1
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Park SC, Lee JK, Kim YM, Lee JR. Effects of structural changes on antibacterial activity and cytotoxicity due to proline substitutions in chimeric peptide HnMc. Biochem Biophys Res Commun 2023; 679:139-144. [PMID: 37696067 DOI: 10.1016/j.bbrc.2023.09.013] [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: 08/10/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023]
Abstract
Owing to the rapidly increasing emergence of multidrug-resistant pathogens, antimicrobial peptides (AMPs) are being explored as next-generation antibiotics. However, AMPs present in nature are highly toxic and exhibit low antibacterial activity. Simple modifications, such as amino acid substitution, can enhance antimicrobial activity and cell selectivity. Herein, we show that HnMc-W, substituted by the Phe1Trp analog of HnMc, a chimeric peptide, resulted in membranolytic antibacterial action and enhanced salt tolerance, whereas HnMc-WP1 with one Ser9Pro substitution resulted in a proline-kink helical structure that increased salt-tolerant antibacterial effects and reduced cytotoxicity. In addition, the HnMc-WP2 peptide, designed with a PXXP motif, had a flexible central hinge in its α-helical structure due to the introduction of two Pro and two Gln (X positions, by deletion of two Gln at positions 16 and 17) residues instead of Ser at position. HnMc-WP2 exhibited excellent antibacterial effects without cytotoxicity in vitro. Moreover, its potent antibacterial activity was demonstrated in a drug-resistant Pseudomonas aeruginosa-infected mouse model in vivo. Our findings provide valuable information for the design of peptides with high antibacterial activity and cell selectivity.
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Affiliation(s)
- Seong-Cheol Park
- Department of Chemical Engineering, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Jong-Kook Lee
- Department of Chemical Engineering, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Young-Min Kim
- Department of Chemical Engineering, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Jung Ro Lee
- LMO Team, National Institute of Ecology (NIE), Seocheon, 33657, Republic of Korea; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA.
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2
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Peptidomic analysis of the host-defense peptides in skin secretions of the Amazon River frog Lithobates palmipes (Ranidae). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101069. [PMID: 36868141 DOI: 10.1016/j.cbd.2023.101069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/18/2023] [Accepted: 02/19/2023] [Indexed: 03/05/2023]
Abstract
Skin secretions of certain frog species represent a source of host-defense peptides (HDPs) with therapeutic potential and their primary structures provide insight into taxonomic and phylogenetic relationships. Peptidomic analysis was used to characterize the HDPs in norepinephrine-stimulated skin secretions from the Amazon River frog Lithobates palmipes (Ranidae) collected in Trinidad. A total of ten peptides were purified and identified on the basis of amino acid similarity as belonging to the ranatuerin-2 family (ranatuerin-2PMa, -2PMb, -2PMc, and-2PMd), the brevinin-1 family (brevinin-1PMa, -1PMb, -1PMc and des(8-14)brevinin-1PMa) and the temporin family (temporin-PMa in C-terminally amidated and non-amidated forms). Deletion of the sequence VAAKVLP from brevinin-1PMa (FLPLIAGVAAKVLPKIFCAISKKC) in des[(8-14)brevinin-1PMa resulted in a 10-fold decrease in potency against Staphylococcus aureus (MIC = 31 μM compared with 3 μM) and a > 50-fold decrease in hemolytic activity but potency against Echerichia coli was maintained (MIC = 62.5 μM compared with 50 μM). Temporin-PMa (FLPFLGKLLSGIF.NH2) inhibited growth of S. aureus (MIC = 16 μM) but the non-amidated form of the peptide lacked antimicrobial activity. Cladistic analysis based upon the primary structures of ranaturerin-2 peptides supports the division of New World frogs of the family Ranidae into the genera Lithobates and Rana. A sister-group relationship between L. palmipes and Warszewitsch's frog Lithobates warszewitschii is indicated within a clade that includes the Tarahumara frog Lithobates tarahumarae. The study has provided further evidence that peptidomic analysis of HDPs in frog skin secretions is a valuable approach to elucidation of the evolutionary history of species within a particular genus.
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3
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Wen R, Wang K, Yang D, Yu T, Zan X, Meng Q. The novel aciniform silk protein (AcSp2-v2) reveals the unique repetitive domain with high acid and thermal stability and self-assembly capability. Int J Biol Macromol 2021; 202:91-101. [PMID: 34973994 DOI: 10.1016/j.ijbiomac.2021.12.088] [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: 09/21/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 12/01/2022]
Abstract
Orb-weaving spiders spin a mechanically and functionally diverse range of silk fibers, each composed of one or more specific silk proteins. Of all silk types, wrapping silk combines high strength and extensibility and is made of multiple aciniform silk proteins (AcSp) that can be grouped into two AcSp types (AcSp1 and AcSp2) according to their distinct repetitive regions. Here, we present a novel and complete AcSp gene from orb weaving spider Araneus ventricosus. Phylogenetic analysis of the terminal regions of spidroins reveals that the new silk protein and the published A. ventricosus AcSp2 together form a subclade, indicating that this protein is a member of AcSp2 subclass and therefore named AcSp2 variant 2 (AcSp2-v2). The repetitive region of A. ventricosus AcSp2-v2 contains 24 cysteine residues, which is the first time that cysteine has been found in repetitive regions of spidroins. Moreover, the discovery of the ability of AcSp2-v2 repetitive domain to self-assemble into silk fibers expands the repertoire of known self-assembling sequences.
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Affiliation(s)
- Rui Wen
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China; School of Ophthalmology and Optometry, Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang Province 325035, China; Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai 201620, China
| | - Kangkang Wang
- School of Ophthalmology and Optometry, Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang Province 325035, China
| | - Dong Yang
- School of Ophthalmology and Optometry, Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang Province 325035, China
| | - Tiantian Yu
- School of Ophthalmology and Optometry, Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang Province 325035, China
| | - Xingjie Zan
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China; School of Ophthalmology and Optometry, Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang Province 325035, China
| | - Qing Meng
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai 201620, China.
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4
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Kim MI, Pham TK, Kim D, Park M, Kim BO, Cho YH, Kim YW, Lee C. Identification of brevinin-1EMa-derived stapled peptides as broad-spectrum virus entry blockers. Virology 2021; 561:6-16. [PMID: 34089997 DOI: 10.1016/j.virol.2021.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
Based on the previously reported 13-residue antibacterial peptide analog, brevinin-1EMa (FLGWLFKVASKVL, peptide B), we attempted to design a novel class of antiviral peptides. For this goal, we synthesized three peptides with different stapling positions (B-2S, B-8S, and B-5S). The most active antiviral peptide with the specific stapling position (B-5S) was further modified in combination with either cysteine (B-5S3C, B-5S7C, and B-5S10C) or hydrophilic amino acid substitution (Bsub and Bsub-5S). Overall, B, B-5S, and Bsub-5S peptides showed superior antiviral activities against enveloped viruses such as retrovirus, lentivirus, hepatitis C virus, and herpes simplex virus with EC50 values of 1-5 μM. Murine norovirus, a non-enveloped virus, was not susceptible to the virucidal actions of these peptides, suggesting the virus membrane disruption as their main antiviral mechanisms of action. We believe that these three novel peptides could serve as promising candidates for further development of membrane-targeting antiviral drugs in the future.
