Abstract
Recent emergence of plant derived peptide cyclotides, characterized with a cyclized head-to-tail backbone and three disulfide bonds forming cyclic cystine knot, has advanced the field of biopharmaceutics to next level. This conserved structural feature of cyclotides holds responsible for its outstanding resistance towards thermal, chemical and enzymatic degradation. Besides, the cyclotides are preferred widely in current research to develop them as potent peptide therapeutics, where the improvement of structural stability is a demanding task in pharmaceutical firm. Hence, in this work, the structural stability of six cyclotides of kalata family (kalata B1, kalata B2, kalata B5, kalata B7, kalata B8 and kalata B12) was investigated. Among all, maximum number of intra-molecular interactions was observed only in kalata B1 (kB1). In addition, geometrical observables using conformational sampling of six kalata cyclotides also revealed that kB1 exhibited statistically significant structural stability in terms of contours of root mean square fluctuation, gyration radius, ovality and surface area (polar and non-polar). Furthermore, the distance of disulfide bridges (S–S within 2.2 Å) also confirmed that kB1 achieved maximum strength in terms of structural stability and accomplished remarkable functionality in terms of ovality as compared to other five kalata cyclotides. Accordingly, kB1 could be demonstrated as a stable template for the advancement of peptide therapeutics.
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References
Adamczak M (2003) Synthesis, properties, and application of lipase from Candida antarctica for high yield monoacylglycerol biosynthesis. Pol J Food Nutr Sci 12:3–8
Adejoro IA, Akintemi E, Adeboye OO, Ibeji C (2014) Quantum mechanical studies of the structure-activity relationship and electronic vibration of some dietary flavonoids. Asian J Appl Sci 7:117–128. doi:10.3923/ajaps.2014.117.128
Ahmed A, Rippmann F, Barnickel G, Gohlke H (2011) A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. J Chem Inf Model 51:1604–1622. doi:10.1021/ci100461k
Berman HM, Westbrook J, Feng Z et al (2000) The protein data bank. Nucleic Acids Res 28:235–242
Carlsen M, Koehl P, Røgen P (2014) On the importance of the distance measures used to train and test knowledge-based potentials for proteins. PLoS One 9:e109335. doi:10.1371/journal.pone.0109335
Carrascoza F, Zaric S, Silaghi-Dumitrescu R (2014) Computational study of protein secondary structure elements: ramachandran plots revisited. J Mol Graph Model 50:125–133. doi:10.1016/j.jmgm.2014.04.001
Čemažar M, Craik DJ (2006) Factors Influencing the stability of cyclotides: proteins with a circular backbone and cystine knot motif. Int J Pept Res Ther 12:253–260. doi:10.1007/s10989-006-9019-2
Colgrave ML, Craik DJ (2004) Thermal, chemical, and enzymatic stability of the cyclotide kalata B1: the importance of the cyclic cystine knot. Biochemistry (Mosc) 43:5965–5975. doi:10.1021/bi049711q
Colgrave ML, Huang Y-H, Craik DJ, Kotze AC (2010) Cyclotide interactions with the nematode external surface. Antimicrob Agents Chemother 54:2160–2166. doi:10.1128/AAC.01306-09
Craik DJ (2010) Discovery and applications of the plant cyclotides. Toxicon 56:1092–1102. doi:10.1016/j.toxicon.2010.02.021
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 Mol Biol 294:1327–1336
Craik DJ, Anderson MA, Barry DG et al (2001a) Discovery and structures of the cyclotides: novel macrocyclic peptides from plants. Lett Pept Sci 8:119–128. doi:10.1023/A:1016262020925
Craik DJ, Daly NL, Waine C (2001b) The cystine knot motif in toxins and implications for drug design. Toxicon Off J Int Soc Toxinol 39:43–60
Daly NL, Clark RJ, Göransson U, Craik DJ (2003) Diversity in the disulfide folding pathways of cystine knot peptides. Lett Pept Sci 10:523–531. doi:10.1007/s10989-004-2417-4
Daly NL, Clark RJ, Plan MR, Craik DJ (2006) Kalata B8, a novel antiviral circular protein, exhibits conformational flexibility in the cystine knot motif. Biochem J 393:619–626. doi:10.1042/BJ20051371
