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Musin KG. ANTIMICROBIAL PEPTIDES — A POTENTIAL REPLACEMENT FOR TRADITIONAL ANTIBIOTICS. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2018. [DOI: 10.15789/2220-7619-2018-3-295-308] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Antimicrobial peptides are a heterogeneous group of molecules involved in the innate and acquired immune response of various organisms, ranging from prokaryotes to mammals, including humans. They consist of 12–50 amino acid residues; have different physico-chemical and biological properties. The most common feature is their ability to destroy the prokaryotic cell membrane, which causes cell death. In the action, the molecules of antimicrobial peptides are embedded in the target bacteriological cells and change their conformation, forming structures in some cases resembling channels. Some other molecules of antimicrobial peptides can cover the surface of a bacteriological cell and form a carpet, when they reach a critical mass they act like detergents. In addition, being positively charged molecules of such peptides, penetrating through the membranes of parasitic and bacteriological cells, bind to polyanionic RNA and DNA molecules. Among the benefits of antimicrobial peptides is their high metabolic activity, low probability of occurrence of addictions and side effects. In addition, bacteriological pathogens that previously did not have resistance to any antimicrobial peptide are difficult to develop a strategy to control them. In this connection, these peptides are the most promising moleculessubstitutes for traditional antibiotics. The article discusses the approaches and strategies of therapeutic use, the studies of antimicrobial peptides identified in recent years; The most frequently encountered mechanisms of interaction of antimicrobial peptides and a bacteriological membrane are described, the physicochemical properties of peptide molecules are described; the results of studies on the detection of resistance of some strains of bacteria to antimicrobial peptides and antibiotics in general are summarized.
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52
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Mondal J. A brief appraisal of computational modeling of antimicrobial peptides’ activity. Drug Dev Res 2018; 80:28-32. [DOI: 10.1002/ddr.21472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/16/2018] [Accepted: 08/27/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences; Hyderabad 500107 India
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53
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Antibacterial activity and its mechanisms of a recombinant Funme peptide against Cronobacter sakazakii in powdered infant formula. Food Res Int 2018; 116:258-265. [PMID: 30716944 DOI: 10.1016/j.foodres.2018.08.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/23/2018] [Accepted: 08/11/2018] [Indexed: 12/30/2022]
Abstract
Cronobacter sakazakii (Cs) is a typical foodborne bacterium that infect powdered infant formula (PIF) worldwide. In this study, a recombinant antimicrobial peptide, branded as Funme peptide (FP)was applied to protect PIF from Cs contamination. The result from the antimicrobial activity assay showed that the minimum inhibitory concentration (MIC) of BMAP-27 peptide, FP and Ampicillin against Cs were 250.0, 125.0 and 15.6 μg/mL, respectively, indicating FP possessed higher MIC than that of Ampicillin, and lower MIC than that of BMAP-27. The minimum biofilm eradication concentration (MBEC) assay showed that FP at 2 × MIC (250.0 μg/mL) could completely eradicated Cs biofilms. The antibacterial activity of FP might be due to the increasing permeability and the release of cytoplasmic β-galactosidase of Cs. The results acquired from transmission electron microscopy and scanning electron microscopy indicated that FP induced the disruption and dysfunction of cell walls and membranes. Moreover, safety assay showed that FP had low cytotoxicity to human erythrocytes. The present study investigated the antibacterial effects and mechanisms of FP against Cs, providing promising evidence to apply this novel antimicrobial agent against Cs contamination in foods and food processing facilities.
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54
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Wen PC, Mahinthichaichan P, Trebesch N, Jiang T, Zhao Z, Shinn E, Wang Y, Shekhar M, Kapoor K, Chan CK, Tajkhorshid E. Microscopic view of lipids and their diverse biological functions. Curr Opin Struct Biol 2018; 51:177-186. [PMID: 30048836 DOI: 10.1016/j.sbi.2018.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/27/2018] [Accepted: 07/05/2018] [Indexed: 12/21/2022]
Abstract
Biological membranes and their diverse lipid constituents play key roles in a broad spectrum of cellular and physiological processes. Characterization of membrane-associated phenomena at a microscopic level is therefore essential to our fundamental understanding of such processes. Due to the semi-fluid and dynamic nature of lipid bilayers, and their complex compositions, detailed characterization of biological membranes at an atomic scale has been refractory to experimental approaches. Computational modeling and simulation offer a highly complementary toolset with sufficient spatial and temporal resolutions to fill this gap. Here, we review recent molecular dynamics studies focusing on the diversity of lipid composition of biological membranes, or aiming at the characterization of lipid-protein interaction, with the overall goal of dissecting how lipids impact biological roles of the cellular membranes.
