Prediction of linear cationic antimicrobial peptides based on characteristics responsible for their interaction with the membranes

Journal of Chemical Information and Modeling

Volumn 54, Issue 5, 2014, Pages 1512-1523

  Vishnepolsky, Boris ^a   Pirtskhalava, Malak ^a  

^a Georgia   (Georgia)

Author keywords

[No Author keywords available]

Indexed keywords

EFFICIENCY; FORECASTING; HYDROPHOBICITY; MEMBRANES; MICROORGANISMS; PEPTIDES;

ANIONIC MEMBRANES; ANTIMICROBIAL PEPTIDE; CATIONIC ANTIMICROBIAL PEPTIDES; DISCRIMINATIVE METHODS; DISORDERED STRUCTURES; MACHINE LEARNING APPROACHES; PHYSICOCHEMICAL CHARACTERISTICS; PREDICTION METHODS;

LEARNING SYSTEMS;

ANTIMICROBIAL CATIONIC PEPTIDE; PROTEIN BINDING;

BIOLOGY; CELL MEMBRANE; CHEMISTRY; METABOLISM; PROCEDURES;

ANTIMICROBIAL CATIONIC PEPTIDES; CELL MEMBRANE; COMPUTATIONAL BIOLOGY; PROTEIN BINDING;

EID: 84901642563     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci4007003     Document Type: Article

References (44)

