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Stephani J, Gerhards L, Khairalla B, Solov’yov IA, Brand I. How do Antimicrobial Peptides Interact with the Outer Membrane of Gram-Negative Bacteria? Role of Lipopolysaccharides in Peptide Binding, Anchoring, and Penetration. ACS Infect Dis 2024; 10:763-778. [PMID: 38259029 PMCID: PMC10862549 DOI: 10.1021/acsinfecdis.3c00673] [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: 12/05/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
Gram-negative bacteria possess a complex structural cell envelope that constitutes a barrier for antimicrobial peptides that neutralize the microbes by disrupting their cell membranes. Computational and experimental approaches were used to study a model outer membrane interaction with an antimicrobial peptide, melittin. The investigated membrane included di[3-deoxy-d-manno-octulosonyl]-lipid A (KLA) in the outer leaflet and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) in the inner leaflet. Molecular dynamics simulations revealed that the positively charged helical C-terminus of melittin anchors rapidly into the hydrophilic headgroup region of KLA, while the flexible N-terminus makes contacts with the phosphate groups of KLA, supporting melittin penetration into the boundary between the hydrophilic and hydrophobic regions of the lipids. Electrochemical techniques confirmed the binding of melittin to the model membrane. To probe the peptide conformation and orientation during interaction with the membrane, polarization modulation infrared reflection absorption spectroscopy was used. The measurements revealed conformational changes in the peptide, accompanied by reorientation and translocation of the peptide at the membrane surface. The study suggests that melittin insertion into the outer membrane affects its permeability and capacitance but does not disturb the membrane's bilayer structure, indicating a distinct mechanism of the peptide action on the outer membrane of Gram-negative bacteria.
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Affiliation(s)
- Justus
C. Stephani
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Bishoy Khairalla
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
- Research
Center Neurosensory Science, Carl von Ossietzky
University of Oldenburg, 26111 Oldenburg, Germany
- CeNaD—Center
for Nanoscale Dynamics, Carl von Ossietzky
University of Oldenburg, 26111 Oldenburg, Germany
| | - Izabella Brand
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
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2
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Nomura K, Mori S, Shimamoto K. Roles of a Glycolipid MPIase in Sec-Independent Membrane Protein Insertion. MEMBRANES 2024; 14:48. [PMID: 38392675 PMCID: PMC10890265 DOI: 10.3390/membranes14020048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Membrane protein integrase (MPIase), an endogenous glycolipid in Escherichia coli (E. coli) membranes, is essential for membrane protein insertion in E. coli. We have examined Sec-independent membrane protein insertion mechanisms facilitated by MPIase using physicochemical analytical techniques, namely solid-state nuclear magnetic resonance, fluorescence measurements, and surface plasmon resonance. In this review, we outline the physicochemical characteristics of membranes that may affect membrane insertion of proteins. Subsequently, we introduce our results verifying the effects of membrane lipids on insertion and estimate the impact of MPIase. Although MPIase is a minor component of E. coli membranes, it regulates insertion by altering the physicochemical properties of the membrane. In addition, MPIase promotes insertion by interacting with substrate proteins. We propose comprehensive mechanisms for the membrane insertion of proteins involving MPIase, which provide a physicochemical basis for understanding the roles of glycolipids in protein translocation.
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Affiliation(s)
- Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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3
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Ball HL, Said H, Chapman K, Fu R, Xiong Y, Burk JA, Rosenbaum D, Veneziano R, Cotten ML. Orexin A, an amphipathic α-helical neuropeptide involved in pleiotropic functions in the nervous and immune systems: Synthetic approach and biophysical studies of the membrane-bound state. Biophys Chem 2023; 297:107007. [PMID: 37037119 DOI: 10.1016/j.bpc.2023.107007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/11/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023]
Abstract
This research reports on the membrane interactions of orexin A (OXA), an α-helical and amphipathic neuropeptide that contains 33 residues and two disulfide bonds in the N-terminal region. OXA, which activates the orexins 1 and 2 receptors in neural and immune cell membranes, has essential pleiotropic physiological effects, including at the levels of arousal, sleep/wakefulness, energy balance, neuroprotection, lipid signaling, the inflammatory response, and pain. As a result, the orexin system has become a prominent target to treat diseases such as sleep disorders, drug addiction, and inflammation. While the high-resolution structure of OXA has been investigated in water and bound to micelles, there is a lack of information about its conformation bound to phospholipid membranes and its receptors. NMR is a powerful method to investigate peptide structures in a membrane environment. To facilitate the NMR structural studies of OXA exposed to membranes, we present a novel synthetic scheme, leading to the production of isotopically-labeled material at high purity. A receptor activation assay shows that the 15N-labeled peptide is biologically active. Biophysical studies are performed using surface plasmon resonance, circular dichroism, and NMR to investigate the interactions of OXA with phospholipid bilayers. The results demonstrate a strong interaction between the peptide and phospholipids, an increase in α-helical content upon membrane binding, and an in-plane orientation of the C-terminal region critical to function. This new knowledge about structure-activity relationships in OXA could inspire the design of novel therapeutics that leverage the anti-inflammatory and neuro-protective functions of OXA, and therefore could help address neuroinflammation, a major issue associated with neurological disorders such as Alzheimer's disease.
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Affiliation(s)
- Haydn L Ball
- Department of Chemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hooda Said
- Department of Bioengineering, College of Engineering and Computing, George Mason University, Fairfax, VA 22030, USA
| | - Karen Chapman
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Yawei Xiong
- Department of Applied Science, William & Mary, Williamsburg, VA 23185, USA
| | - Joshua A Burk
- Department of Psychological Sciences, William & Mary, Williamsburg, VA 23185, USA
| | - Daniel Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Remi Veneziano
- Department of Bioengineering, College of Engineering and Computing, George Mason University, Fairfax, VA 22030, USA
| | - Myriam L Cotten
- Department of Applied Science, William & Mary, Williamsburg, VA 23185, USA.
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4
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Strandberg E, Wadhwani P, Bürck J, Anders P, Mink C, van den Berg J, Ciriello RAM, Melo MN, Castanho MARB, Bardají E, Ulmschneider JP, Ulrich AS. Temperature-Dependent Re-alignment of the Short Multifunctional Peptide BP100 in Membranes Revealed by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations. Chembiochem 2023; 24:e202200602. [PMID: 36454659 DOI: 10.1002/cbic.202200602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/02/2022]
Abstract
BP100 is a cationic undecamer peptide with antimicrobial and cell-penetrating activities. The orientation of this amphiphilic α-helix in lipid bilayers was examined under numerous conditions using solid-state 19 F, 15 N and 2 H NMR. At high temperatures in saturated phosphatidylcholine lipids, BP100 lies flat on the membrane surface, as expected. Upon lowering the temperature towards the lipid phase transition, the helix is found to flip into an upright transmembrane orientation. In thin bilayers, this inserted state was stable at low peptide concentration, but thicker membranes required higher peptide concentrations. In the presence of lysolipids, the inserted state prevailed even at high temperature. Molecular dynamics simulations suggest that BP100 monomer insertion can be stabilized by snorkeling lysine side chains. These results demonstrate that even a very short helix like BP100 can span (and thereby penetrate through) a cellular membrane under suitable conditions.
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Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Patrick Anders
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Christian Mink
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.,Present address: Syngenta Crop Protection AG, 4333, Münchwilen, Switzerland
| | - Jonas van den Berg
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Raffaele A M Ciriello
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Manuel N Melo
- Instituto de Medicina Molecular Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal.,Present address: ITQB Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Miguel A R B Castanho
- Instituto de Medicina Molecular Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Eduard Bardají
- LIPPSO, Department of Chemistry, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Jakob P Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany.,Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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5
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Length matters: Functional flip of the short TatA transmembrane helix. Biophys J 2022:S0006-3495(22)03926-1. [PMID: 36523158 DOI: 10.1016/j.bpj.2022.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The twin arginine translocase (Tat) exports folded proteins across bacterial membranes. The putative pore-forming or membrane-weakening component (TatAd in B. subtilis) is anchored to the lipid bilayer via an unusually short transmembrane α-helix (TMH), with less than 16 residues. Its tilt angle in different membranes was analyzed under hydrophobic mismatch conditions, using synchrotron radiation circular dichroism and solid-state NMR. Positive mismatch (introduced either by reconstitution in short-chain lipids or by extending the hydrophobic TMH length) increased the helix tilt of the TMH as expected. Negative mismatch (introduced either by reconstitution in long-chain lipids or by shortening the TMH), on the other hand, led to protein aggregation. These data suggest that the TMH of TatA is just about long enough for stable membrane insertion. At the same time, its short length is a crucial factor for successful translocation, as demonstrated here in native membrane vesicles using an in vitro translocation assay. Furthermore, when reconstituted in model membranes with negative spontaneous curvature, the TMH was found to be aligned parallel to the membrane surface. This intrinsic ability of TatA to flip out of the membrane core thus seems to play a key role in its membrane-destabilizing effect during Tat-dependent translocation.
