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Sani MA, Rajput S, Keizer DW, Separovic F. NMR techniques for investigating antimicrobial peptides in model membranes and bacterial cells. Methods 2024; 224:10-20. [PMID: 38295893 DOI: 10.1016/j.ymeth.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/05/2024] Open
Abstract
AMPs are short, mainly cationic membrane-active peptides found in all living organism. They perform diverse roles including signaling and acting as a line of defense against bacterial infections. AMPs have been extensively investigated as templates to facilitate the development of novel antimicrobial therapeutics. Understanding the interplay between these membrane-active peptides and the lipid membranes is considered to be a significant step in elucidating the specific mechanism of action of AMPs against prokaryotic and eukaryotic cells to aid the development of new therapeutics. In this review, we have provided a brief overview of various NMR techniques commonly used for studying AMP structure and AMP-membrane interactions in model membranes and whole cells.
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Affiliation(s)
- Marc-Antoine Sani
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Sunnia Rajput
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - David W Keizer
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Frances Separovic
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia; School of Chemistry, University of Melbourne, Melbourne, VIC 3010, Australia
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Sani MA, Le Brun AP, Rajput S, Attard T, Separovic F. The membrane activity of the antimicrobial peptide caerin 1.1 is pH dependent. Biophys J 2023; 122:1058-1067. [PMID: 36680343 PMCID: PMC10111263 DOI: 10.1016/j.bpj.2023.01.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/09/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Antimicrobial peptides are an important class of membrane-active peptides that can provide alternatives or complements to classic antibiotics. Among the many classes of AMPs, the histidine-rich family is of particular interest since they may induce pH-sensitive interactions with cell membranes. The AMP caerin 1.1 (Cae-1), from Australian tree frogs, has three histidine residues, and thus we studied the pH dependence of its interactions with model cell membranes. Using NMR spectroscopy and molecular dynamics simulations, we showed that Cae-1 induced greater perturbation of the lipid dynamics and water penetrations within the membrane interior in an acidic environment compared with physiological conditions. Using 31P solid-state NMR, the packing, chemical environment, and dynamics of the lipid headgroup were monitored. 2H solid-state NMR showed that Cae-1 ordered the acyl chains of the hydrophobic core of the bilayer. These results supported the molecular dynamics data, which showed that Cae-1 was mainly inserted within the lipid bilayer for both neutral and negatively charged membranes, with the charged residues pulling the water and phosphate groups inward. This could be an early step in the mechanism of membrane disruption by histidine-rich antimicrobial peptides and indicated that Cae-1 acts via a transmembrane mechanism in bilayers of neutral and anionic phospholipid membranes, especially in acidic conditions.
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Affiliation(s)
- Marc-Antoine Sani
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
| | - Anton P Le Brun
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Kirrawee, New South Wales, Australia
| | - Sunnia Rajput
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Troy Attard
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Frances Separovic
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia.
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Gelenter M, Bax A. Recombinant Expression and Chemical Amidation of Isotopically Labeled Native Melittin. J Am Chem Soc 2023; 145:3850-3854. [PMID: 36753641 PMCID: PMC9951214 DOI: 10.1021/jacs.2c12631] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Indexed: 02/10/2023]
Abstract
Post-translational modifications are ubiquitous in the eukaryotic proteome. However, these modifications are rarely incorporated in NMR studies of eukaryotic proteins, which are typically produced through recombinant expression in E. coli. Melittin is the primary peptide in honey bee venom. Its native C-terminal amide significantly affects its equilibrium structure and dynamics in solution and is thus a prerequisite for studying its native structure and function. Here, we present a method for producing triply isotopically labeled (2H, 13C, and 15N) native melittin through recombinant expression followed by chemical amidation. We then show that structural models produced with AlphaFold-Multimer are in even better agreement with experimental residual dipolar couplings than the 2.0 Å resolution X-ray crystal structure for residues G3-K23.