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Affiliation(s)
- Po-Chao Wen
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Noah Trebesch
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhiyu Zhao
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Eric Shinn
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuhang Wang
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mrinal Shekhar
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Karan Kapoor
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chun Kit Chan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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55
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Lai PK, Kaznessis YN. Insights into Membrane Translocation of Protegrin Antimicrobial Peptides by Multistep Molecular Dynamics Simulations. ACS OMEGA 2018; 3:6056-6065. [PMID: 29978143 PMCID: PMC6026836 DOI: 10.1021/acsomega.8b00483] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Protegrin-1 (PG-1) is a cationic arginine-rich antimicrobial peptide. It is widely accepted that PG-1 induces membrane disruption by forming pores that lead to cell death. However, the insertion mechanism for these highly cationic peptides into the hydrophobic membrane environment is still poorly understood at the molecular scale. It has previously been determined that the association of arginine guanidinium and lipid phosphate groups results in strong bidentate bonds that stabilize peptide-lipid complexes. It has also been suggested that arginine residues are able to drag phosphate groups as they insert inside the membrane to form a toroidal pore. However, whether bidentate bonds play a significant role in inducing a pore formation remains unclear. To investigate the role of bidentate complexes in PG-1 translocation, we conducted molecular dynamics simulations. Two computational electroporation methods were implemented to examine the translocation process. We found that PG-1 could insert into the membrane, provided the external electric potential is large enough to first induce a water column or a pore within the lipid bilayer membrane. We also found that the highly charged PG-1 is capable in itself of inducing molecular electroporation. Substitution of arginines with charge-equivalent lysines showed a markedly reduced tendency for insertion. This indicates that the guanidinium group likely facilitates PG-1 translocation. Potential of mean force calculations suggests that peptide insertion inside the hydrophobic environment of the membrane core is not favored. We found that formation of a water column or a pore might be a prerequisite for PG-1 translocation. We also found that PG-1 can stabilize the pore after insertion. We suggest that PG-1 could be a pore inducer and stabilizer. This work sheds some light on PG-1 translocation mechanisms at the molecular level. Methods presented in this study may be extended to other arginine-rich antimicrobial and cell-penetrating peptides.
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56
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Cipcigan F, Carrieri AP, Pyzer-Knapp EO, Krishna R, Hsiao YW, Winn M, Ryadnov MG, Edge C, Martyna G, Crain J. Accelerating molecular discovery through data and physical sciences: Applications to peptide-membrane interactions. J Chem Phys 2018; 148:241744. [DOI: 10.1063/1.5027261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Flaviu Cipcigan
- IBM Research UK, Hartree Centre, Daresbury WA4 4AD, United Kingdom
| | | | | | - Ritesh Krishna
- IBM Research UK, Hartree Centre, Daresbury WA4 4AD, United Kingdom
| | - Ya-Wen Hsiao
- STFC Daresbury Laboratories, Daresbury WA4 4AD, United Kingdom
| | - Martyn Winn
- STFC Daresbury Laboratories, Daresbury WA4 4AD, United Kingdom
| | - Maxim G. Ryadnov
- National Physical Laboratory, Hampton Road, Teddington, United Kingdom
| | - Colin Edge
- GSK Medicines Research Centre, Stevenage SG1 2NY, United Kingdom
| | - Glenn Martyna
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Jason Crain
- IBM Research UK, Hartree Centre, Daresbury WA4 4AD, United Kingdom
- Maxwell Centre, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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57
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Nelson N, Schwartz DK. Single-Molecule Resolution of Antimicrobial Peptide Interactions with Supported Lipid A Bilayers. Biophys J 2018; 114:2606-2616. [PMID: 29874611 PMCID: PMC6129183 DOI: 10.1016/j.bpj.2018.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 03/16/2018] [Accepted: 04/12/2018] [Indexed: 01/12/2023] Open