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Affiliation(s)
- Mi Il Kim
- College of Pharmacy, Dongguk University, Goyang, Republic of Korea
| | - Thanh K Pham
- College of Pharmacy, Dongguk University, Goyang, Republic of Korea
| | - Dahee Kim
- College of Pharmacy, Dongguk University, Goyang, Republic of Korea
| | - Minkyung Park
- College of Pharmacy, Dongguk University, Goyang, Republic of Korea
| | - Bi-O Kim
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Republic of Korea
| | - You-Hee Cho
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Republic of Korea
| | - Young-Woo Kim
- College of Pharmacy, Dongguk University, Goyang, Republic of Korea.
| | - Choongho Lee
- College of Pharmacy, Dongguk University, Goyang, Republic of Korea.
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5
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Brevinin-1GHd: a novel Hylarana guentheri skin secretion-derived Brevinin-1 type peptide with antimicrobial and anticancer therapeutic potential. Biosci Rep 2021; 40:222871. [PMID: 32347293 PMCID: PMC7225409 DOI: 10.1042/bsr20200019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/02/2020] [Accepted: 04/20/2020] [Indexed: 12/24/2022] Open
Abstract
Host-defense antimicrobial peptides (AMPs) from amphibians are usually considered as one of the most promising next-generation antibiotics because of their excellent antimicrobial properties and low cytotoxicity. In the present study, one novel Brevinin-1 type peptide, Brevinin-1GHd, was isolated and characterized from the skin secretion of the frog, Hylarana guentheri. Brevinin-1GHd was found to possess a wide range of antimicrobial activity through penetrating the bacterial membrane within a short time while showing low hemolysis at bactericidal concentrations, even against the resistant strains. It also inhibited and eradicated biofilms that are thought to be closely related to the rise in resistance. Meanwhile, Brevinin-1GHd exhibited wide-spectrum anti-proliferation activity toward human cancer lines. Taken together, these results indicate that Brevinin-1GHd with its excellent antimicrobial and anticancer activities is a promising candidate for a novel antibiotic agent, and study of its structure–activity relationships also provided a rational template for further research and peptide analog design.
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6
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Zhou X, Liu Y, Gao Y, Wang Y, Xia Q, Zhong R, Ma C, Zhou M, Xi X, Shaw C, Chen T, Wu D, Kwok HF, Wang L. Enhanced Antimicrobial Activity of N-Terminal Derivatives of a Novel Brevinin-1 Peptide from The Skin Secretion of Odorrana schmackeri. Toxins (Basel) 2020; 12:E484. [PMID: 32751489 PMCID: PMC7472354 DOI: 10.3390/toxins12080484] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial peptides (AMPs) are promising therapeutic alternatives compared to conventional antibiotics for the treatment of drug-resistant bacterial infections. However, the application of the overwhelming majority of AMPs is limited because of the high toxicity and high manufacturing costs. Amphibian skin secretion has been proven to be a promising source for the discovery and development of novel AMPs. Herein, we discovered a novel AMP from the skin secretion of Odorrana schmackeri, and designed the analogues by altering the key factors, including conformation, net charge and amphipathicity, to generate short AMPs with enhanced therapeutic efficacy. All the peptides were chemically synthesised, followed by evaluating their biological activity, stability and cytotoxicity. OSd, OSe and OSf exhibited broad-spectrum antibacterial effects, especially OSf, which presented the highest therapeutic index for the tested bacteria. Moreover, these peptides displayed good stability. The results from scanning electron microscopy and transmission electron microscopy studies, indicated that brevinin-OS, OSd, OSe and OSf possessed rapid bactericidal ability by disturbing membrane permeability and causing the release of cytoplasmic contents. In addition, OSd, OSe and OSf dramatically decreased the mortality of waxworms acutely infected with MRSA. Taken together, these data suggested that a balance between positive charge, degrees of α-helicity and hydrophobicity, is necessary for maintaining antimicrobial activity, and these data successfully contributed to the design of short AMPs with significant bactericidal activity and cell selectivity.
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Affiliation(s)
- Xiaowei Zhou
- Department of Nutrition, Henry Fok School of Food Science and Engineering, Shaoguan University; Shaoguan 512005, China; (X.Z.); (R.Z.)
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University, Belfast BT9 7BL, Northern Ireland, UK; (Y.L.); (C.M.); (M.Z.); (C.S.); (T.C.); (L.W.)
| | - Yue Liu
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University, Belfast BT9 7BL, Northern Ireland, UK; (Y.L.); (C.M.); (M.Z.); (C.S.); (T.C.); (L.W.)
| | - Yitian Gao
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China;
| | - Yuanxing Wang
- State Key Lab of Food Science and Technology, Nanchang University, Nanchang 330047, China;
| | - Qiang Xia
- Department of Food Science and Engineering, Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China;
| | - Ruimin Zhong
- Department of Nutrition, Henry Fok School of Food Science and Engineering, Shaoguan University; Shaoguan 512005, China; (X.Z.); (R.Z.)
| | - Chengbang Ma
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University, Belfast BT9 7BL, Northern Ireland, UK; (Y.L.); (C.M.); (M.Z.); (C.S.); (T.C.); (L.W.)
| | - Mei Zhou
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University, Belfast BT9 7BL, Northern Ireland, UK; (Y.L.); (C.M.); (M.Z.); (C.S.); (T.C.); (L.W.)
| | - Xinping Xi
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University, Belfast BT9 7BL, Northern Ireland, UK; (Y.L.); (C.M.); (M.Z.); (C.S.); (T.C.); (L.W.)
| | - Chris Shaw
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University, Belfast BT9 7BL, Northern Ireland, UK; (Y.L.); (C.M.); (M.Z.); (C.S.); (T.C.); (L.W.)
| | - Tianbao Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University, Belfast BT9 7BL, Northern Ireland, UK; (Y.L.); (C.M.); (M.Z.); (C.S.); (T.C.); (L.W.)
| | - Di Wu
- Chemical Biology Research Centre, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou 325035, China;
| | - Hang Fai Kwok
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR
| | - Lei Wang
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University, Belfast BT9 7BL, Northern Ireland, UK; (Y.L.); (C.M.); (M.Z.); (C.S.); (T.C.); (L.W.)