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6
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Matching amino acids membrane preference profile to improve activity of antimicrobial peptides. Commun Biol 2022; 5:1199. [PMID: 36347951 PMCID: PMC9643456 DOI: 10.1038/s42003-022-04164-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Antimicrobial peptides (AMPs) are cationic antibiotics that can kill multidrug-resistant bacteria via membrane insertion. However, their weak activity limits their clinical use. Ironically, the cationic charge of AMPs is essential for membrane binding, but it obstructs membrane insertion. In this study, we postulate that this problem can be overcome by locating cationic amino acids at the energetically preferred membrane surface. All amino acids have an energetically preferred or less preferred membrane position profile, and this profile is strongly related to membrane insertion. However, most AMPs do not follow this profile. One exception is protegrin-1, a powerful but neglected AMP. In the present study, we found that a potent AMP, WCopW5, strongly resembles protegrin-1 and that the match between its sequence and the preferred position profile closely correlates with its antimicrobial activity. One of its derivatives, WCopW43, has antimicrobial activity comparable to that of the most effective AMPs in clinical use.
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7
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Membranolytic Mechanism of Amphiphilic Antimicrobial β-Stranded [KL]n Peptides. Biomedicines 2022; 10:biomedicines10092071. [PMID: 36140173 PMCID: PMC9495826 DOI: 10.3390/biomedicines10092071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Amphipathic peptides can act as antibiotics due to membrane permeabilization. KL peptides with the repetitive sequence [Lys-Leu]n-NH2 form amphipathic β-strands in the presence of lipid bilayers. As they are known to kill bacteria in a peculiar length-dependent manner, we suggest here several different functional models, all of which seem plausible, including a carpet mechanism, a β-barrel pore, a toroidal wormhole, and a β-helix. To resolve their genuine mechanism, the activity of KL peptides with lengths from 6–26 amino acids (plus some inverted LK analogues) was systematically tested against bacteria and erythrocytes. Vesicle leakage assays served to correlate bilayer thickness and peptide length and to examine the role of membrane curvature and putative pore diameter. KL peptides with 10–12 amino acids showed the best therapeutic potential, i.e., high antimicrobial activity and low hemolytic side effects. Mechanistically, this particular window of an optimum β-strand length around 4 nm (11 amino acids × 3.7 Å) would match the typical thickness of a lipid bilayer, implying the formation of a transmembrane pore. Solid-state 15N- and 19F-NMR structure analysis, however, showed that the KL backbone lies flat on the membrane surface under all conditions. We can thus refute any of the pore models and conclude that the KL peptides rather disrupt membranes by a carpet mechanism. The intriguing length-dependent optimum in activity can be fully explained by two counteracting effects, i.e., membrane binding versus amyloid formation. Very short KL peptides are inactive, because they are unable to bind to the lipid bilayer as flexible β-strands, whereas very long peptides are inactive due to vigorous pre-aggregation into β-sheets in solution.
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8
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Role of a bacterial glycolipid in Sec-independent membrane protein insertion. Sci Rep 2022; 12:12231. [PMID: 35851412 PMCID: PMC9293918 DOI: 10.1038/s41598-022-16304-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/07/2022] [Indexed: 11/08/2022] Open
Abstract
Non-proteinaceous components in membranes regulate membrane protein insertion cooperatively with proteinaceous translocons. An endogenous glycolipid in the Escherichia coli membrane called membrane protein integrase (MPIase) is one such component. Here, we focused on the Sec translocon-independent pathway and examined the mechanisms of MPIase-facilitated protein insertion using physicochemical techniques. We determined the membrane insertion efficiency of a small hydrophobic protein using solid-state nuclear magnetic resonance, which showed good agreement with that determined by the insertion assay using an in vitro translation system. The observed insertion efficiency was strongly correlated with membrane physicochemical properties measured using fluorescence techniques. Diacylglycerol, a trace component of E. coli membrane, reduced the acyl chain mobility in the core region and inhibited the insertion, whereas MPIase restored them. We observed the electrostatic intermolecular interactions between MPIase and the side chain of basic amino acids in the protein, suggesting that the negatively charged pyrophosphate of MPIase attracts the positively charged residues of a protein near the membrane surface, which triggers the insertion. Thus, this study demonstrated the ingenious approach of MPIase to support membrane insertion of proteins by using its unique molecular structure in various ways.
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9
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Talandashti R, Mehrnejad F, Rostamipour K, Doustdar F, Lavasanifar A. Molecular Insights into Pore Formation Mechanism, Membrane Perturbation, and Water Permeation by the Antimicrobial Peptide Pleurocidin: A Combined All-Atom and Coarse-Grained Molecular Dynamics Simulation Study. J Phys Chem B 2021; 125:7163-7176. [PMID: 34171196 DOI: 10.1021/acs.jpcb.1c01954] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The antimicrobial peptide (AMP) pleurocidin has a broad antimicrobial activity against Gram-negative and Gram-positive bacteria by perturbation and permeabilizing their membranes; however, understanding the mechanism of action of pleurocidin, a promising AMP for replacing current antibiotic agents, has tremendous importance for future applications. Hence, we applied all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations to provide molecular-level insights into the pore-forming process. The early stages of pore formation were examined by 500 ns AA simulations. The results demonstrated that pleurocidin has the ability to create a pore with two peptides through which water molecules can flow. However, the results of the 25 μs CG simulations indicate that the final pore will be created by accumulation of more than two peptides. The results show that after 2.5 μs of simulations, peptides will aggregate and create a channel-like pore across the membrane. Pleurocidin can construct a more efficient and stable pore in the anionic membranes than in the zwitterionic membranes. Moreover, the structure amphipathicity, polarity, and basic residues play crucial roles in the pore formation and flow of water molecules across the lipid bilayers. In general, the findings revealed that based on the lipid compositions of the membranes, pleurocidin could act by forming either toroidal or disordered toroidal pores with different peptide arrangements.
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Affiliation(s)
- Reza Talandashti
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, P. O. Box: 1985717443 Tehran, Iran.,Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Kiana Rostamipour
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Farahnoosh Doustdar
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 14395-1561, Iran.,Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | - Afsaneh Lavasanifar
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
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10
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Felício MR, Silveira GGOS, Oshiro KGN, Meneguetti BT, Franco OL, Santos NC, Gonçalves S. Polyalanine peptide variations may have different mechanisms of action against multidrug-resistant bacterial pathogens. J Antimicrob Chemother 2021; 76:1174-1186. [PMID: 33501992 DOI: 10.1093/jac/dkaa560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/15/2020] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The number of bacterial pathogens resistant to the currently available antibiotics has dramatically increased, with antimicrobial peptides (AMPs) being among the most promising potential new drugs. In this study, the applicability and mechanisms of action of Pa-MAP 2 and Pa-MAP 1.9, two AMPs synthetically designed based on a natural AMP template, were evaluated. METHODS Pa-MAP 2 and Pa-MAP 1.9 were tested against a clinically isolated multidrug-resistant (MDR) Escherichia coli strain. Biophysical approaches were used to evaluate the preference of both peptides for specific lipid membranes, and bacterial surface changes imaged by atomic force microscopy (AFM). The efficacy of both peptides was assessed both in vitro and in vivo. RESULTS Experimental results showed that both peptides have antimicrobial activity against the E. coli MDR strain. Zeta potential and surface plasmon resonance assays showed that they interact extensively with negatively charged membranes, changing from a random coil structure, when free in solution, to an α-helical structure after membrane interaction. The antibacterial efficacy was evaluated in vitro, by several techniques, and in vivo, using a wound infection model, showing a concentration-dependent antibacterial effect. Different membrane properties were evaluated to understand the mechanism underlying peptide action, showing that both promote destabilization of the bacterial surface, as imaged by AFM, and change properties such as membrane surface and dipole potential. CONCLUSIONS Despite their similarity, data indicate that the mechanisms of action of the peptides are different, with Pa-MAP 1.9 being more effective than Pa-MAP 2. These results highlight their potential use as antimicrobial agents against MDR bacteria.