Abstract
The molecular interactions between antimicrobial peptides (AMPs) and lipid A-containing supported lipid bilayers were probed using single-molecule total internal reflection fluorescence microscopy. Hybrid supported lipid bilayers with lipid A outer leaflets and phospholipid (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)) inner leaflets were prepared and characterized, and the spatiotemporal trajectories of individual fluorescently labeled LL37 and Melittin AMPs were determined as they interacted with the bilayer surfaces comprising either monophosphoryl or diphosphoryl lipid A (from Escherichia coli) to determine the impact of electrostatic interactions. Large numbers of trajectories were obtained and analyzed to obtain the distributions of surface residence times and the statistics of the spatial trajectories. Interestingly, the AMP species were sensitive to subtle differences in the charge of the lipid, with both peptides diffusing more slowly and residing longer on the diphosphoryl lipid A. Furthermore, the single-molecule dynamics indicated a qualitative difference between the behavior of AMPs on hybrid Lipid A bilayers and on those composed entirely of DOPE. Whereas AMPs interacting with a DOPE bilayer exhibited two-dimensional Brownian diffusion with a diffusion coefficient of ∼1.7 μm2/s, AMPs adsorbed to the lipid A surface exhibited much slower apparent diffusion (on the order of ∼0.1 μm2/s) and executed intermittent trajectories that alternated between two-dimensional Brownian diffusion and desorption-mediated three-dimensional flights. Overall, these findings suggested that bilayers with lipid A in the outer leaflet, as it is in bacterial outer membranes, are valuable model systems for the study of the initial stage of AMP-bacterium interactions. Furthermore, single-molecule dynamics was sensitive to subtle differences in electrostatic interactions between cationic AMPs and monovalent or divalent anionic lipid A moieties.
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Affiliation(s)
- Nathaniel Nelson
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado.
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58
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Tse CH, Comer J, Wang Y, Chipot C. Link between Membrane Composition and Permeability to Drugs. J Chem Theory Comput 2018; 14:2895-2909. [PMID: 29771515 DOI: 10.1021/acs.jctc.8b00272] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Prediction of membrane permeability to small molecules represents an important aspect of drug discovery. First-principles calculations of this quantity require an accurate description of both the thermodynamics and kinetics that underlie translocation of the permeant across the lipid bilayer. In this contribution, the membrane permeability to three drugs, or drug-like molecules, namely, 9-anthroic acid (ANA), 2',3'-dideoxyadenosine (DDA), and hydrocortisone (HYL), are estimated in a pure 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) and in a POPC:cholesterol (2:1) mixture. On the basis of independent 2-5-μs free-energy calculations combined with a time-fractional Smoluchowski determination of the diffusivity, the estimated membrane permeabilities to these chemically diverse permeants fall within an order of magnitude from the experimental values obtained in egg-lecithin bilayers, with the exception of HYL in pure POPC. This exception is particularly interesting because the calculated permeability of the sterol-rich bilayer to HYL, in close agreement with the experimental value, is about 600 times lower than that of the pure POPC bilayer to HYL. In contrast, the permeabilities to ANA and DDA differ by less than a factor of 10 between the pure POPC and POPC:cholesterol bilayers. The unusual behavior of HYL, a large, amphiphilic compound, may be linked with the longer range perturbation of the lipid bilayer it induces, compared to ANA and DDA, suggestive of a possibly different translocation mechanism. We find that the tendency of lower permeabilities of the POPC:cholesterol bilayer relative to those of the pure POPC one is a consequence of increased free-energy barriers. Beyond reporting accurate estimates of the membrane permeability, the present contribution also demonstrates that rigorous free-energy calculations and a fractional-diffusion model are key in revealing the molecular phenomena linking the composition of a membrane to its permeability to drugs.
