] [Accepted: 03/28/2019] [Indexed: 11/22/2022]
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18
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Schmitt C, Bafna JA, Schmid B, Klingl S, Baier S, Hemmis B, Wagner R, Winterhalter M, Voll LM. Manipulation of charge distribution in the arginine and glutamate clusters of the OmpG pore alters sugar specificity and ion selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183021. [PMID: 31306626 DOI: 10.1016/j.bbamem.2019.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 01/08/2023]
Abstract
OmpG is a general diffusion pore in the E. coli outer membrane with a molecular architecture comprising a 14-stranded β-barrel scaffold and unique structural features. In contrast to other non-specific porins, OmpG lacks a central constriction zone and has an exceptionally wide pore diameter of about 13 Å. The equatorial plane of OmpG harbors an annulus of four alternating basic and acidic patches whose function is only poorly characterized. We have investigated the role of charge distribution for ion selectivity and sugar transport with the help of OmpG variants mutated in the annulus. Substituting the glutamate residues of the annulus for histidines or alanines led to a strong reduction in cation selectivity. Replacement of the glutamates in the annulus by histidine residues also disfavored the passage of pentoses and hexoses relative to disaccharides. Our results demonstrate that despite the wide pore diameter, an annulus only consisting of two opposing basic patches confers reduced cation and monosaccharide transport compared to OmpG wild type. Furthermore, randomization of charged residues in the annulus had the potential to abolish pH-dependency of sugar transport. Our results indicate that E15, E31, R92, R111 and R211 in the annulus form electrostatic interactions with R228, E229 and D232 in loop L6 that influence pH-dependency of sugar transport.
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Affiliation(s)
- Christine Schmitt
- Division of Biochemistry and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany; Department Biology, Division of Plant Physiology, Philipps-University Marburg, D-35043 Marburg, Germany.
| | - Jayesh Arun Bafna
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719 Bremen, Germany.
| | - Benedikt Schmid
- Division of Biotechnology and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany.
| | - Stefan Klingl
- Division of Biotechnology and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany.
| | - Steffen Baier
- Division of Biochemistry and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany
| | - Birgit Hemmis
- Department of Biology and Chemistry, University of Osnabrück, D-49069 Osnabrück, Germany
| | - Richard Wagner
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719 Bremen, Germany; Department of Biology and Chemistry, University of Osnabrück, D-49069 Osnabrück, Germany.
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719 Bremen, Germany.
| | - Lars M Voll
- Division of Biochemistry and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany; Department Biology, Division of Plant Physiology, Philipps-University Marburg, D-35043 Marburg, Germany.
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19
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Vigani G, Solti ÏDM, Thomine SB, Philippar K. Essential and Detrimental - an Update on Intracellular Iron Trafficking and Homeostasis. PLANT & CELL PHYSIOLOGY 2019; 60:1420-1439. [PMID: 31093670 DOI: 10.1093/pcp/pcz091] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/06/2019] [Indexed: 05/22/2023]
Abstract
Chloroplasts, mitochondria and vacuoles represent characteristic organelles of the plant cell, with a predominant function in cellular metabolism. Chloroplasts are the site of photosynthesis and therefore basic and essential for photoautotrophic growth of plants. Mitochondria produce energy during respiration and vacuoles act as internal waste and storage compartments. Moreover, chloroplasts and mitochondria are sites for the biosynthesis of various compounds of primary and secondary metabolism. For photosynthesis and energy generation, the internal membranes of chloroplasts and mitochondria are equipped with electron transport chains. To perform proper electron transfer and several biosynthetic functions, both organelles contain transition metals and here iron is by far the most abundant. Although iron is thus essential for plant growth and development, it becomes toxic when present in excess and/or in its free, ionic form. The harmful effect of the latter is caused by the generation of oxidative stress. As a consequence, iron transport and homeostasis have to be tightly controlled during plant growth and development. In addition to the corresponding transport and homeostasis proteins, the vacuole plays an important role as an intracellular iron storage and release compartment at certain developmental stages. In this review, we will summarize current knowledge on iron transport and homeostasis in chloroplasts, mitochondria and vacuoles. In addition, we aim to integrate the physiological impact of intracellular iron homeostasis on cellular and developmental processes.
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Affiliation(s)
- Gianpiero Vigani
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, via Quarello 15/A, Turin I, Italy
| | - Ï Dï M Solti
- Department of Plant Physiology and Molecular Plant Biology, E�tv�s Lor�nd University, Budapest H, Hungary
| | - Sï Bastien Thomine
- Institut de Biologie Int�grative de la Cellule, CNRS, Avenue de la Terrasse, Gif-sur-Yvette, France
| | - Katrin Philippar
- Plant Biology, Center for Human- and Molecular Biology (ZHMB), Saarland University, Campus A2.4, Saarbr�cken D, Germany
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20
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Abstract
This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD, and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of nonbiological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well-characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Last, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.