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7
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Brožek R, Kabelka I, Vácha R. Effect of Helical Kink on Peptide Translocation across Phospholipid Membranes. J Phys Chem B 2020; 124:5940-5947. [PMID: 32603116 DOI: 10.1021/acs.jpcb.0c03291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Biological membranes present a major obstacle for the delivery of therapeutic agents into cells. Some peptides have been shown to translocate across the membrane spontaneously, and they could be thus used as drug-carriers. However, the advantageous peptide properties for the translocation remain unclear. Of particular interest is the effect of a proline-induced kink in α-helical peptides, because the kink was previously reported to both increase and decrease the antimicrobial activity. The antimicrobial activity of peptides could be related to their translocation across the membrane as is the case of the buforin 2 peptide investigated here. Using computer simulations with two independent models, we consistently showed that the presence of the kink has (1) no effect on the translocation barrier, (2) reduces the peptide affinity to the membrane, and (3) disfavors the transmembrane state. Moreover, we were able to determine that these effects are mainly caused by the peptide increased polarity, not the increased flexibility of the kink. The provided molecular understanding can be utilized for the design of cell-penetrating and drug-carrying peptides.
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Affiliation(s)
- Radim Brožek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Ivo Kabelka
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Robert Vácha
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
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8
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Tuerkova A, Kabelka I, Králová T, Sukeník L, Pokorná Š, Hof M, Vácha R. Effect of helical kink in antimicrobial peptides on membrane pore formation. eLife 2020; 9:47946. [PMID: 32167466 PMCID: PMC7069690 DOI: 10.7554/elife.47946] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 02/18/2020] [Indexed: 12/19/2022] Open
Abstract
Every cell is protected by a semipermeable membrane. Peptides with the right properties, for example Antimicrobial peptides (AMPs), can disrupt this protective barrier by formation of leaky pores. Unfortunately, matching peptide properties with their ability to selectively form pores in bacterial membranes remains elusive. In particular, the proline/glycine kink in helical peptides was reported to both increase and decrease antimicrobial activity. We used computer simulations and fluorescence experiments to show that a kink in helices affects the formation of membrane pores by stabilizing toroidal pores but disrupting barrel-stave pores. The position of the proline/glycine kink in the sequence further controls the specific structure of toroidal pore. Moreover, we demonstrate that two helical peptides can form a kink-like connection with similar behavior as one long helical peptide with a kink. The provided molecular-level insight can be utilized for design and modification of pore-forming antibacterial peptides or toxins.
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Affiliation(s)
- Alzbeta Tuerkova
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Ivo Kabelka
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Tereza Králová
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice, Czech Republic
| | - Lukáš Sukeník
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská, Czech Republic
| | - Šárka Pokorná
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Hof
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská, Czech Republic
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9
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Structural and positional studies of the antimicrobial peptide brevinin‐1BYa in membrane‐mimetic environments. J Pept Sci 2019; 25:e3208. [DOI: 10.1002/psc.3208] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/04/2019] [Accepted: 07/12/2019] [Indexed: 11/07/2022]
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10
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Insights into conformation and membrane interactions of the acyclic and dicarba-bridged brevinin-1BYa antimicrobial peptides. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:701-710. [DOI: 10.1007/s00249-019-01395-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/10/2019] [Accepted: 08/13/2019] [Indexed: 02/03/2023]
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11
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Rajasekaran G, Kumar SD, Yang S, Shin SY. Improving Cell Selectivity of Fowlicidin‐1 by Swapping Residues between Pro‐7 and Tyr‐20. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ganesan Rajasekaran
- Department of Medical Science, Graduate School, School of MedicineChosun University Gwangju 61452 Republic of Korea
| | - S. Dinesh Kumar
- Department of Medical Science, Graduate School, School of MedicineChosun University Gwangju 61452 Republic of Korea
| | - Sungtae Yang
- Department of Medical Science, Graduate School, School of MedicineChosun University Gwangju 61452 Republic of Korea
- Department of Microbiology, School of MedicineChosun University Gwangju 61452 Republic of Korea
| | - Song Yub Shin
- Department of Medical Science, Graduate School, School of MedicineChosun University Gwangju 61452 Republic of Korea
- Department of Cellular and Molecular Medicine, School of MedicineChosun University Gwangju 61452 Republic of Korea
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12
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BHARALII KRISHNA, KALITA DJ, BORA P, SAIKIA DP, DEVI B, DAS L. Characterization of defensin gene of Asom hill goat and in-silico designing of novel antimicrobial peptides. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i5.79945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tissue samples of tongue were collected from apparently healthy Asom hill goat from local slaughter house. Total RNA was extracted and reverse transcribed to cDNA. Size of the amplified products of defensin gene with specific primer were 266 bp. Positive clones were sequenced and analyzed using DNA Star software. At nucleotide level, the Asom hill goat LAP cDNA showed a variation of two nucleotides at 37 and 194 with Capra hircus LAP. Nucleotide sequence of Asom hill goat LAP showed highest similarity of 99% with Capra hircus LAP followed by 95.4% with Capra hircus EBD and 91.3% with sheep BD2. The predicted peptide of Asom hill goat LAP comprised 64 amino acids. Analysis of mature domain of Asom hill goat LAP revealed the presence of 13 basic, 20 hydrophobic, 3 proline and 1 histidine amino acid. Support Vector Machine (SVM) algorithm was used for designing and prediction of antimicrobial potency and amino acids in between 25-39 of mature domain of Asom hill goat LAP predicted to be most potent among all the designed peptide.
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13
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Zhang L, Chen X, Zhang Y, Ma C, Xi X, Wang L, Zhou M, Burrows JF, Chen T. Identification of novel Amurin-2 variants from the skin secretion of Rana amurensis, and the design of cationicity-enhanced analogues. Biochem Biophys Res Commun 2018; 497:943-949. [PMID: 29366784 DOI: 10.1016/j.bbrc.2018.01.124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 01/19/2018] [Indexed: 01/21/2023]
Abstract
Rana amurensis is important in Chinese medicine as its skin secretions contain abundant bioactive peptides. Here, we have identified the antimicrobial peptide Amurin-2 and three highly-conserved variants, Amurin-2a, Amurin-2b and Amurin-2c through a combination of molecular cloning and MS/MS fragmentation sequencing. Synthetic replicates of these peptides demonstrate potent antimicrobial activity against S. aureus, whilst some have activity against C.albicans and even resistant bacterial MRSA. Furthermore, two Lys-analogues (K4-Amurin-2 and K11-Amurin-2) were designed to improve the bioactive function and the antimicrobial activity of K4-Amurin-2 against E.coli was enhanced distinctly. In addition, the two modified peptides also showed more potent activity against S. aureus, C. albicans and MRSA strains. Meanwhile, these peptides showed inhibitory effect on the cell viability of several cancer cells. As a result, these structural and functional studies of Amurin-2 variants and analogues could provide insights for future antimicrobial peptide design.
