1
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Miyazaki Y, Shinoda W. pSPICA Force Field Extended for Proteins and Peptides. J Chem Inf Model 2024; 64:532-542. [PMID: 38156656 DOI: 10.1021/acs.jcim.3c01611] [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: 01/03/2024]
Abstract
Many coarse-grained (CG) molecular dynamics (MD) studies have been performed to investigate biological processes involving proteins and lipids. CG force fields (FFs) in these MD studies often use implicit or nonpolar water models to reduce computational costs. CG-MD using water models cannot properly describe electrostatic screening effects owing to the hydration of ionic segments and thus cannot appropriately describe molecular events involving water channels and pores through lipid membranes. To overcome this issue, we developed a protein model in the pSPICA FF, in which a polar CG water model showing the proper dielectric response was adopted. The developed CG model greatly improved the transfer free energy profiles of charged side chain analogues across the lipid membrane. Application studies on melittin-induced membrane pores and mechanosensitive channels in lipid membranes demonstrated that CG-MDs using the pSPICA FF correctly reproduced the structure and stability of the pores and channels. Furthermore, the adsorption behavior of the highly charged nona-arginine peptides on lipid membranes changed with salt concentration, indicating the pSPICA FF is also useful for simulating protein adsorption on membrane surfaces.
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Affiliation(s)
- Yusuke Miyazaki
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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2
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Izumi K, Saito C, Kawano R. Liposome Deformation Induced by Membrane-Binding Peptides. MICROMACHINES 2023; 14:373. [PMID: 36838073 PMCID: PMC9967443 DOI: 10.3390/mi14020373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
This paper presents an investigation of liposome deformation and shape distortion using four membrane-binding peptides: TAT and C105Y as cell-penetrating peptides (CPPs), and melittin and ovispirin as antimicrobial peptides (AMPs). Liposome deformation was monitored utilizing fluorescent microscopy, while the binding of peptides to the DOPC membrane was estimated through capacitance measurements. The degree of liposome deformation and shape distortion was found to be higher for the CPPs compared to the AMPs. Additionally, it was observed that C105Y did not induce liposome rupture, unlike the other three peptides. We propose that these variations in liposome distortion may be attributed to differences in secondary structure, specifically the presence of an α-helix or random coil. Our studies offer insight into the use of peptides to elicit control of liposome architecture and may offer a promising approach for regulating the bodies of liposomal molecular robots.
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3
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Miyazaki Y, Shinoda W. Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183955. [PMID: 35526599 DOI: 10.1016/j.bbamem.2022.183955] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/09/2022] [Accepted: 04/29/2022] [Indexed: 12/29/2022]
Abstract
We conducted a series of coarse-grained molecular dynamics (CG-MD) simulations to investigate the complicated actions of melittin, which is an antimicrobial peptide (AMP) derived from honey bee venom, on a lipid membrane. To accurately simulate the AMP action, we developed and used a protein CG model as an extension of the pSPICA force field (FF), which was designed to reproduce several thermodynamic quantities and structural properties. At a low peptide-to-lipid (P/L) ratio (1/102), no defect was detected. At P/L = 1/51, toroidal pore formation was observed due to collective insertion of multiple melittin peptides from the N-termini. The pore formation was initiated by a local increase in membrane curvature in the vicinity of the peptide aggregate. At a higher P/L ratio (1/26), two more modes were detected, seemingly not controlled by the P/L ratio but by a local arrangement of melittin peptides: 1. Pore formation accompanied by lipid extraction by melittin peptides:a detergent-like mechanism. 2. A rapidly formed large pore in a significantly curved membrane: bursting. Thus, we observed three pore formation modes (toroidal pore formation, lipid extraction, and bursting) depending on the peptide concentration and local arrangement. These observations were consistent with experimental observations and hypothesized melittin modes. Through this study, we found that the local arrangements and population of melittin peptides and the area expansion rate by membrane deformation were key to the initiation of and competition among the multiple pore formation mechanisms.