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Affiliation(s)
- Mário R Felício
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Gislaine G O S Silveira
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Karen G N Oshiro
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil
| | - Beatriz T Meneguetti
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Octávio L Franco
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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11
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Li M, Heller WT, Liu CH, Gao CY, Cai Y, Hou Y, Nieh MP. Effects of fluidity and charge density on the morphology of a bicellar mixture - A SANS study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183315. [PMID: 32304755 DOI: 10.1016/j.bbamem.2020.183315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 04/11/2020] [Accepted: 04/13/2020] [Indexed: 01/28/2023]
Abstract
The spontaneously formed structures of physiologically relevant lipid model membranes made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) and 1,2-hexanoyl-sn-glycero-3-phosphocholine have been evaluated in depth using small angle neutron scattering. Although a common molar ratio of long- to short- chain phospholipids (~4) as reported in many bicellar mixtures was used, discoidal bicelles were not found as the major phase throughout the range of lipid concentration and temperature studied, indicating that the required condition for the formation of bicelle is the immiscibility between the long- and short- chain lipids, which were in the gel and Lα phases, respectively, in previous reports. In this study, all lipids are in the Lα phase. The characterization outcome suggests that the spontaneous structures tie strongly with the physical parameters of the system such as melting transition temperature of the long-chain lipid, total lipid concentration and charge density of the system. Multilamellar vesicles, unilamellar vesicles, ribbons and perforated lamellae can be obtained based on the analysis of the small angle neutron scattering results, leading to the construction of structural diagrams. This report provides the important map to choose suitable lipid systems for the structural study of membrane-associated proteins, design of theranostic nanocarriers or other related research fields.
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Affiliation(s)
- Ming Li
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, 06269, USA
| | - William T Heller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chung-Hao Liu
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, 06269, USA
| | - Carrie Y Gao
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yutian Cai
- Department of Polymer Material Science and Engineering, College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410000, China
| | - Yiming Hou
- Department of Polymer Material Science and Engineering, College of Materials Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410000, China
| | - Mu-Ping Nieh
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, 06269, USA; Department of Chemical & Biomolecular Engineering, University of Connecticut, Storrs 06269, USA; Department of Biomedical Engineering, University of Connecticut, Storrs 06269, USA.
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12
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Strandberg E, Bentz D, Wadhwani P, Bürck J, Ulrich AS. Terminal charges modulate the pore forming activity of cationic amphipathic helices. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183243. [DOI: 10.1016/j.bbamem.2020.183243] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/14/2020] [Accepted: 02/18/2020] [Indexed: 11/15/2022]
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13
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Strandberg E, Bentz D, Wadhwani P, Ulrich AS. Chiral supramolecular architecture of stable transmembrane pores formed by an α-helical antibiotic peptide in the presence of lyso-lipids. Sci Rep 2020; 10:4710. [PMID: 32170095 PMCID: PMC7070102 DOI: 10.1038/s41598-020-61526-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/20/2020] [Indexed: 01/10/2023] Open
Abstract
The amphipathic α-helical antimicrobial peptide MSI-103 (aka KIA21) can form stable transmembrane pores when the bilayer takes on a positive spontaneous curvature, e.g. by the addition of lyso-lipids. Solid-state 31P- and 15N-NMR demonstrated an enrichment of lyso-lipids in these toroidal wormholes. Anionic lyso-lipids provided additional stabilization by electrostatic interactions with the cationic peptides. The remaining lipid matrix did not affect the nature of the pore, as peptides maintained the same orientation independent of lipid charge, and a change in membrane thickness did not considerably affect their tilt angle. Under optimized conditions (i.e. in the presence of lyso-lipids and appropriate bilayer thickness), stable and well-aligned pores could be obtained for solid-state 2H-NMR analysis. These data revealed for the first time the complete 3D alignment of this representative amphiphilic peptide in fluid membranes, which is compatible with either monomeric helices as constituents, or left-handed supercoiled dimers as building blocks from which the overall toroidal wormhole is assembled.
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Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - David Bentz
- KIT, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany. .,KIT, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.
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14
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Tan P, Lai Z, Zhu Y, Shao C, Akhtar MU, Li W, Zheng X, Shan A. Multiple Strategy Optimization of Specifically Targeted Antimicrobial Peptide Based on Structure-Activity Relationships to Enhance Bactericidal Efficiency. ACS Biomater Sci Eng 2019; 6:398-414. [PMID: 33463238 DOI: 10.1021/acsbiomaterials.9b00937] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Unlike traditional broad-spectrum antibacterial agents, specifically targeted antimicrobial peptides (STAMPs) are difficult for bacteria to develop resistance to due to their unique membrane lytic mechanism. Additionally, STAMPs can maintain a normal ecological balance and provide long-term protection to the body. However, therapeutic applications of STAMPS are hindered by their weak activity and imperfect specificity, as well as lack of knowledge in understanding their structure-activity relationships. To investigate the effects of different parameters on the biological activities of STAMPs, a peptide sequence, WKKIWKDPGIKKWIK, was truncated, extended, and provided with an increased charge and altered amphipathicity. In addition, a novel template modification method for attaching a phage-displayed peptide, which recognized and bound to Escherichia coli (E. coli) cells, to the end of the sequence was introduced. Compared with the traditional template modification method, peptide 13, which contained a phage-displayed peptide at the C-terminus, exhibited superior narrow-spectrum antibacterial activity against E. coli compared to that of parental peptide 2, and the activity and specificity of peptide 13 were increased by 5.0 and 2.4 times, respectively. Additionally, peptide 13 showed low cytotoxicity and relatively desirable salt, serum, acid, alkaline and heat stability. In this study, peptide 13 specifically killed E. coli by causing cytoplasmic membrane rupture and cytosol leakage. In summary, these findings are useful for improving the activity and specificity of STAMPs and show that peptide 13 is able to combat the growing threat of E. coli infections.
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Affiliation(s)
- Peng Tan
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Zhenheng Lai
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Yongjie Zhu
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Changxuan Shao
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Muhammad Usman Akhtar
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Weifen Li
- Institute of Animal Nutrition and Feed Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Xin Zheng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Anshan Shan
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
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15
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Kubyshkin V, Grage SL, Ulrich AS, Budisa N. Bilayer thickness determines the alignment of model polyproline helices in lipid membranes. Phys Chem Chem Phys 2019; 21:22396-22408. [PMID: 31577299 DOI: 10.1039/c9cp02996f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Our understanding of protein folds relies fundamentally on the set of secondary structures found in the proteomes. Yet, there also exist intriguing structures and motifs that are underrepresented in natural biopolymeric systems. One example is the polyproline II helix, which is usually considered to have a polar character and therefore does not form membrane spanning sections of membrane proteins. In our work, we have introduced specially designed polyproline II helices into the hydrophobic membrane milieu and used 19F NMR to monitor the helix alignment in oriented lipid bilayers. Our results show that these artificial hydrophobic peptides can adopt several different alignment states. If the helix is shorter than the thickness of the hydrophobic core of the membrane, it is submerged into the bilayer with its long axis parallel to the membrane plane. The polyproline helix adopts a transmembrane alignment when its length exceeds the bilayer thickness. If the peptide length roughly matches the lipid thickness, a coexistence of both states is observed. We thus show that the lipid thickness plays a determining role in the occurrence of a transmembrane polyproline II helix. We also found that the adaptation of polyproline II helices to hydrophobic mismatch is in some notable aspects different from α-helices. Finally, our results prove that the polyproline II helix is a competent structure for the construction of transmembrane peptide segments, despite the fact that no such motif has ever been reported in natural systems.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany and Department of Chemistry, University of Manitoba, Dysart Rd. 144, Winnipeg MB R3T 2N2, Canada.
| | - Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O.B. 3640, Karlsruhe 76021, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O.B. 3640, Karlsruhe 76021, Germany and Institute of Organic Chemistry, KIT, Fritz-Haber-Weg 6, Karlsruhe 76131, Germany
| | - Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany and Department of Chemistry, University of Manitoba, Dysart Rd. 144, Winnipeg MB R3T 2N2, Canada.
