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Hosseinpour S, Roeters SJ, Bonn M, Peukert W, Woutersen S, Weidner T. Structure and Dynamics of Interfacial Peptides and Proteins from Vibrational Sum-Frequency Generation Spectroscopy. Chem Rev 2020; 120:3420-3465. [DOI: 10.1021/acs.chemrev.9b00410] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Saman Hosseinpour
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | | | - Mischa Bonn
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Sander Woutersen
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 EP Amsterdam, The Netherlands
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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2
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Shi J, So LY, Chen F, Liang J, Chow HY, Wong KY, Wan S, Jiang T, Yu R. Influences of disulfide connectivity on structure and antimicrobial activity of tachyplesin I. J Pept Sci 2018; 24:e3087. [PMID: 29870123 DOI: 10.1002/psc.3087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 12/15/2022]
Abstract
Tachyplesin I is a potent antimicrobial peptide with broad spectrum of antimicrobial activity. It has 2 disulfide bonds and can form 3 disulfide bond isomers. In this study, the structure and antimicrobial activity of 3 tachyplesin I isomers (tachyplesin I, 3C12C, 3C7C) were investigated using molecular dynamic simulations, circular dichroism structural study, as well as antimicrobial activity and hemolysis assay. Our results suggest that in comparison to the native peptide, the 2 isomers (3C12C, 3C7C) have substantial structural and activity variations. The native peptide is in the ribbon conformation, while 3C12C and 3C7C possess remarkably different secondary structures, which are referred as "globular" and "beads" isomers, respectively. The substantially decreased hemolysis effects for these 2 isomers is accompanied by significantly decreased anti-gram-positive bacterial activity.
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Affiliation(s)
- Juan Shi
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Lok-Yan So
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hong Kong
| | - Fangling Chen
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Jiazhen Liang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Ho-Yin Chow
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hong Kong
| | - Kwok-Yin Wong
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hong Kong
| | - Shengbiao Wan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Tao Jiang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
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3
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Ohto T, Hunger J, Backus EHG, Mizukami W, Bonn M, Nagata Y. Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations. Phys Chem Chem Phys 2017; 19:6909-6920. [DOI: 10.1039/c6cp07284d] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Vibrational spectroscopy and molecular simulations revealed the hydrophilicity and hydrophobicity of TMAO in aqueous solution.
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Affiliation(s)
- Tatsuhiko Ohto
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | | | | | - Wataru Mizukami
- Department of Energy and Material Sciences
- Faculty of Engineering Sciences
- Kyushu University
- Fukuoka
- Japan
| | - Mischa Bonn
- Max Planck Institute for Polymer Research
- 55128 Mainz
- Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research
- 55128 Mainz
- Germany
- Department of Theoretical and Computational Molecular Science
- Institute for Molecular Science
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4
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Han E, Lee H. Structural effects of tachyplesin I and its linear derivative on their aggregation and mobility in lipid bilayers. J Mol Graph Model 2015; 59:123-8. [DOI: 10.1016/j.jmgm.2015.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/09/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
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5
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Soblosky L, Ramamoorthy A, Chen Z. Membrane interaction of antimicrobial peptides using E. coli lipid extract as model bacterial cell membranes and SFG spectroscopy. Chem Phys Lipids 2015; 187:20-33. [PMID: 25707312 DOI: 10.1016/j.chemphyslip.2015.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 12/17/2022]
Abstract
Supported lipid bilayers are used as a convenient model cell membrane system to study biologically important molecule-lipid interactions in situ. However, the lipid bilayer models are often simple and the acquired results with these models may not provide all pertinent information related to a real cell membrane. In this work, we use sum frequency generation (SFG) vibrational spectroscopy to study molecular-level interactions between the antimicrobial peptides (AMPs) MSI-594, ovispirin-1 G18, magainin 2 and a simple 1,2-dipalmitoyl-d62-sn-glycero-3-phosphoglycerol (dDPPG)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) bilayer. We compared such interactions to those between the AMPs and a more complex dDPPG/Escherichia coli (E. coli) polar lipid extract bilayer. We show that to fully understand more complex aspects of peptide-bilayer interaction, such as interaction kinetics, a heterogeneous lipid composition is required, such as the E. coli polar lipid extract. The discrepancy in peptide-bilayer interaction is likely due in part to the difference in bilayer charge between the two systems since highly negative charged lipids can promote more favorable electrostatic interactions between the peptide and lipid bilayer. Results presented in this paper indicate that more complex model bilayers are needed to accurately analyze peptide-cell membrane interactions and demonstrates the importance of using an appropriate lipid composition to study AMP interaction properties.