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Affiliation(s)
- Luyao Zhang
- School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK
| | - Xiaoling Chen
- School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK
| | - Ying Zhang
- School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK; Clinical Trial Center, Beijing Hospital, Beijing, 100730, China
| | - Chengbang Ma
- School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
| | - Xinping Xi
- School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
| | - Lei Wang
- School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK
| | - Mei Zhou
- School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK
| | - James F Burrows
- School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK
| | - Tianbao Chen
- School of Pharmacy, Queen's University, Belfast BT9 7BL, Northern Ireland, UK
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14
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Rajasekaran G, Shin SY. Fowlicidin-3 Analog with Improved Cell Selectivity Synthesized by Shifting a PXXP Motif from the N-Terminus to a Central Position. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ganesan Rajasekaran
- Department of Cellular & Molecular Medicine; School of Medicine, Chosun University; Gwangju 501-759 Republic of Korea
| | - Song Yub Shin
- Department of Cellular & Molecular Medicine; School of Medicine, Chosun University; Gwangju 501-759 Republic of Korea
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15
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Chanu KV, Thakuria D, Kumar S. Antimicrobial peptides of buffalo and their role in host defenses. Vet World 2018; 11:192-200. [PMID: 29657403 PMCID: PMC5891874 DOI: 10.14202/vetworld.2018.192-200] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/16/2018] [Indexed: 01/07/2023] Open
Abstract
Antimicrobial peptides (AMPs) are highly conserved components of the innate immune system found among all classes of life. Buffalo (Bubalus bubalis), an important livestock for milk and meat production, is known to have a better resistance to many diseases as compared to cattle. They are found to express many AMPs such as defensins, cathelicidins, and hepcidin which play an important role in neutralizing the invading pathogens. Buffalo AMPs exhibit broad-spectrum antimicrobial activity against both Gram-positive and Gram-negative bacteria. Similar to its natural form, synthetic analogs of buffalo AMPs are also antimicrobial against bacteria and even fungus making them a good target for the development of therapeutic antimicrobials. In addition to its antimicrobial effect, AMPs have been demonstrated to have a number of immunomodulatory functions, and their genes are responsive to infections. Further, induction of their gene expression by external factors may help in preventing infectious diseases. This review briefly discusses the AMPs of buffalo identified to date and their possible role in innate immunity.
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Affiliation(s)
| | - Dimpal Thakuria
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal - 263 136, Uttarakhand, India
| | - Satish Kumar
- ICAR-Indian Veterinary Research Institute, Bareilly - 243 122, Uttar Pradesh, India
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16
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Pal I, Brahmkhatri VP, Bera S, Bhattacharyya D, Quirishi Y, Bhunia A, Atreya HS. Enhanced stability and activity of an antimicrobial peptide in conjugation with silver nanoparticle. J Colloid Interface Sci 2016; 483:385-393. [DOI: 10.1016/j.jcis.2016.08.043] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 11/27/2022]
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17
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Kozić M, Vukičević D, Simunić J, Rončević T, Antcheva N, Tossi A, Juretić D. Predicting the Minimal Inhibitory Concentration for Antimicrobial Peptides with Rana-Box Domain. J Chem Inf Model 2015; 55:2275-87. [PMID: 26332863 DOI: 10.1021/acs.jcim.5b00161] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The global spreading of multidrug resistance has motivated the search for new antibiotic classes including different types of antimicrobial peptides (AMPs). Computational methods for predicting activity in terms of the minimal inhibitory concentration (MIC) of AMPs can facilitate "in silico" design and reduce the cost of synthesis and testing. We have used an original method for separating training and test data sets, both of which contain the sequences and measured MIC values of non-homologous anuran peptides having the Rana-box disulfide motif at their C-terminus. Using a more flexible profiling methodology (sideways asymmetry moment, SAM) than the standard hydrophobic moment, we have developed a two-descriptor model to predict the bacteriostatic activity of Rana-box peptides against Gram-negative bacteria--the first multilinear quantitative structure-activity relationship model capable of predicting MIC values for AMPs of widely different lengths and low identity using such a small number of descriptors. Maximal values for SAMs, as defined and calculated in our method, furthermore offer new structural insight into how different segments of a peptide contribute to its bacteriostatic activity, and this work lays the foundations for the design of active artificial AMPs with this type of disulfide bridge.
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Affiliation(s)
- Mara Kozić
- Institute of Integrative Biology, University of Liverpool , Liverpool L69 7ZB, U.K
| | - Damir Vukičević
- Faculty of Science, University of Split , 21000 Split, Croatia
| | - Juraj Simunić
- Mediterranean Institute for Life Sciences , 21000 Split, Croatia
| | | | - Nikolinka Antcheva
- Department of Life Sciences, University of Trieste , 34127 Trieste, Italy
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste , 34127 Trieste, Italy
| | - Davor Juretić
- Faculty of Science, University of Split , 21000 Split, Croatia
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18
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Xu X, Lai R. The chemistry and biological activities of peptides from amphibian skin secretions. Chem Rev 2015; 115:1760-846. [PMID: 25594509 DOI: 10.1021/cr4006704] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Xueqing Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology , Kunming 650223, Yunnan, China
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19
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Evaristo G, Pinkse M, Wang L, Zhou M, Wu Y, Wang H, Chen T, Shaw C, Verhaert P. The chains of the heterodimeric amphibian skin antimicrobial peptide, distinctin, are encoded by separate messenger RNAs. J Proteomics 2013; 78:245-53. [DOI: 10.1016/j.jprot.2012.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/12/2012] [Accepted: 09/14/2012] [Indexed: 10/27/2022]
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20
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Seo MD, Won HS, Kim JH, Mishig-Ochir T, Lee BJ. Antimicrobial peptides for therapeutic applications: a review. Molecules 2012; 17:12276-86. [PMID: 23079498 PMCID: PMC6268056 DOI: 10.3390/molecules171012276] [Citation(s) in RCA: 325] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 10/08/2012] [Accepted: 10/17/2012] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial peptides (AMPs) have been considered as potential therapeutic sources of future antibiotics because of their broad-spectrum activities and different mechanisms of action compared to conventional antibiotics. Although AMPs possess considerable benefits as new generation antibiotics, their clinical and commercial development still have some limitations, such as potential toxicity, susceptibility to proteases, and high cost of peptide production. In order to overcome those obstacles, extensive efforts have been carried out. For instance, unusual amino acids or peptido-mimetics are introduced to avoid the proteolytic degradation and the design of short peptides retaining antimicrobial activities is proposed as a solution for the cost issue. In this review, we focus on small peptides, especially those with less than twelve amino acids, and provide an overview of the relationships between their three-dimensional structures and antimicrobial activities. The efforts to develop highly active AMPs with shorter sequences are also described.