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Affiliation(s)
- Chi Hang Tse
- Shenzhen Research Institute , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China.,Department of Physics , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
| | - Jeffrey Comer
- Institute of Computational Comparative Medicine and Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology , Kansas State University , Manhattan , Kansas 66506 , United States
| | - Yi Wang
- Shenzhen Research Institute , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China.,Department of Physics , The Chinese University of Hong Kong , Shatin , Hong Kong SAR , China
| | - Christophe Chipot
- Laboratoire International Associé Centre, National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7019 , Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex , France.,Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , 405 North Mathews Avenue , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
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59
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Wan M, Gao L, Fang W. Implicit-solvent dissipative particle dynamics force field based on a four-to-one coarse-grained mapping scheme. PLoS One 2018; 13:e0198049. [PMID: 29795682 PMCID: PMC5967728 DOI: 10.1371/journal.pone.0198049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/12/2018] [Indexed: 11/30/2022] Open
Abstract
A new set of efficient solvent-free dissipative particle dynamics (DPD) force fields was developed for phospholipids and peptides. To enhance transferability, this model maps around four heavy atoms and their connected hydrogen atoms into a coarse-grained elementary bead based on functional group. The effective hybrid potential between any pair of beads is composed of a short-range repulsive soft-core potential that directly adopts the form of an explicit-solvent DPD model and a long-range attractive hydrophobic potential. The parameters of the attractive potentials for lipid molecules were obtained by fitting the explicit-solvent DPD simulation of one bead of any type in a water box, then finely tuning it until the bilayer membrane properties obtained in the explicit-solvent model were matched. These parameters were further extended to amino acids according to bead type. The structural and elastic properties of bilayer membranes, free energy profiles for a lipid flip-flop and amino acid analogues translocating across the membrane, and membrane pore formation induced by antimicrobial peptides obtained from this solvent-free DPD force field considerably agreed with the explicit-solvent DPD results. Importantly, the efficiency of this method is guaranteed to accelerate the assembly of vesicles composed of several thousand lipids by up to 50-fold, rendering the experimental liposome dynamics as well as membrane-peptide interactions feasible at accessible computational expense.
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Affiliation(s)
- Mingwei Wan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Lianghui Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
- * E-mail:
| | - Weihai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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60
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Hsiao YW, Hedström M, Losasso V, Metz S, Crain J, Winn M. Cooperative Modes of Action of Antimicrobial Peptides Characterized with Atomistic Simulations: A Study on Cecropin B. J Phys Chem B 2018; 122:5908-5921. [PMID: 29737852 DOI: 10.1021/acs.jpcb.8b01957] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Antimicrobial peptides (AMPs) are widely occurring host defense agents of interest as one route for addressing the growing problem of multidrug-resistant pathogens. Understanding the mechanisms behind their antipathogen activity is instrumental in designing new AMPs. Herein, we present an all-atom molecular dynamics and free energy study on cecropin B (CB) and its constituent domains. We find a cooperative mechanism in which CB inserts into an anionic model membrane with its amphipathic N-terminal segment, supported by the hydrophobic C-terminal segment of a second peptide. The two peptides interact via a Glu···Lys salt bridge and together sustain a pore in the membrane. Using a modified membrane composition, we demonstrate that when the lower leaflet is overall neutral, insertion of the cationic segment is retarded and thus this mode of action is membrane specific. The observed mode of action utilizes a flexible hinge, a common structural motif among AMPs, which allows CB to insert into the membrane using either or both termini. Data from both unbiased trajectories and enhanced sampling simulations indicate that a requirement for CB to be an effective AMP is the interaction of its hydrophobic C-terminal segment with the membrane. Simulations of these segments in isolation reveal their aggregation in the membrane and a different mechanism of supporting pore formation. Together, our results show the complex interaction of different structural motifs of AMPs and, in particular, a potential role for electronegative side chains in an overall cationic AMP.