1. Sang, Y.; Blecha, F. Antimicrobial peptides and bacteriocins: alternatives to traditional antibiotics Anim. Health Res. Rev. 2008, 9, 227-235
2. Hancock, R. E. W.; Rozek, A. Role of membranes in the activities of antimicrobial cationic peptides FEMS Microbiol. Lett. 2002, 206 (2) 143-149
3. Fjell, C. D.; Hiss, J. A.; Hancock, R. E.; Schneider, G. Designing antimicrobial peptides: form follows function Nat. Rev. Drug Discovery 2011, 11 (1) 37-51
4. Torrent, M.; Andreu, D.; Nogués, V. M.; Boix, E. Connecting Peptide Physicochemical and Antimicrobial Properties by a Rational Prediction Model PLoS One 2011, 6 (2) e16968
5. Wang, P.; Hu, L.; Liu, G.; Jiang, N.; Chen, X.; Xu, J.; Zheng, W.; Li, L.; Tan, M.; Chen, Z.; Song, H.; Cai, Y.; Chouet, K. Prediction of Antimicrobial Peptides Based on Sequence Alignment and Feature Selection Methods PLoS One 2011, 6 (4) e18476
6. Frecer, V.; Ho, B.; Ding, J. L. De novo design of potent antimicrobial peptides Antimicrob. Agents Chemother. 2004, 48, 3349-3357
7. Jenssen, H.; Lejon, T.; Hilpert, K.; Fjell, C. D.; Cherkasov, A.; Hancock, R. E. W. Evaluating different descriptors for model design of antimicrobial peptides with enhanced activity toward P. aeruginosa Chem. Biol. Drug Des. 2007, 70, 134-142
8. Jenssen, H.; Fjell, C. D.; Cherkasov, A.; Hancock, R. E. QSAR modeling and computer-aided design of antimicrobial peptides J. Pept. Sci. 2008, 14, 110-114
9. Frecer, V. QSAR analysis of antimicrobial and haemolytic effects of cyclic cationic antimicrobial peptides derived from protegrin-1 Bioorg. Med. Chem. 2006, 14, 6065-6074
10. Cherkasov, A.; Jankovic, B. Application of 'inductive' QSAR descriptors for quantification of antibacterial activity of cationic polypeptides Molecules 2004, 9, 1034-1052
11. Waghu, F. H.; Gopi, L.; Barai, R. S.; Ramteke, P.; Nizami, B.; Idicula-Thomas, S. CAMP: Collection of sequences and structures of antimicrobial peptides Nucleic Acids Res. 2014, 42, D1154-D1158
12. Taboureau, O.; Olsen, O. H.; Nielsen, J. D.; Raventos, D.; Mygind, P. H.; Kristensen, H. H. Design of novispirin antimicrobial peptides by quantitative structure-activity relationship Chem. Biol. Drug Des. 2006, 68, 48-57
13. White, S. H.; Wimley, W. C. Membrane protein folding and stability: physical principles Annu. Rev. Biophys. Biomol. Struct. 1999, 28, 319-365
14. Jayasinghe, S.; Hristova, K.; White, S. H. Energetics, stability, and prediction of transmembrane helices J. Mol. Biol. 2001, 312, 927-934
15. Scocchi, M.; Tossi, A.; Gennaro, R. Proline-rich antimicrobial peptides: converging to a non-lytic mechanism of action Cell. Mol. Life Sci. 2011, 68, 2317-30
16. Kragol, G.; Hoffmann, R.; Chattergoon, M. A.; Lovas, S.; Cudic, M.; Bulet, P.; Condie, B. A.; Rosengren, K. J.; Montaner, L. J.; Otvos, L. Identification of crucial residues for the antibacterial activity of the proline-rich peptide, pyrrhocoricin Eur. J. Biochem. 2002, 269, 4226-4237
17. Wang, Z.; Wang, G. APD: the Antimicrobial Peptide Database Nucleic Acids Res. 2004, 32, D590-D592
18. Fjell, C. D.; Hancock, R. E.; Cherkasov, A. AMPer: a database and an automated discovery tool for antimicrobial peptides Bioinformatics 2007, 23, 1148-1155
19. Hammami, R.; Zouhir, A.; Ben Hamida, J.; Fliss, I. BACTIBASE: a new web-accessible database for bacteriocin characterization BMC Microbiol. 2007, 7, 89
20. Hammami, R.; Zouhir, A.; Le Lay, C.; Ben Hamida, J.; Fliss, I. BACTIBASE second release: a database and tool platform for bacteriocin characterization BMC Microbiol. 2010, 10, 22
21. Hammami, R.; Ben Hamida, J.; Vergoten, G.; Fliss, I. PhytAMP: a database dedicated to antimicrobial plant peptides Nucleic Acids Res. 2009, 37, D963-968
22. Lata, S.; Sharma, B. K.; Raghava, G. P. Analysis and prediction of antibacterial peptides BMC Bioinf. 2007, 8, 263 (2007)
23. Lata, S.; Mishra, N. K.; Raghava, G. P. AntiBP2: improved version of antibacterial peptide prediction BMC Bioinf. 2010, 11 (Suppl 1) S19
24. Bioinformatics 2005, 59, 252-265.
25. Tusnády, G. E.; Dosztányi, Z.; Simon, I. PDB-TM: selection and membrane localization of transmembrane proteins in the protein data bank Bioinformatics 2004, 20 (17) 2964-2972
26. Kozma, D.; Simon, I.; Tusnády, G. E. PDBTM: Protein Data Bank of transmembrane proteins after 8 years Nucleic Acids Res. 2013, 41 (D1) D524-D529
27. Yeaman, M. R.; Yount, N. Y. Unifying themes in host defence effector polypeptides Nat. Rev. Microbiol. 2007, 5, 727-740
28. Kyte, J.; Doolittle, R. F. A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 1982, 157 (1) 105-132
29. Wimley, W. C.; White, S. H. Experimentally determined hydrophobicity scale for proteins at membrane interfaces Nat. Struct. Biol. 1996, 3, 842-848
30. Koehler, J.; Woetzel, N.; Staritzbichler, R.; Sanders, C. R.; Meiler, J. A unified hydrophobicity scale for multispan membrane proteins Proteins 2009, 76, 13-29
31. Hessa, T.; Meindl-Beinker, N. M.; Bernsel, A.; Kim, H.; Sato, Y.; Lerch-Bader, M.; Nilsson, I.; White, S. H.; von Heijne, G. Molecular code for transmembrane-helix recognition by the Sec61 translocon Nature 2007, 450, U1026-U1032
32. Eisenberg, D.; Weiss, R. M.; Terwilliger, T. C. The hydrophobic moment detects periodicity in protein hydrophobicity Proc. Natl. Acad. Sci. U. S. A. 1984, 81 (1) 140-144
33. Moon, C. P.; Fleming, K. G. Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (25) 10174-10177
34. Yeaman, M. R.; Yount, N. Y. Mechanisms of antimicrobial peptide action and resistance Pharmacol. Rev. 2003, 55 (1) 27-55
35. Eisenberg, D.; Weiss, R. M.; Terwilliger, T. C. The helical hydrophobic moment: a measure of the amphiphilicity of a helix Nature 1982, 299 (5881) 371-374
36. Senes, A.; Chadi, D. C.; Law, P. B.; Walters, R. F. S.; Nanda, V.; DeGrado, W. F. Ez, a Depth-dependent Potential for Assessing the Energies of Insertion of Amino Acid Side-chains into Membranes: Derivation and Applications to Determining the Orientation of Transmembrane and Interfacial Helices J. Mol. Biol. 2007, 366, 436-448
37. Shai, Y. Mode of action of membrane active antimicrobial peptides Biopolymers 2002, 66, 236-248
38. Uversky, V.; Gillespie, J.; Fink, A. Why are "natively unfolded" proteins unstructured under physiological conditions? Proteins: Struct. Funct. Gen. 2000, 41 (3) 415-427
39. Fernandez-Escamilla, A. M.; Rousseau, F.; Schymkowitz, J.; Serrano, L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins Nat. Biotechnol. 2004, 22, 1302-1306
40. Conchillo-Sole, O.; de Groot, N. S.; Aviles, F. X.; Vendrell, J.; Daura, X.; Ventura, S. AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides BMC Bioinf. 2007, 8, 65
41. Bechinger, B. The structure, dynamics and orientation of antimicrobial peptides in membranes by multidimensional solid-state NMR spectroscopy Biochim. Biophys. Acta 1999, 1462 (1-2) 157-83
42. Mitaku, S.; Hirokava, T.; Tsuji, T. Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces Bioinformatics 2002, 18, 608-16
43. Ulmschneider, M. B.; Sansom, M. S. P.; Di Nola, A. Properties of Integral Membrane Protein Structures:Derivation of an Implicit Membrane Potential Proteins: Struct., Funct., Bioinf. 2005, 59, 252-262
44. Wimley, W. C. Describing the Mechanism of Antimicrobial Peptide Action with the Interfacial Activity Model ACS Chem. Biol. 2010, 5, 905-917