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Affiliation(s)
- Richard M Venable
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Andreas Krämer
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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21
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Wilson J, Sarthak K, Si W, Gao L, Aksimentiev A. Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model. ACS Sens 2019; 4:634-644. [PMID: 30821441 DOI: 10.1021/acssensors.8b01375] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nanopore sensing has emerged as a versatile approach to detection and identification of biomolecules. Presently, researchers rely on experience and intuition for choosing or modifying the nanopores to detect a target analyte. The field would greatly benefit from a computational method that could relate the atomic-scale geometry of the nanopores and analytes to the blockade nanopore currents they produce. Existing computational methods are either computationally too expensive to be used routinely in experimental laboratories or not sensitive enough to account for the atomic structure of the pore and the analytes. Here, we demonstrate a robust and inexpensive computational approach-the steric exclusion model (SEM) of nanopore conductance-that is orders of magnitude more efficient than all-atom MD and yet is sensitive enough to account for the atomic structure of the nanopore and the analyte. The method combines the computational efficiency of a finite element solver with the atomic precision of a nanopore conductance map to yield unprecedented speed and accuracy of ionic current prediction. We validate our SEM approach through comparison with the current blockades computed using the all-atom molecular dynamics method for a range of proteins confined to a solid-state nanopore, biological channels embedded in a lipid bilayer membranes, and blockade currents produced by DNA homopolymers in MspA. We illustrate potential applications of SEM by computing blockade currents produced by nucleosome proteins in a solid-state nanopore, individual amino acids in MspA, and by testing the effect of point mutations on amino acid distinguishability. We expect our SEM approach to become an integral part of future development of the nanopore sensing field.
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Affiliation(s)
| | | | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing, 210096, China
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22
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Golla VK, Sans-Serramitjana E, Pothula KR, Benier L, Bafna JA, Winterhalter M, Kleinekathöfer U. Fosfomycin Permeation through the Outer Membrane Porin OmpF. Biophys J 2019; 116:258-269. [PMID: 30616836 PMCID: PMC6350074 DOI: 10.1016/j.bpj.2018.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/21/2018] [Accepted: 12/03/2018] [Indexed: 01/14/2023] Open
Abstract
Fosfomycin is a frequently prescribed drug in the treatment of acute urinary tract infections. It enters the bacterial cytoplasm and inhibits the biosynthesis of peptidoglycans by targeting the MurA enzyme. Despite extensive pharmacological studies and clinical use, the permeability of fosfomycin across the bacterial outer membrane is largely unexplored. Here, we investigate the fosfomycin permeability across the outer membrane of Gram-negative bacteria by electrophysiology experiments as well as by all-atom molecular dynamics simulations including free-energy and applied-field techniques. Notably, in an electrophysiological zero-current assay as well as in the molecular simulations, we found that fosfomycin can rapidly permeate the abundant Escherichia coli porin OmpF. Furthermore, two triple mutants in the constriction region of the porin have been investigated. The permeation rates through these mutants are slightly lower than that of the wild type but fosfomycin can still permeate. Altogether, this work unravels molecular details of fosfomycin permeation through the outer membrane porin OmpF of E. coli and moreover provides hints for understanding the translocation of phosphonic acid antibiotics through other outer membrane pores.
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Affiliation(s)
- Vinaya Kumar Golla
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | | | | | - Lorraine Benier
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Jayesh Arun Bafna
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany.
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23
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Abstract
The transport of small molecules across membranes is essential for the import of nutrients and other energy sources into the cell and, for the export of waste and other potentially harmful byproducts out of the cell. While hydrophobic molecules are permeable to membranes, ions and other small polar molecules require transport via specialized membrane transport proteins . The two major classes of membrane transport proteins are transporters and channels. With our focus here on porins-major class of non-specific diffusion channel proteins , we will highlight some recent structural biology reports and functional assays that have substantially contributed to our understanding of the mechanism that mediates uptake of small molecules, including antibiotics, across the outer membrane of Enterobacteriaceae . We will also review advances in the regulation of porin expression and porin biogenesis and discuss these pathways as new therapeutic targets.
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Affiliation(s)
- Muriel Masi
- UMR_MD1, Inserm U1261, IRBA, Membranes et Cibles Thérapeutiques, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | | | - Jean-Marie Pagès
- UMR_MD1, Inserm U1261, IRBA, Membranes et Cibles Thérapeutiques, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France.