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Affiliation(s)
- Ya-Wen Hsiao
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , U.K
| | - Magnus Hedström
- Clay Technology AB , Ideon Science Park , SE-223 70 Lund , Sweden
| | - Valeria Losasso
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , U.K
| | - Sebastian Metz
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , U.K
| | - Jason Crain
- IBM Research , Hartree Centre , Daresbury WA4 4AD , U.K
| | - Martyn Winn
- Scientific Computing Department , STFC Daresbury Laboratory , Keckwick Lane, Daresbury , Warrington WA4 4AD , U.K
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61
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Ulmschneider JP, Ulmschneider MB. Molecular Dynamics Simulations Are Redefining Our View of Peptides Interacting with Biological Membranes. Acc Chem Res 2018; 51:1106-1116. [PMID: 29667836 DOI: 10.1021/acs.accounts.7b00613] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Ever since the first molecular mechanics computer simulations of biological molecules became possible, there has been the dream to study all complex biological phenomena in silico, simply bypassing the enormous experimental challenges and their associated costs. For this, two inherent requirements need to be met: First, the time scales achievable in simulations must reach up to the millisecond range and even longer. Second, the computational model must accurately reproduce what is measured experimentally. Despite some recent successes, the general consensus in the field to date has been that neither of these conditions have yet been met and that the dream will be realized, if at all, only in the distant future. In this Account, we show that this view is wrong; instead, we are actually in the middle of the in silico molecular dynamics (MD) revolution, which is reshaping how we think about protein function. The example explored in this Account is a recent advance in the field of membrane-active peptides (MAPs). MD simulations have succeeded in accurately capturing the process of peptide binding, folding, and partitioning into lipid bilayers as well as revealing how channels form spontaneously from polypeptide fragments and conduct ionic and other cargo across membranes, all at atomic resolution. These game-changing advances have been made possible by a combination of steadily advancing computational power, more efficient algorithms and techniques, clever accelerated sampling schemes, and thorough experimental verifications. The great advantage of MD is the spatial and temporal resolution, directly providing a molecular movie of a protein undergoing folding and cycling through a functional process. This is especially important for proteins with transitory functional states, such as pore-forming MAPs. Recent successes are demonstrated here for the large class of antimicrobial peptides (AMPs). These short peptides are an essential part of the nonadaptive immune system for many organisms, ubiquitous in nature, and of particular interest to the pharmaceutical industry in the age of rising bacterial resistance to conventional antibiotic treatments. Unlike integral membrane proteins, AMPs are sufficiently small to allow converged sampling with the unbiased high-temperature sampling methodology outlined here and are relatively easy to handle experimentally. At the same time, AMPs exhibit a wealth of complex and poorly understood interactions with lipid bilayers, which allow not only tuning and validation of the simulation methodology but also advancement of our knowledge of protein-lipid interactions at a fundamental level. Space constraints limit our discussion to AMPs, but the MD methodologies outlined here can be applied to all phenomena involving peptides in membranes, including cell-penetrating peptides, signaling peptides, viral channel forming peptides, and fusion peptides, as well as ab initio membrane protein folding and assembly. For these systems, the promise of MD simulations to predict the structure of channels and to provide complete-atomic-detail trajectories of the mechanistic processes underlying their biological functions appears to rapidly become a reality. The current challenge is to design joint experimental and computational benchmarks to verify and tune MD force fields. With this, MD will finally fulfill its promise to become an inexpensive, powerful, and easy-to-use tool providing atomic-detail insights to researchers as part of their investigations into membrane biophysics and beyond.
