메뉴 건너뛰기




Volumn 4, Issue , 2014, Pages

Defining the membrane disruption mechanism of kalata B1 via coarse-grained molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

ANTIMICROBIAL CATIONIC PEPTIDE; CYCLOTIDE; KALATA B1; LIPID BILAYER; PROTEIN BINDING; VEGETABLE PROTEIN; WATER;

EID: 84893841488     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep03933     Document Type: Article
Times cited : (34)

References (53)
  • 1
    • 70349583511 scopus 로고    scopus 로고
    • Discovery Structure and biological activities of cyclotides
    • Daly, N. L., Rosengren, K. J. & Craik, D. J. Discovery, structure and biological activities of cyclotides. Adv Drug Deliv Rev 61, 918-930 (2009)
    • (2009) Adv Drug Deliv Rev , vol.61 , pp. 918-930
    • Daly, N.L.1    Rosengren, K.J.2    Craik, D.J.3
  • 2
    • 0033579483 scopus 로고    scopus 로고
    • Plant cyclotides: A unique family of cyclic and knotted proteins that defines the cyclic cystine knot structural motif
    • DOI 10.1006/jmbi.1999.3383
    • Craik, D. J., Daly, N. L., Bond, T. & Waine, C. Plant cyclotides: A unique family of cyclic and knotted proteins that defines the cyclic cystine knot structural motif. J Mol Biol 294, 1327-1336 (1999) (Pubitemid 30008803)
    • (1999) Journal of Molecular Biology , vol.294 , Issue.5 , pp. 1327-1336
    • Craik, D.J.1    Daly, N.L.2    Bond, T.3    Waine, C.4
  • 3
    • 0037424506 scopus 로고    scopus 로고
    • Twists, knots, and rings in proteins: Structural definition of the cyclotide framework
    • DOI 10.1074/jbc.M211147200
    • Rosengren, K. J., Daly, N. L., Plan, M. R., Waine, C. & Craik, D. J. Twists, knots, and rings in proteins. Structural definition of the cyclotide framework. J Biol Chem 278, 8606-8616 (2003) (Pubitemid 36800615)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.10 , pp. 8606-8616
    • Rosengren, K.J.1    Daly, N.L.2    Plan, M.R.3    Waine, C.4    Craik, D.J.5
  • 4
    • 34447633710 scopus 로고    scopus 로고
    • Plant cyclotides: An unusual class of defense compounds
    • DOI 10.1016/j.peptides.2007.04.025, PII S0196978107001593
    • Pelegrini, P. B., Quirino, B. F. & Franco, O. L. Plant cyclotides: an unusual class of defense compounds. Peptides 28, 1475-1481 (2007) (Pubitemid 47088738)
    • (2007) Peptides , vol.28 , Issue.7 , pp. 1475-1481
    • Pelegrini, P.B.1    Quirino, B.F.2    Franco, O.L.3
  • 5
    • 2442715239 scopus 로고    scopus 로고
    • Thermal, chemical, and enzymatic stability of the cyclotide kalata B1: The importance of the cyclic cystine knot
    • DOI 10.1021/bi049711q
    • Colgrave, M. L. & Craik, D. J. Thermal, chemical, and enzymatic stability of the cyclotide kalata B1: the importance of the cyclic cystine knot. Biochemistry 43, 5965-5975 (2004) (Pubitemid 38669464)
    • (2004) Biochemistry , vol.43 , Issue.20 , pp. 5965-5975
    • Colgrave, M.L.1    Craik, D.J.2
  • 6
    • 33745832676 scopus 로고    scopus 로고
    • Factors influencing the stability of cyclotides: Proteins with a circular backbone and cystine knot motif
    • DOI 10.1007/s10989-006-9019-2
    • C? emaz?ar, M. & Craik, D. Factors Influencing the Stability of Cyclotides: Proteins with a Circular Backbone and Cystine KnotMotif. Int J Pept Res Ther 12, 253-260 (2006) (Pubitemid 44035104)
    • (2006) International Journal of Peptide Research and Therapeutics , vol.12 , Issue.3 , pp. 253-260
    • Cemazar, M.1    Craik, D.J.2
  • 8
    • 77953454570 scopus 로고    scopus 로고
    • Design and therapeutic applications of cyclotides
    • Daly, N. L. & Craik, D. J. Design and therapeutic applications of cyclotides. Future Med Chem 1, 1613-1622 (2009)
    • (2009) Future Med Chem , vol.1 , pp. 1613-1622
