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Volovik MV, Batishchev OV. Membrane Activity of Melittin and Magainin-I at Low Peptide-to-Lipid Ratio: Different Types of Pores and Translocation Mechanisms. Biomolecules 2024; 14:1118. [PMID: 39334885 PMCID: PMC11430820 DOI: 10.3390/biom14091118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 09/01/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
Antimicrobial peptides (AMPs) are believed to be a prominent alternative to the common antibiotics. However, despite decades of research, there are still no good clinical examples of peptide-based antimicrobial drugs for system application. The main reasons are loss of activity in the human body, cytotoxicity, and low selectivity. To overcome these challenges, a well-established structure-function relationship for AMPs is critical. In the present study, we focused on the well-known examples of melittin and magainin to investigate in detail the initial stages of AMP interaction with lipid membranes at low peptide-to-lipid ratio. By combining the patch-clamp technique with the bioelectrochemical method of intramembrane field compensation, we showed that these peptides interact with the membrane in different ways: melittin inserts deeper into the lipid bilayer than magainin. This difference led to diversity in pore formation. While magainin, after a threshold concentration, formed the well-known toroidal pores, allowing the translocation of the peptide through the membrane, melittin probably induced predominantly pure lipidic pores with a very low rate of peptide translocation. Thus, our results shed light on the early stages of peptide-membrane interactions and suggest new insights into the structure-function relationship of AMPs based on the depth of their membrane insertion.
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Affiliation(s)
- Marta V Volovik
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
| | - Oleg V Batishchev
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia
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2
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Sun L, Wang S, Tian F, Zhu H, Dai L. Organizations of melittin peptides after spontaneous penetration into cell membranes. Biophys J 2022; 121:4368-4381. [PMID: 36199252 PMCID: PMC9703044 DOI: 10.1016/j.bpj.2022.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/16/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
Abstract
The antimicrobial peptide, melittin, is a potential next-generation antibiotic because melittin can spontaneously form pores in bacterial cell membranes and cause cytoplasm leakage. However, the organizations of melittin peptides in cell membranes remain elusive, which impedes the understanding of the poration mechanism. In this work, we use coarse-grained and all-atom molecular dynamics (MD) simulations to investigate the organizations of melittin peptides during and after spontaneous penetration into DPPC/POPG lipid bilayers. We find that the peptides in lipid bilayers adopt either a transmembrane conformation or a U-shaped conformation, which are referred to as T- and U-peptides, respectively. Several U-peptides and/or T-peptides aggregate to form stable pores. We analyze a T-pore consisting of four T-peptides and a U-pore consisting of three U-peptides and one T-peptide. In both pores, peptides are organized in a manner such that polar residues face inward and hydrophobic residues face outward, which stabilizes the pores and produces water channels. Compared with the U-pore, the T-pore has lower energy, larger pore diameter, and higher permeability. However, the T-pore occurs less frequently than the U-pore in our simulations, probably because the formation of the T-pore is kinetically slower than the U-pore. The stability and permeability of both pores are confirmed by 300 ns all-atom MD simulations. The peptide organizations obtained in this work should deepen the understanding of the stability, poration mechanism, and permeability of melittin, and facilitate the optimization of melittin to enhance the antibacterial ability.
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Affiliation(s)
- Liang Sun
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Simin Wang
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China.
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3
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Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method. Sci Rep 2021; 11:11406. [PMID: 34075115 PMCID: PMC8169667 DOI: 10.1038/s41598-021-90907-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 05/07/2021] [Indexed: 11/29/2022] Open
Abstract
The stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to the search for the most stable biomolecular complexes in water by using the MARTINI coarse-grained (CG) model. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as an EpCAM adaptor for an EpA (AptEpA) benchmark target molecule. The effects of two adsorption positions on the EpCAM were analysed, and it is found that the AptEpA adsorption configuration located within the EpCAM pocket-like structure is more stable and the energy barrier is lower due to the interaction with water. By the root mean square deviation (RMSD), the configuration of EpCAM in water is more conservative when the AptEpA binds to EpCAM by attaching to the pocket space of the EpCAM dimer. For AptEpA, the root mean square fluctuation (RMSF) analysis result indicates Nucleobase 1 and Nucleobase 2 display higher flexibility during the CGMD simulation. Finally, from the binding energy contour maps and histogram plots of EpCAM and each AptEpA nucleobase, it is clear that the binding energy adsorbed to the pocket-like structure is more continuous than that energy not adsorbed to the pocket-like structure. This study has proposed a new numerical process for applying the STUN-BH-DMD with the CG model, which can reduce computational details and directly find a more stable AptEpA/EpCAM complex in water.