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16
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Mihailescu M, Sorci M, Seckute J, Silin VI, Hammer J, Perrin BS, Hernandez JI, Smajic N, Shrestha A, Bogardus KA, Greenwood AI, Fu R, Blazyk J, Pastor RW, Nicholson LK, Belfort G, Cotten ML. Structure and Function in Antimicrobial Piscidins: Histidine Position, Directionality of Membrane Insertion, and pH-Dependent Permeabilization. J Am Chem Soc 2019; 141:9837-9853. [PMID: 31144503 DOI: 10.1021/jacs.9b00440] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Piscidins are histidine-enriched antimicrobial peptides that interact with lipid bilayers as amphipathic α-helices. Their activity at acidic and basic pH in vivo makes them promising templates for biomedical applications. This study focuses on p1 and p3, both 22-residue-long piscidins with 68% sequence identity. They share three histidines (H3, H4, and H11), but p1, which is significantly more permeabilizing, has a fourth histidine (H17). This study investigates how variations in amphipathic character associated with histidines affect the permeabilization properties of p1 and p3. First, we show that the permeabilization ability of p3, but not p1, is strongly inhibited at pH 6.0 when the conserved histidines are partially charged and H17 is predominantly neutral. Second, our neutron diffraction measurements performed at low water content and neutral pH indicate that the average conformation of p1 is highly tilted, with its C-terminus extending into the opposite leaflet. In contrast, p3 is surface bound with its N-terminal end tilted toward the bilayer interior. The deeper membrane insertion of p1 correlates with its behavior at full hydration: an enhanced ability to tilt, bury its histidines and C-terminus, induce membrane thinning and defects, and alter membrane conductance and viscoelastic properties. Furthermore, its pH-resiliency relates to the neutral state favored by H17. Overall, these results provide mechanistic insights into how differences in the histidine content and amphipathicity of peptides can elicit different directionality of membrane insertion and pH-dependent permeabilization. This work features complementary methods, including dye leakage assays, NMR-monitored titrations, X-ray and neutron diffraction, oriented CD, molecular dynamics, electrochemical impedance spectroscopy, surface plasmon resonance, and quartz crystal microbalance with dissipation.
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Affiliation(s)
- Mihaela Mihailescu
- Institute for Bioscience and Biotechnology Research , University of Maryland , Rockville , Maryland 20850 , United States
| | - Mirco Sorci
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Jolita Seckute
- Department of Molecular Biology and Genetics , Cornell University , Ithaca , New York 14853 , United States
| | - Vitalii I Silin
- Institute for Bioscience and Biotechnology Research , University of Maryland , Rockville , Maryland 20850 , United States
| | - Janet Hammer
- Department of Biomedical Sciences , Ohio University , Athens , Ohio 45701 , United States
| | - B Scott Perrin
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Jorge I Hernandez
- Department of Bioengineering , Clemson University , Clemson , South Carolina 29634 , United States
| | - Nedzada Smajic
- Department of Chemistry , Hamilton College , Clinton , New York 13323 , United States
| | - Akritee Shrestha
- Department of Chemistry , Hamilton College , Clinton , New York 13323 , United States
| | - Kimberly A Bogardus
- Department of Chemistry , Hamilton College , Clinton , New York 13323 , United States
| | - Alexander I Greenwood
- Department of Applied Science , College of William and Mary , Williamsburg , Virginia 23185 , United States
| | - Riqiang Fu
- National High Magnetic Field Laboratory , Tallahassee , Florida 32310 , United States
| | - Jack Blazyk
- Department of Biomedical Sciences , Ohio University , Athens , Ohio 45701 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Linda K Nicholson
- Department of Molecular Biology and Genetics , Cornell University , Ithaca , New York 14853 , United States
| | - Georges Belfort
- Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Myriam L Cotten
- Department of Applied Science , College of William and Mary , Williamsburg , Virginia 23185 , United States
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17
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Baeriswyl S, Gan BH, Siriwardena TN, Visini R, Robadey M, Javor S, Stocker A, Darbre T, Reymond JL. X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes. ACS Chem Biol 2019; 14:758-766. [PMID: 30830745 DOI: 10.1021/acschembio.9b00047] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Herein, we report X-ray crystal structures of 11-13 residue antimicrobial peptides (AMPs) active against Pseudomonas aeruginosa as complexes of fucosylated d-enantiomeric sequences with the P. aeruginosa lectin LecB. These represent the first crystal structures of short AMPs. In 24 individual structures of eight different peptides, we found mostly α-helices assembled as two-helix or four-helix bundles with a hydrophobic core and cationic residues pointing outside. Two of the analogs formed an extended structure engaging in multiple contacts with the lectin. Molecular dynamics (MD) simulations showed that α-helices are stabilized by bundle formation and suggested that the N-terminal acyl group present in the linker to the fucosyl group can extend the helix by one additional H-bond and increase α-helix amphiphilicity. Investigating N-terminal acylation led to AMPs with equivalent and partly stronger antibacterial effects compared to the free peptide.
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Affiliation(s)
- Stéphane Baeriswyl
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Bee-Ha Gan
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Thissa N. Siriwardena
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Ricardo Visini
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Maurane Robadey
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Sacha Javor
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Achim Stocker
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Tamis Darbre
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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18
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Yamamoto T, Umegawa Y, Yamagami M, Suzuki T, Tsuchikawa H, Hanashima S, Matsumori N, Murata M. The Perpendicular Orientation of Amphotericin B Methyl Ester in Hydrated Lipid Bilayers Supports the Barrel-Stave Model. Biochemistry 2019; 58:2282-2291. [PMID: 30973009 DOI: 10.1021/acs.biochem.9b00180] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The clinically important antibiotic amphotericin B (AmB) is a membrane-active natural product that targets membrane sterol. The antimicrobial activity of AmB is generally attributed to its membrane permeabilization, which occurs when a pore is formed across a lipid bilayer. In this study, the molecular orientation of AmB was investigated using solid-state nuclear magnetic resonance (NMR) to better understand the mechanism of antifungal activity. The methyl ester of AmB (AME) labeled with NMR isotopes, d3-AME, and its fluorinated and/or 13C-labeled derivatives were prepared. All of the AmB derivatives showed similar membrane-disrupting activities and ultraviolet spectra in phospholipid liposomes, suggesting that their molecular assemblies in membranes closely mimic those of AmB. Solid-state 2H NMR measurements of d3-AME in a hydrated membrane showed that the mobility of AME molecules depends on concentration and temperature. At a 1:5:45 AME:Erg:dimyristoylphosphatidylcholine ratio, AME became sufficiently mobilized to observe the motional averaging of quadrupole coupling. On the basis of the rotational averaging effect of 19F chemical shift anisotropy, 2H quadrupolar splitting, and 13C-19F dipolar coupling of 14β-F-AMEs, we deduced that the molecular axis of AME is predominantly parallel to the normal of a lipid bilayer. This result supports the barrel-stave model as a molecular assembly of AmB in membranes.
