1
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Macias ALD, Alecrim LC, Almeida FCL, Giordano RJ. Understanding the Structural Requirements of Peptide-Protein Interaction and Applications for Peptidomimetic Development. Methods Mol Biol 2024; 2793:65-82. [PMID: 38526724 DOI: 10.1007/978-1-0716-3798-2_5] [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] [Indexed: 03/27/2024]
Abstract
Protein-protein interaction is at the heart of most biological processes, and small peptides that bind to protein binding sites are resourceful tools to explore and understand the structural requirements for these interactions. In that sense, phage display is a well-suited technology to study protein-protein interactions, as it allows for unbiased screening of billions of peptides in search for those that interact with a protein binding domain. Here, we will illustrate how two distinct but complementary approaches, phage display and nuclear magnetic resonance (NMR), can be utilized to unveil structural details of peptide-protein interaction. Finally, knowledge derived from phage mutagenesis and NMR studies can be streamlined for quick peptidomimetic design and synthesis using the retroinversion approach to validate using in vitro and in vivo assays the therapeutic potential of peptides identified by phage display.
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Affiliation(s)
| | - Lilian Costa Alecrim
- Biochemistry Department, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil
| | - Fabio C L Almeida
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo Jose Giordano
- Biochemistry Department, Institute of Chemistry, University of Sao Paulo, Sao Paulo, Brazil.
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2
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Membrane interactions of the anuran antimicrobial peptide HSP1-NH 2: Different aspects of the association to anionic and zwitterionic biomimetic systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183449. [PMID: 32828849 DOI: 10.1016/j.bbamem.2020.183449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/08/2020] [Accepted: 08/17/2020] [Indexed: 11/21/2022]
Abstract
Studies have suggested that antimicrobial peptides act by different mechanisms, such as micellisation, self-assembly of nanostructures and pore formation on the membrane surface. This work presents an extensive investigation of the membrane interactions of the 14 amino-acid antimicrobial peptide hylaseptin P1-NH2 (HSP1-NH2), derived from the tree-frog Hyla punctata, which has stronger antifungal than antibacterial potential. Biophysical and structural analyses were performed and the correlated results were used to describe in detail the interactions of HSP1-NH2 with zwitterionic and anionic detergent micelles and phospholipid vesicles. HSP1-NH2 presents similar well-defined helical conformations in both zwitterionic and anionic micelles, although NMR spectroscopy revealed important structural differences in the peptide N-terminus. 2H exchange experiments of HSP1-NH2 indicated the insertion of the most N-terminal residues (1-3) in the DPC-d38 micelles. A higher enthalpic contribution was verified for the interaction of the peptide with anionic vesicles in comparison with zwitterionic vesicles. The pore formation ability of HSP1-NH2 (examined by dye release assays) and its effect on the size and surface charge as well as on the lipid acyl chain ordering (evaluated by Fourier-transform infrared spectroscopy) of anionic phospholipid vesicles showed membrane disruption even at low peptide-to-phospholipid ratios, and the effect increases proportionately to the peptide concentration. On the other hand, these biophysical investigations showed that a critical peptide-to-phospholipid ratio around 0.6 is essential for promoting disruption of zwitterionic membranes. In conclusion, this study demonstrates that the binding process of the antimicrobial HSP1-NH2 peptide depends on the membrane composition and peptide concentration.
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3
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Fluorine-19 NMR spectroscopy of fluorinated analogs of tritrpticin highlights a distinct role for Tyr residues in antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183260. [DOI: 10.1016/j.bbamem.2020.183260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 02/08/2023]
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4
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Ghazarian H, Hu W, Mao A, Nguyen T, Vaidehi N, Sligar S, Shively JE. NMR analysis of free and lipid nanodisc anchored CEACAM1 membrane proximal peptides with Ca 2+/CaM. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:787-797. [PMID: 30639287 DOI: 10.1016/j.bbamem.2019.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/16/2018] [Accepted: 01/08/2019] [Indexed: 11/28/2022]
Abstract
CEACAM1, a homotypic transmembrane receptor with 12 or 72 amino acid cytosolic domain isoforms, is converted from inactive cis-dimers to active trans-dimers by calcium-calmodulin (Ca2+/CaM). Previously, the weak binding of Ca2+/CaM to the human 12 AA cytosolic domain was studied using C-terminal anchored peptides. We now show the binding of 15N labeled Phe-454 cytosolic domain peptides in solution or membrane anchored using NMR demonstrates a significant role for the lipid bilayer. Although binding is increased by the mutation Phe454Ala, this mutation was previously shown to abrogate actin binding. On the other hand, Ca2+/CaM binding is abrogated by phosphorylation of nearby Thr-457, a post-translation modification required for actin binding and subsequent in vitro lumen formation. Binding of Ca2+/CaM to a membrane proximal peptide from the long 72 AA cytosolic domain anchored to lipid nanodiscs was very weak compared to lipid free conditions, suggesting membrane specific effects between the two isoforms. NMR analysis of 15N labeled Ca2+/CaM with unlabeled peptides showed the C-lobe of Ca2+/CaM is involved in peptide interactions, and hydrophobic residues such as Met-109, Val-142 and Met-144 play important roles in binding peptide. This information was incorporated into transmembrane models of CEACAM1 binding to Ca2+/CaM. The lack of Ca2+/CaM binding to phosphorylated Thr-457, a residue we have previously shown to be phosphorylated by CaMK2D, also dependent on Ca2+/CaM, suggests stepwise binding of the cytosolic domain first to Ca2+/CaM and then to actin.