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Affiliation(s)
- Yusuke Miyazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan; Department of Chemistry, Faculty of Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
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4
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Lohan S, Mandal D, Choi W, Konshina AG, Tiwari RK, Efremov RG, Maslennikov I, Parang K. Small Amphiphilic Peptides: Activity Against a Broad Range of Drug-Resistant Bacteria and Structural Insight into Membranolytic Properties. J Med Chem 2022; 65:665-687. [PMID: 34978443 DOI: 10.1021/acs.jmedchem.1c01782] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the synthesis and antibacterial activities of a series of amphiphilic membrane-active peptides composed, in part, of various nongenetically coded hydrophobic amino acids. The lead cyclic peptides, 8C and 9C, showed broad-spectrum activity against drug-resistant Gram-positive (minimum inhibitory concentration (MIC) = 1.5-6.2 μg/mL) and Gram-negative (MIC = 12.5-25 μg/mL) bacteria. The cytotoxicity study showed the predominant lethal action of the peptides against bacteria as compared with mammalian cells. A plasma stability study revealed approximately 2-fold higher stability of lead cyclic peptides as compared to their linear counterparts after 24 h of incubation. A calcein dye leakage experiment revealed the membranolytic effect of the cyclic peptides. Nuclear magnetic resonance spectroscopy and molecular dynamics simulation studies of the interaction of the peptides with the phospholipid bilayer provided a solid structural basis to explain the membranolytic action of the peptides with atomistic details. These results highlight the potential of newly designed amphiphilic peptides as the next generation of peptide-based antibiotics.
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Affiliation(s)
- Sandeep Lohan
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, 9401 Jeronimo Road, Irvine, California 92618, United States.,AJK Biopharmaceutical, 5270 California Avenue, Irvine, California 92617, United States
| | - Dindyal Mandal
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, 9401 Jeronimo Road, Irvine, California 92618, United States.,AJK Biopharmaceutical, 5270 California Avenue, Irvine, California 92617, United States.,School of Biotechnology, KIIT Deemed to be University, Bhubaneswar 751024, India
| | - Wonsuk Choi
- Structural Biology Research Center, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, 9401 Jeronimo Road, Irvine, California 92618, United States
| | - Anastasia G Konshina
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russia
| | - Rakesh K Tiwari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, 9401 Jeronimo Road, Irvine, California 92618, United States
| | - Roman G Efremov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russia.,National Research University Higher School of Economics, Myasnitskaya ul. 20, Moscow 101000, Russia.,Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701 Moscow, Oblast, Russia
| | - Innokentiy Maslennikov
- Structural Biology Research Center, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, 9401 Jeronimo Road, Irvine, California 92618, United States
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, 9401 Jeronimo Road, Irvine, California 92618, United States
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5
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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6
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Velasco-Bolom JL, Garduño-Juárez R. Computational studies of membrane pore formation induced by Pin2. J Biomol Struct Dyn 2021; 40:5060-5068. [PMID: 33397200 DOI: 10.1080/07391102.2020.1867640] [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: 10/22/2022]
Abstract
Understanding, at the molecular level, the effect of AMPs on biological membranes is of crucial importance given the increasing number of multidrug-resistant bacteria. Being part of an ancient type of innate immunity system, AMPs have emerged as a potential solution for which bacteria have not developed resistance. Traditional antibiotics specifically act on biosynthetic pathways, while AMPs may directly destabilize the lipid membrane, but it is unclear how AMPs affect the membrane's stability. We performed multiscale molecular dynamics simulations to investigate the structural features leading to membrane pores formation on zwitterionic and anionic membranes by the antimicrobial peptide (AMP) Pandinin 2 (Pin2). Some experimental reports propose that Pin2 could form barrel-stave pores, while others suggest that it could form toroidal pores. Since there is no conclusive evidence of which type of pore is formed by Pin2 on bilayers, performing molecular dynamics simulations on these systems could shed some light on whether or not or what type of pore Pin2 forms on model membranes. Our results are focused on a detailed description of the pore formation by Pin2 in POPC and POPE:POPG membranes., which strongly suggest that Pin2 forms a toroidal pore and not a barrel-shaped pore; this type of pore also affects the membrane properties. In the process, a phospholipid remodeling in the POPE:POPG membrane takes place. Moreover, the pores formed by Pin2 indicate that they are selective for the chlorine ion. There are no previous ion selectivity reports for other AMPs with similar physicochemical properties, such as melittin and magainin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- José-Luis Velasco-Bolom