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Affiliation(s)
- Tomoya Yamamoto
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,JST-ERATO Lipid Active Structure Project, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,JST-ERATO Lipid Active Structure Project, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Fundamental Science Research Center, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Masaki Yamagami
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Taiga Suzuki
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Department of Chemistry, Graduate School of Sciences , Kyushu University , Fukuoka 819-0395 , Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,JST-ERATO Lipid Active Structure Project, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan.,Fundamental Science Research Center, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
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19
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Ermakova E, Kurbanov R, Zuev Y. Coarse-grained molecular dynamics of membrane semitoroidal pore formation in model lipid-peptide systems. J Mol Graph Model 2019; 87:1-10. [DOI: 10.1016/j.jmgm.2018.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 12/31/2022]
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20
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Reißer S, Strandberg E, Steinbrecher T, Elstner M, Ulrich AS. Best of Two Worlds? How MD Simulations of Amphiphilic Helical Peptides in Membranes Can Complement Data from Oriented Solid-State NMR. J Chem Theory Comput 2018; 14:6002-6014. [PMID: 30289704 DOI: 10.1021/acs.jctc.8b00283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The membrane alignment of helical amphiphilic peptides in oriented phospholipid bilayers can be obtained as ensemble and time averages from solid state 2H NMR by fitting the quadrupolar splittings to ideal α-helices. At the same time, molecular dynamics (MD) simulations can provide atomistic insight into peptide-membrane systems. Here, we evaluate the potential of MD simulations to complement the experimental NMR data that is available on three exemplary systems: the natural antimicrobial peptide PGLa and the two designer-made peptides MSI-103 and KIA14, whose sequences were derived from PGLa. Each peptide was simulated for 1 μs in a DMPC lipid bilayer. We calculated from the MD simulations the local angles which define the side chain geometry with respect to the peptide helix. The peptide orientation was then calculated (i) directly from the simulation, (ii) from back-calculated MD-derived NMR splittings, and (iii) from experimental 2H NMR splittings. Our findings are that (1) the membrane orientation and secondary structure of the peptides found in the NMR analysis are generally well reproduced by the simulations; (2) the geometry of the side chains with respect to the helix backbone can deviate significantly from the ideal structure depending on the specific residue, but on average all side chains have the same orientation; and (3) for all of our peptides, the azimuthal rotation angle found from the MD-derived splittings is about 15° smaller than the experimental value.
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Affiliation(s)
- Sabine Reißer
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
| | - Thomas Steinbrecher
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Anne S Ulrich
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany.,Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
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21
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Strandberg E, Grau-Campistany A, Wadhwani P, Bürck J, Rabanal F, Ulrich AS. Helix Fraying and Lipid-Dependent Structure of a Short Amphipathic Membrane-Bound Peptide Revealed by Solid-State NMR. J Phys Chem B 2018; 122:6236-6250. [DOI: 10.1021/acs.jpcb.8b02661] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Ariadna Grau-Campistany
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Francesc Rabanal
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
- KIT, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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22
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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: 73] [Impact Index Per Article: 12.2] [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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23
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Oluwole AO, Klingler J, Danielczak B, Babalola JO, Vargas C, Pabst G, Keller S. Formation of Lipid-Bilayer Nanodiscs by Diisobutylene/Maleic Acid (DIBMA) Copolymer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:14378-14388. [PMID: 29160078 DOI: 10.1021/acs.langmuir.7b03742] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Membrane proteins usually need to be extracted from their native environment and separated from other membrane components for in-depth in vitro characterization. The use of styrene/maleic acid (SMA) copolymers to solubilize membrane proteins and their surrounding lipids into bilayer nanodiscs is an attractive approach toward this goal. We have recently shown that a diisobutylene/maleic acid (DIBMA) copolymer similarly solubilizes model and cellular membranes but, unlike SMA(3:1), has a mild impact on lipid acyl-chain order and thermotropic phase behavior. Here, we used fluorescence spectroscopy, small-angle X-ray scattering, size-exclusion chromatography, dynamic light scattering, and 31P nuclear magnetic resonance spectroscopy to examine the self-association of DIBMA and its membrane-solubilization properties against lipids differing in acyl-chain length and saturation. Although DIBMA is less hydrophobic than commonly used SMA(3:1) and SMA(2:1) copolymers, it efficiently formed lipid-bilayer nanodiscs that decreased in size with increasing polymer/lipid ratio while maintaining the overall thickness of the membrane. DIBMA fractions of different molar masses were similarly efficient in solubilizing a saturated lipid. Coulomb screening at elevated ionic strength or reduced charge density on the polymer at low pH enhanced the solubilization efficiency of DIBMA. The free-energy penalty for transferring phospholipids from vesicular bilayers into nanodiscs became more unfavorable with increasing acyl-chain length and unsaturation. Altogether, these findings provide a rational framework for using DIBMA in membrane-protein research by shedding light on the effects of polymer and lipid properties as well as experimental conditions on membrane solubilization.
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Affiliation(s)
- Abraham Olusegun Oluwole
- Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
- Department of Chemistry, University of Ibadan , 200284 Ibadan, Nigeria
| | - Johannes Klingler
- Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Bartholomäus Danielczak
- Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | | | - Carolyn Vargas
- Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Georg Pabst
- Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, University of Graz , Humboldtstr. 50/III, 8010 Graz, Austria
- BioTechMed-Graz , 8010 Graz, Austria
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
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Structure analysis of the membrane-bound dermcidin-derived peptide SSL-25 from human sweat. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2308-2318. [DOI: 10.1016/j.bbamem.2017.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/11/2017] [Accepted: 09/05/2017] [Indexed: 11/24/2022]
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25
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Molecular mechanism of synergy between the antimicrobial peptides PGLa and magainin 2. Sci Rep 2017; 7:13153. [PMID: 29030606 PMCID: PMC5640672 DOI: 10.1038/s41598-017-12599-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/08/2017] [Indexed: 12/19/2022] Open
Abstract
PGLa and magainin 2 (MAG2) are amphiphilic α-helical membranolytic peptides from frog skin with known synergistic antimicrobial activity. By systematically mutating residues in the two peptides it was possible to identify the ones crucial for the synergy, as monitored by biological assays, fluorescence vesicle leakage, and solid-state 15N-NMR. Electrostatic interactions between anionic groups in MAG2 and cationic residues in PGLa enhance synergy but are not necessary for the synergistic effect. Instead, two Gly residues (7 and 11) in a so-called GxxxG motif in PGLa are necessary for synergy. Replacing either of them with Ala or another hydrophobic residue completely abolishes synergy according to all three methods used. The designer-made peptide MSI-103, which has a similar sequence as PGLa, shows no synergy with MAG2, but by introducing two Gly mutations it was possible to make it synergistic. A molecular model is proposed for the functionally active PGLa-MAG2 complex, consisting of a membrane-spanning antiparallel PGLa dimer that is stabilized by intimate Gly-Gly contacts, and where each PGLa monomer is in contact with one MAG2 molecule at its C-terminus.
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26
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Stutz K, Müller AT, Hiss JA, Schneider P, Blatter M, Pfeiffer B, Posselt G, Kanfer G, Kornmann B, Wrede P, Altmann KH, Wessler S, Schneider G. Peptide-Membrane Interaction between Targeting and Lysis. ACS Chem Biol 2017; 12:2254-2259. [PMID: 28763193 DOI: 10.1021/acschembio.7b00504] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Certain cationic peptides interact with biological membranes. These often-complex interactions can result in peptide targeting to the membrane, or in membrane permeation, rupture, and cell lysis. We investigated the relationship between the structural features of membrane-active peptides and these effects, to better understand these processes. To this end, we employed a computational method for morphing a membranolytic antimicrobial peptide into a nonmembranolytic mitochondrial targeting peptide by "directed simulated evolution." The results obtained demonstrate that superficially subtle sequence modifications can strongly affect the peptides' membranolytic and membrane-targeting abilities. Spectroscopic and computational analyses suggest that N- and C-terminal structural flexibility plays a crucial role in determining the mode of peptide-membrane interaction.
