Dynamic scenario of membrane binding process of Kalata B1

PLoS ONE

Volumn 9, Issue 12, 2014, Pages

  Nawae, Wanapinun ^a   Hannongbua, Supa ^b   Ruengjitchatchawalya, Marasri ^a  

^a KING MONGKUT'S UNIVERSITY OF TECHNOLOGY THONBURI   (Thailand)

^b KASETSART UNIVERSITY   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BINDING PROTEIN; CYCLOTIDE; KALATA B1 PROTEIN; TRP19 PROTEIN; UNCLASSIFIED DRUG; KALATA B1; PLANT PROTEIN; PROTEIN BINDING;

ARTICLE; BINDING AFFINITY; BIOENGINEERING; BIOLOGICAL ACTIVITY; CONTROLLED STUDY; MEMBRANE BINDING; MEMBRANE INTERFACIAL ZONE; MEMBRANE STRUCTURE; MOLECULAR DYNAMICS; OLIGOMERIZATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; CELL MEMBRANE; CHEMISTRY; OLDENLANDIA; PROTEIN DOMAIN; PROTEIN QUATERNARY STRUCTURE;

CELL MEMBRANE; CYCLOTIDES; MOLECULAR DYNAMICS SIMULATION; OLDENLANDIA; PLANT PROTEINS; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, QUATERNARY;

EID: 84915749222     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0114473     Document Type: Article

References (55)

