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Lyu Y, Yang C, Chen T, Shang L, Yang Y, Li J, Shan A, Xiang W, Cheng B, Zhang L. Characterization of an antibacterial dodecapeptide from pig as a potential food preservative and its antibacterial mechanism. Food Funct 2020; 11:4090-4102. [DOI: 10.1039/d0fo00380h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A membrane-active dodecapeptide was generated from porcine antimicrobial peptide with promising antimicrobial activity for application in the food industry as a potential bio-preservative to prevent microbial spoilage.
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Affiliation(s)
- Yinfeng Lyu
- Institute of Animal Nutrition
- Northeast Agricultural University
- Harbin
- P.R. China
| | - Chengyi Yang
- Institute of Animal Nutrition
- Northeast Agricultural University
- Harbin
- P.R. China
| | - Tingting Chen
- Institute of Animal Nutrition
- Northeast Agricultural University
- Harbin
- P.R. China
| | - Lu Shang
- Institute of Animal Nutrition
- Northeast Agricultural University
- Harbin
- P.R. China
| | - Yang Yang
- Institute of Animal Nutrition
- Northeast Agricultural University
- Harbin
- P.R. China
| | - Jiawei Li
- Institute of Animal Nutrition
- Northeast Agricultural University
- Harbin
- P.R. China
| | - Anshan Shan
- Institute of Animal Nutrition
- Northeast Agricultural University
- Harbin
- P.R. China
| | - Wensheng Xiang
- School of Life Science
- Northeast Agricultural University
- Harbin
- P.R. China
| | - Baojing Cheng
- Institute of Animal Nutrition
- Northeast Agricultural University
- Harbin
- P.R. China
| | - Licong Zhang
- Institute of Animal Nutrition
- Northeast Agricultural University
- Harbin
- P.R. China
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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Anderson JM, Kier BL, Jurban B, Byrne A, Shu I, Eidenschink LA, Shcherbakov AA, Hudson M, Fesinmeyer RM, Andersen NH. Aryl-aryl interactions in designed peptide folds: Spectroscopic characteristics and optimal placement for structure stabilization. Biopolymers 2016; 105:337-356. [PMID: 26850220 PMCID: PMC5638712 DOI: 10.1002/bip.22821] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 01/27/2023]
Abstract
We have extended our studies of Trp/Trp to other Aryl/Aryl through-space interactions that stabilize hairpins and other small polypeptide folds. Herein we detail the NMR and CD spectroscopic features of these types of interactions. NMR data remains the best diagnostic for characterizing the common T-shape orientation. Designated as an edge-to-face (EtF or FtE) interaction, large ring current shifts are produced at the edge aryl ring hydrogens and, in most cases, large exciton couplets appear in the far UV circular dichroic (CD) spectrum. The preference for the face aryl in FtE clusters is W ≫ Y ≥ F (there are some exceptions in the Y/F order); this sequence corresponds to the order of fold stability enhancement and always predicts the amplitude of the lower energy feature of the exciton couplet in the CD spectrum. The CD spectra for FtE W/W, W/Y, Y/W, and Y/Y pairs all include an intense feature at 225-232 nm. An additional couplet feature seen for W/Y, W/F, Y/Y, and F/Y clusters, is a negative feature at 197-200 nm. Tyr/Tyr (as well as F/Y and F/F) interactions produce much smaller exciton couplet amplitudes. The Trp-cage fold was employed to search for the CD effects of other Trp/Trp and Trp/Tyr cluster geometries: several were identified. In this account, we provide additional examples of the application of cross-strand aryl/aryl clusters for the design of stable β-sheet models and a scale of fold stability increments associated with all possible FtE Ar/Ar clusters in several structural contexts. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 337-356, 2016.