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Affiliation(s)
- Katharina Stutz
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Alex T. Müller
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Jan A. Hiss
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Markus Blatter
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Bernhard Pfeiffer
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Gernot Posselt
- Department
of Molecular Biology, Division of Microbiology, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Gil Kanfer
- Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), Otto-Stern-Weg-3, 8093 Zurich, Switzerland
| | - Benoît Kornmann
- Institute of Biochemistry, Swiss Federal Institute of Technology (ETH), Otto-Stern-Weg-3, 8093 Zurich, Switzerland
| | - Paul Wrede
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Silja Wessler
- Department
of Molecular Biology, Division of Microbiology, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
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27
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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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28
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Perrin BS, Fu R, Cotten ML, Pastor RW. Simulations of Membrane-Disrupting Peptides II: AMP Piscidin 1 Favors Surface Defects over Pores. Biophys J 2017; 111:1258-1266. [PMID: 27653484 DOI: 10.1016/j.bpj.2016.08.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/29/2016] [Accepted: 08/10/2016] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial peptides (AMPs) that disrupt bacterial membranes are promising therapeutics against the growing number of antibiotic-resistant bacteria. The mechanism of membrane disruption by the AMP piscidin 1 was examined with multimicrosecond all-atom molecular dynamics simulations and solid-state NMR spectroscopy. The primary simulation was initialized with 20 peptides in four barrel-stave pores in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol bilayer. The four pores relaxed to toroidal by 200 ns, only one porelike structure containing two transmembrane helices remained at 26 μs, and none of the 18 peptides released to the surface reinserted to form pores. The simulation was repeated at 413 K with an applied electric field and all peptides were surface-bound by 200 ns. Trajectories of surface-bound piscidin with and without applied fields at 313 and 413 K and totaling 6 μs show transient distortions of the bilayer/water interface (consistent with (31)P NMR), but no insertion to transmembrane or pore states. (15)N chemical shifts confirm a fully surface-bound conformation. Taken together, the simulation and experimental results imply that transient defects rather than stable pores are responsible for membrane disruption by piscidin 1, and likely other AMPs.
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Affiliation(s)
- B Scott Perrin
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, Florida
| | - Myriam L Cotten
- Department of Applied Science, The College of William & Mary, Williamsburg, Virginia
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
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29
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Strandberg E, Horn D, Reißer S, Zerweck J, Wadhwani P, Ulrich AS. 2H-NMR and MD Simulations Reveal Membrane-Bound Conformation of Magainin 2 and Its Synergy with PGLa. Biophys J 2017; 111:2149-2161. [PMID: 27851939 DOI: 10.1016/j.bpj.2016.10.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 02/04/2023] Open
Abstract
Magainin 2 (MAG2) and PGLa are two α-helical antimicrobial peptides found in the skin of the African frog Xenopus laevis. They act by permeabilizing bacterial membranes and exhibit an exemplary synergism. Here, we determined the detailed molecular alignment and dynamical behavior of MAG2 in oriented lipid bilayers by using 2H-NMR on Ala-d3-labeled peptides, which yielded orientation-dependent quadrupolar splittings of the labels. The amphiphilic MAG2 helix was found to lie flat on the membrane surface in 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC)/1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol (DMPG) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG), as expected, with a tilt angle close to 90°. This orientation fits well with all-atom molecular-dynamics simulations of MAG2 performed in DMPC and DMPC/DMPG. In the presence of an equimolar amount of PGLa, the NMR analysis showed that MAG2 becames tilted at an angle of 120°, and its azimuthal rotation angle also changes. Since this interaction was found to occur in a concentration range where the peptides per se do not interact with their own type, we propose that MAG2 forms a stable heterodimer with PGLa. Given that the PGLa molecules in the complex are known to be flipped into a fully upright orientation, with a helix tilt close to 180°, they must make up the actual transmembrane pore. We thus suggest that the two negative charges on the C-terminus of the obliquely tilted MAG2 peptides neutralize some of the cationic groups on the upright PGLa helices. This would stabilize the assembly of PGLa into a toroidal pore with an overall reduced charge density, which could explain the mechanism of synergy.
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Affiliation(s)
- Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Diana Horn
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sabine Reißer
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany; Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jonathan Zerweck
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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30
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Gagnon MC, Strandberg E, Grau-Campistany A, Wadhwani P, Reichert J, Bürck J, Rabanal F, Auger M, Paquin JF, Ulrich AS. Influence of the Length and Charge on the Activity of α-Helical Amphipathic Antimicrobial Peptides. Biochemistry 2017; 56:1680-1695. [PMID: 28282123 DOI: 10.1021/acs.biochem.6b01071] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrophobic mismatch is important for pore-forming amphipathic antimicrobial peptides, as demonstrated recently [Grau-Campistany, A., et al. (2015) Sci. Rep. 5, 9388]. A series of different length peptides have been generated with the heptameric repeat sequence KIAGKIA, called KIA peptides, and it was found that only those helices sufficiently long to span the hydrophobic thickness of the membrane could induce leakage in lipid vesicles; there was also a clear length dependence of the antimicrobial and hemolytic activities. For the original KIA sequences, the cationic charge increased with peptide length. The goal of this work is to examine whether the charge also has an effect on activity; hence, we constructed two further series of peptides with a sequence similar to those of the KIA peptides, but with a constant charge of +7 for all lengths from 14 to 28 amino acids. For both of these new series, a clear length dependence similar to that of KIA peptides was observed, indicating that charge has only a minor influence. Both series also showed a distinct threshold length for peptides to be active, which correlates directly with the thickness of the membrane. Among the longer peptides, the new series showed activities only slightly lower than those of the original KIA peptides of the same length that had a higher charge. Shorter peptides, in which Gly was replaced with Lys, showed activities similar to those of KIA peptides of the same length, but peptides in which Ile was replaced with Lys lost their helicity and were less active.
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Affiliation(s)
- Marie-Claude Gagnon
- Department of Chemistry, PROTEO, CGCC, Université Laval , 1045 avenue de la Médecine, Québec, Canada G1V 0A6.,Department of Chemistry, PROTEO, CERMA, CQMF, Université Laval , 1045 avenue de la Médecine, Québec, Canada G1V 0A6
| | - Erik Strandberg
- Karlsruhe Institute of Technology (KIT) , Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Ariadna Grau-Campistany
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona , Barcelona, Spain
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT) , Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Johannes Reichert
- Karlsruhe Institute of Technology (KIT) , Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT) , Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Francesc Rabanal
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona , Barcelona, Spain
| | - Michèle Auger
- Department of Chemistry, PROTEO, CERMA, CQMF, Université Laval , 1045 avenue de la Médecine, Québec, Canada G1V 0A6
| | - Jean-François Paquin
- Department of Chemistry, PROTEO, CGCC, Université Laval , 1045 avenue de la Médecine, Québec, Canada G1V 0A6
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT) , Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany.,KIT , Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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31
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Thurotte A, Brüser T, Mascher T, Schneider D. Membrane chaperoning by members of the PspA/IM30 protein family. Commun Integr Biol 2017. [PMCID: PMC5333519 DOI: 10.1080/19420889.2016.1264546] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
PspA, IM30 (Vipp1) and LiaH, which all belong to the PspA/IM30 protein family, form high molecular weight oligomeric structures. For all proteins membrane binding and protection of the membrane structure and integrity has been shown or postulated. Here we discuss the possible membrane chaperoning activity of PspA, IM30 and LiaH and propose that larger oligomeric structures bind to stressed membrane regions, followed by oligomer disassembly and membrane stabilization by protein monomers or smaller/different oligomeric scaffolds.
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Affiliation(s)
- Adrien Thurotte
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Thomas Brüser
- Institut für Mikrobiologie, Leibniz Universität Hannover, Hannover, Germany
| | - Thorsten Mascher
- Institut für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Dirk Schneider
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
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32
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Cuevas Arenas R, Klingler J, Vargas C, Keller S. Influence of lipid bilayer properties on nanodisc formation mediated by styrene/maleic acid copolymers. NANOSCALE 2016; 8:15016-26. [PMID: 27471007 DOI: 10.1039/c6nr02089e] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Copolymers of styrene and maleic acid (SMA) have gained great attention as alternatives to conventional detergents, as they offer decisive advantages for studying membrane proteins and lipids in vitro. These polymers self-insert into artificial and biological membranes and, at sufficiently high concentrations, solubilise them into disc-shaped nanostructures containing a lipid bilayer core surrounded by a polymer belt. We have used (31)P nuclear magnetic resonance spectroscopy and dynamic light scattering to systematically study the solubilisation of vesicles composed of saturated or unsaturated phospholipids by an SMA copolymer with a 3 : 1 styrene/maleic acid molar ratio at different temperatures. Solubilisation was thermodynamically rationalised in terms of a three-stage model that treats various lipid/polymer aggregates as pseudophases. The solubilising capacity of SMA(3 : 1) towards a saturated lipid is higher in the gel than in the liquid-crystalline state of the membrane even though solubilisation is slower. Although the solubilisation of mixed fluid membranes is non-selective, the presence of a non-bilayer phospholipid lowers the threshold at which the membrane becomes saturated with SMA(3 : 1) but raises the polymer concentration required for complete solubilisation. Both of these trends can be explained by considering the vesicle-to-nanodisc transfer free energies of the lipid and the polymer. On the basis of the phase diagrams thus obtained, re-association of polymer-solubilised lipids with vesicles is possible under mild conditions, which has implications for the reconstitution of proteins and lipids from nanodiscs into vesicular membranes. Finally, the phase diagrams provide evidence for the absence of free SMA(3 : 1) in vesicular lipid suspensions.