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Affiliation(s)
- Jakob P. Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
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62
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Lipkin R, Lazaridis T. Computational studies of peptide-induced membrane pore formation. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630158 DOI: 10.1098/rstb.2016.0219] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Richard Lipkin
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Graduate Program in Chemistry, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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63
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Dong X, Qiao Q, Qian Z, Wei G. Recent computational studies of membrane interaction and disruption of human islet amyloid polypeptide: Monomers, oligomers and protofibrils. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018. [PMID: 29530482 DOI: 10.1016/j.bbamem.2018.03.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The amyloid deposits of human islet amyloid polypeptide (hIAPP) are found in type 2 diabetes patients. hIAPP monomer is intrinsically disordered in solution, whereas it can form amyloid fibrils both in vivo and in vitro. Extensive evidence suggests that hIAPP causes the disruption of cellular membrane, and further induces cytotoxicity and the death of islet β-cells in pancreas. The presence of membrane also accelerates the hIAPP fibril formation. hIAPP oligomers and protofibrils in the early stage of aggregation were reported to be the most cytotoxic, disrupting the membrane integrity and giving rise to the pathological process. The detailed molecular mechanisms of hIAPP-membrane interactions and membrane disruption are complex and remain mostly unknown. Here in this review, we focus on recent computational studies that investigated the interactions of full length and fragmentary hIAPP monomers, oligomers and protofibrils with anionic, zwitterionic and mixed anionic-zwitterionic lipid bilayers. We mainly discuss the binding orientation of monomers at membrane surface, the conformational ensemble and the oligomerization of hIAPP inside membranes, the effect of lipid composition on hIAPP oligomers/protofibrils-membrane interactions, and the hIAPP-induced membrane perturbation. This review provides mechanistic insights into the interactions between hIAPP and lipid bilayers with different lipid composition at an atomistic level, which is helpful to understand the hIAPP cytotoxicity mediated by membrane. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, China
| | - Qin Qiao
- Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Shanghai 200032, China.
| | - Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, China.
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64
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Deplazes E. Molecular simulations of venom peptide-membrane interactions: Progress and challenges. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Evelyne Deplazes
- School of Pharmacy and Biomedical Sciences; Curtin Health Innovation Research Institute, Curtin Institute for Computation, Curtin University; Bentley, Perth WA 6102 Australia
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65
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Pokhrel N, Maibaum L. Free Energy Calculations of Membrane Permeation: Challenges Due to Strong Headgroup-Solute Interactions. J Chem Theory Comput 2018; 14:1762-1771. [PMID: 29406707 DOI: 10.1021/acs.jctc.7b01159] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased molecular dynamics computer simulations to calculate and compare the free energy profiles of translocation of several small molecules across 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC) lipid bilayers as a first step toward determining the most efficient method for free energy calculations. We study the translocation of arginine, a sodium ion, alanine, and a single water molecule using the metadynamics, umbrella sampling, and replica exchange umbrella sampling techniques. Within the fixed lengths of our simulations, we find that all methods produce similar results for charge-neutral permeants, but not for polar or positively charged molecules. We identify the long relaxation time scale of electrostatic interactions between lipid headgroups and the solute to be the principal cause of this difference and show that this slow process can lead to an erroneous dependence of computed free energy profiles on the initial system configuration. We demonstrate the use of committor analysis to validate the proper sampling of the presumed transition state, which in our simulations is achieved only in replica exchange calculations. On the basis of these results we provide some useful guidance to perform and evaluate free energy calculations of membrane permeation.
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Affiliation(s)
- Nihit Pokhrel
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Lutz Maibaum
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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66
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Pore formation and the key factors in antibacterial activity of aurein 1.2 and LLAA inside lipid bilayers, a molecular dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:347-356. [DOI: 10.1016/j.bbamem.2017.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 11/20/2022]
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67
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Charged Antimicrobial Peptides Can Translocate across Membranes without Forming Channel-like Pores. Biophys J 2017; 113:73-81. [PMID: 28700927 DOI: 10.1016/j.bpj.2017.04.056] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/18/2017] [Accepted: 04/26/2017] [Indexed: 01/08/2023] Open
Abstract
How can highly charged, cationic antimicrobial peptides (AMPs) translocate across hydrophobic lipid bilayers despite the prohibitive energetic penalty to do so? A common explanation has been the formation of peptide-lined channels. However, for most AMPs, no structures of membrane pores have been found despite clear evidence of membrane leakage and antimicrobial activity. The study here suggests an alternative and simple reason: for the AMP PGLa from Xenopus laevis (charge +5), such pores are not needed to explain both leakage and peptide translocation. Elevated-temperature multimicrosecond equilibrium simulations at all-atomistic level reveal that peptides spontaneously translocate across the membrane individually on a timescale of tens of microseconds, without forming pores. Both surface-bound peptides and lipids assist in the one-by-one translocation of the charged side chains. Single peptides can remain in a transmembrane orientation for many microseconds, snorkeling some charged residues to one interface and some to the opposite, but without inducing a water channel. Instead of stable pores, short-lived water bridges occur when two or three peptides connect at their termini, allowing both ion translocation and lipid flip-flop via a brushlike mechanism usually involving the C terminus of one peptide. The results here suggest that for some specific antimicrobial and other membrane active peptides, pore formation may not have to be invoked at all to explain peptide translocation and membrane permeabilization, which may explain why no channel structures for them have been determined experimentally.