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Affiliation(s)
- Lauren Soblosky
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhan Chen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
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6
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Wang X, Yang P, Mondiot F, Li Y, Miller DS, Chen Z, Abbott NL. Interfacial ordering of thermotropic liquid crystals triggered by the secondary structures of oligopeptides. Chem Commun (Camb) 2015; 51:16844-7. [DOI: 10.1039/c5cc06996c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ordering at phospholipid-decorated interfaces of liquid crystals is influenced by the secondary structure of oligopeptides.
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Affiliation(s)
- Xiaoguang Wang
- Department of Chemical and Biological Engineering
- University of Wisconsin-Madison
- Madison
- USA
| | - Pei Yang
- Department of Chemistry
- University of Michigan
- Ann Arbor
- USA
| | - Frederic Mondiot
- Department of Chemical and Biological Engineering
- University of Wisconsin-Madison
- Madison
- USA
| | - Yaoxin Li
- Department of Chemistry
- University of Michigan
- Ann Arbor
- USA
| | - Daniel S. Miller
- Department of Chemical and Biological Engineering
- University of Wisconsin-Madison
- Madison
- USA
| | - Zhan Chen
- Department of Chemistry
- University of Michigan
- Ann Arbor
- USA
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering
- University of Wisconsin-Madison
- Madison
- USA
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7
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Hu P, Zhang X, Zhang C, Chen Z. Molecular interactions between gold nanoparticles and model cell membranes. Phys Chem Chem Phys 2015; 17:9873-84. [DOI: 10.1039/c5cp00477b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Direct observations of the lipid flip-flop induced by Au NP – model mammalian cell membrane interactions.
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Affiliation(s)
- Peipei Hu
- Department of Chemistry
- University of Michigan
- Michigan 48109
- USA
| | - Xiaoxian Zhang
- Department of Chemistry
- University of Michigan
- Michigan 48109
- USA
| | - Chi Zhang
- Department of Chemistry
- University of Michigan
- Michigan 48109
- USA
| | - Zhan Chen
- Department of Chemistry
- University of Michigan
- Michigan 48109
- USA
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Lipkin RB, Lazaridis T. Implicit Membrane Investigation of the Stability of Antimicrobial Peptide β-Barrels and Arcs. J Membr Biol 2014; 248:469-86. [PMID: 25430621 DOI: 10.1007/s00232-014-9759-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 11/18/2014] [Indexed: 12/31/2022]
Abstract
Previous simulations showed that the β-hairpin antimicrobial peptide (AMP) protegrin-1 can form stable octameric β-barrels and tetrameric arcs (half barrels) in both implicit and explicit membranes. Here, we extend this investigation to several AMPs of similar structure: tachyplesin, androctonin, polyphemusin, gomesin, and the retrocyclin θ-defensin. These peptides form short β-hairpins stabilized by 2-3 disulfide bonds. We also examine synthetic β-sheet peptides selected from a combinatorial library for their ability or inability to form pores in lipid membranes. When heptameric, octameric, and decameric β-barrels and tetrameric arcs of these peptides were embedded in pre-formed neutral or anionic lipid pores (i.e., pores in neutral or anionic membranes, respectively), a variety of behaviors and membrane binding energies were observed. Due to the cationic charge of the peptides, more favorable transfer energies and more stable binding were observed in anionic than neutral pores. The synthetic peptides bound very strongly and formed stable barrels and arcs in both neutral and anionic pores. The natural AMPs exhibited unfavorable or marginally favorable binding energy and kinetic stability in neutral pores, consistent with the lower hemolytic activity of some of them compared with protegrin-1. Binding to anionic pores was more favorable, but significant distortions of the barrel or arc structures were sometimes noted. These results are discussed in light of the available experimental data. The diversity of behaviors obtained makes it unlikely that the barrel and arc mechanisms are valid for the entire family of β-hairpin AMPs.