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Affiliation(s)
- Haike Ghazarian
- Department of Molecular Imaging and Therapy, Diabetes, Metabolism and Research Institute of City of Hope, 1450 East Duarte Road, Duarte, CA 91010, United States of America; City of Hope Irell and Manella Graduate School of Biological Sciences, 1450 East Duarte road, Duarte, CA 91010, United States of America
| | - Weidong Hu
- Department of Molecular Imaging and Therapy, Diabetes, Metabolism and Research Institute of City of Hope, 1450 East Duarte Road, Duarte, CA 91010, United States of America
| | - Allen Mao
- Department of Molecular Imaging and Therapy, Diabetes, Metabolism and Research Institute of City of Hope, 1450 East Duarte Road, Duarte, CA 91010, United States of America
| | - Tung Nguyen
- Department of Molecular Imaging and Therapy, Diabetes, Metabolism and Research Institute of City of Hope, 1450 East Duarte Road, Duarte, CA 91010, United States of America
| | - Nagarajan Vaidehi
- Department of Molecular Imaging and Therapy, Diabetes, Metabolism and Research Institute of City of Hope, 1450 East Duarte Road, Duarte, CA 91010, United States of America
| | - Stephen Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States of America
| | - John E Shively
- Department of Molecular Imaging and Therapy, Diabetes, Metabolism and Research Institute of City of Hope, 1450 East Duarte Road, Duarte, CA 91010, United States of America.
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5
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Bondaryk M, Staniszewska M, Zielińska P, Urbańczyk-Lipkowska Z. Natural Antimicrobial Peptides as Inspiration for Design of a New Generation Antifungal Compounds. J Fungi (Basel) 2017; 3:E46. [PMID: 29371563 PMCID: PMC5715947 DOI: 10.3390/jof3030046] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/16/2017] [Accepted: 08/22/2017] [Indexed: 12/16/2022] Open
Abstract
Invasive fungal infections are associated with high mortality rates, despite appropriate antifungal therapy. Limited therapeutic options, resistance development and the high mortality of invasive fungal infections brought about more concern triggering the search for new compounds capable of interfering with fungal viability and virulence. In this context, peptides gained attention as promising candidates for the antimycotics development. Variety of structural and functional characteristics identified for various natural antifungal peptides makes them excellent starting points for design novel drug candidates. Current review provides a brief overview of natural and synthetic antifungal peptides.
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Affiliation(s)
- Małgorzata Bondaryk
- National Institute of Public Health-National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland.
| | - Monika Staniszewska
- National Institute of Public Health-National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland.
| | - Paulina Zielińska
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
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6
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Arias M, Nguyen LT, Kuczynski AM, Lejon T, Vogel HJ. Position-Dependent Influence of the Three Trp Residues on the Membrane Activity of the Antimicrobial Peptide, Tritrpticin. Antibiotics (Basel) 2014; 3:595-616. [PMID: 27025758 PMCID: PMC4790384 DOI: 10.3390/antibiotics3040595] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/23/2014] [Accepted: 10/23/2014] [Indexed: 01/30/2023] Open
Abstract
Antimicrobial peptides (AMPs) constitute promising candidates for the development of new antibiotics. Among the ever-expanding family of AMPs, tritrpticin has strong antimicrobial activity against a broad range of pathogens. This 13-residue peptide has an unusual amino acid sequence that is almost symmetrical and features three central Trp residues with two Arg residues near each end of the peptide. In this work, the role of the three sequential Trp residues in tritrpticin was studied in a systematic fashion by making a series of synthetic peptides with single-, double- and triple-Trp substitutions to Tyr or Ala. 1H NMR and fluorescence spectroscopy demonstrated the ability of all of the tritrpticin-analog peptides to interact with negatively-charged membranes. Consequently, most tritrpticin analogs exhibited the ability to permeabilize synthetic ePC:ePG (egg-yolk phosphatidylcholine (ePC), egg-yolk phosphatidylglycerol (ePG)) vesicles and live Escherichia coli bacteria. The membrane perturbation characteristics were highly dependent on the location of the Trp residue substitution, with Trp6 being the most important residue and Trp8 the least. The membrane permeabilization activity of the peptides in synthetic and biological membranes was directly correlated with the antimicrobial potency of the peptides against E. coli. These results contribute to the understanding of the role of each of the three Trp residues to the antimicrobial activity of tritrpticin.
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Affiliation(s)
- Mauricio Arias
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada.
| | - Leonard T Nguyen
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada.
| | - Andrea M Kuczynski
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada.
| | - Tore Lejon
- Department of Chemistry, Faculty of Science, UiT-The Artic University of Norway, Tromsø N-9037, Norway.
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada.