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.,Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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7
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Balatti GE, Domene C, Martini MF, Pickholz M. Differential Stability of Aurein 1.2 Pores in Model Membranes of Two Probiotic Strains. J Chem Inf Model 2020; 60:5142-5152. [PMID: 32815723 DOI: 10.1021/acs.jcim.0c00855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Aurein 1.2 is an antimicrobial peptide from the skin secretion of an Australian frog. In the previous experimental work, we reported a differential action of aurein 1.2 on two probiotic strains Lactobacillus delbrueckii subsp. bulgaricus (CIDCA 331) and Lactobacillus delbrueckii subsp. lactis (CIDCA 133). The differences found were attributed to the bilayer compositions. Cell cultures and CIDCA 331-derived liposomes showed higher susceptibility than the ones derived from the CIDCA 133 strain, leading to content leakage and structural disruption. Here, we used molecular dynamics simulations to explore these systems at the atomistic level. We hypothesize that if the antimicrobial peptides organized themselves to form a pore, it will be more stable in membranes that emulate the CIDCA 331 strain than in those of the CIDCA 133 strain. To test this hypothesis, we simulated preassembled aurein 1.2 pores embedded into bilayer models that emulate the two probiotic strains. It was found that the general behavior of the systems depends on the composition of the membrane rather than the preassemble system characteristics. Overall, it was observed that aurein 1.2 pores are more stable in the CIDCA 331 model membranes. This fact coincides with the high susceptibility of this strain against antimicrobial peptide. In contrast, in the case of the CIDCA 133 model membranes, peptides migrate to the water-lipid interphase, the pore shrinks, and the transport of water through the pore is reduced. The tendency of glycolipids to make hydrogen bonds with peptides destabilizes the pore structures. This feature is observed to a lesser extent in CIDCA 331 due to the presence of anionic lipids. Glycolipid transverse diffusion (flip-flop) between monolayers occurs in the pore surface region in all the cases considered. These findings expand our understanding of the antimicrobial peptide resistance properties of probiotic strains.
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Affiliation(s)
- Galo E Balatti
- Departamento de Física Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 1, Buenos Aires 1428, Argentina.,IFIBA, CONICET-UBA, Ciudad Universitaria, Pabellón 1, Buenos Aires 1428, Argentina
| | - Carmen Domene
- Department of Chemistry, University of Bath, 1 South Bldg., Claverton Down, Bath BA27AY, The United Kingdom.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, The United Kingdom
| | - M Florencia Martini
- Facultad de Farmacia y Bioquímica, Departamento de Farmacología, Universidad de Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina.,Instituto de Química y Metabolismo del Fármaco, Fac. de Farmacia y Bioquímica, (Universidad de Buenos Aires, IQUIMEFA-CONICET), Junín 956, C1113AAD Buenos Aires, Argentina
| | - Monica Pickholz
- Departamento de Física Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 1, Buenos Aires 1428, Argentina.,IFIBA, CONICET-UBA, Ciudad Universitaria, Pabellón 1, Buenos Aires 1428, Argentina
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8
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Miyazaki Y, Okazaki S, Shinoda W. Free energy analysis of membrane pore formation process in the presence of multiple melittin peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1409-1419. [PMID: 30885804 DOI: 10.1016/j.bbamem.2019.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 11/30/2022]
Abstract
Understanding the molecular mechanism underlying pore formation in lipid membranes by antimicrobial peptides is of great importance in biological sciences as well as in drug design applications. Melittin has been widely studied as a pore forming peptide, though the molecular mechanism for pore formation is still illusive. We examined the free energy barrier for the creation of a pore in lipid membranes with and without multiple melittin peptides. It was found that six melittin peptides significantly stabilized a pore, though a small barrier (a few kBT) for the formation still existed. With five melittin peptides or fewer, the pore formation barrier was much higher, though the established pore was in a local energy minimum. Although seven melittins effectively reduced the free energy barrier, a single melittin peptide left the pore after a long time MD simulation probably because of the overcrowded environment around the bilayer pore. Thus, it is highly selective for the number of melittin peptides to stabilize the membrane pore, as was also suggested by the line tension evaluations. The free energy cost required to insert a single melittin into the membrane is too high to explain the one-by-one insertion mechanism for pore formation, which also supports the collective melittin mechanism for pore formation.