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Affiliation(s)
- Richard B Lipkin
- Department of Chemistry, City College of the City University of New York, 160 Convent Ave., New York, NY, 10031, USA
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Carr JK, Wang L, Roy S, Skinner JL. Theoretical Sum Frequency Generation Spectroscopy of Peptides. J Phys Chem B 2014; 119:8969-83. [PMID: 25203677 PMCID: PMC4516311 DOI: 10.1021/jp507861t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Vibrational sum frequency generation (SFG) has become a very promising technique for the study of proteins at interfaces, and it has been applied to important systems such as anti-microbial peptides, ion channel proteins, and human islet amyloid polypeptide. Moreover, so-called "chiral" SFG techniques, which rely on polarization combinations that generate strong signals primarily for chiral molecules, have proven to be particularly discriminatory of protein secondary structure. In this work, we present a theoretical strategy for calculating protein amide I SFG spectra by combining line-shape theory with molecular dynamics simulations. We then apply this method to three model peptides, demonstrating the existence of a significant chiral SFG signal for peptides with chiral centers, and providing a framework for interpreting the results on the basis of the dependence of the SFG signal on the peptide orientation. We also examine the importance of dynamical and coupling effects. Finally, we suggest a simple method for determining a chromophore's orientation relative to the surface using ratios of experimental heterodyne-detected signals with different polarizations, and test this method using theoretical spectra.
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Affiliation(s)
- Joshua K Carr
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Lu Wang
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Santanu Roy
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - James L Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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Yan ECY, Fu L, Wang Z, Liu W. Biological Macromolecules at Interfaces Probed by Chiral Vibrational Sum Frequency Generation Spectroscopy. Chem Rev 2014; 114:8471-98. [DOI: 10.1021/cr4006044] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Elsa C. Y. Yan
- Department of Chemistry, Yale University, 225 Prospect
Street, New Haven, Connecticut 06520, United States
| | - Li Fu
- Department of Chemistry, Yale University, 225 Prospect
Street, New Haven, Connecticut 06520, United States
| | - Zhuguang Wang
- Department of Chemistry, Yale University, 225 Prospect
Street, New Haven, Connecticut 06520, United States
| | - Wei Liu
- Department of Chemistry, Yale University, 225 Prospect
Street, New Haven, Connecticut 06520, United States
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11
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Roy S, Covert PA, FitzGerald WR, Hore DK. Biomolecular Structure at Solid–Liquid Interfaces As Revealed by Nonlinear Optical Spectroscopy. Chem Rev 2014; 114:8388-415. [DOI: 10.1021/cr400418b] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sandra Roy
- Department
of Chemistry, University of Victoria, Victoria, British Columbia, V8W 3V6 Canada
| | - Paul A. Covert
- Department
of Chemistry, University of Victoria, Victoria, British Columbia, V8W 3V6 Canada
| | - William R. FitzGerald
- Department
of Chemistry, University of Victoria, Victoria, British Columbia, V8W 3V6 Canada
| | - Dennis K. Hore
- Department
of Chemistry, University of Victoria, Victoria, British Columbia, V8W 3V6 Canada
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12
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Han E, Lee H. Effects of PEGylation on the binding interaction of magainin 2 and tachyplesin I with lipid bilayer surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14214-14221. [PMID: 24160865 DOI: 10.1021/la4036985] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Poly(ethylene glycol) (PEG)-grafted magainin 2 and tachyplesin I were simulated with lipid bilayers. In the simulations of PEGylated magainin 2 and tachyplesin I in water, both peptides are wrapped by PEG chains. The α-helical structure of PEGylated magainin 2 is broken in water, while the β-sheet of PEGylated tachyplesin I keeps stable, similar to the structural behavior of unPEGylated peptides, in agreement with experiments. Simulations of PEGylated peptides with lipid bilayers show that PEG chains block the electrostatic interaction between cationic residues of peptides and anionic phosphates of lipids, leading to the less binding of the peptide to the bilayer surface, which is observed more significantly for magainin 2 than for tachyplesin I. Since the random-coiled magainin 2 can be more completely covered by PEGs than does the β-sheet tachyplesin I, the PEGylation effect on the decreased binding is larger for magainin 2, showing the dependence of PEGylation on the peptide structure. These simulation findings qualitatively support the experimental observation of the different extents of the reduced membrane-permeabilizing activity for PEGylated magainin 2 and tachyplesin I.
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Affiliation(s)
- Eol Han
- Department of Chemical Engineering, Dankook University , Yongin 448-701, South Korea
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13
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Nano-bio interfaces probed by advanced optical spectroscopy: From model system studies to optical biosensors. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-5700-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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