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7
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Iannucci NB, Curto LM, Albericio F, Cascone O, Delfino JM. Structural glance into a novel anti-staphylococcal peptide. Biopolymers 2014; 102:49-57. [DOI: 10.1002/bip.22394] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/20/2013] [Accepted: 07/24/2013] [Indexed: 11/11/2022]
Affiliation(s)
- N. B. Iannucci
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry; University of Buenos Aires; Junín 956, C1113AAD Buenos Aires, Argentina
- Therapeutic Peptides Research and Development Laboratory; Chemo-Romikin, Carlos Villate 5148, B1605AXL, Buenos Aires; Argentina
| | - L. M. Curto
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry; University of Buenos Aires; Junín 956, C1113AAD Buenos Aires, Argentina
| | - F. Albericio
- Institute for Research in Biomedicine; Barcelona Science Park, c/Baldiri Reixac 10, 08028; Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering; Biomaterials and Nanomedicine, Barcelona Science Park, c/Baldiri Reixac 10, 08028; Barcelona, Spain
- Department of Organic Chemistry, School of Chemistry; University of Barcelona, Martí i Franquès 1-11, 08028; Barcelona, Spain
- School of Chemistry and Physics; University of KwaZulu-Natal; Westville Campus, University Road, Westville, 4001-Durban South Africa
| | - O. Cascone
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry; University of Buenos Aires; Junín 956, C1113AAD Buenos Aires, Argentina
| | - J. M. Delfino
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry; University of Buenos Aires; Junín 956, C1113AAD Buenos Aires, Argentina
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8
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Gomes-Neto F, Valente AP, Almeida FCL. Modeling the interaction of dodecylphosphocholine micelles with the anticoccidial peptide PW2 guided by NMR data. Molecules 2013; 18:10056-80. [PMID: 23966088 PMCID: PMC6270265 DOI: 10.3390/molecules180810056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial peptides are highly dynamic entities that acquire structure upon binding to a membrane interface. To better understand the structure and the mechanism for the molecular recognition of dodecylphosphocholine (DPC) micelles by the anticoccidial peptide PW2, we performed molecular dynamics (MD) simulations guided by NMR experimental data, focusing on strategies to explore the transient nature of micelles, which rearrange on a millisecond to second timescale. We simulated the association of PW2 with a pre-built DPC micelle and with free-DPC molecules that spontaneously forms micelles in the presence of the peptide along the simulation. The simulation with spontaneous micelle formation provided the adequate environment which replicated the experimental data. The unrestrained MD simulations reproduced the NMR structure for the entire 100 ns MD simulation time. Hidden discrete conformational states could be described. Coulomb interactions are important for initial approximation and hydrogen bonds for floating the aromatic region at the interface, being essential for the stabilization of the interaction. Arg9 is strongly attached with phosphate. We observed a helix elongation process stabilized by the intermolecular peptide-micelle association. Full association that mimics the experimental data only happens after complete micelle re-association. Fast micelle dynamics without dissociation of surfactants leads to only superficial binding.
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Affiliation(s)
- Francisco Gomes-Neto
- Laboratory of Toxinology, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21045-900, Brazil; E-Mail:
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro - Institute of Structural Biology and Bioimaging, Rio de Janeiro 21941-920, Brazil; E-Mail:
| | - Ana Paula Valente
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro - Institute of Structural Biology and Bioimaging, Rio de Janeiro 21941-920, Brazil; E-Mail:
| | - Fabio C. L. Almeida
- Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro - Institute of Structural Biology and Bioimaging, Rio de Janeiro 21941-920, Brazil; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +55-21-3104-2326; Fax: +55-21-3104-2326
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9
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Yu HY, Huang KC, Yip BS, Tu CH, Chen HL, Cheng HT, Cheng JW. Rational design of tryptophan-rich antimicrobial peptides with enhanced antimicrobial activities and specificities. Chembiochem 2011; 11:2273-82. [PMID: 20865718 DOI: 10.1002/cbic.201000372] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Trp-rich antimicrobial peptides play important roles in the host innate defense mechanism of many plants and animals. A series of short Trp-rich peptides derived from the C-terminal region of Bothrops asper myothoxin II, a Lys49 phospholipase A(2) (PLA(2)), were found to reproduce the antimicrobial activities of their parent molecule. Of these peptides, KKWRWWLKALAKK-designated PEM-2-was found to display improved activity against both Gram-positive and Gram-negative bacteria. To improve the antimicrobial activity of PEM-2 for potential clinical applications further, we determined the solution structure of PEM-2 bound to membrane-mimetic dodecylphosphocholine (DPC) micelles by two-dimensional NMR methods. The DPC micelle-bound structure of PEM-2 adopts an α-helical conformation and the positively charged residues are clustered together to form a hydrophilic patch. The surface electrostatic potential map indicates that two of the three tryptophan residues are packed against the peptide backbone and form a hydrophobic face with Leu7, Ala9, and Leu10. A variety of biophysical and biochemical experiments, including circular dichroism, fluorescence spectroscopy, and microcalorimetry, were used to show that PEM-2 interacted with negatively charged phospholipid vesicles and efficiently induced dye release from these vesicles, suggesting that the antimicrobial activity of PEM-2 could be due to interactions with bacterial membranes. Potent analogues of PEM-2 with enhanced antimicrobial and less pronounced hemolytic activities were designed with the aid of these structural studies.
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Affiliation(s)
- Hui-Yuan Yu
- Institute of Biotechnology, Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
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10
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Young AW, Liu Z, Zhou C, Totsingan F, Jiwrajka N, Shi Z, Kallenbach NR. Structure and antimicrobial properties of multivalent short peptides. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00247j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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11
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Gregor CR, Cerasoli E, Tulip PR, Ryadnov MG, Martyna GJ, Crain J. Autonomous folding in the membrane proximal HIV peptide gp41659–671: pH tuneability at micelle interfaces. Phys Chem Chem Phys 2011; 13:127-35. [DOI: 10.1039/c0cp01502d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Joshi S, Bisht GS, Rawat DS, Kumar A, Kumar R, Maiti S, Pasha S. Interaction studies of novel cell selective antimicrobial peptides with model membranes and E. coli ATCC 11775. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1864-75. [DOI: 10.1016/j.bbamem.2010.06.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 06/04/2010] [Accepted: 06/16/2010] [Indexed: 10/19/2022]
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13
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Kim JK, Lee SA, Shin S, Lee JY, Jeong KW, Nan YH, Park YS, Shin SY, Kim Y. Structural flexibility and the positive charges are the key factors in bacterial cell selectivity and membrane penetration of peptoid-substituted analog of Piscidin 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1913-25. [PMID: 20603100 DOI: 10.1016/j.bbamem.2010.06.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 06/11/2010] [Accepted: 06/25/2010] [Indexed: 01/25/2023]
Abstract
Piscidin 1 (Pis-1) is a novel cytotoxic peptide with a cationic alpha-helical structure isolated from the mast cells of hybrid striped bass. In our previous study, we showed that Pis-1[PG] with a substitution of Pro(8) for Gly(8) in Pis-1 had higher bacterial cell selectivity than Pis-1. We designed peptoid residue-substituted peptide, Pis-1[NkG], in which Gly(8) of Pis-1 was replaced with Nlys (Lys peptoid residue). Pis-1[NkG] had higher antibacterial activity and lower cytotoxicity against mammalian cells than Pis-1 and Pis-1[PG]. We determined the tertiary structure of Pis-1[PG] and Pis-1[NkG] in the presence of DPC micelles by NMR spectroscopy. Both peptides had a three-turn helix in the C-terminal region and a bent structure in the center. Pis-1[PG] has a rigid bent structure at Pro(8) whereas Pis-1[NkG] existed as a dynamic equilibrium of two conformers with a flexible hinge structure at Nlys(8). Depolarization of the membrane potential of Staphylococcus aureus and confocal laser-scanning microscopy study revealed that Pis-1[NkG] effectively penetrated the bacterial cell membrane and accumulated in the cytoplasm, whereas Pis-1[PG] did not penetrate the membrane but remained outside or on the cell surface. Introduction of a lysine peptoid at position 8 of Pis-1 provided conformational flexibility and increased the positive charge at the hinge region; both factors facilitated penetration of the bacterial cell membrane and conferred bacterial cell selectivity on Pis-1[NkG].