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Affiliation(s)
- Rodrigo Cuevas Arenas
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany.
| | - Johannes Klingler
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany.
| | - Carolyn Vargas
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany.
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany.
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33
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Grage SL, Afonin S, Kara S, Buth G, Ulrich AS. Membrane Thinning and Thickening Induced by Membrane-Active Amphipathic Peptides. Front Cell Dev Biol 2016; 4:65. [PMID: 27595096 PMCID: PMC4999517 DOI: 10.3389/fcell.2016.00065] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/09/2016] [Indexed: 11/13/2022] Open
Abstract
Membrane thinning has been discussed as a fundamental mechanism by which antimicrobial peptides can perturb cellular membranes. To understand which factors play a role in this process, we compared several amphipathic peptides with different structures, sizes and functions in their influence on the lipid bilayer thickness. PGLa and magainin 2 from X. laevis were studied as typical representatives of antimicrobial cationic amphipathic α-helices. A 1:1 mixture of these peptides, which is known to possess synergistically enhanced activity, allowed us to evaluate whether and how this synergistic interaction correlates with changes in membrane thickness. Other systems investigated here include the α-helical stress-response peptide TisB from E. coli (which forms membrane-spanning dimers), as well as gramicidin S from A. migulanus (a natural antibiotic), and BP100 (designer-made antimicrobial and cell penetrating peptide). The latter two are very short, with a circular β-pleated and a compact α-helical structure, respectively. Solid-state (2)H-NMR and grazing incidence small angle X-ray scattering (GISAXS) on oriented phospholipid bilayers were used as complementary techniques to access the hydrophobic thickness as well as the bilayer-bilayer repeat distance including the water layer in between. This way, we found that magainin 2, gramicidin S, and BP100 induced membrane thinning, as expected for amphiphilic peptides residing in the polar/apolar interface of the bilayer. PGLa, on the other hand, decreased the hydrophobic thickness only at very high peptide:lipid ratios, and did not change the bilayer-bilayer repeat distance. TisB even caused an increase in the hydrophobic thickness and repeat distance. When reconstituted as a mixture, PGLa and magainin 2 showed a moderate thinning effect which was less than that of magainin 2 alone, hence their synergistically enhanced activity does not seem to correlate with a modulation of membrane thickness. Overall, the absence of a typical thinning response in the case of PGLa, and the increase in the repeat distance and membrane thickening observed for TisB, demonstrate that the concept of peptide-induced membrane thinning cannot be generalized. Instead, these results suggest that different factors contribute to the resulting changes in membrane thickness, such as the peptide orientation in the bilayer, and/or bilayer adaptation to hydrophobic mismatch.
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Affiliation(s)
- Stephan L Grage
- Karlsruhe Institute of Technology, Institute of Biological Interfaces Karlsruhe, Germany
| | - Sergii Afonin
- Karlsruhe Institute of Technology, Institute of Biological Interfaces Karlsruhe, Germany
| | - Sezgin Kara
- Karlsruhe Institute of Technology, Institute of Organic Chemistry Karlsruhe, Germany
| | - Gernot Buth
- Karlsruhe Institute of Technology, Institute for Accelerator Physics and Technology Karlsruhe, Germany
| | - Anne S Ulrich
- Karlsruhe Institute of Technology, Institute of Biological InterfacesKarlsruhe, Germany; Karlsruhe Institute of Technology, Institute of Organic ChemistryKarlsruhe, Germany
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34
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Molecular mechanisms of membrane targeting antibiotics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:980-7. [DOI: 10.1016/j.bbamem.2015.10.018] [Citation(s) in RCA: 270] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/07/2015] [Accepted: 10/23/2015] [Indexed: 01/17/2023]
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35
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Grau-Campistany A, Strandberg E, Wadhwani P, Rabanal F, Ulrich AS. Extending the Hydrophobic Mismatch Concept to Amphiphilic Membranolytic Peptides. J Phys Chem Lett 2016; 7:1116-1120. [PMID: 26963560 DOI: 10.1021/acs.jpclett.6b00136] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A series of nine amphiphilic, pore-forming α-helical KIA peptides (KIAGKIA repeats) with lengths between 14 and 28 residues were studied by solid-state (15)N NMR to determine their alignment in oriented lipid bilayers. In a 2:1 mixture of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) with its corresponding 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine (lyso-MPC), which has a highly positive spontaneous curvature, the helix tilt angle was found to vary steadily with peptide length. The shortest peptide was aligned transmembrane and upright, while the longer ones successively became tilted away from the membrane normal. This behavior is in agreement with the hydrophobic matching concept, conceived so far only for hydrophobic helices. In 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine, with a negative spontaneous curvature, all KIA peptides remained flat on the bilayer surface, while the cylindrical DMPC lipids permitted a slight tilt. Peptide insertion thus depends critically on the intrinsic lipid curvature, and helix orientation is then fine-tuned by membrane thickness. A refined toroidal pore model is proposed.
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Affiliation(s)
- Ariadna Grau-Campistany
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona , Barcelona, Spain
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
| | - Francesc Rabanal
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona , Barcelona, Spain
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT) , POB 3640, 76021 Karlsruhe, Germany
- Institute of Organic Chemistry , KIT , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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36
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Zerweck J, Strandberg E, Bürck J, Reichert J, Wadhwani P, Kukharenko O, Ulrich AS. Homo- and heteromeric interaction strengths of the synergistic antimicrobial peptides PGLa and magainin 2 in membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:535-47. [PMID: 27052218 DOI: 10.1007/s00249-016-1120-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/01/2016] [Accepted: 02/16/2016] [Indexed: 12/11/2022]
Abstract
PGLa and magainin 2 (MAG2) are amphiphilic α-helical frog peptides with synergistic antimicrobial activity. In vesicle leakage assays we observed the strongest synergy for equimolar mixtures of PGLa and MAG2. This result was consistent with solid-state (15)N-NMR data on the helix alignment in model membranes. The Hill coefficients determined from the vesicle leakage data showed that the heterodimeric (PGLa-MAG2) interactions were stronger than the homodimeric (PGLa-PGLa and MAG2-MAG2) interactions. This result was also reflected in the free energy of dimerization determined from oriented circular dichroism and quantitative solid-state (19)F-NMR analysis.
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Affiliation(s)
- Jonathan Zerweck
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Erik Strandberg
- KIT, Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Jochen Bürck
- KIT, Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Johannes Reichert
- KIT, Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Parvesh Wadhwani
- KIT, Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany
| | - Olga Kukharenko
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany. .,KIT, Institute of Biological Interfaces (IBG-2), POB 3640, 76021, Karlsruhe, Germany.
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Zamora-Carreras H, Strandberg E, Mühlhäuser P, Bürck J, Wadhwani P, Jiménez MÁ, Bruix M, Ulrich AS. Alanine scan and (2)H NMR analysis of the membrane-active peptide BP100 point to a distinct carpet mechanism of action. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1328-38. [PMID: 26975251 DOI: 10.1016/j.bbamem.2016.03.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/23/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
The short membrane-active peptide BP100 [KKLFKKILKYL-NH2] is known as an effective antimicrobial and cell penetrating agent. For a functional alanine scan each of the 11 amino acids was replaced with deuterated Ala-d3, one at a time. MIC assays showed that a substitution of Lys did not affect the antimicrobial activity, but it decreased when a hydrophobic residue was replaced. In most cases, a reduction in hydrophobicity led to a decrease in hemolysis, and some peptide analogues had an improved therapeutic index. Circular dichroism showed that BP100 folds as an amphiphilic α-helix in a bilayer. Its alignment was determined from (2)H NMR in oriented membranes of different composition. The azimuthal rotation angle was the same under all conditions, but the average helix tilt angle and the dynamical behavior of the peptide varied in a systematic manner. In POPC/POPG bilayers, with a negative spontaneous curvature, the peptide was found to lie flat on the bilayer surface, and with little wobble. In DMPC/DMPG, with a positive spontaneous curvature, BP100 at higher concentrations became tilted obliquely into the membrane, with the uncharged C-terminus inserted more deeply into the lipid bilayer, experiencing significant fluctuations in tilt angle. In DMPC/DMPG/lyso-MPC, with a pronounced positive spontaneous curvature, the helix tilted even further and became even more mobile. The 11-mer BP100 is obviously too short to form transmembrane pores. We conclude that BP100 operates via a carpet mechanism, whereby the C-terminus gets inserted into the hydrophobic core of the bilayer, which leads to membrane perturbation and induces transient permeability.
