메뉴 건너뛰기




Volumn 97, Issue 3, 2009, Pages 787-795

Comparative molecular dynamics simulation studies of protegrin-1 monomer and dimer in two different lipid bilayers

Author keywords

[No Author keywords available]

Indexed keywords

1,2 DILAUROYLPHOSPHATIDYLCHOLINE; 2 OLEOYL 1 PALMITOYLPHOSPHATIDYLCHOLINE; DIMER; GLYCEROPHOSPHOLIPID; MONOMER; PROTEGRIN; PROTEGRIN 1; UNCLASSIFIED DRUG;

EID: 68949116194     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.05.029     Document Type: Article
Times cited : (23)

References (41)
  • 1
    • 0037165196 scopus 로고    scopus 로고
    • Antimicrobial peptides of multicellular organisms
    • Zasloff, M. 2002. Antimicrobial peptides of multicellular organisms. Nature. 415:389-395.
    • (2002) Nature , vol.415 , pp. 389-395
    • Zasloff, M.1
  • 2
    • 23444437935 scopus 로고    scopus 로고
    • A review of antimicrobial peptides and their therapeutic potential as anti-infective drugs
    • Gordon, Y. J., E. G. Romanowski, and A. M. McDermott. 2005. A review of antimicrobial peptides and their therapeutic potential as anti-infective drugs. Curr. Eye Res. 30:505-515.
    • (2005) Curr. Eye Res , vol.30 , pp. 505-515
    • Gordon, Y.J.1    Romanowski, E.G.2    McDermott, A.M.3
  • 3
    • 0347755460 scopus 로고    scopus 로고
    • APD: The Antimicrobial Peptide Database
    • Wang, Z., and G. S. Wang. 2004. APD: the Antimicrobial Peptide Database. Nucleic Acids Res. 32:D590-D592.
    • (2004) Nucleic Acids Res , vol.32
    • Wang, Z.1    Wang, G.S.2
  • 5
    • 0027169823 scopus 로고
    • Protegrins: Leukocyte antimicrobial peptides that combine features of corticostatic defensins and tachyplesins
    • Kokryakov, V. N., S. S. L. Harwig, E. A. Panyutich, A. A. Shevchenko, G. M. Aleshina, et al. 1993. Protegrins: leukocyte antimicrobial peptides that combine features of corticostatic defensins and tachyplesins. FEBS Lett. 327:231-236.
    • (1993) FEBS Lett , vol.327 , pp. 231-236
    • Kokryakov, V.N.1    Harwig, S.S.L.2    Panyutich, E.A.3    Shevchenko, A.A.4    Aleshina, G.M.5
  • 6
    • 0030198873 scopus 로고    scopus 로고
    • Solution structure of protegrin-1, a broad-spectrum antimicrobial peptide from porcine leukocytes
    • Fahrner, R. L., T. Dieckmann, S. S. Harwig, R. I. Lehrer, D. Eisenberg, et al. 1996. Solution structure of protegrin-1, a broad-spectrum antimicrobial peptide from porcine leukocytes. Chem. Biol. 3:543-550.
    • (1996) Chem. Biol , vol.3 , pp. 543-550
    • Fahrner, R.L.1    Dieckmann, T.2    Harwig, S.S.3    Lehrer, R.I.4    Eisenberg, D.5
  • 7
    • 0028334888 scopus 로고
    • Role of hemocyte-derived granular components in invertebrate defense
    • Iwanaga, S., T. Muta, T. Shigenaga, Y. Miura, N. Seki, et al. 1994. Role of hemocyte-derived granular components in invertebrate defense. Ann. N. Y. Acad. Sci. 15:102-116.
    • (1994) Ann. N. Y. Acad. Sci , vol.15 , pp. 102-116
    • Iwanaga, S.1    Muta, T.2    Shigenaga, T.3    Miura, Y.4    Seki, N.5
  • 8
    • 0031925507 scopus 로고    scopus 로고
    • β-sheet antibiotic peptides as potential dental therapeutics
    • Miyasaki, K. T., and R. I. Lehrer. 1998. β-sheet antibiotic peptides as potential dental therapeutics. Int. J. Antimicrob. Agents. 9: 269-280.
    • (1998) Int. J. Antimicrob. Agents , vol.9 , pp. 269-280
    • Miyasaki, K.T.1    Lehrer, R.I.2
  • 10
    • 0037031254 scopus 로고    scopus 로고
    • Solid-state NMR investigations of peptide-lipid interaction and orientation of a ss-sheet antimicrobial peptide, protegrin
    • Yamaguchi, S., T. Hong, A. Waring, R. I. Lehrer, and M. Hong. 2002. Solid-state NMR investigations of peptide-lipid interaction and orientation of a ss-sheet antimicrobial peptide, protegrin. Biochemistry. 41:9852-9862.
    • (2002) Biochemistry , vol.41 , pp. 9852-9862
    • Yamaguchi, S.1    Hong, T.2    Waring, A.3    Lehrer, R.I.4    Hong, M.5
  • 11
    • 16244391442 scopus 로고    scopus 로고
    • Determination of peptide oligomerization in lipid bilayers using F-19 spin diffusion NMR
    • Buffy, J. J., A. J. Waring, and M. Hong. 2005. Determination of peptide oligomerization in lipid bilayers using F-19 spin diffusion NMR. J. Am. Chem. Soc. 127:4477-4483.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 4477-4483
    • Buffy, J.J.1    Waring, A.J.2    Hong, M.3
  • 12
    • 33745855891 scopus 로고    scopus 로고