    • Daly, N.L.1    Craik, D.J.2
  • 9
    • 78650009505 scopus 로고    scopus 로고
    • Biological activities of natural and engineered cyclotides, a novel molecular scaffold for peptide-based therapeutics
    • Garcia, A. E. & Camarero, J. A. Biological activities of natural and engineered cyclotides, a novel molecular scaffold for peptide-based therapeutics. Curr Mol Pharmacol 3, 153-163 (2010)
    • (2010) Curr Mol Pharmacol , vol.3 , pp. 153-163
    • Garcia, A.E.1    Camarero, J.A.2
  • 10
    • 78649987052 scopus 로고    scopus 로고
    • Cyclotides, a promising molecular scaffold for peptide-based therapeutics
    • Jagadish, K. & Camarero, J. A. Cyclotides, a promising molecular scaffold for peptide-based therapeutics. Biopolymers 94, 611-616 (2010)
    • (2010) Biopolymers , vol.94 , pp. 611-616
    • Jagadish, K.1    Camarero, J.2
  • 11
    • 73749087526 scopus 로고    scopus 로고
    • Cyclotides as templates in drug design
    • Henriques, S. T. & Craik, D. J. Cyclotides as templates in drug design. Drug Discov Today 15, 57-64 (2010)
    • (2010) Drug Discov Today , vol.15 , pp. 57-64
    • Henriques, S.T.1    Craik, D.J.2
  • 13
    • 4444331457 scopus 로고    scopus 로고
    • The role of the cyclic peptide backbone in the anti-HIV activity of the cyclotide kalata B1
    • DOI 10.1016/j.febslet.2004.08.007, PII S001457930400986X
    • Daly, N. L., Gustafson, K. R. & Craik, D. J. The role of the cyclic peptide backbone in the anti-HIV activity of the cyclotide kalata B1. FEBS Lett 574, 69-72 (2004) (Pubitemid 39200896)
    • (2004) FEBS Letters , vol.574 , Issue.1-3 , pp. 69-72
    • Daly, N.L.1    Gustafson, K.R.2    Craik, D.J.3
  • 15
    • 79959914450 scopus 로고    scopus 로고
    • Decoding the membrane activity of the cyclotide kalata B1: The importance of phosphatidylethanolamine phospholipids and lipid organization on hemolytic and anti-HIV activities
    • Henriques, S. T. et al. 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 (2011)
    • (2011) J Biol Chem , vol.286 , pp. 24231-24241
    • Henriques, S.T.1
  • 16
    • 79955567660 scopus 로고    scopus 로고
    • Anticancer and chemosensitizing abilities of cycloviolacin 02 from Viola odorata and psyle cyclotides from Psychotria leptothyrsa
    • Gerlach, S. L. et al. Anticancer and chemosensitizing abilities of cycloviolacin 02 from Viola odorata and psyle cyclotides from Psychotria leptothyrsa. Biopolymers 94, 617-625 (2010)
    • (2010) Biopolymers , vol.94 , pp. 617-625
    • Gerlach, S.L.1
  • 17
    • 0001166316 scopus 로고    scopus 로고
    • Cyclotides: A novel type of cytotoxic agents
    • Lindholm, P. et al. Cyclotides: a novel type of cytotoxic agents. Mol Cancer Ther 1, 365-369 (2002)
    • (2002) Mol Cancer Ther , vol.1 , pp. 365-369
    • Lindholm, P.1
  • 18
    • 0346422447 scopus 로고    scopus 로고
    • A Comparison of the Self-association Behavior of the Plant Cyclotides Kalata B1 and Kalata B2 via Analytical Ultracentrifugation
    • DOI 10.1074/jbc.M306826200
    • Nourse, A., Trabi, M., Daly, N. L. & Craik, D. J. A comparison of the selfassociation behavior of the plant cyclotides kalata B1 and kalata B2 via analytical ultracentrifugation. J Biol Chem 279, 562-570 (2004) (Pubitemid 38044859)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.1 , pp. 562-570
    • Nourse, A.1    Trabi, M.2    Daly, N.L.3    Craik, D.J.4
  • 19
    • 11844280405 scopus 로고    scopus 로고
    • Studies on the membrane interactions of the cyclotides kalata B1 and kalata B6 on model membrane systems by surface plasmon resonance
    • DOI 10.1016/j.ab.2004.10.028, PII S0003269704008462