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68
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Triana-Vidal LE, Castro MS, Pires Júnior OR, Álvares ACM, de Freitas SM, Fontes W, Vargas JAG, Zúñiga-Baos JA, Correia Batista IDF, Grellier P, Charneau S. Dendropsophin 1, a novel antimicrobial peptide from the skin secretion of the endemic Colombian frog Dendropsophus columbianus. Nat Prod Res 2017; 32:1383-1389. [DOI: 10.1080/14786419.2017.1346646] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Luz Elena Triana-Vidal
- Laboratório de Bioquímica e Química de proteínas, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Mariana Souza Castro
- Laboratório de Bioquímica e Química de proteínas, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
- Laboratório de Toxinologia, Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Osmindo Rodrigues Pires Júnior
- Laboratório de Toxinologia, Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Alice Cunha Morales Álvares
- Laboratório de Biofísica, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Sonia Maria de Freitas
- Laboratório de Biofísica, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Wagner Fontes
- Laboratório de Bioquímica e Química de proteínas, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Jimmy Alexander Guerrero Vargas
- Departamento de Biología, Universidad del Cauca, Grupo de Investigaciones Herpetológicas y Toxinológicas (GIHT), Popayán, Colombia
| | - Jorge Alberto Zúñiga-Baos
- Departamento de Biología, Universidad del Cauca, Grupo de Investigaciones Herpetológicas y Toxinológicas (GIHT), Popayán, Colombia
| | | | - Philippe Grellier
- Muséum National d’Histoire Naturelle,UMR 7245 CNRS – Molécules de Communication et Adaptation des Micro-organismes, Paris, France
| | - Sébastien Charneau
- Laboratório de Bioquímica e Química de proteínas, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
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69
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Rice A, Wereszczynski J. Probing the disparate effects of arginine and lysine residues on antimicrobial peptide/bilayer association. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1941-1950. [PMID: 28583830 DOI: 10.1016/j.bbamem.2017.06.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/08/2017] [Accepted: 06/01/2017] [Indexed: 10/19/2022]
Abstract
Antimicrobial peptides (AMPs) are key components of the innate immune response and represent promising templates for the development of broad-spectrum alternatives to conventional antibiotics. Most AMPs are short, cationic peptides that interact more strongly with negatively charged prokaryotic membranes than net neutral eukaryotic ones. Both AMPs and synthetic analogues with arginine-like side chains are more active against bacteria than those with lysine-like amine groups, though the atomistic mechanism for this increase in potency remains unclear. To examine this, we conducted comparative molecular dynamics simulations of a model negatively-charged membrane system interacting with two mutants of the AMP KR-12: one with lysine residues mutated to arginines (R-KR12) and one with arginine residues mutated to lysine (K-KR12). Simulations show that both partition analogously to the bilayer and display similar preferences for hydrogen bonding with the anionic POPGs. However, R-KR12 binds stronger to the bilayer than K-KR12 and forms significantly more hydrogen bonds, leading to considerably longer interaction times. Additional simulations with methylated R-KR12 and charge-modified K-KR12 mutants show that the extensive interaction seen in the R-KR12 system is partly due to arginine's strong atomic charge distribution, rather than being purely an effect of the greater number of hydrogen bond donors. Finally, free energy simulations reveal that both peptides are disordered in solution but form an amphipathic α-helix when inserted into the bilayer headgroup region. Overall, these results highlight the role of charge and hydrogen bond strength in peptide bilayer insertion, and offer potential insights for designing more potent analogues in the future.
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Affiliation(s)
- A Rice
- Department of Physics and The Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, USA
| | - J Wereszczynski
- Department of Physics and The Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois 60616, USA.