1. Daly NL, Rosengren KJ, Craik DJ (2009) Discovery, structure and biological activities of cyclotides. Adv Drug Deliv Rev 61: 918-930.
2. Craik DJ (2010) Discovery and applications of the plant cyclotides. Toxicon 56: 1092-1102.
3. Craik DJ, Daly NL, Bond T, Waine C (1999) Plant cyclotides: A unique family of cyclic and knotted proteins that defines the cyclic cystine knot structural motif. J Biol Chem 294: 1327-1336.
4. Tam JP, Lu YA, Yang JL, Chiu KW (1999) An unusual structural motif of antimicrobial peptides containing end-to-end macrocycle and cystine-knot disulfides. Proc Natl Acad Sci USA 96: 8913-8918.
5. Wang CK, Colgrave ML, Gustafson KR, Ireland DC, Goransson U, et al. (2008) Anti-HIV cyclotides from the Chinese medicinal herb Viola yedoensis. J Nat Prod 71: 47-52.
6. Daly NL, Gustafson KR, Craik DJ (2004) The role of the cyclic peptide backbone in the anti-HIV activity of the cyclotide kalata B1. FEBS Lett 574: 69-72.
7. Gerlach SL, Rathinakumar R, Chakravarty G, Goransson U, Wimley WC, et al. (2010) Anticancer and chemosensitizing abilities of cycloviolacin O2 from Viola odorata and psyle cyclotides from Psychotria leptothyrsa. Biopolymers 94: 617-625.
8. Clark RJ, Daly NL, Craik DJ (2006) Structural plasticity of the cyclic-cystine-knot framework: implications for biological activity and drug design. Biochem J 394: 85-93.
9. Garcia AE, Camarero JA (2010) Biological activities of natural and engineered cyclotides, a novel molecular scaffold for peptide-based therapeutics. Curr Mol Pharmacol 3: 153-163.
10. Jagadish K, Camarero JA (2010) Cyclotides, a promising molecular scaffold for peptide-based therapeutics. Biopolymers 94: 611-616.
11. Henriques ST, Craik DJ (2010) Cyclotides as templates in drug design. Drug Discov Today 15: 57-64.
12. Gould A, Ji Y, Aboye TL, Camarero JA (2011) Cyclotides, a novel ultrastable polypeptide scaffold for drug discovery. Curr Pharm Des 17: 4294-4307.
13. Poth AG, Chan LY, Craik DJ (2013) Cyclotides as grafting frameworks for protein engineering and drug design applications. Biopolymers 100: 480-491.
14. Thongyoo P, Roque-Rosell N, Leatherbarrow RJ, Tate EW (2008) Chemical and biomimetic total syntheses of natural and engineered MCoTI cyclotides. Org Biomol Chem 6: 1462-1470.
15. Thongyoo P, Bonomelli C, Leatherbarrow RJ, Tate EW (2009) Potent inhibitors of beta-tryptase and human leukocyte elastase based on the MCoTI-II scaffold. J Med Chem 52: 6197-6200.
16. Sommerhoff CP, Avrutina O, Schmoldt HU, Gabrijelcic-Geiger D, Diederichsen U, et al. (2010) Engineered cystine knot miniproteins as potent inhibitors of human mast cell tryptase beta. J Mol Biol 395: 167-175.
17. Chan LY, Gunasekera S, Henriques ST, Worth NF, Le SJ, et al. (2011) Engineering pro-angiogenic peptides using stable, disulfide-rich cyclic scaffolds. Blood 118: 6709-6717.
18. Kimura RH, Teed R, Hackel BJ, Pysz MA, Chuang CZ, et al. (2012) Pharmacokinetically stabilized cystine knot peptides that bind alpha-v-beta-6 integrin with single-digit nanomolar affinities for detection of pancreatic cancer. Clin Cancer Res 18: 839-849.
19. Aboye TL, Ha H, Majumder S, Christ F, Debyser Z, et al. (2012) Design of a novel cyclotide-based CXCR4 antagonist with anti-human immunodeficiency virus (HIV)-1 activity. J Med Chem 55: 10729-10734.
20. Mulvenna JP, Wang C, Craik DJ (2006) CyBase: a database of cyclic protein sequence and structure. Nucleic Acids Res 34: D192-194.
21. Gunasekera S, Foley FM, Clark RJ, Sando L, Fabri LJ, et al. (2008) Engineering stabilized vascular endothelial growth factor-A antagonists: synthesis, structural characterization, and bioactivity of grafted analogues of cyclotides. J Med Chem 51: 7697-7704.
22. Getz JA, Rice JJ, Daugherty PS (2011) Protease-resistant peptide ligands from a knottin scaffold library. ACS Chem Biol 6: 837-844.
23. Eliasen R, Daly NL, Wulff BS, Andresen TL, Conde-Frieboes KW, et al. (2012) Design, synthesis, structural and functional characterization of novel melanocortin agonists based on the cyclotide kalata B1. J Biol Chem 287: 40493-40501.
24. Gran L (1973) On the effect of a polypeptide isolated from ''Kalata-Kalata'' (Oldenlandia affinis DC) on the oestrogen dominated uterus. Acta Pharmacol Toxicol (Copenh) 33: 400-408.
25. Simonsen SM, Sando L, Rosengren KJ, Wang CK, Colgrave ML, et al. (2008) Alanine scanning mutagenesis of the prototypic cyclotide reveals a cluster of residues essential for bioactivity. J Biol Chem 283: 9805-9813.