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Affiliation(s)
- Jin-Kyoung Kim
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Korea
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14
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Maupetit J, Derreumaux P, Tufféry P. A fast method for large-scale de novo peptide and miniprotein structure prediction. J Comput Chem 2010; 31:726-38. [PMID: 19569182 DOI: 10.1002/jcc.21365] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although peptides have many biological and biomedical implications, an accurate method predicting their equilibrium structural ensembles from amino acid sequences and suitable for large-scale experiments is still missing. We introduce a new approach-PEP-FOLD-to the de novo prediction of peptides and miniproteins. It first predicts, in the terms of a Hidden Markov Model-derived structural alphabet, a limited number of local conformations at each position of the structure. It then performs their assembly using a greedy procedure driven by a coarse-grained energy score. On a benchmark of 52 peptides with 9-23 amino acids, PEP-FOLD generates lowest-energy conformations within 2.8 and 2.3 A Calpha root-mean-square deviation from the full nuclear magnetic resonance structures (NMR) and the NMR rigid cores, respectively, outperforming previous approaches. For 13 miniproteins with 27-49 amino acids, PEP-FOLD reaches an accuracy of 3.6 and 4.6 A Calpha root-mean-square deviation for the most-native and lowest-energy conformations, using the nonflexible regions identified by NMR. PEP-FOLD simulations are fast-a few minutes only-opening therefore, the door to in silico large-scale rational design of new bioactive peptides and miniproteins.
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Affiliation(s)
- Julien Maupetit
- MTi, INSERM UMR-S973 and RPBS, Université Paris Diderot - Paris 7, 5 rue Marie-Andrée Lagroua Weill-Halle, 75205 Paris, Cedex 13, France
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15
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Onoda A, Suzuki T, Ishizuka H, Sugiyama R, Ariyasu S, Yamamura T. Minimal motif peptide structure of metzincin clan zinc peptidases in micelles. J Pept Sci 2010; 15:832-41. [PMID: 19830795 DOI: 10.1002/psc.1184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
It is well known that the functions of metalloproteins generally originate from their metal-binding motifs. However, the intrinsic nature of individual motifs remains unknown, particularly the details about metal-binding effects on the folding of motifs; the converse is also unknown, although there is no doubt that the motif is the core of the reactivity for each metalloprotein. In this study, we focused our attention on the zinc-binding motif of the metzincin clan family, HEXXHXXGXXH; this family contains the general zinc-binding sequence His-Glu-Xaa-Xaa-His (HEXXH) and the extended GXXH region. We adopted the motif sequence of stromelysin-1 and investigated the folding properties of the Trp-labeled peptides WAHEIAHSLGLFHA (STR-W1), AWHEIAHSLGLFHA (STR-W2), AHEIAHSLGWFHA (STR-W11), and AHEIAHSLGLFHWA (STR-W14) in the presence and absence of zinc ions in hydrophobic micellar environments by circular dichroism (CD) measurements. We accessed successful incorporation of these zinc peptides into micelles using quenching of Trp fluorescence. Results of CD studies indicated that two of the Trp-incorporated peptides, STR-W1 and STR-W14, exhibited helical folding in the hydrophobic region of cetyltrimethylammonium chloride micelle. The NMR structural analysis of the apo STR-W14 revealed that the conformation in the C-terminus GXXH region significantly differred between the apo state in the micelle and the reported Zn-bound state of stromelysin-1 in crystal structures. The structural analyses of the qualitative Zn-binding properties of this motif peptide provide an interesting Zn-binding mechanism: the minimum consensus motif in the metzincin clan, a basic zinc-binding motif with an extended GXXH region, has the potential to serve as a preorganized Zn binding scaffold in a hydrophobic environment.