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Affiliation(s)
- Yusuke Miyazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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9
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Zhang Y, Chen T, Pan Z, Sun X, Yin X, He M, Xiao S, Liang H. Theoretical Insights into the Interactions between Star-Shaped Antimicrobial Polypeptides and Bacterial Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:13438-13448. [PMID: 30350688 DOI: 10.1021/acs.langmuir.8b02677] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A structurally nanoengineered antimicrobial polypeptide consisting of lysine and valine residues is a new class of antimicrobial agent with superior antibacterial activity against multidrug-resistant bacteria and low toxicity toward mammalian cells. Utilizing coarse-grained models, we studied the interactions of microbial cytoplasmic membranes with polypeptides of either (K2V1)5 (star-KV) or CM15 (star-CM15). Our computational results verify the low toxicity of polypeptides of (K2V1)5 toward the dipalmitoyl phosphatidylcholine bilayer. This low toxicity is demonstrated to originate from weakened hydrophobicity combined with its random coil conformation for (K2V1)5 because of the highly abundant valine residues, compared with the typical antimicrobial peptides, such as CM15. In the interactions with a palmitoyl-oleoyl-phosphatidylethanolamine/palmitoyl-oleoyl-phosphatidylglycerol bilayer, star-KV has greater ability in phase separation and generation of phase boundary defects not only in lipid redistribution but also in lateral dynamic movements, although both star-KV and star-CM15 can extract the phosphatidylglycerol lipids and purify the phosphatidylethanolamine lipids into continuum domains. We suggest that the polypeptide of (K2V1)5 can nondisruptively kill bacteria by hampering bacterial metabolism through reorganizing lipid domain distribution and simultaneously "freezing" lipid movement.
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Affiliation(s)
| | | | - Zhimeng Pan
- School of Computing , University of Utah , Salt Lake City , Utah 84112 , United States
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10
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Patel SJ, Van Lehn RC. Characterizing the Molecular Mechanisms for Flipping Charged Peptide Flanking Loops across a Lipid Bilayer. J Phys Chem B 2018; 122:10337-10348. [PMID: 30376710 DOI: 10.1021/acs.jpcb.8b06613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cell membrane largely prevents the passive diffusion of charged molecules due to the large free energy barrier associated with translocating charged groups across the hydrophobic lipid bilayer core. Despite this barrier, some peptides can interconvert between transmembrane and surface-adsorbed states by "flipping" charged flanking loops across the bilayer on a surprisingly rapid second-minute time scale. The transmembrane helices of some multispanning membrane proteins undergo similar reorientation processes, suggesting that loop-flipping may be a mechanism for regulating membrane protein topology; however, the molecular mechanisms underlying this behavior remain unknown. In this work, we study the loop-flipping behavior exhibited by a peptide with a hydrophobic transmembrane helix, charged flanking loops, and a central, membrane-exposed aspartate residue of varying protonation state. We utilize all-atom temperature accelerated molecular dynamics simulations to predict the likelihood of loop-flipping without predefining specific loop-flipping pathways. We demonstrate that this approach can identify multiple possible flipping pathways, with the prevalence of each pathway depending on the protonation state of the central residue. In particular, we find that a charged central residue facilitates loop-flipping by stabilizing membrane water defects, enabling the "self-catalysis" of charge translocation. These findings provide detailed molecular-level insights into charged loop-flipping pathways that may generalize to other charge translocation processes, such as lipid flip-flop or the large-scale conformational rearrangements of multispanning membrane proteins.