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Affiliation(s)
- Min-Duk Seo
- College of Pharmacy, Ajou University, Suwon 443-749, Korea
| | - Hyung-Sik Won
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk 380-701, Korea
| | - Ji-Hun Kim
- Center for Structural Biology and Departments of Biochemistry and Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | | | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
- Author to whom correspondence should be addressed; ; Tel.: +82-2-880-7869; Fax: +82-2-872-3632
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21
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Ningsih Z, Hossain MA, Wade JD, Clayton AHA, Gee ML. Slow insertion kinetics during interaction of a model antimicrobial peptide with unilamellar phospholipid vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:2217-2224. [PMID: 22148887 DOI: 10.1021/la203770j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The mechanism of interaction between a model antimicrobial peptide and phospholipid unilamellar vesicle membranes was studied using fluorescence spectroscopy, fluorescence lifetime measurements, and light scattering. The peptide, a mellitin mutant, was labeled at position K14 with the polarity-sensitive probe AlexaFluor 430. The kinetics of the interaction of this derivative with various concentrations of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) vesicles was examined. Our work unveiled two novel aspects of peptide-lipid interactions. First, the AB plot or phasor analysis of the fluorescence lifetime studies revealed at least three different peptide states, the population of which depended on the lipid to peptide (L:P) concentration ratio. Second, complex fluorescence kinetics were observed over extended time-scales from 30 s to 2 h. The extended kinetics was only observed at particular lipid concentrations (L:P ratios 20:1 and 10:1) and not at others (30, 40, 50 and 100:1 L:P ratio). Analysis of the complex kinetics revealed several intermediates. We assign these to distinct states of the peptide formed during helix insertion into the vesicle membrane that are intermediate to lytic pore formation.
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Affiliation(s)
- Zubaidah Ningsih
- School of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
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22
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Keller RCA. New user-friendly approach to obtain an Eisenberg plot and its use as a practical tool in protein sequence analysis. Int J Mol Sci 2011; 12:5577-91. [PMID: 22016610 PMCID: PMC3189734 DOI: 10.3390/ijms12095577] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 08/22/2011] [Accepted: 08/22/2011] [Indexed: 12/26/2022] Open
Abstract
The Eisenberg plot or hydrophobic moment plot methodology is one of the most frequently used methods of bioinformatics. Bioinformatics is more and more recognized as a helpful tool in Life Sciences in general, and recent developments in approaches recognizing lipid binding regions in proteins are promising in this respect. In this study a bioinformatics approach specialized in identifying lipid binding helical regions in proteins was used to obtain an Eisenberg plot. The validity of the Heliquest generated hydrophobic moment plot was checked and exemplified. This study indicates that the Eisenberg plot methodology can be transferred to another hydrophobicity scale and renders a user-friendly approach which can be utilized in routine checks in protein–lipid interaction and in protein and peptide lipid binding characterization studies. A combined approach seems to be advantageous and results in a powerful tool in the search of helical lipid-binding regions in proteins and peptides. The strength and limitations of the Eisenberg plot approach itself are discussed as well. The presented approach not only leads to a better understanding of the nature of the protein–lipid interactions but also provides a user-friendly tool for the search of lipid-binding regions in proteins and peptides.
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Affiliation(s)
- Rob C A Keller
- Section Chemistry, Charlemagne College, Wilhelminastraat 13-15, 6524 AJ Nijmegen, The Netherlands; E-Mail: ; Tel.: +0031-243820460
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23
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Synthesis, conformational analysis and biological properties of a dicarba derivative of the antimicrobial peptide, brevinin-1BYa. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:555-64. [DOI: 10.1007/s00249-011-0679-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 01/11/2011] [Accepted: 01/25/2011] [Indexed: 10/18/2022]
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24
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Galloux M, Libersou S, Alves ID, Marquant R, Salgado GF, Rezaei H, Lepault J, Delmas B, Bouaziz S, Morellet N. NMR structure of a viral peptide inserted in artificial membranes: a view on the early steps of the birnavirus entry process. J Biol Chem 2010; 285:19409-21. [PMID: 20385550 PMCID: PMC2885221 DOI: 10.1074/jbc.m109.076083] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 03/08/2010] [Indexed: 11/06/2022] Open
Abstract
Nonenveloped virus must penetrate the cellular membrane to access the cytoplasm without the benefit of membrane fusion. For birnavirus, one of the peptides present in the virus capsid, pep46 for infectious bursal disease virus, is able to induce pores into membranes as an intermediate step of the birnavirus-penetration pathway. Using osmotic protection experiments, we demonstrate here that pep46 and its pore-forming N-terminal moiety (pep22) form pores of different diameters, 5-8 and 2-4 nm, respectively, showing that both pep46 moieties participate to pore formation. The solution structures of pep46, pep22, and pep24 (the pep46 C-terminal moiety) in different hydrophobic environments and micelles determined by (1)H NMR studies provide structural insights of the pep46 domain interaction. In CDCl(3)/CD(3)OH mixture and in dodecylphosphocholine micelles, the N-terminal domain of pep46 is structured in a long kinked helix, although the C terminus is structured in one or two helices depending upon the solvents used. We also show that the folding and the proline isomerization status of pep46 depend on the type of hydrophobic environment. NMR spectroscopy with labeled phospholipid micelles, differential scanning calorimetry, and plasmon waveguide resonance studies show the peptides lie parallel to the lipid-water interface, perturbing the fatty acid chain packing. All these data lead to a model in which the two domains of pep46 interact with the membrane to form pores.