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24
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Lopes-Rodrigues M, Zanuy D, Alemán C, Michaux C, Perpète EA. 3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes. J Biomol Struct Dyn 2018; 37:3923-3935. [DOI: 10.1080/07391102.2018.1529627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Maximilien Lopes-Rodrigues
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - David Zanuy
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Carlos Alemán
- Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, Barcelona, Spain
- Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Eric A. Perpète
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium
- Namur Institute of Structured Matter, University of Namur, Namur, Belgium
- Institute of Life-Earth-Environment, University of Namur, Namur, Belgium
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25
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Ahumada JC, Alemán C, Soto-Delgado J, Torras J. Ion–Ion Repulsions and Charge-Shielding Effects Dominate the Permeation Mechanism through the OmpF Porin Channel. J Phys Chem B 2018; 123:86-94. [DOI: 10.1021/acs.jpcb.8b09549] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juan Carlos Ahumada
- Department of Chemical Engineering (EEBE) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10−14, 08019 Barcelona, Spain
- Departamento de Química, Universidad Técnica Federico Santa María, Casilla 110-V, 2390123 Valparaíso, Chile
| | - Carlos Alemán
- Department of Chemical Engineering (EEBE) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10−14, 08019 Barcelona, Spain
| | - Jorge Soto-Delgado
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Quillota 980, 2531015 Viña del Mar, Chile
| | - Juan Torras
- Department of Chemical Engineering (EEBE) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10−14, 08019 Barcelona, Spain
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26
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Hollingsworth SA, Dror RO. Molecular Dynamics Simulation for All. Neuron 2018; 99:1129-1143. [PMID: 30236283 PMCID: PMC6209097 DOI: 10.1016/j.neuron.2018.08.011] [Citation(s) in RCA: 980] [Impact Index Per Article: 163.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/17/2018] [Accepted: 08/07/2018] [Indexed: 12/12/2022]
Abstract
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery has expanded dramatically in recent years. These simulations capture the behavior of proteins and other biomolecules in full atomic detail and at very fine temporal resolution. Major improvements in simulation speed, accuracy, and accessibility, together with the proliferation of experimental structural data, have increased the appeal of biomolecular simulation to experimentalists-a trend particularly noticeable in, although certainly not limited to, neuroscience. Simulations have proven valuable in deciphering functional mechanisms of proteins and other biomolecules, in uncovering the structural basis for disease, and in the design and optimization of small molecules, peptides, and proteins. Here we describe, in practical terms, the types of information MD simulations can provide and the ways in which they typically motivate further experimental work.
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Affiliation(s)
- Scott A Hollingsworth
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.
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27
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Lee J, Pothula KR, Kleinekathöfer U, Im W. Simulation Study of Occk5 Functional Properties in Pseudomonas aeruginosa Outer Membranes. J Phys Chem B 2018; 122:8185-8192. [DOI: 10.1021/acs.jpcb.8b07109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Joonseong Lee
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Karunakar R. Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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28
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Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins. ISME JOURNAL 2018; 12:2389-2402. [PMID: 29899515 DOI: 10.1038/s41396-018-0191-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/11/2018] [Accepted: 04/14/2018] [Indexed: 01/17/2023]
Abstract
Surface layers (S-layers) are two-dimensional, proteinaceous, porous lattices that form the outermost cell envelope component of virtually all archaea and many bacteria. Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. However, the precise function of S-layers, or the role of charged SLPs and how they relate to cellular metabolism is unknown. Nano-scale lattices affect the diffusion behavior of low-concentration solutes, even if they are significantly smaller than the pore size. Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ammonia-oxidizing archaea (AOA) as a model for S-layer geometry, and a 2D electrodiffusion reaction computational framework to simulate diffusion and consumption of the charged solute ammonium (NH4+), we find that the characteristic length scales of nanoporous S-layers elevate the concentration of NH4+ in the pseudo-periplasmic space. Our simulations suggest an evolutionary, mechanistic basis for S-layer charge and shed light on the unique ability of some AOA to oxidize ammonia in environments with nanomolar NH4+ availability, with broad implications for comparisons of ecologically distinct populations.