Daly NL, Rosengren KJ, Craik DJ (2009) Discovery, structure and biological activities of cyclotides. Adv Drug Deliv Rev 61:918–930. doi:10.1016/j.addr.2009.05.003
Delaney JS (2005) Predicting aqueous solubility from structure. Drug Discov Today 10:289–295
Gaillard P, Carrupt PA, Testa B, Boudon A (1994) Molecular lipophilicity potential, a tool in 3D QSAR: method and applications. J Comput Aided Mol Des 8:83–96
Gunasekera S, Daly NL, Anderson MA, Craik DJ (2006) Chemical synthesis and biosynthesis of the cyclotide family of circular proteins. IUBMB Life 58:515–524. doi:10.1080/15216540600889532
Gunasekera S, Aboye TL, Madian WA et al (2013) Making ends meet: microwave-accelerated synthesis of cyclic and disulfide rich proteins via in situ thioesterification and native chemical ligation. Int J Pept Res Ther 19:43–54. doi:10.1007/s10989-012-9331-y
Hennemann H, Wirths S, Carl C (2014) Cell-based peptide screening to access the undruggable target space. Eur J Med Chem. doi:10.1016/j.ejmech.2014.10.038
Henriques ST, Huang Y-H, Rosengren KJ et al (2011) Decoding the membrane activity of the cyclotide kalata B1: the importance of phosphatidylethanolamine phospholipids and lipid organization on hemolytic and anti-HIV activities. J Biol Chem 286:24231–24241. doi:10.1074/jbc.M111.253393
Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins 44:150–165
Kaewklom S, Euanorasetr J, Intra B et al (2015) Antimicrobial activities of novel peptides derived from defensin genes of brassica hybrid cv pule. Int J Pept Res Ther 22:93–100. doi:10.1007/s10989-015-9488-2
Kamaraj B, Rajendran V, Sethumadhavan R, Purohit R (2013) In-silico screening of cancer associated mutation on PLK1 protein and its structural consequences. J Mol Model 19:5587–5599. doi:10.1007/s00894-013-2044-0
Kempner ES (1993) Movable lobes and flexible loops in proteins. Structural deformations that control biochemical activity. FEBS Lett 326:4–10
Koehbach J, O’Brien M, Muttenthaler M et al (2013) Oxytocic plant cyclotides as templates for peptide G protein-coupled receptor ligand design. Proc Natl Acad Sci USA 110:21183–21188. doi:10.1073/pnas.1311183110
Kruger DM, Ahmed A, Gohlke H (2012) NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins. Nucleic Acids Res 40:W310–W316. doi:10.1093/nar/gks478
Kruskal WH (1952) A nonparametric test for the several sample problem. Ann Math Stat 23:525–540. doi:10.1214/aoms/1177729332
Kumar A, Purohit R (2014) Use of long term molecular dynamics simulation in predicting cancer associated SNPs. PLoS Comput Biol 10:e1003318. doi:10.1371/journal.pcbi.1003318
Kumar A, Rajendran V, Sethumadhavan R, Purohit R (2013) Roadmap to determine the point mutations involved in cardiomyopathy disorder: a Bayesian approach. Gene 519:34–40. doi:10.1016/j.gene.2013.01.056
Larios A, Garcia HS, Oliart RM, Valerio-Alfaro G (2004) Synthesis of flavor and fragrance esters using Candida antarctica lipase. Appl Microbiol Biotechnol 65:373–376. doi:10.1007/s00253-004-1602-x
Lindahl E, Azuara C, Koehl P, Delarue M (2006) NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res 34:W52–W56. doi:10.1093/nar/gkl082
Maaß F, Wüstehube-Lausch J, Dickgießer S et al (2015) Cystine-knot peptides targeting cancer-relevant human cytotoxic T lymphocyte-associated antigen 4 (CTLA-4). J Pept Sci 21:651–660. doi:10.1002/psc.2782
McPhee JB, Hancock REW (2005) Function and therapeutic potential of host defence peptides. J Pept Sci Off Publ Eur Pept Soc 11:677–687. doi:10.1002/psc.704
Nick Pace C, Trevino S, Prabhakaran E, Martin Scholtz J (2004) Protein structure, stability and solubility in water and other solvents. Philos Trans R Soc B Biol Sci 359:1225–1235. doi:10.1098/rstb.2004.1500
Nick Pace C, Scholtz JM, Grimsley GR (2014) Forces stabilizing proteins. FEBS Lett 588:2177–2184. doi:10.1016/j.febslet.2014.05.006
Pace CN, Fu H, Fryar KL et al (2011) Contribution of hydrophobic interactions to protein stability. J Mol Biol 408:514–528. doi:10.1016/j.jmb.2011.02.053