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Affiliation(s)
- Marie Galloux
- From the Unité de Pharmacologie Chimique et Génétique, CNRS, UMR 8151, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 4 Avenue de l'Observatoire, Paris, F-75270 Cedex 06
- the Unité de Virologie et Immunologie Moléculaires, UR892, Bâtiment de Biotechnologies, INRA, Domaine de Vilvert, F-78350 Jouy-en-Josas
| | - Sonia Libersou
- the CNRS UMR 2472, INRA 1157, Virologie Moléculaire et Structurale, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Isabel D. Alves
- the UPMC Paris 06, CNRS, UMR 7203, Laboratoire des BioMolécules, FR 2769, Case Courier 182, 4 Place Jussieu, 75252 Paris Cedex 05, and
| | - Rodrigue Marquant
- From the Unité de Pharmacologie Chimique et Génétique, CNRS, UMR 8151, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 4 Avenue de l'Observatoire, Paris, F-75270 Cedex 06
| | - Gilmar F. Salgado
- the UPMC Paris 06, CNRS, UMR 7203, Laboratoire des BioMolécules, FR 2769, Case Courier 182, 4 Place Jussieu, 75252 Paris Cedex 05, and
| | - Human Rezaei
- the Unité de Virologie et Immunologie Moléculaires, UR892, Bâtiment de Biotechnologies, INRA, Domaine de Vilvert, F-78350 Jouy-en-Josas
| | - Jean Lepault
- the CNRS UMR 2472, INRA 1157, Virologie Moléculaire et Structurale, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Bernard Delmas
- the Unité de Virologie et Immunologie Moléculaires, UR892, Bâtiment de Biotechnologies, INRA, Domaine de Vilvert, F-78350 Jouy-en-Josas
| | - Serge Bouaziz
- From the Unité de Pharmacologie Chimique et Génétique, CNRS, UMR 8151, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 4 Avenue de l'Observatoire, Paris, F-75270 Cedex 06
| | - Nelly Morellet
- From the Unité de Pharmacologie Chimique et Génétique, CNRS, UMR 8151, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 4 Avenue de l'Observatoire, Paris, F-75270 Cedex 06
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25
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Henriques ST, Castanho MARB, Pattenden LK, Aguilar MI. Fast membrane association is a crucial factor in the peptide pep-1 translocation mechanism: a kinetic study followed by surface plasmon resonance. Biopolymers 2010; 94:314-22. [PMID: 20049920 DOI: 10.1002/bip.21367] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The use of peptide carriers, termed "cell-penetrating peptides (CPPs)" has attracted much attention due to their potential for cellular delivery of hydrophilic molecules with pharmacological interest, overcoming the membrane barrier. These peptides are able to deliver attached cargos in a nontoxic manner, with the uptake mechanisms being either endosomally or physically driven. Pep-1 is a CPP of particular interest, not only due to outstanding delivery rates but also because its mechanism of membrane translocation is exclusively physically driven which appears to be dependent on a very high affinity for the phospholipid bilayer in the cell membrane. In this study, pep-1-lipid interactions were further explored by characterization of the pep-1-lipid association/dissociation by surface plasmon resonance. Although a high affinity of pep-1 for lipid bilayers was observed in all conditions tested, negatively charged phospholipids resulted in a larger peptide/lipid ratio. We also show that pep-1-membrane interaction is a fast process described by a multistep model initiated by peptide adsorption, primarily governed by electrostatic attractions, and followed by peptide insertion in the hydrophobic membrane core. In the context of a cell-based process, the translocation of pep-1 is a physical mechanism promoted by peptide primary amphipathicity and asymmetric properties of the membrane. This explains the high efficiency rates of pep-1 when compared with other CPPs.
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Affiliation(s)
- Sónia Troeira Henriques
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal.
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26
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Kang SJ, Won HS, Choi WS, Lee BJ. De novo generation of antimicrobial LK peptides with a single tryptophan at the critical amphipathic interface. J Pept Sci 2009; 15:583-8. [PMID: 19544481 DOI: 10.1002/psc.1149] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
De novo design of amphipathic model peptides has been successful for generating many antimicrobial peptides with various lengths and amino acid compositions. Here, we suggest a very simple strategy to design antimicrobial peptides with a short length and a simple amino acid composition. Amphipathic helical properties were conferred by using only leucines and lysines and a single tryptophan was positioned at the critical amphipathic interface between the hydrophilic ending side and the hydrophobic starting side, in the helical wheel projection. According to this rule, the model peptides with 7 to 13 residues exhibited antimicrobial activity. Among them, the most potent activity against both Gram-positive and Gram-negative bacteria, covering all of the nine bacterial strains tested in this study, was found for the 11-mer sequences having a 1:1 (L(5)K(5)W(6)) or a 3:2 (L(6)K(4)W(6)) ratio of leucines to lysines. In particular, the former peptide L(5)K(5)W(6) could be evaluated as the most useful agent, as it showed no significant hemolytic activity with a broad-spectrum of antimicrobial activity.
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Affiliation(s)
- Su-Jin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
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27
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Grip S, Johansson J, Hedhammar M. Engineered disulfides improve mechanical properties of recombinant spider silk. Protein Sci 2009; 18:1012-22. [PMID: 19388023 DOI: 10.1002/pro.111] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Nature's high-performance polymer, spider silk, is composed of specific proteins, spidroins, which form solid fibers. So far, fibers made from recombinant spidroins have failed in replicating the extraordinary mechanical properties of the native material. A recombinant miniature spidroin consisting of four poly-Ala/Gly-rich tandem repeats and a nonrepetitive C-terminal domain (4RepCT) can be isolated in physiological buffers and undergoes self assembly into macrofibers. Herein, we have made a first attempt to improve the mechanical properties of 4RepCT fibers by selective introduction of AA --> CC mutations and by letting the fibers form under physiologically relevant redox conditions. Introduction of AA --> CC mutations in the first poly-Ala block in the miniature spidroin increases the stiffness and tensile strength without changes in ability to form fibers, or in fiber morphology. These improved mechanical properties correlate with degree of disulfide formation. AA --> CC mutations in the forth poly-Ala block, however, lead to premature aggregation of the protein, possibly due to disulfide bonding with a conserved Cys in the C-terminal domain. Replacement of this Cys with a Ser, lowers thermal stability but does not interfere with dimerization, fiber morphology or tensile strength. These results show that mutagenesis of 4RepCT can reveal spidroin structure-activity relationships and generate recombinant fibers with improved mechanical properties.
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Affiliation(s)
- S Grip
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, The Biomedical Centre, Uppsala 751 23, Sweden
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28
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Won HS, Kang SJ, Lee BJ. Action mechanism and structural requirements of the antimicrobial peptides, gaegurins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1788:1620-9. [PMID: 19059199 DOI: 10.1016/j.bbamem.2008.10.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 10/20/2008] [Accepted: 10/28/2008] [Indexed: 12/27/2022]
Abstract
Gaegurins (GGNs) are a family of cationic, alpha-helical, antimicrobial peptides that were isolated from a Korean frog, Glandirana emeljanovi (formerly classified as Rana rugosa) and represent one of the structurally well-characterized groups. Among six gaegurins, gaegurin 4 (renamed herein esculentin-2EM), gaegurin 5 (brevinin-1EMa), and gaegurin 6 (brevinin-1EMb) have been investigated comprehensively in terms of structure-activity relationships. In this paper, we first suggest renaming of gaegurins according to a recently raised rule of systematic nomenclature. Then, the current understanding of gaegurins is reviewed by summarizing their structure-activity relationships. In particular competing arguments on gaegurins are synthetically inspected. Finally their action mechanism and structural requirements will be discussed.
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Affiliation(s)
- Hyung-Sik Won
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk 380-701, South Korea.