    • Kamimori, H., Hall, K., Craik, D. J. & Aguilar, M. I. Studies on the membrane interactions of the cyclotides kalata B1 and kalata B6 on model membrane systems by surface plasmon resonance. Anal Biochem 337, 149-153 (2005) (Pubitemid 40092791)
    • (2005) Analytical Biochemistry , vol.337 , Issue.1 , pp. 149-153
    • Kamimori, H.1    Hall, K.2    Craik, D.J.3    Aguilar, M.-I.4
  • 20
    • 33745227238 scopus 로고    scopus 로고
    • Conformation and mode of membrane interaction in cyclotides Spatial structure of kalata B1 bound to a dodecylphosphocholine micelle
    • Shenkarev, Z. O. et al. Conformation and mode of membrane interaction in cyclotides. Spatial structure of kalata B1 bound to a dodecylphosphocholine micelle. FEBS J 273, 2658-2672 (2006)
    • (2006) FEBS J , vol.273 , pp. 2658-2672
    • Shenkarev, Z.O.1
  • 22
    • 43949138210 scopus 로고    scopus 로고
    • Alanine scanning mutagenesis of the prototypic cyclotide reveals a cluster of residues essential for bioactivity
    • Simonsen, S. M. et al. Alanine scanning mutagenesis of the prototypic cyclotide reveals a cluster of residues essential for bioactivity. J Biol Chem 283, 9805-9813 (2008)
    • (2008) J Biol Chem , vol.283 , pp. 9805-9813
    • Simonsen, S.M.1
  • 23
    • 68949120908 scopus 로고    scopus 로고
    • The biological activity of the prototypic cyclotide kalata b1 is modulated by the formation of multimeric pores
    • Huang, Y. H. et al. The Biological Activity of the Prototypic Cyclotide Kalata B1 Is Modulated by the Formation of Multimeric Pores. J Biol Chem 284, 20699-20707 (2009)
    • (2009) J Biol Chem , vol.284 , pp. 20699-20707
    • Huang, Y.H.1
  • 24
    • 77951247943 scopus 로고    scopus 로고
    • Lysinescanning Mutagenesis Reveals an Amendable Face of the Cyclotide Kalata B1 for the Optimization of Nematocidal Activity
    • Huang, Y. H., Colgrave, M. L., Clark, R. J., Kotze, A. C. & Craik, D. J. Lysinescanning Mutagenesis Reveals an Amendable Face of the Cyclotide Kalata B1 for the Optimization of Nematocidal Activity. J Biol Chem 285, 10797-10805 (2010)
    • (2010) J Biol Chem , vol.285 , pp. 10797-10805
    • Huang, Y.H.1    Colgrave, M.L.2    Clark, R.J.3    Kotze, A.C.4
  • 25
    • 80052265881 scopus 로고    scopus 로고
    • Cyclotidemembrane interactions: Defining factors of membrane binding, depletion and disruption
    • Burman, R., Stromstedt, A. A., Malmsten, M. & Goransson, U. Cyclotidemembrane interactions: defining factors of membrane binding, depletion and disruption. Biochim Biophys Acta 1808, 2665-2673 (2011)
    • (2011) Biochim Biophys Acta , vol.1808 , pp. 2665-2673
    • Burman, R.1    Stromstedt, A.A.2    Malmsten, M.3    Goransson, U.4
  • 26
    • 84871548747 scopus 로고    scopus 로고
    • Cyclotides insert into lipid bilayers to form membrane pores and destabilize the membrane through hydrophobic and phosphoethanolamine-specific interactions
    • Wang, C. K., Wacklin, H. P. & Craik, D. J. 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 (2012)
    • (2012) J Biol Chem , vol.287 , pp. 43884-43898
    • Wang, C.K.1    Wacklin, H.P.2    Craik, D.J.3
  • 27
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • DOI 10.1038/nsb0902-646
    • Karplus, M. & McCammon, J. A. Molecular dynamics simulations of biomolecules. Nat Struct Biol 9, 646-652 (2002) (Pubitemid 34977295)
    • (2002) Nature Structural Biology , vol.9 , Issue.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 28
    • 33947139278 scopus 로고    scopus 로고
    • Setting up and running molecular dynamics simulations of membrane proteins
    • DOI 10.1016/j.ymeth.2006.08.006, PII S1046202306001873
    • Kandt, C., Ash, W. L. & Tieleman, D. P. Setting up and running molecular dynamics simulations of membrane proteins. Methods 41, 475-488 (2007) (Pubitemid 46400527)