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Affiliation(s)
- Samarthaben J Patel
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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11
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Ma Z, Han J, Chang B, Gao L, Lu Z, Lu F, Zhao H, Zhang C, Bie X. Membrane-Active Amphipathic Peptide WRL3 with in Vitro Antibiofilm Capability and in Vivo Efficacy in Treating Methicillin-Resistant Staphylococcus aureus Burn Wound Infections. ACS Infect Dis 2017; 3:820-832. [PMID: 28885829 DOI: 10.1021/acsinfecdis.7b00100] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has become increasingly prevalent in hospitals, clinics, and the community. MRSA can cause significant and even lethal infections, especially in skin burn wounds. The currently available topical agents have largely failed to eliminate MRSA infections due to resistance. Therefore, there is an urgent need for new and effective approaches for treating MRSA. Here, we show that a novel engineered amphipathic peptide, WRL3 (WLRAFRRLVRRLARGLRR-NH2), exhibits potent antimicrobial activity against MRSA, even in the presence of various salts or serum. The cell selectivity of WRL3 was demonstrated by its ability to specifically eliminate MRSA cells over host cells in a coculture model. Additionally, WRL3 showed a synergistic effect against MRSA when combined with ceftriaxone and effectively inhibited sessile biofilm bacteria growth leading to a reduction in biomass. Fluorescent measurements and microscopic observations of live bacterial cells and artificial membranes revealed that WRL3 exerted its bactericidal activity possibly by destroying the bacterial membrane. In vivo studies indicate that WRL3 is able to control proliferation of MRSA in wound tissue and reduce bioburden and provides a more favorable environment for wound healing. Collectively, our data suggest that WRL3 has enormous potential as a novel antimicrobial agent for the treatment of clinical MRSA infections of skin burn wounds.
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Affiliation(s)
- Zhi Ma
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu
District, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Jinzhi Han
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu
District, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Bingxue Chang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu
District, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Ling Gao
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu
District, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu
District, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu
District, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu
District, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Chong Zhang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu
District, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Xuanwu
District, Nanjing, Jiangsu 210095, People’s Republic of China
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12
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Sun D, Forsman J, Woodward CE. Molecular Simulations of Melittin-Induced Membrane Pores. J Phys Chem B 2017; 121:10209-10214. [PMID: 29035531 DOI: 10.1021/acs.jpcb.7b07126] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Membrane-active peptides (MAPs) are able to induce pores in cell membranes via molecular mechanisms, which are still subject to ongoing research. In this work, we present molecular dynamics simulations that suggest a precursor membrane defect plays an important role in the pore-inducing activity of the prototypical antimicrobial peptide melittin. The simulations reveal that the hydrophobic N-terminus of melittin is able to recognize and insert into the membrane defect in the lipid bilayer and that this leads to a cascading transfer of adsorbed peptides to the membrane defect, leading to peptide aggregation in the pore. We show that this mechanism also acts in the case of a melittin mutant without the flexible central proline hinge, thus indicating the latter is not crucial to the activity of melittin, which is consistent with experiments.
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Affiliation(s)
- Delin Sun
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra, ACT 2600, Australia
| | - Jan Forsman
- Theoretical Chemistry, Chemical Centre, Lund University , P.O. Box 124, S-221 00 Lund, Sweden
| | - Clifford E Woodward
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra, ACT 2600, Australia
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13
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Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations. Molecules 2017; 22:molecules22101775. [PMID: 29053635 PMCID: PMC6151434 DOI: 10.3390/molecules22101775] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/17/2017] [Indexed: 01/05/2023] Open
Abstract
In this work; we investigated the differential interaction of amphiphilic antimicrobial peptides with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid structures by means of extensive molecular dynamics simulations. By using a coarse-grained (CG) model within the MARTINI force field; we simulated the peptide-lipid system from three different initial configurations: (a) peptides in water in the presence of a pre-equilibrated lipid bilayer; (b) peptides inside the hydrophobic core of the membrane; and (c) random configurations that allow self-assembled molecular structures. This last approach allowed us to sample the structural space of the systems and consider cooperative effects. The peptides used in our simulations are aurein 1.2 and maculatin 1.1; two well-known antimicrobial peptides from the Australian tree frogs; and molecules that present different membrane-perturbing behaviors. Our results showed differential behaviors for each type of peptide seen in a different organization that could guide a molecular interpretation of the experimental data. While both peptides are capable of forming membrane aggregates; the aurein 1.2 ones have a pore-like structure and exhibit a higher level of organization than those conformed by maculatin 1.1. Furthermore; maculatin 1.1 has a strong tendency to form clusters and induce curvature at low peptide-lipid ratios. The exploration of the possible lipid-peptide structures; as the one carried out here; could be a good tool for recognizing specific configurations that should be further studied with more sophisticated methodologies.