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29
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Kalita DJ, Kumar A. Molecular cloning and characterization of lingual antimicrobial peptide cDNA of Bubalus bubalis. Res Vet Sci 2008; 86:91-7. [PMID: 18558415 DOI: 10.1016/j.rvsc.2008.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2007] [Revised: 04/24/2008] [Accepted: 05/02/2008] [Indexed: 12/17/2022]
Abstract
Antimicrobial peptides form a crucial component of innate immune system, making it a highly effective first line of defense in animals. In the study, lingual antimicrobial peptide cDNA of Bubalus bubalis has been characterized. The characterized cDNA has complete ORF of 195 bases. The signal sequence of buffalo LAP comprised of N-terminal 1-20 amino acids and mature peptide from 23-64 amino acids. The percentage of similarity of buffalo LAP and buffalo EBD at nucleotide and amino acid level was 96.4% and 92.3% respectively. The identity of buffalo LAP with cattle LAP and TAP at nucleotide level was 92.8% and 90.3%. Both at nucleotide and amino acid level buffalo LAP is closer to buffalo EBD followed by cattle LAP and TAP. Phylogenetic tree at nucleotide and amino acid level also showed close relationship of buffalo LAP with buffalo EBD, cattle LAP and TAP. The synthesized LAP fragment had antibacterial activity.
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Affiliation(s)
- Dhruba Jyoti Kalita
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India
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30
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Fázio MA, Jouvensal L, Vovelle F, Bulet P, Miranda MTM, Daffre S, Miranda A. Biological and structural characterization of new linear gomesin analogues with improved therapeutic indices. Biopolymers 2007; 88:386-400. [PMID: 17183513 DOI: 10.1002/bip.20660] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gomesin (Gm) is a potent antimicrobial peptide isolated from the spider Acanthoscurria gomesiana. The two disulfide bridges Cys(2,15) and Cys(6,11) facilitate the folding of the molecule in a beta-hairpin structure, conferring on the peptide a high stability in human plasma. We report herein biological and structural features of new linear Gm analogues, obtained by combining the removal of both disulfide bridges and the incorporation of a D- or L-proline. Regarding their biological properties, two analogues, namely, [D-Thr(2,6,11,15), Pro(9)]-D-Gm and [Thr(2,6,11,15), D-Pro(9)]-Gm, are as potent as Gm against Candida albicans and only fourfold less against Staphylococcus aureus and Escherichia coli. In addition, at 100 microM they are approximately threefold less hemolytic than Gm. The best therapeutic indices were found for [D-Thr(2,6,11,15), Pro(9)]-D-Gm and for [(Des-pGlu(1), -Thr(2), -Arg(3)), Thr(6,11,15), D-Pro(9)]-Gm with a 32-fold increase of their activity against bacteria, and from 128- to 512-fold against yeast when compared with Gm. Regarding the stability, [D-Thr(2,6,11,15), Pro(9)]-D-Gm appeared to be the most resistant in human serum, along with [D-Thr(2,6,11,15), Pro(8)]-D-Gm and [Thr(2,6,11,15), D-Arg(4,16), D-Pro(9)]-Gm. When evaluating their conformation by CD spectroscopy in sodium dodecyl sulfate (SDS), most linear analogues display beta-conformation characteristics. Moreover, considering its high therapeutic index and stability in serum, [D-Thr(2,6,11,15), Pro(9)]-D-Gm was further analyzed by NMR spectroscopy. (1)H NMR experiments in SDS micelles demonstrated that [D-Thr(2,6,11,15), Pro(9)]-D-Gm presents a conformation very similar to that of Gm. In our search for Gm analogues with enhanced potential for drug development, we demonstrated that designing cysteine-free analogues can improve the therapeutic index of Gm derivatives.
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Affiliation(s)
- Marcos A Fázio
- Department of Biophysics, UNIFESP, 04044-020 São Paulo, SP, Brazil
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31
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Park S, Son WS, Kim YJ, Kwon AR, Lee BJ. NMR Spectroscopic Assessment of the Structure and Dynamic Properties of an Amphibian Antimicrobial Peptide (Gaegurin 4) Bound to SDS Micelles. BMB Rep 2007; 40:261-9. [PMID: 17394777 DOI: 10.5483/bmbrep.2007.40.2.261] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structure and dynamics of a 37-residue antimicrobial peptide gaegurin 4 (GGN4) isolated from the skin of the native Korean frog, Rana rugosa, was determined in SDS micelles by NMR spectroscopy. The solution structure of the peptide in SDS micelles was determined from 352 NOE-derived distance constraints and 22 backbone torsion angle constraints. Dynamic properties for the amide backbone were characterized by (1)H-(15)N heteronuclear NOE experiments. The structural study revealed two amphipathic helices spanning residues 2-10 and 16-32 and that the helices were connected by a flexible loop. An intraresidue disulfide bridge was formed between residues Cys31 and Cys37 near the C-terminus. The loop region (11-15) connecting the two helices are were slightly more flexible than these helices themselves. From the fact that since there is no contact NOEs between two helices, it is implied that the GGN4 peptide shows an independent motion of both helices which has an angle of about 60 degrees -120 degrees from each other.
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Affiliation(s)
- Sangho Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, San 56-1, Shillim-dong, Gwanak-gu, Seoul 151-742, Republic of Korea
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Yount NY, Yeaman MR. Structural congruence among membrane-active host defense polypeptides of diverse phylogeny. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:1373-86. [PMID: 16725105 DOI: 10.1016/j.bbamem.2006.03.027] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2006] [Revised: 03/08/2006] [Accepted: 03/15/2006] [Indexed: 11/17/2022]
Abstract
A requisite for efficacious host defense against pathogens and predators has prioritized evolution of effector molecules thereof. A recent multidimensional analysis of physicochemical properties revealed a novel, unifying structural signature among virtually all classes of cysteine-containing antimicrobial peptides. This motif, termed the gamma-core, is seen in host defense peptides from organisms spanning more than 2.6 billion years of evolution. Interestingly, many toxins possess the gamma-core signature, consistent with discoveries of their direct antimicrobial activity. Many microbicidal chemokines (kinocidins) likewise contain iterations of the gamma-core motif, reconciling their antimicrobial efficacy. Importantly, these polypeptide classes have evolved to target and modulate biomembranes in protecting respective hosts against unfavorable interactions with potential pathogens or predators. Extending on this concept, the current report addresses the hypothesis that antimicrobial peptides, kinocidins, and polypeptide toxins are structurally congruent and share a remarkably close phylogenetic relationship, paralleling their roles in host-pathogen relationships. Analyses of their mature amino acid sequences demonstrated that cysteine-stabilized antimicrobial peptides, kinocidins, and toxins share ancient evolutionary relatedness stemming from early precursors of the gamma-core signature. Moreover, comparative 3-D structure analysis revealed recurring iterations of antimicrobial peptide gamma-core motifs within kinocidins and toxins. However, despite such congruence in gamma-core motifs, the kinocidins diverged in overall homology from microbicidal peptides or toxins. These findings are consistent with observations that chemokines are not toxic to mammalian cells, in contrast to many antimicrobial peptides and toxins. Thus, specific functions of these molecular effectors may be governed by specific configurations of structural modules associated with a common gamma-core motif. These concepts are consistent with the hypothesis that the gamma-core is an archetype determinant in polypeptides that target or regulate with biological membranes, with specific iterations optimized to unique or cognate host defense contexts. Quantitative and qualitative data suggest these protein families emerged through both parallel and divergent processes of modular evolution. Taken together, the current and prior findings imply that the gamma-core motif contributes to conserved structures and functions of host defense polypeptides. The presence of this unifying molecular signature in otherwise diverse categories of membrane-active host defense peptides implies an ancient and essential role for such a motif in effector molecules governing host-pathogen relationships.