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Ma H, Khan A, Nangia S. Dynamics of OmpF Trimer Formation in the Bacterial Outer Membrane of Escherichia coli. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5623-5634. [PMID: 29166022 DOI: 10.1021/acs.langmuir.7b02653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The self-assembly of outer membrane protein F (OmpF) in the outer membrane of Escherichia coli Gram-negative bacteria was studied using multiscale molecular dynamics simulations. To accommodate the long time scale required for protein assembly, coarse-grained parametrization of E. coli outer membrane lipids was first developed. The OmpF monomers formed stable dimers at specific protein-protein interactions sites irrespective of the lipid membrane environment. The dimer intermediate was asymmetric but provided a template to form a symmetric trimer. Superposition analysis of the self-assembled trimer with the X-ray crystal structure of the trimer available in the protein data bank showed excellent agreement with global root-mean-square deviation of less than 2.2 Å. The free energy change associated with dimer formation was -26 ± 1 kcal mol-1, and for a dimer to bind to a monomer and to form a trimer yielded -56 ± 4 kcal mol-1. Based on thermodynamic data, an alternate path to trimer formation via interaction of two dimers is also presented.
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Affiliation(s)
- Huilin Ma
- Department of Biomedical and Chemical Engineering , Syracuse University , Syracuse , New York 13244 , United States
| | - Aliza Khan
- Department of Biomedical and Chemical Engineering , Syracuse University , Syracuse , New York 13244 , United States
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering , Syracuse University , Syracuse , New York 13244 , United States
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30
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Ghai I, Bajaj H, Arun Bafna J, El Damrany Hussein HA, Winterhalter M, Wagner R. Ampicillin permeation across OmpF, the major outer-membrane channel in Escherichia coli. J Biol Chem 2018. [PMID: 29540483 DOI: 10.1074/jbc.ra117.000705] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The outer cell wall of the Gram-negative bacteria is a crucial barrier for antibiotics to reach their target. Here, we show that the chemical stability of the widely used antibiotic ampicillin is a major factor in the permeation across OmpF to reach the target in the periplasm. Using planar lipid bilayers we investigated the interactions and permeation of OmpF with ampicillin, its basic pH-induced primary degradation product (penicilloic acid), and the chemically more stable benzylpenicillin. We found that the solute-induced ion current fluctuation is 10 times higher with penicilloic acid than with ampicillin. Furthermore, we also found that ampicillin can easily permeate through OmpF, at an ampicillin gradient of 10 μm and a conductance of Gamp ≅ 3.8 fS, with a flux rate of roughly 237 molecules/s of ampicillin at Vm = 10 mV. The structurally related benzylpenicillin yields a lower conductance of Gamp ≅ 2 fS, corresponding to a flux rate of ≈120 molecules/s. In contrast, the similar sized penicilloic acid was nearly unable to permeate through OmpF. MD calculations show that, besides their charge difference, the main differences between ampicillin and penicilloic acid are the shape of the molecules, and the strength and direction of the dipole vector. Our results show that OmpF can impose selective permeation on similar sized molecules based on their structure and their dipolar properties.
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Affiliation(s)
- Ishan Ghai
- From the Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | - Harsha Bajaj
- From the Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | - Jayesh Arun Bafna
- From the Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | | | - Mathias Winterhalter
- From the Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | - Richard Wagner
- From the Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
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31
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Shearer J, Khalid S. Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations. Sci Rep 2018; 8:1805. [PMID: 29379141 PMCID: PMC5789016 DOI: 10.1038/s41598-018-20227-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/04/2018] [Indexed: 01/09/2023] Open
Abstract
We use coarse-grain molecular simulations to investigate the structural and dynamics differences between an asymmetric and a symmetrical membrane, both containing beta barrel transmembrane proteins. We find in where the dynamics of the two leaflets differ greatly, the slowest leaflet dominates the structural effects and importance of protein-lipid interactions.
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Affiliation(s)
- Jonathan Shearer
- University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Syma Khalid
- University of Southampton, Southampton, SO17 1BJ, United Kingdom.
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32
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Prajapati JD, Solano CJF, Winterhalter M, Kleinekathöfer U. Enrofloxacin Permeation Pathways across the Porin OmpC. J Phys Chem B 2018; 122:1417-1426. [PMID: 29307192 DOI: 10.1021/acs.jpcb.7b12568] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In Gram-negative bacteria, the lack or quenching of antibiotic translocation across the outer membrane is one of the main factors for acquiring antibiotic resistance. An atomic-level comprehension of the key features governing the transport of drugs by outer-membrane protein channels would be very helpful in developing the next generation of antibiotics. In a previous study [ J. D. Prajapati et al. J. Chem. Theory Comput. 2017 , 13 , 4553 ], we characterized the diffusion pathway of a ciprofloxacin molecule through the outer membrane porin OmpC of Escherichia coli by combining metadynamics and a zero-temperature string method. Here, we evaluate the diffusion route through the OmpC porin for a similar fluoroquinolone, that is, the enrofloxacin molecule, using the previously developed protocol. As a result, it was found that the lowest-energy pathway was similar to that for ciprofloxacin; namely, a reorientation was required on the extracellular side with the carboxyl group ahead before enrofloxacin reached the constriction region. In turn, the free-energy basins for both antibiotics are located at similar positions in the space defined by selected reaction coordinates, and their affinity sites share a wide number of porin residues. However, there are some important deviations due to the chemical differences of these two drugs. On the one hand, a slower diffusion process is expected for enrofloxacin, as the permeation pathway exhibits higher overall energy barriers, mainly in the constriction region. On the other hand, enrofloxacin needs to replace some polar interactions in its affinity sites with nonpolar ones. This study demonstrates how minor chemical modifications can qualitatively affect the translocation mechanism of an antibiotic molecule.