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Henderson JM, Waring AJ, Separovic F, Lee KYC. Antimicrobial Peptides Share a Common Interaction Driven by Membrane Line Tension Reduction. Biophys J 2017; 111:2176-2189. [PMID: 27851941 DOI: 10.1016/j.bpj.2016.10.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/30/2016] [Accepted: 10/05/2016] [Indexed: 12/30/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a class of host-defense molecules that neutralize a broad range of pathogens. Their membrane-permeabilizing behavior has been commonly attributed to the formation of pores; however, with the continuing discovery of AMPs, many are uncharacterized and their exact mechanism remains unknown. Using atomic force microscopy, we previously characterized the disruption of model membranes by protegrin-1 (PG-1), a cationic AMP from pig leukocytes. When incubated with zwitterionic membranes of dimyristoylphosphocholine, PG-1 first induced edge instability at low concentrations, then porous defects at intermediate concentrations, and finally worm-like micelle structures at high concentrations. These rich structural changes suggested that pore formation constitutes only an intermediate state along the route of PG-1's membrane disruption process. The formation of these structures could be best understood by using a mesophase framework of a binary mixture of lipids and peptides, where PG-1 acts as a line-active agent in lowering interfacial bilayer tensions. We have proposed that rather than being static pore formers, AMPs share a common ability to lower interfacial tensions that promote membrane transformations. In a study of 13 different AMPs, we found that peptide line-active behavior was not driven by the overall charge, and instead was correlated with their adoption of imperfect secondary structures. These peptide structures commonly positioned charged residues near the membrane interface to promote deformation favorable for their incorporation into the membrane. Uniquely, the data showed that barrel-stave-forming peptides such as alamethicin are not line-active, and that the seemingly disparate models of toroidal pores and carpet activity are actually related. We speculate that this interplay between peptide structure and the distribution of polar residues in relation to the membrane governs AMP line activity in general and represents a novel, to our knowledge, avenue for the rational design of new drugs.
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Affiliation(s)
- J Michael Henderson
- Department of Chemistry, The University of Chicago, Chicago, Illinois; Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois; The James Frank Institute, The University of Chicago, Chicago, Illinois
| | - Alan J Waring
- Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Ka Yee C Lee
- Department of Chemistry, The University of Chicago, Chicago, Illinois; Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois; The James Frank Institute, The University of Chicago, Chicago, Illinois.