26. Huang YH, Colgrave ML, Clark RJ, Kotze AC, Craik DJ (2010) Lysine-scanning mutagenesis reveals an amendable face of the cyclotide kalata B1 for the optimization of nematocidal activity. J Biol Chem 285: 10797-10805.
27. Huang YH, Colgrave ML, Daly NL, Keleshian A, Martinac B, et al. (2009) The Biological Activity of the Prototypic Cyclotide Kalata B1 Is Modulated by the Formation of Multimeric Pores. J Biol Chem 284: 20699-20707.
28. Wang CK, Wacklin HP, Craik DJ (2012) Cyclotides insert into lipid bilayers to form membrane pores and destabilize the membrane through hydrophobic and phosphoethanolamine-specific interactions. J Biol Chem 287: 43884-43898.
29. Nawae W, Hannongbua S, Ruengjitchatchawalya M (2014) Defining the membrane disruption mechanism of kalata B1 via coarse-grained molecular dynamics simulations. Sci Rep 4: 3933.
30. Takada S (2012) Coarse-grained molecular simulations of large biomolecules. Curr Opin Struct Biol 22: 130-137.
31. Khalfa A, Tarek M (2010) On the Antibacterial Action of Cyclic Peptides: Insights from Coarse-Grained MD Simulations. J Phys Chem B 114: 2676-2684.
32. Su Z-Y, Wang Y-T (2010) Coarse-Grained Molecular Dynamics Simulations of Cobra Cytotoxin A3 Interactions with a Lipid Bilayer: Penetration of Loops into Membranes. J Phys Chem B 115: 796-802.
33. Gkeka P, Sarkisov L (2009) Interactions of Phospholipid Bilayers with Several Classes of Amphiphilic a- Helical Peptides: Insights from Coarse-Grained Molecular Dynamics Simulations. J Phys Chem B 114: 826-839.
34. Zhao J, Zhao C, Liang G, Zhang M, Zheng J (2013) Engineering Antimicrobial Peptides with Improved Antimicrobial and Hemolytic Activities. J Chem Inf Model 53: 3280-3296.
35. Kästner J (2011) Umbrella sampling. WIREs Comput Mol Sci 1: 932-942.
36. Wimley WC (2010) Describing the mechanism of antimicrobial peptide action with the interfacial activity model. ACS Chem Biol 5: 905-917.
37. Shenkarev ZO, Nadezhdin KD, Sobol VA, Sobol AG, Skjeldal L, et al. (2006) Conformation and mode of membrane interaction in cyclotides. Spatial structure of kalata B1 bound to a dodecylphosphocholine micelle. FEBS J 273: 2658-2672.
38. Rosengren KJ, Daly NL, Harvey PJ, Craik DJ (2013) The self-association of the cyclotide kalata B2 in solution is guided by hydrophobic interactions. Biopolymers 100: 453-460.
39. Yau WM, Wimley WC, Gawrisch K, White SH (1998) The preference of tryptophan for membrane interfaces. Biochemistry 37: 14713-14718.
40. de Jesus AJ, Allen TW (2013) The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch. Biochim Biophys Acta 1828: 864-876.
41. Kaas Q, Craik DJ (2010) Analysis and classification of circular proteins in CyBase. Biopolymers 94: 584-591.
42. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, et al. (2005) GROMACS: fast, flexible, and free. J Comput Chem 26: 1701-1718.
43. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulations. J Chem Theory Comput 4: 435-447.
44. Marrink SJ, de Vries AH, Mark AE (2003) Coarse Grained Model for Semiquantitative Lipid Simulations. J Phys Chem B 108: 750-760.
45. Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH (2007) The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111: 7812-7824.
46. Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, et al. (2008) The MARTINI Coarse-Grained Force Field: Extension to Proteins. J Chem Theory Comput 4: 819-834.
47. Berendsen HJC, Postma JPM, van Gunsteren, WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81: 3684-3690.
48. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Molec Graphics 14: 33- 38, 27-38.
49. Rosengren KJ, Daly NL, Plan MR, Waine C, Craik DJ (2003) Twists, knots, and rings in proteins. Structural definition of the cyclotide framework. J Biol Chem 278: 8606-8616.
50. Risselada HJ, Marrink SJ (2008) The molecular face of lipid rafts in model membranes. Proc Natl Acad Sci USA 105: 17367-17372.
51. Fantini J, Garmy N, Mahfoud R, Yahi N (2002) Lipid rafts: structure, function and role in HIV, Alzheimer's and prion diseases. Expert Rev Mol Med 4: 1-22.
52. Aloia RC, Tian H, Jensen FC (1993) Lipid composition and fluidity of the human immunodeficiency virus envelope and host cell plasma membranes. Proc Natl Acad Sci USA 90: 5181-5185.
53. Scott KA, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, et al. (2008) Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly. Structure 16: 621-630.
54. Kumar S, Rosenberg JM, Bouzida D, Swendsen RH, Kollman PA (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem 13: 1011-1021.
55. Hub JS, de Groot BL, van der Spoel D (2010) g-wham-A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates. J Chem Theory Comput 6: 3713-3720.