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Affiliation(s)
- Jigneshkumar Dahyabhai Prajapati
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Carlos José Fernández Solano
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Mathias Winterhalter
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences and ‡Department of Life Sciences and Chemistry, Jacobs University Bremen , 28759 Bremen, Germany
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33
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Yao Y, Kanai Y. Free Energy Profile of NaCl in Water: First-Principles Molecular Dynamics with SCAN and ωB97X-V Exchange–Correlation Functionals. J Chem Theory Comput 2018; 14:884-893. [DOI: 10.1021/acs.jctc.7b00846] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yi Yao
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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34
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Citak F, Ghai I, Rosenkötter F, Benier L, Winterhalter M, Wagner R. Probing transport of fosfomycin through substrate specific OprO and OprP from Pseudomonas aeruginosa. Biochem Biophys Res Commun 2018; 495:1454-1460. [DOI: 10.1016/j.bbrc.2017.11.188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 11/28/2017] [Indexed: 10/18/2022]
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35
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Moritz C, Tröster A, Dellago C. Interplay of fast and slow dynamics in rare transition pathways: The disk-to-slab transition in the 2d Ising model. J Chem Phys 2017; 147:152714. [DOI: 10.1063/1.4997479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Clemens Moritz
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Andreas Tröster
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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36
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Ható Z, Valiskó M, Kristóf T, Gillespie D, Boda D. Multiscale modeling of a rectifying bipolar nanopore: explicit-water versus implicit-water simulations. Phys Chem Chem Phys 2017; 19:17816-17826. [PMID: 28657634 DOI: 10.1039/c7cp01819c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore at two modeling levels. In an all-atom model, we use explicit water to simulate ion transport directly with the molecular dynamics technique. In a reduced model, we use implicit water and apply the Local Equilibrium Monte Carlo method together with the Nernst-Planck transport equation. This hybrid method makes the fast calculation of ion transport possible at the price of lost details. We show that the implicit-water model is an appropriate representation of the explicit-water model when we look at the system at the device (i.e., input vs. output) level. The two models produce qualitatively similar behavior of the electrical current for different voltages and model parameters. Looking at the details of concentration and potential profiles, we find profound differences between the two models. These differences, however, do not influence the basic behavior of the model as a device because they do not influence the z-dependence of the concentration profiles which are the main determinants of current. These results then address an old paradox: how do reduced models, whose assumptions should break down in a nanoscale device, predict experimental data? Our simulations show that reduced models can still capture the overall device physics correctly, even though they get some important aspects of the molecular-scale physics quite wrong; reduced models work because they include the physics that is necessary from the point of view of device function. Therefore, reduced models can suffice for general device understanding and device design, but more detailed models might be needed for molecular level understanding.
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Affiliation(s)
- Zoltán Ható
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary. and Institute of Advanced Studies Köszeg (iASK), Chernel st. 14, H-9730 Köszeg, Hungary
| | - Mónika Valiskó
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary.
| | - Tamás Kristóf
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary.
| | - Dirk Gillespie
- Department of Physiology and Biophysics, Rush University Medical Center, Chicago, IL, USA
| | - Dezsö Boda
- Department of Physical Chemistry, University of Pannonia, P. O. Box 158, H-8201 Veszprém, Hungary. and Institute of Advanced Studies Köszeg (iASK), Chernel st. 14, H-9730 Köszeg, Hungary
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37
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Lee J, Patel DS, Kucharska I, Tamm LK, Im W. Refinement of OprH-LPS Interactions by Molecular Simulations. Biophys J 2017; 112:346-355. [PMID: 28122220 DOI: 10.1016/j.bpj.2016.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/27/2016] [Accepted: 12/05/2016] [Indexed: 12/16/2022] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is composed of lipopolysaccharide (LPS) in the outer leaflet and phospholipids in the inner leaflet. The outer membrane protein H (OprH) of Pseudomonas aeruginosa provides an increased stability to the OMs by directly interacting with LPS. Here we report the influence of various P. aeruginosa and, for comparison, Escherichia coli LPS environments on the physical properties of the OMs and OprH using all-atom molecular dynamics simulations. The simulations reveal that although the P. aeruginosa OMs are thinner hydrophobic bilayers than the E. coli OMs, which is expected from the difference in the acyl chain length of their lipid A, this effect is almost imperceptible around OprH due to a dynamically adjusted hydrophobic match between OprH and the OM. The structure and dynamics of the extracellular loops of OprH show distinct behaviors in different LPS environments. Including the O-antigen greatly reduces the flexibility of the OprH loops and increases the interactions between these loops and LPS. Furthermore, our study shows that the interactions between OprH and LPS mainly depend on the secondary structure of OprH and the chemical structure of LPS, resulting in distinctive patterns in different LPS environments.