Pedretti A, Villa L, Vistoli G (2004) VEGA–an open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. J Comput Aided Mol Des 18:167–173
Pei J, Kim B-H, Grishin NV (2008) PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res 36:2295–2300. doi:10.1093/nar/gkn072
Purohit R (2014) Role of ELA region in auto-activation of mutant KIT receptor: a molecular dynamics simulation insight. J Biomol Struct Dyn 32:1033–1046. doi:10.1080/07391102.2013.803264
Rajendran V, Sethumadhavan R (2014) Drug resistance mechanism of PncA in Mycobacterium tuberculosis. J Biomol Struct Dyn 32:209–221. doi:10.1080/07391102.2012.759885
Rajendran V, Purohit R, Sethumadhavan R (2012) In silico investigation of molecular mechanism of laminopathy caused by a point mutation (R482 W) in lamin A/C protein. Amino Acids 43:603–615. doi:10.1007/s00726-011-1108-7
Rosengren KJ (2003) Twists, knots, and rings in proteins. structural definition of the cyclotide framework. J Biol Chem 278:8606–8616. doi:10.1074/jbc.M211147200
Rosengren KJ, Daly NL, Plan MR et al (2003) Twists, knots, and rings in proteins. Structural definition of the cyclotide framework. J Biol Chem 278:8606–8616. doi:10.1074/jbc.M211147200
Schöne D, Schade B, Böttcher C, Koksch B (2015) Impact of multivalent charge presentation on peptide–nanoparticle aggregation. Beilstein J Org Chem 11:792–803. doi:10.3762/bjoc.11.89
Senthilkumar B, Kumar P, Rajasekaran R (2015) In-silico template selection of in vitro evolved kalata B1 of Oldenlandia affinis for scaffolding peptide based drug design. J Cell Biochem. doi:10.1002/jcb.25248
Stenberg P, Luthman K, Artursson P (1999) Prediction of membrane permeability to peptides from calculated dynamic molecular surface properties. Pharm Res 16:205–212. doi:10.1023/A:1018816122458
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
Thapa P, Espiritu MJ, Cabalteja C, Bingham J-P (2014) The emergence of cyclic peptides: the potential of bioengineered peptide drugs. Int J Pept Res Ther 20:545–551. doi:10.1007/s10989-014-9421-0
Tina KG, Bhadra R, Srinivasan N (2007) PIC: protein interactions calculator. Nucleic Acids Res 35:W473–W476. doi:10.1093/nar/gkm423
Unsworth LD, van der Oost J, Koutsopoulos S (2007) Hyperthermophilic enzymes−stability, activity and implementation strategies for high temperature applications: properties and applications of hyperthermozymes. FEBS J 274:4044–4056. doi:10.1111/j.1742-4658.2007.05954.x
Vogt G, Argos P (1997) Protein thermal stability: hydrogen bonds or internal packing? Fold Des 2:S40–S46
Vogt G, Woell S, Argos P (1997) Protein thermal stability, hydrogen bonds, and ion pairs. J Mol Biol 269:631–643
Wang CK, Colgrave ML, Ireland DC et al (2009) Despite a conserved cystine knot motif, different cyclotides have different membrane binding modes. Biophys J 97:1471–1481. doi:10.1016/j.bpj.2009.06.032
Wang CKL, Clark RJ, Harvey PJ et al (2011) The role of conserved Glu residue on cyclotide stability and activity: a structural and functional study of Kalata B12, a naturally occurring Glu to Asp mutant. Biochemistry (Mosc) 50:4077–4086. doi:10.1021/bi2004153
Wang CK, Northfield SE, Swedberg JE et al (2015) Exploring experimental and computational markers of cyclic peptides: charting islands of permeability. Eur J Med Chem 97:202–213. doi:10.1016/j.ejmech.2015.04.049
Witherup KM, Bogusky MJ, Anderson PS et al (1994) Cyclopsychotride A, a biologically active, 31-residue cyclic peptide isolated from psychotria longipes. J Nat Prod 57:1619–1625. doi:10.1021/np50114a002
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Senthilkumar, B., Rajasekaran, R. Analysis of the Structural Stability Among Cyclotide Members Through Cystine Knot Fold that Underpins Its Potential Use as a Drug Scaffold. Int J Pept Res Ther 23, 1–11 (2017). https://doi.org/10.1007/s10989-016-9537-5
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DOI: https://doi.org/10.1007/s10989-016-9537-5