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Affiliation(s)
- Akira Onoda
- Faculty of Science, Department of Chemistry, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan
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Li MY, Wang J, Lai GY. Effect of a dentifrice containing the peptide of streptococcal antigen I/II on the adherence of mutans streptococcus. Arch Oral Biol 2009; 54:1068-73. [DOI: 10.1016/j.archoralbio.2009.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 08/03/2009] [Accepted: 08/12/2009] [Indexed: 10/20/2022]
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17
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Giuseppe Rizzello C, Coda R, De Angelis M, Di Cagno R, Carnevali P, Gobbetti M. Long-term fungal inhibitory activity of water-soluble extract from Amaranthus spp. seeds during storage of gluten-free and wheat flour breads. Int J Food Microbiol 2009; 131:189-96. [DOI: 10.1016/j.ijfoodmicro.2009.02.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 02/11/2009] [Accepted: 02/20/2009] [Indexed: 11/28/2022]
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18
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Wu JM, Wei SY, Chen HL, Weng KY, Cheng HT, Cheng JW. Solution structure of a novel D-naphthylalanine substituted peptide with potential antibacterial and antifungal activities. Biopolymers 2008; 88:738-45. [PMID: 17410595 DOI: 10.1002/bip.20736] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A new type of Trp-rich peptide, Ac-KWRRWVRWI-NH2, designated as Pac-525, was found to possess improved activity against both gram-positive and negative bacteria. We have synthesized two Pac-525 analogues, D-Pac-525 containing all D-amino acids and D-Nal-Pac-525, the D-Pac-525 analogue with tryptophan replaced by D-beta-naphthylalanine. We have determined the solution structure of D-Nal-Pac-525 bound to membrane-mimetic DPC micelles by two-dimensional NMR methods. The DPC micelle-bound structure of D-Nal-Pac-525 adopts a left-hand alpha-helical segment and the positively charged residues are clustered together to form a hydrophilic patch. The surface electrostatic potential map indicates the three D-beta-naphthylalanines are packed against the peptide backbone and form an amphipathic structure. A variety of biophysical and biochemical experiments, including circular dichroism, fluorescence spectroscopy, and microcalorimetry, were used to show that D-Nal-Pac-525 interacted strongly with negatively charged phospholipid vesicles and induced efficient dye release from these vesicles, suggesting that the strong antimicrobial activity of D-Nal-Pac-525 may be due to interactions with bacterial and fungus membranes.
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Affiliation(s)
- Jiun-Ming Wu
- Institute of Biotechnology and Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan
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19
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Tinoco LW, Gomes-Neto F, Valente AP, Almeida FCL. Effect of micelle interface on the binding of anticoccidial PW2 peptide. JOURNAL OF BIOMOLECULAR NMR 2007; 39:315-322. [PMID: 17926009 DOI: 10.1007/s10858-007-9202-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Revised: 09/18/2007] [Accepted: 09/18/2007] [Indexed: 05/25/2023]
Abstract
PW2 is an anticoccidial peptide active against Eimeria acervulina and Eimeria tenella. We determined the structure of PW2 in dodecylphosphocholine micelles. The structure showed two distinct regions: an amphipathic N-terminal 3(10) helix and an aromatic region containing WWR interface-binding motif. The aromatic region acted as a scaffold of the protein in the interface and shared the same structure in both DPC and SDS micelles. N-terminal helix interacted with DPC but not with SDS interface. Chemical shift change was slow when SDS was added to PW2 in DPC and fast when DPC was added to PW2 in SDS, indicating that interaction with DPC micelles was kinetically more stable than with SDS micelles. Also, DPC interface was able to accommodate PW2, but it maintained the conformational arrangement in the aromatic region observed for SDS micelles. This behavior, which is different from that observed for other antimicrobial peptides with WWR motif, may be associated with the absence of PW2 antibacterial activity and its selectivity for Eimeria parasites.
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Affiliation(s)
- Luzineide W Tinoco
- Nucleo de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-590, Brazil
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20
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Siddiqui AA, Singh N, Sharma YD. Expression and purification of a Plasmodium vivax antigen - PvTARAg55 tryptophan- and alanine-rich antigen and its immunological responses in human subjects. Vaccine 2007; 26:96-107. [PMID: 18054126 DOI: 10.1016/j.vaccine.2007.10.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/11/2007] [Accepted: 10/18/2007] [Indexed: 01/16/2023]
Abstract
Despite the immense global efforts, the malaria vaccine is not yet available and requires the identification of newer target molecules. Since tryptophan-rich proteins of P. yoelii have been proposed as vaccine candidates, we describe here the expression, purification and immunological characterization of a 55kDa Plasmodium vivax tryptophan- and alanine-rich antigen (PvTARAg55). This protein consists of 480 aa residues with a calculated molecular mass of 55.0kDa. It shows 42% aa sequence identity (64% homology) with PyPAg1 of P. yoelii and shares positional conservation of tryptophan residues. Sequence analysis of PvTARAg55 from different P. vivax isolates revealed that typtophan-rich domain which contains most of the B-cell epitopes was highly conserved in the parasite population while the alanine-rich domain showed polymorphism. Exon-2 covering major part (420 aa) of the protein including both the domains was PCR amplified, cloned, expressed in Escherichia coli, and the recombinant protein purified to its homogeneity. Majority of P. vivax-infected individuals (82.5%, n=40) produced antibodies against this antigen. Proliferative responses to the recombinant PvTARAg55 were observed in 60% (n=20) of individuals who had recently been exposed to the P. vivax infection. Measurement of Th1- (IFN-gamma, TNF-alpha, and IL-12) and Th2-type (IL-4 and IL-10) cytokine production in response to this recombinant antigen revealed a mixed type T-cell response with a Th2 response being more pronounced. These results demonstrate that PvTARAg55 elicits high humoral and cellular immune responses thus establishes its immunogenecity in humans.