    • (2007) Methods , vol.41 , Issue.4 , pp. 475-488
    • Kandt, C.1    Ash, W.L.2    Peter Tieleman, D.3
  • 29
    • 56249119219 scopus 로고    scopus 로고
    • The molecular face of lipid rafts in model membranes
    • Risselada, H. J. & Marrink, S. J. The molecular face of lipid rafts in model membranes. Proc Natl Acad Sci U S A 105, 17367-17372 (2008)
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 17367-17372
    • Risselada, H.J.1    Marrink, S.J.2
  • 30
    • 33746085241 scopus 로고    scopus 로고
    • Rafts defined: A report on the Keystone symposium on lipid rafts and cell function
    • DOI 10.1194/jlr.E600002-JLR200
    • Pike, L. J. Rafts defined: a report on the Keystone Symposium on Lipid Rafts and Cell Function. J Lipid Res 47, 1597-1598 (2006) (Pubitemid 44079915)
    • (2006) Journal of Lipid Research , vol.47 , Issue.7 , pp. 1597-1598
    • Pike, L.J.1
  • 31
    • 79952153989 scopus 로고    scopus 로고
    • Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes
    • Schafer, L. V. et al. Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes. Proc Natl Acad Sci U S A 108, 1343-1348 (2011)
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 1343-1348
    • Schafer, L.V.1
  • 32
    • 84861438588 scopus 로고    scopus 로고
    • Organization, dynamics, and segregation of Ras nanoclusters in membrane domains
    • Janosi, L., Li, Z., Hancock, J. F. & Gorfe, A. A. Organization, dynamics, and segregation of Ras nanoclusters in membrane domains. Proc Natl Acad Sci U S A 109, 8097-8102 (2012)
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 8097-8102
    • Janosi, L.1    Li, Z.2    Hancock, J.F.3    Gorfe, A.A.4
  • 33
    • 77749298088 scopus 로고    scopus 로고
    • On the antibacterial action of cyclic peptides: Insights from coarse-grained MD simulations
    • Khalfa, A. & Tarek, M. On the antibacterial action of cyclic peptides: insights from coarse-grained MD simulations. J Phys Chem B 114, 2676-2684 (2010)
    • (2010) J Phys Chem B , vol.114 , pp. 2676-2684
    • Khalfa, A.1    Tarek, M.2
  • 34
    • 77958085274 scopus 로고    scopus 로고
    • Describing the mechanism of antimicrobial peptide action with the interfacial activity model
    • Wimley, W. C. Describing the mechanism of antimicrobial peptide action with the interfacial activity model. ACS Chem Biol 5, 905-917 (2010)
    • (2010) ACS Chem Biol , vol.5 , pp. 905-917
    • Wimley, W.C.1
  • 35
    • 79955669580 scopus 로고    scopus 로고
    • Antimicrobial peptides: Successes, challenges and unanswered questions
    • Wimley, W. C. & Hristova, K. Antimicrobial peptides: successes, challenges and unanswered questions. J Membr Biol 239, 27-34 (2011)
    • (2011) J Membr Biol , vol.239 , pp. 27-34
    • Wimley, W.C.1    Hristova, K.2
  • 36
    • 1642485164 scopus 로고    scopus 로고
    • Coarse grained model for semiquantitative lipid simulations
    • Marrink, S. J., de Vries, A. H. & Mark, A. E. Coarse Grained Model for Semiquantitative Lipid Simulations. J. Phys. Chem. B 108, 750-760 (2003)
    • (2003) J. Phys. Chem , vol.B108 , pp. 750-760
    • Marrink, S.J.1    De Vries, A.H.2    Mark, A.E.3
  • 39
    • 79952838963 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of cobra cytotoxin A3 interactions with a lipid bilayer: Penetration of loops into membranes
    • Su, Z. Y. &Wang, Y. T. 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 (2011)
    • (2011) J Phys Chem B , vol.115 , pp. 796-802
    • Su, Z.Y.1    Wang, Y.T.2
  • 40
    • 84865782103 scopus 로고    scopus 로고
    • Bending membranes
    • Kirchhausen, T. Bending membranes. Nat Cell Biol 14, 906-908 (2012)
    • (2012) Nat Cell Biol , vol.14 , pp. 906-908