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Affiliation(s)
- Joonseong Lee
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania; Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Dhilon S Patel
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania; Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania
| | - Iga Kucharska
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Lukas K Tamm
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia; Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania; Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania.
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38
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Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD, Klauda JB, Qi Y, Im W. CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem 2017; 38:1114-1124. [PMID: 27862047 PMCID: PMC5403596 DOI: 10.1002/jcc.24660] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 10/04/2016] [Accepted: 10/18/2016] [Indexed: 12/16/2022]
Abstract
CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sunhwan Jo
- Leadership Computing Facility, Argonne National Laboratory, 9700 Cass Ave, Argonne, Illinois
| | - Xi Cheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China
| | - Jumin Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Seonghoon Kim
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Sang-Jun Park
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Dhilon S Patel
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Andrew H Beaven
- Department of Chemistry, The University of Kansas, Lawrence, Kansas
| | - Kyu Il Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Huan Rui
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Soohyung Park
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Hui Sun Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Jeffrey B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland College Park, Maryland
| | - Yifei Qi
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
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39
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Richter MF, Drown BS, Riley AP, Garcia A, Shirai T, Svec RL, Hergenrother PJ. Predictive compound accumulation rules yield a broad-spectrum antibiotic. Nature 2017; 545:299-304. [PMID: 28489819 DOI: 10.1038/nature22308] [Citation(s) in RCA: 588] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 03/23/2017] [Indexed: 12/22/2022]
Abstract
Most small molecules are unable to rapidly traverse the outer membrane of Gram-negative bacteria and accumulate inside these cells, making the discovery of much-needed drugs against these pathogens challenging. Current understanding of the physicochemical properties that dictate small-molecule accumulation in Gram-negative bacteria is largely based on retrospective analyses of antibacterial agents, which suggest that polarity and molecular weight are key factors. Here we assess the ability of over 180 diverse compounds to accumulate in Escherichia coli. Computational analysis of the results reveals major differences from the retrospective studies, namely that the small molecules that are most likely to accumulate contain an amine, are amphiphilic and rigid, and have low globularity. These guidelines were then applied to convert deoxynybomycin, a natural product that is active only against Gram-positive organisms, into an antibiotic with activity against a diverse panel of multi-drug-resistant Gram-negative pathogens. We anticipate that these findings will aid in the discovery and development of antibiotics against Gram-negative bacteria.
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Affiliation(s)
- Michelle F Richter
- University of Illinois, Department of Chemistry and Institute for Genomic Biology, Urbana, Illinois 61801, USA
| | - Bryon S Drown
- University of Illinois, Department of Chemistry and Institute for Genomic Biology, Urbana, Illinois 61801, USA
| | - Andrew P Riley
- University of Illinois, Department of Chemistry and Institute for Genomic Biology, Urbana, Illinois 61801, USA
| | - Alfredo Garcia
- University of Illinois, Department of Chemistry and Institute for Genomic Biology, Urbana, Illinois 61801, USA
| | - Tomohiro Shirai
- University of Illinois, Department of Chemistry and Institute for Genomic Biology, Urbana, Illinois 61801, USA
| | - Riley L Svec
- University of Illinois, Department of Chemistry and Institute for Genomic Biology, Urbana, Illinois 61801, USA
| | - Paul J Hergenrother
- University of Illinois, Department of Chemistry and Institute for Genomic Biology, Urbana, Illinois 61801, USA
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40
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Patel DS, Qi Y, Im W. Modeling and simulation of bacterial outer membranes and interactions with membrane proteins. Curr Opin Struct Biol 2017; 43:131-140. [DOI: 10.1016/j.sbi.2017.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 12/08/2016] [Accepted: 01/11/2017] [Indexed: 10/20/2022]
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41
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Fluctuation-Driven Transport in Biological Nanopores. A 3D Poisson–Nernst–Planck Study. ENTROPY 2017. [DOI: 10.3390/e19030116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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42