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70
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Edler E, Schulze E, Stein M. Membrane localization and dynamics of geranylgeranylated Rab5 hypervariable region. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1335-1349. [PMID: 28455099 DOI: 10.1016/j.bbamem.2017.04.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/18/2017] [Accepted: 04/23/2017] [Indexed: 12/11/2022]
Abstract
The small GTPase Rab5 is a key regulator of endosomal trafficking processes and a marker for the early endosome. The C-terminal hypervariable region (HVR) of Rab5 is post-translationally modified at residues Cys212 and Cys213 to accommodate two geranylgeranyl anchors (C20 carbon chain length) in order to associate Rab5 with the membrane. The structural role of the HVR regarding protein-early endosome membrane recruitment is not resolved due to its high degree of flexibility and lack of crystallographic information. Here, full-atomistic and coarse-grained molecular dynamics simulations of the truncated Rab5 HVR206-215 in three model membranes of increasing complexity (pure phospholipid bilayer, ternary membrane with cholesterol, six-component early endosome) were performed. Specific electrostatic interactions between the HVR206-215 Arg209 residue and the phosphate group of the inositol ring of PI(3)P were detected. This shows that PI(3)P acts as a first contact site of protein recruitment to the early endosome. The free energy change of HVR206-215 extraction from the bilayer was largest for the physiological negatively charged membrane. 5μs coarse-grained simulations revealed an active recruitment of PI(3)P to the HVR206-215 supporting the formation of Rab5- and PI(3)P enriched signaling platforms.
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Affiliation(s)
- Eileen Edler
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Eric Schulze
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; International Max Planck Research School (IMPRS) for Advanced Methods in Process and Systems Engineering, Magdeburg, Germany
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
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71
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Hub JS, Awasthi N. Probing a Continuous Polar Defect: A Reaction Coordinate for Pore Formation in Lipid Membranes. J Chem Theory Comput 2017; 13:2352-2366. [PMID: 28376619 DOI: 10.1021/acs.jctc.7b00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Various biophysical processes involve the formation of aqueous pores over lipid membranes, including processes of membrane fusion, antimicrobial peptide activity, lipid flip-flop, and membrane permeation. Reliable and efficient free-energy calculations of pore formation using molecular dynamics simulations remained challenging due to the lack of good reaction coordinates (RCs) for pore formation. We present a new RC for pore formation that probes the formation and rupture of a continuous polar defect over the membrane. Potential of mean force (PMF) calculations along the new RC rapidly converge and exhibit no hysteresis between pore-opening and pore-closing pathways, in contrast to calculations based on previous RCs. We show that restraints along the new RC may restrain the system tightly to the transition state of pore formation, rationalizing the absence of hysteresis. We observe that the PMF of pore formation in a tension-free membrane of dimyristoylphosphatidylcholine (DMPC) reveals a free-energy barrier for pore nucleation, confirming a long-hypothesized metastable prepore state. We test the influence of the lipid force field, the cutoff distance used for Lennard-Jones interactions, and the lateral membrane size on the free energies of pore formation. In contrast to PMF calculations based on previous RCs, we find that such parameters have a relatively small influence on the free energies of pore nucleation. However, the metastability of the open pore in DMPC may depend on such parameters. The RC has been implemented into an extension of the GROMACS simulation software. The new RC allows for reliable and computationally efficient free-energy calculations of pore formation in lipid membranes.
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Affiliation(s)
- Jochen S Hub
- Institute for Microbiology and Genetics, University of Göttingen , Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
| | - Neha Awasthi
- Institute for Microbiology and Genetics, University of Göttingen , Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
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72
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Ma H, Cummins DD, Edelstein NB, Gomez J, Khan A, Llewellyn MD, Picudella T, Willsey SR, Nangia S. Modeling Diversity in Structures of Bacterial Outer Membrane Lipids. J Chem Theory Comput 2017; 13:811-824. [DOI: 10.1021/acs.jctc.6b00856] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Huilin Ma
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Daniel D. Cummins
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Natalie Brooke Edelstein
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Jerry Gomez
- 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
| | - Masud Dikita Llewellyn
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Tara Picudella
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Sarah Rose Willsey
- 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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