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Affiliation(s)
- Martin
D. Gelenter
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Ad Bax
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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Gu H, Kato T, Kumeta H, Kumaki Y, Tsukamoto T, Kikukawa T, Demura M, Ishida H, Vogel HJ, Aizawa T. Three-Dimensional Structure of the Antimicrobial Peptide Cecropin P1 in Dodecylphosphocholine Micelles and the Role of the C-Terminal Residues. ACS OMEGA 2022; 7:31924-31934. [PMID: 36120057 PMCID: PMC9475619 DOI: 10.1021/acsomega.2c02778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/23/2022] [Indexed: 05/31/2023]
Abstract
Cecropin P1 (CP1) isolated from a large roundworm Ascaris suum, which is found in pig intestines, has been extensively studied as a model antimicrobial peptide (AMP). However, despite being a model AMP, its antibacterial mechanism is not well understood, particularly the function of its C-terminus. By using an Escherichia coli overexpression system with calmodulin as a fusion partner, we succeeded in the mass expression of recombinant peptides, avoiding toxicity to the host and degradation of CP1. The structure of the recombinant 15N- and 13C-labeled CP1 and its C-terminus truncated analogue in dodecylphosphocholine (DPC) micelles was determined by NMR. In this membrane-mimetic environment, CP1 formed an α-helix for almost its entire length, except for a short region at the C-terminus, and there was no evidence of a hinge, which is considered important for the expression of activity in other cecropins. Several NMR analyses showed that the entire length of CP1 was protected from water by micelles. Since the loss of the C-terminus of the analogue had little effect on the NMR structure or its interaction with the micelle, we investigated another role of the C-terminus of CP1 in its antimicrobial activity. The results showed that the C-terminal region affected the DNA-binding capacity of CP1, and this mechanism of action was also newly suggested that it contributed to the antimicrobial activity of CP1.
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Affiliation(s)
- Hao Gu
- Graduate
School of Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo 060-0810, Japan
| | - Takasumi Kato
- Graduate
School of Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo 060-0810, Japan
| | - Hiroyuki Kumeta
- Faculty
of Advanced Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo 060-0810, Japan
| | - Yasuhiro Kumaki
- Faculty
of Advanced Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo 060-0810, Japan
| | - Takashi Tsukamoto
- Faculty
of Advanced Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo 060-0810, Japan
| | - Takashi Kikukawa
- Faculty
of Advanced Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo 060-0810, Japan
| | - Makoto Demura
- Faculty
of Advanced Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo 060-0810, Japan
| | - Hiroaki Ishida
- Department
of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Hans J. Vogel
- Department
of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Tomoyasu Aizawa
- Faculty
of Advanced Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo 060-0810, Japan
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Gardijan L, Miljkovic M, Obradovic M, Borovic B, Vukotic G, Jovanovic G, Kojic M. Redesigned pMAL expression vector for easy and fast purification of active native antimicrobial peptides. J Appl Microbiol 2022; 133:1001-1013. [PMID: 35578999 DOI: 10.1111/jam.15623] [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: 12/19/2021] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this study was to construct the improved pMAL expression vector in order to increase the efficacy of small native peptides purification and their clear-cut separation from MBP tag. The modifications we introduced can be applied to many expression vectors. METHODS AND RESULTS To improve the pMAL expression vector we introduced the His6 tag and the enterokinase cleavage site (Ek) downstream from the MBP tag and Xa cleavage site on the original vector. For cloning of a desired peptide DNA, the enterokinase site contains a unique BsaBI restriction site adjacent to the original multi-cloning-site. This redesigned pMAL vector was optimized for the purification of cytoplasmic (pMALc5HisEk) and periplasmic (pMALp5HisEk) peptides. The purification of native and active peptide (P) was obtained following two-step affinity chromatography. In the first step the entire MBP-His6 -Ek-P fusion protein is purified using the Ni-NTA agarose column. This fusion protein was cleaved with active His6 tagged enterokinase. In the second step, the further purification was performed by column containing the mixture of amylose and Ni-NTA agarose resins. This removes both the MBP-His6 and His6 -enterokinase leaving pure native protein in solution. These new vectors and the two-step purification protocol was successfully applied in purification of active native small antimicrobial peptides (AMPs), lactococcin A and human β-defensin. CONCLUSIONS We constructed the improved pMAL expression vectors and established the pipeline and optimal conditions for their use in efficient purification of large amounts of active native small peptides. SIGNIFICANCE AND IMPACT OF THE STUDY Choice of expression vector impacts on the efficiency of expression and purification of desired proteins. The idea of redesigning pMAL vector was driven by need for rapid purification of larger amounts of active native AMPs. This newly improved pMAL vector, the cloning strategy, expression conditions and two-step purification protocol represent a unique simple approach which can be applied in every laboratory.
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Affiliation(s)
- Lazar Gardijan
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, Belgrade, Serbia
| | - Marija Miljkovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, Belgrade, Serbia
| | - Mina Obradovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, Belgrade, Serbia
| | - Branka Borovic
- Institute of Meat Hygiene and Technology, Kaćanskog 13, Belgrade, Serbia
| | - Goran Vukotic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, Belgrade, Serbia.,Faculty of Biology, University of Belgrade, Studentskitrg16, Belgrade, Serbia
| | - Goran Jovanovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, Belgrade, Serbia
| | - Milan Kojic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444/a, Belgrade, Serbia
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