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Patel DS, Re S, Wu EL, Qi Y, Klebba PE, Widmalm G, Yeom MS, Sugita Y, Im W. Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability. Biophys J 2016; 110:930-8. [PMID: 26910429 DOI: 10.1016/j.bpj.2016.01.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/13/2022] Open
Abstract
The asymmetric outer membrane of Gram-negative bacteria is formed of the inner leaflet with phospholipids and the outer leaflet with lipopolysaccharides (LPS). Outer membrane protein F (OmpF) is a trimeric porin responsible for the passive transport of small molecules across the outer membrane of Escherichia coli. Here, we report the impact of different levels of heterogeneity in LPS environments on the structure and dynamics of OmpF using all-atom molecular dynamics simulations. The simulations provide insight into the flexibility and dynamics of LPS components that are highly dependent on local environments, with lipid A being the most rigid and O-antigen being the most flexible. Increased flexibility of O-antigen polysaccharides is observed in heterogeneous LPS systems, where the adjacent O-antigen repeating units are weakly interacting and thus more dynamic, compared to homogeneous LPS systems in which LPS interacts strongly with each other with limited overall flexibility due to dense packing. The model systems were validated by comparing molecular-level details of interactions between OmpF surface residues and LPS core sugars with experimental data, establishing the importance of LPS core oligosaccharides in shielding OmpF surface epitopes recognized by monoclonal antibodies. There are LPS environmental influences on the movement of bulk ions (K(+) and Cl(-)), but the ion selectivity of OmpF is mainly affected by bulk ion concentration.
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Affiliation(s)
- Dhilon S Patel
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Suyong Re
- RIKEN Theoretical Molecular Science Laboratory, Hirosawa, Wako, Saitama, Japan; RIKEN Quantitative Biology Center (QBiC), IMDA 6F, Chuo-ku, Kobe, Hyogo Prefecture, Japan; RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo Prefecture, Japan
| | - Emilia L Wu
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Phillip E Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas
| | - Göran Widmalm
- Department of Organic Chemistry and Stockholm Center for Biomembrane Research, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information, Yuseong-gu, Daejeon, Korea
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, Hirosawa, Wako, Saitama, Japan; RIKEN Quantitative Biology Center (QBiC), IMDA 6F, Chuo-ku, Kobe, Hyogo Prefecture, Japan; RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo Prefecture, Japan
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
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43
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Xu J, Xie Y, Lu B, Zhang L. Charged Substrate and Product Together Contribute Like a Nonreactive Species to the Overall Electrostatic Steering in Diffusion-Reaction Processes. J Phys Chem B 2016; 120:8147-53. [PMID: 27070411 DOI: 10.1021/acs.jpcb.6b01393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Debye-Hückel limiting law is used to study the binding kinetics of substrate-enzyme system as well as to estimate the reaction rate of a electrostatically steered diffusion-controlled reaction process. It is based on a linearized Poisson-Boltzmann model and known for its accurate predictions in dilute solutions. However, the substrate and product particles are in nonequilibrium states and are possibly charged, and their contributions to the total electrostatic field cannot be explicitly studied in the Poisson-Boltzmann model. Hence the influences of substrate and product on reaction rate coefficient were not known. In this work, we consider all the charged species, including the charged substrate, product, and mobile salt ions in a Poisson-Nernst-Planck model, and then compare the results with previous work. The results indicate that both the charged substrate and product can significantly influence the reaction rate coefficient with different behaviors under different setups of computational conditions. It is interesting to find that when substrate and product are both considered, under an overall neutral boundary condition for all the bulk charged species, the computed reaction rate kinetics recovers a similar Debye-Hückel limiting law again. This phenomenon implies that the charged product counteracts the influence of charged substrate on reaction rate coefficient. Our analysis discloses the fact that the total charge concentration of substrate and product, though in a nonequilibrium state individually, obeys an equilibrium Boltzmann distribution, and therefore contributes as a normal charged ion species to ionic strength. This explains why the Debye-Hückel limiting law still works in a considerable range of conditions even though the effects of charged substrate and product particles are not specifically and explicitly considered in the theory.