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Affiliation(s)
- Asim A Siddiqui
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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21
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NMR structural studies of the antibiotic lipopeptide daptomycin in DHPC micelles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3116-26. [PMID: 17945184 DOI: 10.1016/j.bbamem.2007.08.034] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Revised: 08/30/2007] [Accepted: 08/31/2007] [Indexed: 11/23/2022]
Abstract
Daptomycin is a cyclic anionic lipopeptide that exerts its rapid bactericidal effect by perturbing the bacterial cell membrane, a mode of action different from most other currently commercially available antibiotics (except e.g. polymyxin and gramicidin). Recent work has shown that daptomycin requires calcium in the form of Ca2+ to form a micellar structure in solution and to bind to bacterial model membranes. This evidence sheds light on the initial steps in the mechanism of action of this novel antibiotic. To understand how daptomycin goes on to perturb bacterial membranes, its three-dimensional structure has been determined in the presence of 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) micelles. NMR spectra of daptomycin in DHPC were obtained under two conditions, namely in the presence of Ca2+ as used by Jung et al. [D. Jung, A. Rozek, M. Okon, R.E.W. Hancock, Structural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin, Chem. Biol. 11 (2004) 949-57] to solve the calcium-conjugated structure of daptomycin in solution and in a phosphate buffer as used by Rotondi and Gierasch [K.S. Rotondi, L.M. Gierasch, A well-defined amphipathic conformation for the calcium-free cyclic lipopeptide antibiotic, daptomycin, in aqueous solution, Biopolymers 80 (2005) 374-85] to solve the structure of apo-daptomycin. The structures were calculated using molecular dynamics time-averaged refinement. The different sample conditions used to obtain the NMR spectra are discussed in light of fluorescence data, lipid flip-flop and calcein release assays in PC liposomes, in the presence and absence of Ca2+ [D. Jung, A. Rozek, M. Okon, R.E.W. Hancock, Structural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin, Chem. Biol. 11 (2004) 949-57]. The implications of these results for the membrane perturbation mechanism of daptomycin are discussed.
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22
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Cruzeiro-Silva C, Gomes-Neto F, Tinoco LW, Cilli EM, Barros PVR, Lapido-Loureiro PA, Bisch PM, Almeida FCL, Valente AP. Structural biology of membrane-acting peptides: conformational plasticity of anticoccidial peptide PW2 probed by solution NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3182-92. [PMID: 17927950 DOI: 10.1016/j.bbamem.2007.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 08/22/2007] [Accepted: 08/24/2007] [Indexed: 10/22/2022]
Abstract
The bottleneck for the complete understanding of the structure-function relationship of flexible membrane-acting peptides is its dynamics. At the same time, not only the structure but also the dynamics are the key points for their mechanism of action. Our model is PW2, a TRP-rich, cationic peptide selected from phage display libraries that shows anticoccidial activity against Eimeria acervulina. In this manuscript we used a combination of several NMR techniques to tackle these difficulties. The structural features of the membrane-acting peptide PW2 was studied in several membrane mimetic environments: we compared the structural features of PW2 in SDS and DPC micelles, that were reported earlier, with the structure properties in different lipid vesicles and the peptide free in water. We were able to unify the structural information obtained in each of these systems. The structural constraints of the peptide free in water were fundamental for the understanding of plasticity necessary for the membrane interaction. Our data suggested that the WWR sequence is the region responsible for anchoring the peptide to the interfaces, and that this same region displays some degree of conformational order in solution. For PW2, we found that affinity is related to the aromatic region, by anchoring the peptide to the membrane, and specificity is related to the N- and C-termini, which are able to accommodate in the membrane due to its plasticity.
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Affiliation(s)
- C Cruzeiro-Silva
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Programa de Biologia Estrutural, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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23
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Liu Z, Brady A, Young A, Rasimick B, Chen K, Zhou C, Kallenbach NR. Length effects in antimicrobial peptides of the (RW)n series. Antimicrob Agents Chemother 2006; 51:597-603. [PMID: 17145799 PMCID: PMC1797765 DOI: 10.1128/aac.00828-06] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A class of antimicrobial peptides involved in host defense consists of sequences rich in Arg and Trp-R and -W. Analysis of the pharmacophore in these peptides revealed that chains as short as trimers of sequences such as WRW and RWR have antimicrobial activity (M. B. Strom, B. E. Haug, M. L. Skar, W. Stensen, T. Stiberg, and J. S. Svendsen, J. Med. Chem. 46:1567-1570, 2003). To evaluate the effect of chain length on antimicrobial activity, we synthesized a series of peptides containing simple sequence repeats, (RW)n-NH2 (where n equals 1, 2, 3, 4, or 5), and determined their antimicrobial and hemolytic activity. The antimicrobial activity of the peptides increases with chain length, as does the hemolysis of red blood cells. Within the experimental error, longer peptides (n equals 3, 4, or 5) show similar values for the ratio of hemolytic activity to antibacterial activity, or the hemolytic index. The (RW)3 represents the optimal chain length in terms of the efficacy of synthesis and selectivity as evaluated by the hemolytic index. Circular dichroism spectroscopy indicates that these short peptides appear to be unfolded in aqueous solution but acquire structure in the presence of phospholipids. Interaction of the peptides with model lipid vesicles was examined using tryptophan fluorescence. The (RW)n peptides preferentially interact with bilayers containing the negatively charged headgroup phosphatidylglycerol relative to those containing a zwitterionic headgroup, phosphatidylcholine.