    • Kirchhausen, T.1
  • 41
    • 0041765833 scopus 로고    scopus 로고
    • Mechanisms of membrane deformation
    • DOI 10.1016/S0955-0674(03)00073-5
    • Farsad, K. & De Camilli, P. Mechanisms of membrane deformation. Curr Opin Cell Biol 15, 372-381 (2003) (Pubitemid 36928038)
    • (2003) Current Opinion in Cell Biology , vol.15 , Issue.4 , pp. 372-381
    • Farsad, K.1    De Camilli, P.2
  • 42
    • 48549100003 scopus 로고    scopus 로고
    • Modulation of the spontaneous curvature and bending rigidity of lipid membranes by interfacially adsorbed amphipathic peptides
    • Zemel, A., Ben-Shaul, A. &May, S. Modulation of the spontaneous curvature and bending rigidity of lipid membranes by interfacially adsorbed amphipathic peptides. J Phys Chem B 112, 6988-6996 (2008)
    • (2008) J Phys Chem B , vol.112 , pp. 6988-6996
    • Zemel, A.1    Ben-Shaul, A.2    May, S.3
  • 44
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess, B., Kutzner, C., van der Spoel, D.&Lindahl, E.GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 4, 435-447 (2008)
    • (2008) J. Chem. Theory Comput , vol.4 , pp. 435-447
    • Hess, B.1
  • 45
    • 73949129925 scopus 로고    scopus 로고
    • Coarse-grained models reveal functional dynamics-II. Molecular dynamics simulation at the coarse-grained level-theories and biological applications
    • Chng, C. P. & Yang, L. W. Coarse-grained models reveal functional dynamics-II. Molecular dynamics simulation at the coarse-grained level-theories and biological applications. Bioinform Biol Insights 2, 171-185 (2008)
    • (2008) Bioinform Biol Insights , vol.2 , pp. 171-185
    • Chng, C.P.1    Yang, L.W.2
  • 46
    • 33750587438 scopus 로고
    • Molecular dynamics with coupling to an external bath
    • Berendsen, H. J. C. a. P., J. P. M., van Gunsteren, W. F., DiNola, A. & Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684-3690 (1984)
    • (1984) J. Chem. Phys , vol.81 , pp. 3684-3690
    • Berendsen, H.J.1
  • 49
    • 41449119304 scopus 로고    scopus 로고
    • Coarse-Grained MD simulations of membrane protein-bilayer self-assembly
    • DOI 10.1016/j.str.2008.01.014, PII S0969212608000683
    • Scott, K. A. et al. Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly. Structure 16, 621-630 (2008) (Pubitemid 351458703)
    • (2008) Structure , vol.16 , Issue.4 , pp. 621-630
    • Scott, K.A.1    Bond, P.J.2    Ivetac, A.3    Chetwynd, A.P.4    Khalid, S.5    Sansom, M.S.P.6
  • 50
    • 33847738814 scopus 로고    scopus 로고
    • Lipid rafts: Structure, function and role in HIV, Alzheimer's and prion diseases
    • Fantini, J., Garmy, N.,Mahfoud, R. & Yahi, N. Lipid rafts: structure, function and role in HIV, Alzheimer's and prion diseases. Expert Rev Mol Med 4, 1-22 (2002)
    • (2002) Expert Rev Mol Med , vol.4 , pp. 1-22
    • Fantini, J.1    Garmy N.Mahfoud2
  • 52
    • 0035854701 scopus 로고    scopus 로고
    • Visualizing detergent resistant domains in model membranes with atomic force microscopy
    • PII S0014579301026369
    • Rinia, H. A., Snel, M. M., van der Eerden, J. P.&deKruijff, B. Visualizing detergent resistant domains in model membranes with atomic force microscopy. FEBS Lett 501, 92-96 (2001) (Pubitemid 33712494)
    • (2001) FEBS Letters , vol.501 , Issue.1-3 , pp. 92-96
    • Rinia, H.A.1    Snel, M.M.E.2    Van Der Eerden, J.P.J.M.3    De Kruijf, B.4
  • 53
    • 78349243645 scopus 로고    scopus 로고
    • Role of lipids in spheroidal high density lipoproteins
    • Vuorela, T. et al. Role of lipids in spheroidal high density lipoproteins. PLoS Comput Biol 6, e1000964 (2010)
    • (2010) PLoS Comput Biol , vol.6
    • Vuorela, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.