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Min SH, Wijesinghe S, Lau EY, Berkowitz ML. Damage to Polystyrene Polymer Film by Shock Wave Induced Bubble Collapse. J Phys Chem B 2020; 124:7494-7499. [PMID: 32790408 DOI: 10.1021/acs.jpcb.0c04413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metallic surfaces that are in contact with solutions are commonly used in numerous applications where these surfaces can be damaged by shock wave induced bubble collapse. Use of polymer films that coat such surfaces to prevent them from damage requires a better understanding of how much harm collapsing bubbles produce in the films. In this study, we report the results from coarse-grained molecular dynamics simulations to study the damage to polystyrene (PS) films coating a hard surface. The damage was caused by a collapsing nanobubble located in the proximity of the film and interacting with an impinging shock wave. This collapse produces a high-speed water jet that impacts the PS film with a greater force than the shock front and creates cavities/pits in the PS film. We observed that polymer molecules located in the jet vicinity undergo conformational extension in the direction perpendicular to the jet motion, while chain molecules in the rest of the film undergo compression. We also observed that damage to the film is sensitive to the strength of the shock wave.
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Affiliation(s)
- Sa Hoon Min
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sidath Wijesinghe
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Edmond Y Lau
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Max L Berkowitz
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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5
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Mescola A, Marín-Medina N, Ragazzini G, Accolla M, Alessandrini A. Magainin-H2 effects on the permeabilization and mechanical properties of giant unilamellar vesicles. J Colloid Interface Sci 2019; 553:247-258. [PMID: 31207545 DOI: 10.1016/j.jcis.2019.06.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/28/2019] [Accepted: 06/09/2019] [Indexed: 10/26/2022]
Abstract
Among the potential novel therapeutics to treat bacterial infections, antimicrobial peptides (AMPs) are a very promising substitute due to their broad-spectrum activity and rapid bactericidal action. AMPs strongly interact with the bacterial membrane, and the need to have a correct understanding of the interaction between AMPs and lipid bilayers at a molecular level prompted a wealth of experimental and theoretical studies exploiting a variety of AMPs. Here, we studied the effects of magainin H2 (Mag H2), an analog of the well-known magainin 2 (wt Mag 2) AMP endowed with a higher degree of hydrophobicity, on giant unilamellar vesicles (GUVs) concentrating on its permeabilization activity and the effect on the lipid bilayer mechanical properties. We demonstrated that the increased hydrophobicity of Mag H2 affects its selectivity conferring a strong permeabilization activity also on zwitterionic lipid bilayers. Moreover, when lipid mixtures including PG lipids are considered, PG has a protective effect, at variance from wt Mag 2, suggesting that for Mag H2 the monolayer curvature could prevail over the peptide-membrane electrostatic interaction. We then mechanically characterized GUVs by measuring the effect of Mag H2 on the bending constant of lipid bilayers by flickering spectroscopy and, by using micropipette aspiration technique, we followed the steps leading to vesicle permeabilization. We found that Mag H2, notwithstanding its enhanced hydrophobicity, has a pore formation mechanism compatible with the toroidal pore model similar to that of wt Mag 2.
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Affiliation(s)
- Andrea Mescola
- CNR-Nanoscience Institute-S3, Via Campi 213/A, 41125 Modena, Italy.
| | - Nathaly Marín-Medina
- Department of Physics, University of Los Andes, Carrera 1 N° 18A - 12, Bogotá, Colombia.
| | - Gregorio Ragazzini
- CNR-Nanoscience Institute-S3, Via Campi 213/A, 41125 Modena, Italy; Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Via Campi 213/A, 41125 Modena, Italy.
| | - Maurizio Accolla
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Via Campi 213/A, 41125 Modena, Italy
| | - Andrea Alessandrini
- CNR-Nanoscience Institute-S3, Via Campi 213/A, 41125 Modena, Italy; Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Via Campi 213/A, 41125 Modena, Italy.
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Hong J, Lu X, Deng Z, Xiao S, Yuan B, Yang K. How Melittin Inserts into Cell Membrane: Conformational Changes, Inter-Peptide Cooperation, and Disturbance on the Membrane. Molecules 2019; 24:molecules24091775. [PMID: 31067828 PMCID: PMC6539814 DOI: 10.3390/molecules24091775] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 01/27/2023] Open
Abstract
Antimicrobial peptides (AMPs), as a key component of the immune defense systems of organisms, are a promising solution to the serious threat of drug-resistant bacteria to public health. As one of the most representative and extensively studied AMPs, melittin has exceptional broad-spectrum activities against microorganisms, including both Gram-positive and Gram-negative bacteria. Unfortunately, the action mechanism of melittin with bacterial membranes, especially the underlying physics of peptide-induced membrane poration behaviors, is still poorly understood, which hampers efforts to develop melittin-based drugs or agents for clinical applications. In this mini-review, we focus on recent advances with respect to the membrane insertion behavior of melittin mostly from a computational aspect. Membrane insertion is a prerequisite and key step for forming transmembrane pores and bacterial killing by melittin, whose occurrence is based on overcoming a high free-energy barrier during the transition of melittin molecules from a membrane surface-binding state to a transmembrane-inserting state. Here, intriguing simulation results on such transition are highlighted from both kinetic and thermodynamic aspects. The conformational changes and inter-peptide cooperation of melittin molecules, as well as melittin-induced disturbances to membrane structure, such as deformation and lipid extraction, are regarded as key factors influencing the insertion of peptides into membranes. The associated intermediate states in peptide conformations, lipid arrangements, membrane structure, and mechanical properties during this process are specifically discussed. Finally, potential strategies for enhancing the poration ability and improving the antimicrobial performance of AMPs are included as well.