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Affiliation(s)
- Zhigang Liu
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
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24
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Wei SY, Wu JM, Kuo YY, Chen HL, Yip BS, Tzeng SR, Cheng JW. Solution structure of a novel tryptophan-rich peptide with bidirectional antimicrobial activity. J Bacteriol 2006; 188:328-34. [PMID: 16352849 PMCID: PMC1317575 DOI: 10.1128/jb.188.1.328-334.2006] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Trp-rich antimicrobial peptides play important roles in the host innate defense mechanisms of many plants, insects, and mammals. A new type of Trp-rich peptide, Ac-KWRRWVRWI-NH(2), designated Pac-525, was found to possess improved activity against both gram-positive and -negative bacteria. We have determined that the solution structures of Pac-525 bound to membrane-mimetic sodium dodecyl sulfate (SDS) micelles. The SDS micelle-bound structure of Pac-525 adopts an alpha-helical segment at residues Trp2, Arg3, and Arg4. The positively charged residues are clustered together to form a hydrophilic patch. The three hydrophobic residues Trp2, Val6, and Ile9 form a hydrophobic core. The surface electrostatic potential map indicates the three tryptophan indole rings are packed against the peptide backbone and form an amphipathic structure. Moreover, the reverse sequence of Pac-525, Ac-IWRVWRRWK-NH(2), designated Pac-525(rev), also demonstrates similar antimicrobial activity and structure in membrane-mimetic micelles and vesicles. A variety of biophysical and biochemical methods, including circular dichroism, fluorescence spectroscopy, and microcalorimetry, were used to show that Pac-525 interacted strongly with negatively charged phospholipid vesicles and induced efficient dye release from these vesicles, suggesting that the antimicrobial activity of Pac-525 may be due to interactions with bacterial membranes.
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Affiliation(s)
- Shu-Yi Wei
- Pacgen Biopharmaceuticals Corp., 1730-505 Burrard Street, Vancouver, BC V7X 1M6, Canada
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25
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Uchiyama F, Tanaka Y, Minari Y, Tokui N. Designing scaffolds of peptides for phage display libraries. J Biosci Bioeng 2005; 99:448-56. [PMID: 16233816 DOI: 10.1263/jbb.99.448] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 03/02/2005] [Indexed: 11/17/2022]
Abstract
Phage display is a powerful method for the discovery of peptide ligands that are used for analytical tools, drug discovery, and target validations. Phage display technology can produce a huge number of peptides and generate novel peptide ligands. Recently, phage display technology has successfully managed to create peptide ligands that bind to pharmaceutically difficult targets such as the erythropoietin receptor. As a result of the structural analysis of their ligands, we found that the conformational design of peptides in library is important for selecting high-affinity ligands that bind to every target from a phage peptide library. Key issues concern constraints on the conformation of peptides on the phage and the development of chemically synthesized peptides derived from peptides on phage. This review discusses studies related to the conformation of peptides selected from phage display peptide libraries in addition to the conversion from peptides to non-peptides.
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Affiliation(s)
- Fumiaki Uchiyama
- Department of Nutritional Sciences, Graduate School of Nutritional Sciences, Nakamura Gakuen University, 5-7-1 Befu, Jounan-Ku, Fukuoka 814-0198, Japan.
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26
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Jalah R, Sarin R, Sud N, Alam MT, Parikh N, Das TK, Sharma YD. Identification, expression, localization and serological characterization of a tryptophan-rich antigen from the human malaria parasite Plasmodium vivax. Mol Biochem Parasitol 2005; 142:158-69. [PMID: 15869815 DOI: 10.1016/j.molbiopara.2005.01.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 01/11/2005] [Accepted: 01/26/2005] [Indexed: 11/26/2022]
Abstract
Plasmodium vivax is most common but non-cultivable human malaria parasite which is poorly characterized at the molecular level. Here, we describe the identification and characterization of a P. vivax Tryptophan-Rich Antigen (PvTRAg) which contains unusually high (8.28%) tryptophan residues and is expressed by all blood stages of the parasite. The pvtrag gene comprises a 978bp open reading frame interrupted by two introns. The first intron is located in the 5'-untranslated region while the second one is positioned 174bp downstream to the ATG codon. The encoded approximately 40kDa protein contains a transmembrane domain near the N-terminus followed by a tryptophan-rich domain with significantly high surface probability and antigenic index. It is localized in the parasite cytoplasm as well as in the cytoplasm of the parasitized erythrocyte. The purified E. coli expressed recombinant PvTRAg protein showed a very high seropositivity rate for the presence of antibodies amongst the P. vivax patients, indicating that the antigen generates significant humoral immune response during the natural course of P. vivax infection. Analysis of various field isolates revealed that the tryptophan-rich domain is highly conserved except for three-point mutations. The PvTRAg could be a potential vaccine candidate since similar tryptophan-rich antigens of P. yoelii have shown protection against malaria in murine model.
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Affiliation(s)
- Rashmi Jalah
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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27
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Rozek A, Powers JPS, Friedrich CL, Hancock REW. Structure-based design of an indolicidin peptide analogue with increased protease stability. Biochemistry 2004; 42:14130-8. [PMID: 14640680 DOI: 10.1021/bi035643g] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Indolicidin is an antimicrobial cationic peptide with broad-spectrum activity isolated from bovine neutrophils. An indolicidin analogue CP-11, ILKKWPWWPWRRK-NH(2), with improved activity against Gram-negative bacteria had increased positive charge and amphipathicity while maintaining the short length of the parent molecule. The structure of CP-11 in the presence of dodecylphosphocholine (DPC) micelles was determined using nuclear magnetic resonance spectroscopy. CP-11 was found to be an amphipathic molecule with a U-shaped backbone bringing the N- and C-termini in close proximity. On the basis of this close proximity, a cyclic disulfide-bonded peptide cycloCP-11, ICLKKWPWWPWRRCK-NH(2), was designed to stabilize the lipid-bound structure and to increase protease resistance. The three-dimensional structure of cycloCP-11 was determined under the same conditions as for the linear peptide and was found to be similar to CP-11. Both CP-11 and cycloCP-11 associated with phospholipid membranes in a similar manner as indicated by circular dichroism and fluorescence spectra. The minimal inhibitory concentrations of CP-11 and cycloCP-11 for a range of bacteria differed by no more than 2-fold, and they were nonhemolytic at concentrations up to 256 microg/mL. Cyclization was found to greatly increase protease stability. The half-life of cycloCP-11 in the presence of trypsin was increased by 4.5-fold from 4 to 18 min. More importantly, the antibacterial activity of cycloCP-11, but not that of CP-11, in the presence of trypsin was completely retained up to 90 min since the major degradation product was equally active. A structural comparison of CP-11 and cycloCP-11 revealed that the higher trypsin resistance of cycloCP-11 may be due to the more compact packing of lysine and tryptophan side chains. These findings suggest that cyclization may serve as an important strategy in the rational design of antimicrobial peptides.