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Affiliation(s)
| | - Erik Strandberg
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Philipp Mühlhäuser
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany
| | - M Ángeles Jiménez
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Marta Bruix
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain
| | - Anne S Ulrich
- Karlsruhe Institute for Technology (KIT), Institute for Biological Interfaces (IBG-2), POB 3640, 76021 Karlsruhe, Germany; KIT, Institute of Organic Chemistry and CFN, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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38
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Sanders MR, Clifton LA, Frazier RA, Green RJ. Role of Lipid Composition on the Interaction between a Tryptophan-Rich Protein and Model Bacterial Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:2050-7. [PMID: 26813886 DOI: 10.1021/acs.langmuir.5b04628] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The interaction between tryptophan-rich puroindoline proteins and model bacterial membranes at the air-liquid interface has been investigated by FTIR spectroscopy, surface pressure measurements, and Brewster angle microscopy. The role of different lipid constituents on the interactions between lipid membrane and protein was studied using wild type (Pin-b) and mutant (Trp44 to Arg44 mutant, Pin-bs) puroindoline proteins. The results show differences in the lipid selectivity of the two proteins in terms of preferential binding to specific lipid head groups in mixed lipid systems. Pin-b wild type was able to penetrate mixed layers of phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) head groups more deeply compared to the mutant Pin-bs. Increasing saturation of the lipid tails increased penetration and adsorption of Pin-b wild type, but again the response of the mutant form differed. The results provide insight as to the role of membrane architecture, lipid composition, and fluidity on antimicrobial activity of proteins. Data show distinct differences in the lipid binding behavior of Pin-b as a result of a single residue mutation, highlighting the importance of hydrophobic and charged amino acids in antimicrobial protein and peptide activity.
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Affiliation(s)
- Michael R Sanders
- School of Pharmacy and Department of Food and Nutritional Sciences, University of Reading , PO Box 226, Whiteknights, Reading, Berkshire RG6 6AP, United Kingdom
| | - Luke A Clifton
- ISIS Pulsed Neutron and Muon Source, Science and technology Facilities Council, Rutherford Appleton Laboratory , Harwell Oxford Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Richard A Frazier
- School of Pharmacy and Department of Food and Nutritional Sciences, University of Reading , PO Box 226, Whiteknights, Reading, Berkshire RG6 6AP, United Kingdom
| | - Rebecca J Green
- School of Pharmacy and Department of Food and Nutritional Sciences, University of Reading , PO Box 226, Whiteknights, Reading, Berkshire RG6 6AP, United Kingdom
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Rokitskaya TI, Kotova EA, Naberezhnykh GA, Khomenko VA, Gorbach VI, Firsov AM, Zelepuga EA, Antonenko YN, Novikova OD. Single channel activity of OmpF-like porin from Yersinia pseudotuberculosis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:883-91. [PMID: 26854962 DOI: 10.1016/j.bbamem.2016.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 01/28/2016] [Accepted: 02/04/2016] [Indexed: 11/16/2022]
Abstract
To gain a mechanistic insight in the functioning of the OmpF-like porin from Yersinia pseudotuberculosis (YOmpF), we compared the effect of pH variation on the ion channel activity of the protein in planar lipid bilayers and its binding to lipid membranes. The behavior of YOmpF channels upon acidification was similar to that previously described for Escherichia coli OmpF. In particular, a decrease in pH of the bathing solution resulted in a substantial reduction of YOmpF single channel conductance, accompanied by the emergence of subconductance states. Similar subconductance substates were elicited by the addition of lysophosphatidylcholine. This observation, made with porin channels for the first time, pointed to the relevance of lipid-protein interactions, in particular, the lipid curvature stress, to the appearance of subconductance states at acidic pH. Binding of YOmpF to membranes displayed rather modest dependence on pH, whereas the channel-forming potency of the protein tremendously decreased upon acidification.
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Affiliation(s)
- Tatyana I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1/40, Moscow 119991, Russia
| | - Elena A Kotova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1/40, Moscow 119991, Russia
| | - Gennadiy A Naberezhnykh
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 let Vladivostoku 159, Vladivostok 690022, Russia
| | - Valentina A Khomenko
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 let Vladivostoku 159, Vladivostok 690022, Russia
| | - Vladimir I Gorbach
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 let Vladivostoku 159, Vladivostok 690022, Russia
| | - Alexander M Firsov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1/40, Moscow 119991, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory 1/73, Moscow 119991, Russia
| | - Elena A Zelepuga
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 let Vladivostoku 159, Vladivostok 690022, Russia
| | - Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1/40, Moscow 119991, Russia.
| | - Olga D Novikova
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 let Vladivostoku 159, Vladivostok 690022, Russia.
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Pino-Angeles A, Leveritt JM, Lazaridis T. Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family. PLoS Comput Biol 2016; 12:e1004570. [PMID: 26727376 PMCID: PMC4699650 DOI: 10.1371/journal.pcbi.1004570] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 09/28/2015] [Indexed: 11/18/2022] Open
Abstract
Magainin 2 and PGLa are among the best-studied cationic antimicrobial peptides. They bind preferentially to negatively charged membranes and apparently cause their disruption by the formation of transmembrane pores, whose detailed structure is still unclear. Here we report the results of 5–9 μs all-atom molecular dynamics simulations starting from tetrameric transmembrane helical bundles of these two peptides, as well as their stoichiometric mixture, and the analog MG-H2 in DMPC or 3:1 DMPC/DMPG membranes. The simulations produce pore structures that appear converged, although some effect of the starting peptide arrangement (parallel vs. antiparallel) is still observed on this timescale. The peptides remain mostly helical and adopt tilted orientations. The calculated tilt angles for PGLa are in excellent agreement with recent solid state NMR experiments. The antiparallel dimer structure in the magainin 2 simulations resembles previously determined NMR and crystal structures. More transmembrane orientations and a larger and more ordered pore are seen in the 1:1 heterotetramer with an antiparallel helix arrangement. Insights into the mechanism of synergy between these two peptides are obtained via implicit solvent modeling of homo- and heterodimers and analysis of interactions in the atomistic simulations. This analysis suggests stronger pairwise interactions in the heterodimer than in the two homodimers. The emergence of antibiotic resistance has created a compelling need for new potent antibiotics. Antimicrobial peptides, naturally produced by many organisms, have long been pursued as a means to fill this gap. However, they have not yet realized their practical potential, partly due to a lack of full understanding of their mechanism of action. The formation of pores by these peptides in bacterial membranes has been demonstrated by multiple biophysical approaches, but the detailed structure of these pores is still unclear. The magainin family of antimicrobial peptides have been thoroughly studied over the last three decades. We have generated atomic-resolution models of membrane pores generated by tetrameric assemblies of different magainin peptides by means of molecular dynamics simulations on the multimicrosecond timescale. The results complement previous experimental findings and set the stage for further development of theoretical and experimental approaches that may ultimately allow the rational design of improved antibiotics.
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Affiliation(s)
- Almudena Pino-Angeles
- Department of Chemistry, The City College of New York, New York, New York, United States of America
| | - John M. Leveritt
- Department of Chemistry, The City College of New York, New York, New York, United States of America
| | - Themis Lazaridis
- Department of Chemistry, The City College of New York, New York, New York, United States of America
- * E-mail:
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