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Lipkin R, Lazaridis T. Computational prediction of the optimal oligomeric state for membrane-inserted β-barrels of protegrin-1 and related mutants. J Pept Sci 2017; 23:334-345. [PMID: 28382709 DOI: 10.1002/psc.2992] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 11/07/2022]
Abstract
Protegrin-1 is a widely studied 18-residue β-hairpin antimicrobial peptide. Evidence suggests that it acts via a β-barrel pore formation mechanism, but the exact number of peptides comprising the pore state is unknown. In this study, we performed molecular dynamics simulations of β-barrels of protegrin and three related mutants (v14v16l, v14v16a, and r4n) in NCNC parallel topology in implicit membrane pores of varying radius and curvature for oligomeric numbers 6-14. We then identified the optimal pore radius and curvature values for all constructs and determined the total effective energy and the translational and rotational entropic losses. These, along with an estimate of membrane deformation free energy from experimental line tension values, provided an estimate of the overall energetics of formation of each pore state. The results indicated that oligomeric numbers 7-13 are generally stable, allowing the possibility of a heterogeneous pore state. The optimal oligomeric state for protegrin is the nonamer, shifting to higher numbers for the mutants. Protegrin, v14v16l, and r4n are stable as membrane-inserted β-barrels, but v14v16a seems much less so because of its decreased hydrophobicity. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Richard Lipkin
- Department of Chemistry, City College of New York, 160 Convent Ave., New York, NY, 10031, USA.,Graduate Program in Chemistry, Graduate Center, City University of New York, 365 Fifth Ave, New York, NY, 10016, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, 160 Convent Ave., New York, NY, 10031, USA
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16
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Quan X, Peng C, Zhao D, Li L, Fan J, Zhou J. Molecular Understanding of the Penetration of Functionalized Gold Nanoparticles into Asymmetric Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:361-371. [PMID: 27794619 DOI: 10.1021/acs.langmuir.6b02937] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this work, the interactions between surface-functionalized gold nanoparticles (AuNPs) and asymmetric membranes and the associated cytotoxicity were explored by coarse-grained molecular dynamics simulations. Simulation results show that the surface chemistry of AuNPs and the asymmetry of lipid membranes play significant roles. AuNPs with different signs of charges spontaneously adhere to the membrane surface or penetrate the membrane core. Also, the asymmetric distribution of charged lipids in membranes can facilitate the penetration of cationic AuNPs. Increasing the surface charge density (SCD) of AuNPs can not only improve the penetration efficiency but also lead to more disruption of the membrane structure. Moreover, the flip-flop of charged lipids in the inner leaflet can be observed during the translocation of AuNPs with a high SCD. The breakdown of membrane asymmetry may hinder the cellular internalization of AuNPs in a direct penetration mechanism. More importantly, we demonstrate that the hydrophobic contact between protruding solvent-exposed lipid tails and the hydrophobic moieties of ligands can mediate the insertion of AuNPs with a low SCD into cell membranes, which will exhibit less cytotoxicity in most in vivo applications. This may open a new exciting avenue to developing nanocarriers with a higher translocation efficiency and a lower toxicity simultaneously for biomedical applications.
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Affiliation(s)
- Xuebo Quan
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, P. R. China
| | - Chunwang Peng
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, P. R. China
| | - Daohui Zhao
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, P. R. China
| | - Libo Li
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, P. R. China
| | - Jun Fan
- Department of Physics and Materials Science, City University of Hong Kong , Hong Kong, P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Laboratory for Green Chemical Product Technology, South China University of Technology , Guangzhou 510640, P. R. China
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Gómez-Llobregat J, Elías-Wolff F, Lindén M. Anisotropic Membrane Curvature Sensing by Amphipathic Peptides. Biophys J 2016; 110:197-204. [PMID: 26745422 DOI: 10.1016/j.bpj.2015.11.3512] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/29/2015] [Accepted: 11/11/2015] [Indexed: 12/29/2022] Open
Abstract
Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodeling cell membranes. However, the molecular driving forces behind these processes are not well understood. Here, we describe an approach to study curvature sensing by simulating the interactions of single molecules with a buckled lipid bilayer. We analyze three amphipathic antimicrobial peptides, a class of membrane-associated molecules that specifically target and destabilize bacterial membranes, and find qualitatively different sensing characteristics that would be difficult to resolve with other methods. Our findings provide evidence for direction-dependent curvature sensing mechanisms in amphipathic peptides and challenge existing theories of hydrophobic insertion. The buckling approach is generally applicable to a wide range of curvature-sensing molecules, and our results provide strong motivation to develop new experimental methods to track position and orientation of membrane proteins.