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Affiliation(s)
- Nannette Y Yount
- Division of Infectious Diseases, LAC-Harbor UCLA Medical Center, Torrance, CA 90509, USA
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Pukala TL, Bowie JH, Maselli VM, Musgrave IF, Tyler MJ. Host-defence peptides from the glandular secretions of amphibians: structure and activity. Nat Prod Rep 2006; 23:368-93. [PMID: 16741585 DOI: 10.1039/b512118n] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Tara L Pukala
- Department of Chemistry, The University of Adelaide, South Australia
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Li H, Li F, Qian ZM, Sun H. Structure and topology of the transmembrane domain 4 of the divalent metal transporter in membrane-mimetic environments. ACTA ACUST UNITED AC 2004; 271:1938-51. [PMID: 15128303 DOI: 10.1111/j.1432-1033.2004.04104.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The divalent metal transporter (DMT1) is a 12-transmembrane domain protein responsible for dietary iron uptake in the duodenum and iron acquisition from transferrin in peripheral tissues. The transmembrane domain 4 (TM4) of DMT1 has been shown to be crucial for its biological function. Here we report the 3D structure and topology of the DMT1-TM4 peptide by NMR spectroscopy with simulated annealing calculations in membrane-mimetic environments, e.g. 2,2,2-trifluoroethanol and SDS micelles. The 3D structures of the peptide are similar in both environments, with nonordered and flexible N- and C-termini flanking an ordered helical region. The final set of the 16 lowest energy structures is particularly well defined in the region of residues Leu9-Phe20 in 2,2,2-trifluoroethanol, with a mean pairwise root mean square deviation of 0.23 +/- 0.10 A for the backbone heavy atoms and 0.82 +/- 0.17 A for all heavy atoms. In SDS micelles, the length of the helix is dependent on pH values. In particular, the C-terminus becomes well-structured at low pH (4.0), whereas the N-terminal segment (Arg1-Gly7) is flexible and poorly defined at all pH values studied. The effects of 12-doxylPtdCho spin-label and paramagnetic metal ions on NMR signal intensities demonstrated that both the N-terminus and helical region of the TM4 are embedded into the interior of SDS micelles. Unexpectedly, we observed that amide protons exchanged much faster in SDS than in 2,2,2-trifluoroethanol, indicating that there is possible solvent accessibility in the structure. The paramagnetic metal ions broaden NMR signals from residues both situated in aqueous phase and in the helical region. From these results we speculate that DMT1-TM4s may self-assemble to form a channel through which metal ions are likely to be transported. These results might provide an insight into the structure-function relationship for the integral DMT1.
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Affiliation(s)
- Hongyan Li
- Department of Chemistry and Open Laboratory of Chemical Biology, The University of Hong Kong, China
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Won HS, Jung SJ, Kim HE, Seo MD, Lee BJ. Systematic Peptide Engineering and Structural Characterization to Search for the Shortest Antimicrobial Peptide Analogue of Gaegurin 5. J Biol Chem 2004; 279:14784-91. [PMID: 14739294 DOI: 10.1074/jbc.m309822200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As part of an effort to develop new, low molecular mass peptide antibiotics, we searched for the shortest bioactive analogue of gaegurin 5 (GGN5), a 24-residue antimicrobial peptide. Thirty-one kinds of GGN5 analogues were synthesized, and their biological activities were analyzed against diverse microorganisms and human erythrocytes. The structural properties of the peptides in various solutions were characterized by spectroscopic methods. The N-terminal 13 residues of GGN5 were identified as the minimal requirement for biological activity. The helical stability, the amphipathic property, and the hydrophobic N terminus were characterized as the important structural factors driving the activity. To develop shorter antibiotic peptides, amino acid substitutions in an inactive 11-residue analogue were examined. Single tryptophanyl substitutions at certain positions yielded some active 11-residue analogues. The most effective site for the substitution was the hydrophobic-hydrophilic interface in the amphipathic helical structure. At this position, tryptophan was the most useful amino acid conferring favorable activity to the peptide. The introduced tryptophan played an important anchoring role for the membrane interaction of the peptides. Finally, two 11-residue analogues of GGN5, which exhibited strong bactericidal activity with little hemolytic activity, were obtained as property-optimized candidates for new peptide antibiotic development. Altogether, the present approach not only characterized some important factors for the antimicrobial activity but also provided useful information about peptide engineering to search for potent lead molecules for new peptide antibiotic development.
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Affiliation(s)
- Hyung-Sik Won
- National Research Laboratory for Membrane Protein Structure, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
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Won HS, Lee YH, Kim JH, Shin IS, Lee MH, Lee BJ. Structural Characterization of the Nickel-binding Properties of Bacillus pasteurii Urease Accessory Protein (Ure)E in Solution. J Biol Chem 2004; 279:17466-72. [PMID: 14769802 DOI: 10.1074/jbc.m308390200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Urease activation is critical to the virulence of many human and animal pathogens. Urease possesses multiple, nickel-containing active sites, and UreE, the only nickel-binding protein among the urease accessory proteins, activates urease by transporting nickel ions. We performed NMR experiments to investigate the solution structure and the nickel-binding properties of Bacillus pasteurii (Bp) UreE. The secondary structures and global folds of BpUreE were determined for its metal-free and nickel-bound forms. The results indicated that no major structural change of BpUreE arises from the nickel binding. In addition to the previously identified nickel-binding site (Gly(97)-Cys(103)), the C-terminal tail region (Lys(141)-His(147)) was confirmed for the first time to be involved in the nickel binding. The C-terminally conserved sequence ((144)GHQH(147)) was confirmed to have an inherent nickel-binding ability. Nickel addition to 1.6 mm subunit, a concentration where BpUreE predominantly forms a tetramer upon the nickel binding, induced a biphasic spectral change consistent with binding of up to at least three nickel ions per tetrameric unit. In contrast, nickel addition to 0.1 mm subunit, a concentration at which the protein is primarily a dimer, caused a monophasic spectral change consistent with more than 1 equivalent per dimeric unit. Combined with the equilibrium dialysis results, which indicated 2.5 nickel equivalents binding per dimer at a micromolar protein concentration, the nickel-binding stoichiometry of BpUreE at a physiological concentration could be three nickel ions per dimer. Altogether, the present results provide the first detailed structural data concerning the nickel-binding properties of intact, wild-type BpUreE in solution.
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Affiliation(s)
- Hyung-Sik Won
- National Research Laboratory for Membrane Protein Structure, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
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