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Affiliation(s)
- Jordan M Anderson
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - Brandon L Kier
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - Brice Jurban
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - Aimee Byrne
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - Irene Shu
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | | | | | - Mike Hudson
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - R M Fesinmeyer
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, WA, 98195
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Makwana KM, Mahalakshmi R. Stereopositional Outcome in the Packing of Dissimilar Aromatics in Designed β-Hairpins. Chemistry 2016; 22:4147-56. [DOI: 10.1002/chem.201504428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/15/2015] [Indexed: 01/06/2023]
Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory; Department of Biological Sciences; Indian Institute of Science Education and Research, Bhopal; 462023 Madhya Pradesh India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory; Department of Biological Sciences; Indian Institute of Science Education and Research, Bhopal; 462023 Madhya Pradesh India
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Xu L, Chou S, Wang J, Shao C, Li W, Zhu X, Shan A. Antimicrobial activity and membrane-active mechanism of tryptophan zipper-like β-hairpin antimicrobial peptides. Amino Acids 2015; 47:2385-97. [PMID: 26088720 DOI: 10.1007/s00726-015-2029-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/10/2015] [Indexed: 11/24/2022]
Abstract
Antimicrobial peptides (AMPs) with amphipathic β-hairpin structures have been demonstrated to possess potent antimicrobial activities and great cell selectivities. However, our understanding of β-hairpin antimicrobial peptides lags behind that of α-helices, mainly because it is difficult for short peptides to form robust β-hairpin structures. Tryptophan zipper (trpzip) peptides are among the most stable β-hairpin peptides known to fold spontaneously without requiring covalent disulfide constraint or metal binding. To develop model β-hairpin AMPs with small size and remarkable stability, a series of amphiphilic linear peptides were designed based on the trpzip motif. The sequence of designed peptides is (WK) n (D) PG(KW) n -NH2 (n = 1, 2, 3, 4, 5), and the antimicrobial activity and membrane interaction mechanism of the peptides were evaluated. The results showed that these peptides readily fold into β-hairpin structures in aqueous and membrane-mimicking environments and exhibit broad-spectrum antimicrobial activities against both gram-positive and gram-negative bacteria. The antibacterial potency of the peptides initially increased and then decreased with increasing chain length. WK3, a 14-residue peptide, displayed excellent antimicrobial activity with minimal hemolytic activity and cytotoxicity, suggesting that it possesses great cell selectivity. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), fluorescence spectroscopy, and flow cytometry indicated that representative peptides WK3 and WK4 exert their activities by permeabilizing the microbial membrane and damaging cell membrane integrity. This study reveals the application potential of the designed peptides as promising antimicrobial agents for the control of infectious diseases, and it also provides new insights into the design and optimization of highly stable β-hairpin AMPs with great antimicrobial activities and cell selectivities.
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Affiliation(s)
- Lin Xu
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China.,Heilongjiang Polytechnic, 5 Xuefu Road, Harbin, 150080, China
| | - Shuli Chou
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Jiajun Wang
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Changxuan Shao
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Weizhong Li
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Xin Zhu
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China.
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Makwana KM, Mahalakshmi R. NMR Analysis of Tuning Cross-Strand Phe/Tyr/Trp-Trp Interactions in Designed β-Hairpin Peptides: Terminal Switch from L to D Amino Acid as a Strategy for β-Hairpin Capping. J Phys Chem B 2015; 119:5376-85. [PMID: 25849307 DOI: 10.1021/acs.jpcb.5b00554] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Interaction among the side chains of aromatic amino acids is a well-known mechanism of protein and peptide structure stabilization, particularly in β sheets. Using short β-hairpin models bearing the sequence Ac-Leu-Xxx-Val-DPro-Gly-Leu-Trp-Val-NH2, we report the surprising observation of significant destabilization in aryl–tryptophan interactions, which results in poorly folded peptide populations accompanied by lowering of stability. We find that such destabilization arises from forced occupancy of the indole ring in the shielded Edge position, in T-shaped aryl geometries. We demonstrate that this destabilizing effect can be efficiently salvaged by replacing the N-terminal LLeu with DLeu, which causes an increase in the folded hairpin population, while retaining Trp in the Edge position. Our observation of unique cross strand NOEs and data from temperature-dependent NMR and CD measurements reveals the formation of a locally stabilized aliphatic–aromatic network, leading to an overall increase in ΔGF° by ∼ −0.6 to −1.2 kcal/mol. Our results suggest that a contextual evaluation of stabilization by tryptophan is necessary in β hairpins. Furthermore, we report for the first time that the use of D isomers of aliphatic amino acids at the terminus is stabilizing, which can serve as a new strategy for increasing β-hairpin stability.
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Affiliation(s)
- Kamlesh M Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462023, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462023, India
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Makwana KM, Mahalakshmi R. Comparative analysis of cross strand aromatic–Phe interactions in designed peptide β-hairpins. Org Biomol Chem 2014; 12:2053-61. [DOI: 10.1039/c3ob42247j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Examination of the preferential interaction geometries of the aromatic amino acids Phe, Tyr and Trp with the benzyl ring of Phe in designed octapeptide hairpin scaffolds reveals stabilizing contributions of a Trp–Phe pair, even in amphipathic solvents.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
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Abstract
Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.
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Affiliation(s)
- M Angeles Jiménez
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Química Física Rocasolano (IQFR), Serrano 119, 28006, Madrid, Spain,
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Meyer D, Mutschler C, Robertson I, Batt A, Tatko C. Aromatic interactions with naphthylalanine in a β
-hairpin peptide. J Pept Sci 2013; 19:277-82. [DOI: 10.1002/psc.2496] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 01/22/2013] [Accepted: 01/25/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Meyer
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Caleb Mutschler
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Ian Robertson
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Alexandra Batt
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Chad Tatko
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
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