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Affiliation(s)
- Jordi Gómez-Llobregat
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Federico Elías-Wolff
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Martin Lindén
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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King MJ, Bennett AL, Almeida PF, Lee HS. Coarse-grained simulations of hemolytic peptide δ-lysin interacting with a POPC bilayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:3182-3194. [PMID: 27720634 DOI: 10.1016/j.bbamem.2016.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/17/2016] [Accepted: 10/04/2016] [Indexed: 01/08/2023]
Abstract
δ-lysin, secreted by a Gram-positive bacterium Staphylococcus aureus, is a 26-residue membrane active peptide that shares many common features with antimicrobial peptides (AMPs). However, it possesses a few unique features that differentiate itself from typical AMPs. In particular, δ-lysin has zero net charge, even though it has many charged residues, and it preferentially lyses eukaryotic cells over bacterial cells. Here, we present the results of coarse-grained molecular dynamics simulations of δ-lysin interacting with a zwitterionic membrane over a wide range of peptide concentrations. When the peptides concentration is low, spontaneous dimerization of peptides is observed on the membrane surface, but deep insertion of peptides or pore formation was not observed. However, the calculated free energy of peptide insertion suggests that a small fraction of peptides is likely to be present inside the membrane at the peptide concentrations typically seen in dye efflux experiments. When the simulations with multiple peptides are carried out with a single pre-inserted transmembrane peptide, spontaneous pore formation occurs with a peptide-to-lipid ratio (P/L) as low as P/L=1:42. Inter-peptide salt bridges among the transmembrane peptides seem to play a role in creating compact pores with very low level of hydration. More importantly, the transmembrane peptides making up the pore are constantly pushed to the opposite side of the membrane when the mass imbalance between the two sides of membrane is significant. Thus, the pore is very dynamic, allowing multiple peptides to translocate across the membrane simultaneously.
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Affiliation(s)
- Mariah J King
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States
| | - Ashley L Bennett
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States
| | - Paulo F Almeida
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States
| | - Hee-Seung Lee
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, United States.
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Sun D, Forsman J, Woodward CE. Atomistic Molecular Simulations Suggest a Kinetic Model for Membrane Translocation by Arginine-Rich Peptides. J Phys Chem B 2015; 119:14413-20. [DOI: 10.1021/acs.jpcb.5b08072] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Delin Sun
- School
of Physical, Environmental and Mathematical Sciences, University of New South Wales, Canberra ACT 2600, Australia
| | - Jan Forsman
- Theoretical
Chemistry, Chemical Centre, Lund University, P.O. Box 124, S-221 00 Lund, Sweden
| | - Clifford E. Woodward
- School
of Physical, Environmental and Mathematical Sciences, University of New South Wales, Canberra ACT 2600, Australia
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20
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Sun D, Forsman J, Woodward CE. Multistep Molecular Dynamics Simulations Identify the Highly Cooperative Activity of Melittin in Recognizing and Stabilizing Membrane Pores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:9388-9401. [PMID: 26267389 DOI: 10.1021/acs.langmuir.5b01995] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The prototypical antimicrobial peptide, melittin, is well-known for its ability to induce pores in zwitterionic model lipid membranes. However, the mechanism by which melittin accomplishes this is not fully understood. We have conducted all-atom and coarse-grained molecular dynamics simulations which suggest that melittin employs a highly cooperative mechanism for the induction of both small and large membrane pores. The process by which this peptide induces membrane pores appears to be driven by its affinity to membrane defects via its N-terminus region. In our simulations, a membrane defect was deliberately created through either lipid flip-flop or the reorientation of one adsorbed melittin peptide. In a cooperative response, other melittin molecules also inserted their N-termini into the created defect, thus lowering the overall free energy. The insertion of these peptide molecules ultimately allowed the defect to develop into a small transmembrane pore, with an estimated diameter of ∼1.5 nm and a lifetime of the order of tens of milliseconds. In the presence of a finite membrane tension, we show that this small pore can act as a nucleation site for the stochastic rupture of the lipid bilayer, so as to create a much larger pore. We found that a threshold membrane tension of 25 mN/m was needed to create a ruptured pore. Furthermore, by actively accumulating at its edge, adsorbed peptides are able to cooperatively stabilize this larger pore. The defect-mediated pore formation mechanism revealed in this work may also apply to other amphipathic membrane-active peptides.
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Affiliation(s)
- Delin Sun
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra ACT 2600, Australia
| | - Jan Forsman
- Theoretical Chemistry, Chemical Centre, Lund University , P.O. Box 124, S-221 00 Lund, Sweden
| | - Clifford E Woodward
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales , Canberra ACT 2600, Australia
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