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Affiliation(s)
- Annett Rozek
- Department of Microbiology and Immunology, University of British Columbia, #300-6174 University Boulevard, Vancouver, British Columbia, Canada
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28
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Whitehead TL, Jones LM, Hicks RP. PFG-NMR Investigations of the Binding of Cationic Neuropeptides to Anionic and Zwitterionic Micelles. J Biomol Struct Dyn 2004; 21:567-76. [PMID: 14692800 DOI: 10.1080/07391102.2004.10506949] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The mechanism by which peptides bind to micelles is believed to be a two-phase process, involving (i). initial electrostatic interactions between the peptide and micelle surface, followed by (ii). hydrophobic interactions between peptide side chains and the micelle core. To better characterize the electrostatic portion of this process, a series of pulse field gradient nuclear magnetic resonance (PFG-NMR) spectroscopic experiments were conducted on a group of neuropeptides with varying net cationic charges (+1 to +3) and charge location to determine both their diffusion coefficients and partition coefficients when in the presence of detergent micelles. Two types of micelles were chosen for the study, namely anionic sodium dodecylsulfate (SDS) and zwitterionic dodecylphosphocholine (DPC) micelles. Results obtained from this investigation indicate that in the case of the anionic SDS micelles, peptides with a larger net positive charge bind to a greater extent than those with a lesser net positive charge (bradykinin > substance P > neurokinin A > Met-enkephalin). In contrast, when in the presence of zwitterionic DPC micelles, the degree of mixed-charge nature of the peptide affects binding (neurokinin A > substance P > Met-enkephalin > bradykinin). Partition coefficients between the peptides and the micelles follow similar trends for both micelle types. Diffusion coefficients for the peptides in SDS micelles, when ranked from largest to smallest, follow a trend where increasing net positive charge results in the smallest diffusion coefficient: Met-enkephalin > neurokinin A > bradykinin > substance P. Diffusion coefficients when in the presence of DPC micelles, when ranked from largest to smallest, follow a trend where the presence of negatively-charged side chains results in the smallest diffusion coefficient: bradykinin > Met-enkephalin > substance P > neurokinin A.
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Affiliation(s)
- Tracy L Whitehead
- Department of Chemistry, Mail Stop 9573, Mississippi State University, Mississippi State, Mississippi 39762, USA.
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29
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Powers JPS, Hancock REW. The relationship between peptide structure and antibacterial activity. Peptides 2003; 24:1681-91. [PMID: 15019199 DOI: 10.1016/j.peptides.2003.08.023] [Citation(s) in RCA: 636] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2003] [Accepted: 08/08/2003] [Indexed: 10/26/2022]
Abstract
Cationic antimicrobial peptides are a class of small, positively charged peptides known for their broad-spectrum antimicrobial activity. These peptides have also been shown to possess anti-viral and anti-cancer activity and, most recently, the ability to modulate the innate immune response. To date, a large number of antimicrobial peptides have been chemically characterized, however, few high-resolution structures are available. Structure-activity studies of these peptides reveal two main requirements for antimicrobial activity, (1) a cationic charge and (2) an induced amphipathic conformation. In addition to peptide conformation, the role of membrane lipid composition, specifically non-bilayer lipids, on peptide activity will also be discussed.
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Affiliation(s)
- Jon-Paul S Powers
- Department of Microbiology and Immunology, University of British Columbia, #300-6174 University Boulevard, Vancouver, BC, Canada V6T 1Z3.
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30
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Jing W, Demcoe AR, Vogel HJ. Conformation of a bactericidal domain of puroindoline a: structure and mechanism of action of a 13-residue antimicrobial peptide. J Bacteriol 2003; 185:4938-47. [PMID: 12897014 PMCID: PMC166454 DOI: 10.1128/jb.185.16.4938-4947.2003] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Puroindoline a, a wheat endosperm-specific protein containing a tryptophan-rich domain, was reported to have antimicrobial activities. We found that a 13-residue fragment of puroindoline a (FPVTWRWWKWWKG-NH(2)) (puroA) exhibits activity against both gram-positive and gram-negative bacteria. This suggests that puroA may be a bactericidal domain of puroindoline a. PuroA interacted strongly with negatively charged phospholipid vesicles and induced efficient dye release from these vesicles, suggesting that the microbicidal effect of puroA may be due to interactions with bacterial membranes. A variety of biophysical and biochemical methods, including fluorescence spectroscopy and microcalorimetry, were used to examine the mode of action of puroA. These studies showed that puroA is located at the membrane interface, probably due to its high content of Trp residues that have a high propensity to partition into the membrane interface. The penetration of these Trp residues in negatively charged phospholipid vesicles resembling bacterial membranes was more extensive than the penetration in neutral vesicles mimicking eukaryotic membranes. Peptide binding had a significant influence on the phase behavior of the former vesicles. The three-dimensional structure of micelle-bound puroA determined by two-dimensional nuclear magnetic resonance spectroscopy indicated that all the positively charged residues are oriented close to the face of Trp indole rings, forming energetically favorable cation-pi interactions. This characteristic, along with its well-defined amphipathic structure upon binding to membrane mimetic systems, allows puroA to insert more deeply into bacterial membranes and disrupt the regular membrane bilayer structure.
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Affiliation(s)
- Weiguo Jing
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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