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Affiliation(s)
- Jingjie Xu
- School of Mathematical Sciences, University of Science and Technology of China , Hefei, China
| | - Yan Xie
- State Key Laboratory of Scientific and Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing, China
| | - Benzhuo Lu
- State Key Laboratory of Scientific and Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing, China
| | - Linbo Zhang
- State Key Laboratory of Scientific and Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing, China
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Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA. Challenges in structural approaches to cell modeling. J Mol Biol 2016; 428:2943-64. [PMID: 27255863 PMCID: PMC4976022 DOI: 10.1016/j.jmb.2016.05.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 05/19/2016] [Accepted: 05/24/2016] [Indexed: 11/17/2022]
Abstract
Computational modeling is essential for structural characterization of biomolecular mechanisms across the broad spectrum of scales. Adequate understanding of biomolecular mechanisms inherently involves our ability to model them. Structural modeling of individual biomolecules and their interactions has been rapidly progressing. However, in terms of the broader picture, the focus is shifting toward larger systems, up to the level of a cell. Such modeling involves a more dynamic and realistic representation of the interactomes in vivo, in a crowded cellular environment, as well as membranes and membrane proteins, and other cellular components. Structural modeling of a cell complements computational approaches to cellular mechanisms based on differential equations, graph models, and other techniques to model biological networks, imaging data, etc. Structural modeling along with other computational and experimental approaches will provide a fundamental understanding of life at the molecular level and lead to important applications to biology and medicine. A cross section of diverse approaches presented in this review illustrates the developing shift from the structural modeling of individual molecules to that of cell biology. Studies in several related areas are covered: biological networks; automated construction of three-dimensional cell models using experimental data; modeling of protein complexes; prediction of non-specific and transient protein interactions; thermodynamic and kinetic effects of crowding; cellular membrane modeling; and modeling of chromosomes. The review presents an expert opinion on the current state-of-the-art in these various aspects of structural modeling in cellular biology, and the prospects of future developments in this emerging field.
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Affiliation(s)
- Wonpil Im
- Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66047, United States.
| | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, United States.
| | - Arthur Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, United States.
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, United States.
| | - Ilya A Vakser
- Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66047, United States.
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Park S, Beaven AH, Klauda JB, Im W. How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets? J Chem Theory Comput 2016; 11:3466-77. [PMID: 26575780 PMCID: PMC4685941 DOI: 10.1021/acs.jctc.5b00232] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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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
impacts 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 lower leaflet from no mismatch to a 25%
reduction compared to that 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 upper leaflet
becomes more ordered, and the lower leaflet becomes less ordered.
The mismatch impacts on various bilayer properties are mild up to
5–10% mismatch, and bilayers with fully saturated chains appear
to be more prone to these impacts than those with unsaturated tails.
The nonvanishing 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. On the basis of 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).
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Affiliation(s)
| | | | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland , College Park, Maryland 20742, United States
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Affiliation(s)
- Baron Peters
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106;
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47
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Solano CJF, Pothula KR, Prajapati JD, De Biase PM, Noskov SY, Kleinekathöfer U. BROMOCEA Code: An Improved Grand Canonical Monte Carlo/Brownian Dynamics Algorithm Including Explicit Atoms. J Chem Theory Comput 2016; 12:2401-17. [DOI: 10.1021/acs.jctc.5b01196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos J. F. Solano
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Karunakar R. Pothula
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Jigneshkumar D. Prajapati
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Pablo M. De Biase
- Centre
for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ulrich Kleinekathöfer
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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48
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Why do the outer membrane proteins OmpF from E. coli and OprP from P. aeruginosa prefer trimers? Simulation studies. J Mol Graph Model 2016; 65:1-7. [DOI: 10.1016/j.jmgm.2016.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/18/2015] [Accepted: 02/06/2016] [Indexed: 01/27/2023]
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49
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Pavlova A, Hwang H, Lundquist K, Balusek C, Gumbart JC. Living on the edge: Simulations of bacterial outer-membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1753-9. [PMID: 26826270 DOI: 10.1016/j.bbamem.2016.01.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 01/06/2023]
Abstract
Gram-negative bacteria are distinguished in part by a second, outer membrane surrounding them. This membrane is distinct from others, possessing an outer leaflet composed not of typical phospholipids but rather large, highly charged molecules known as lipopolysaccharides. Therefore, modeling the structure and dynamics of proteins embedded in the outer membrane requires careful consideration of their native environment. In this review, we examine how simulations of such outer-membrane proteins have evolved over the last two decades, culminating most recently in detailed, highly accurate atomistic models of the outer membrane. We also draw attention to how the simulations have coupled with experiments to produce novel insights unattainable through a single approach. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Karl Lundquist
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Curtis Balusek
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States.
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50
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Harris BJ, Cheng X, Frymier P. Structure and Function of Photosystem I–[FeFe] Hydrogenase Protein Fusions: An All-Atom Molecular Dynamics Study. J Phys Chem B 2016; 120:599-609. [DOI: 10.1021/acs.jpcb.5b07812] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bradley J. Harris
- College
of Engineering and Computer Science, University of Tennessee, Chattanooga, Tennessee 37403, United States
| | - Xiaolin Cheng
- Center for
Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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