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Affiliation(s)
- Jiajia Hong
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Xuemei Lu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Zhixiong Deng
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Shufeng Xiao
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Bing Yuan
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
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7
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Effects of the peptide Magainin H2 on Supported Lipid Bilayers studied by different biophysical techniques. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2635-2643. [DOI: 10.1016/j.bbamem.2018.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/02/2018] [Indexed: 11/24/2022]
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Wang J, Dou X, Song J, Lyu Y, Zhu X, Xu L, Li W, Shan A. Antimicrobial peptides: Promising alternatives in the post feeding antibiotic era. Med Res Rev 2018; 39:831-859. [PMID: 30353555 DOI: 10.1002/med.21542] [Citation(s) in RCA: 312] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 12/15/2022]
Abstract
Antimicrobial peptides (AMPs), critical components of the innate immune system, are widely distributed throughout the animal and plant kingdoms. They can protect against a broad array of infection-causing agents, such as bacteria, fungi, parasites, viruses, and tumor cells, and also exhibit immunomodulatory activity. AMPs exert antimicrobial activities primarily through mechanisms involving membrane disruption, so they have a lower likelihood of inducing drug resistance. Extensive studies on the structure-activity relationship have revealed that net charge, hydrophobicity, and amphipathicity are the most important physicochemical and structural determinants endowing AMPs with antimicrobial potency and cell selectivity. This review summarizes the recent advances in AMPs development with respect to characteristics, structure-activity relationships, functions, antimicrobial mechanisms, expression regulation, and applications in food, medicine, and animals.
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Affiliation(s)
- Jiajun Wang
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Xiujing Dou
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Jing Song
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Yinfeng Lyu
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Xin Zhu
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Lin Xu
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Weizhong Li
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Anshan Shan
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
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Ting CL, Müller M. Membrane stress profiles from self-consistent field theory. J Chem Phys 2017; 146:104901. [PMID: 28298095 DOI: 10.1063/1.4977585] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Using self-consistent field theory (SCFT), we develop an accurate, local expression for the stress profiles in membranes and soft matter interfaces, in general. The bond stresses are expressed in terms of pre-computed chain propagators, which are used to describe the statistical weight of the molecules and therefore require minimal additional calculations. In addition, we overcome the resolution limit of the molecular bond length by including the Irving and Kirkwood bond assignment and recover a constant normal stress profile across an interface. Using this theory, we find that the membrane lateral stress profile contains repulsive (positive) stresses in the regions of the head and tail groups, and attractive (negative) stresses near the hydrophobic/hydrophilic interface. We also verify that the zeroth and first moments of the stress profile correspond to the thermodynamic tension and product of the bending modulus and the spontaneous curvature, respectively.
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Affiliation(s)
- Christina L Ting
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Marcus Müller
- Institute for Theoretical Physics, Georg-August University, Göttingen 37077, Germany
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10
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Goliaei A, Adhikari U, Berkowitz ML. Opening of the blood-brain barrier tight junction due to shock wave induced bubble collapse: a molecular dynamics simulation study. ACS Chem Neurosci 2015; 6:1296-301. [PMID: 26075566 DOI: 10.1021/acschemneuro.5b00116] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Passage of a shock wave across living organisms may produce bubbles in the blood vessels and capillaries. It was suggested that collapse of these bubbles imposed by an impinging shock wave can be responsible for the damage or even destruction of the blood-brain barrier. To check this possibility, we performed molecular dynamics computer simulations on systems that contained a model of tight junction from the blood-brain barrier. In our model, we represent the tight junction by two pairs of interacting proteins, claudin-15. Some of the simulations were done in the absence of a nanobubble, some in its presence. Our simulations show that when no bubble is present in the system, no damage to tight junction is observed when the shock wave propagates across it. In the presence of a nanobubble, even when the impulse of the shock wave is relatively low, the implosion of the bubble causes serious damage to our model tight junction.
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Affiliation(s)
- Ardeshir Goliaei
- Department of Biochemistry
and Biophysics and Program
in Molecular and Cellular Biophysics, and ‡Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Upendra Adhikari
- Department of Biochemistry
and Biophysics and Program
in Molecular and Cellular Biophysics, and ‡Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Max L. Berkowitz
- Department of Biochemistry
and Biophysics and Program
in Molecular and Cellular Biophysics, and ‡Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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