    • Membrane-bound dimer structure of a β-hairpin antimicrobial peptide from rotational-echo double-resonance solid-state NMR
    • Mani, R., M. Tang, X. Wu, J. J. Buffy, A. J. Waring, et al. 2006. Membrane-bound dimer structure of a β-hairpin antimicrobial peptide from rotational-echo double-resonance solid-state NMR. Biochemistry. 45:8341-8349.
    • (2006) Biochemistry , vol.45 , pp. 8341-8349
    • Mani, R.1    Tang, M.2    Wu, X.3    Buffy, J.J.4    Waring, A.J.5
  • 13
    • 33750820630 scopus 로고    scopus 로고
    • Membrane-dependent oligomeric structure and pore formation of β-hairpin antimicrobial peptide in lipid bilayers from solid-state NMR
    • Mani, R., S. D. Cady, M. Tang, A. J. Waring, R. I. Lehrert, et al. 2006. Membrane-dependent oligomeric structure and pore formation of β-hairpin antimicrobial peptide in lipid bilayers from solid-state NMR. Proc. Natl. Acad. Sci. USA. 103:16242-16247.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 16242-16247
    • Mani, R.1    Cady, S.D.2    Tang, M.3    Waring, A.J.4    Lehrert, R.I.5
  • 14
    • 34247625467 scopus 로고    scopus 로고
    • Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect
    • Jang, H., B. Ma, and R. Nussinov. 2007. Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect. BMC Struct. Biol. 7:21.
    • (2007) BMC Struct. Biol , vol.7 , pp. 21
    • Jang, H.1    Ma, B.2    Nussinov, R.3
  • 15
    • 41549125949 scopus 로고    scopus 로고
    • On the nature of antimicrobial activity: A model for protegrin-1 pores
    • Langham, A. A., A. S. Ahmad, and Y. N. Kaznessis. 2008. On the nature of antimicrobial activity: a model for protegrin-1 pores. J. Am. Chem. Soc. 130:4338-4346.
    • (2008) J. Am. Chem. Soc , vol.130 , pp. 4338-4346
    • Langham, A.A.1    Ahmad, A.S.2    Kaznessis, Y.N.3
  • 16
    • 58149311146 scopus 로고    scopus 로고
    • Models of toxic β-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic Alzheimer β-amyloid ion channels
    • Jang, H., B. Ma, R. Lal, and R. Nussinov. 2008. Models of toxic β-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic Alzheimer β-amyloid ion channels. Biophys. J. 95:4631-4642.
    • (2008) Biophys. J , vol.95 , pp. 4631-4642
    • Jang, H.1    Ma, B.2    Lal, R.3    Nussinov, R.4
  • 17
    • 33749535555 scopus 로고    scopus 로고
    • Interaction of protegrin-1 with lipid bilayers: Membrane thinning effect
    • Jang, H., B. Ma, T. B. Woolf, and R. Nussinov. 2006. Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Biophys. J. 91:2848-2859.
    • (2006) Biophys. J , vol.91 , pp. 2848-2859
    • Jang, H.1    Ma, B.2    Woolf, T.B.3    Nussinov, R.4
  • 18
    • 33847078068 scopus 로고    scopus 로고
    • Structure of the antimicrobial β-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation
    • Khandelia, H., and Y. N. Kaznessis. 2007. Structure of the antimicrobial β-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation. Biochim. Biophys. Acta. 1768:509-520.
    • (2007) Biochim. Biophys. Acta , vol.1768 , pp. 509-520
    • Khandelia, H.1    Kaznessis, Y.N.2
  • 19
    • 47149096704 scopus 로고    scopus 로고
    • Software news and updates - CHARNIM-GUI: A webased graphical user interface for CHARMM
    • Jo, S., T. Kim, V. G. Iyer, and W. Im. 2008. Software news and updates - CHARNIM-GUI: a webased graphical user interface for CHARMM. J. Comput. Chem. 29:1859-1865.
    • (2008) J. Comput. Chem , vol.29 , pp. 1859-1865
    • Jo, S.1    Kim, T.2    Iyer, V.G.3    Im, W.4
  • 20
    • 41149134824 scopus 로고    scopus 로고
    • Automated builder and database of protein/membrane complexes for molecular dynamics simulations
    • Jo, S., T. Kim, and W. Im. 2007. Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS ONE. 2:e880.
    • (2007) PLoS ONE , vol.2
    • Jo, S.1    Kim, T.2    Im, W.3
  • 21
    • 68949149548 scopus 로고    scopus 로고
    • CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes
    • Jo, S., J. B. Lim, J. B. Klauda, and W. Im. 2009. CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes. Biophys. J. 97:50-58.
    • (2009) Biophys. J , vol.97 , pp. 50-58
    • Jo, S.1    Lim, J.B.2    Klauda, J.B.3    Im, W.4
  • 22
    • 84986512474 scopus 로고
    • Charmm: A program for macromolecular energy, minimization, and dynamics calculations
    • Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, et al. 1983. Charmm: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
    • (1983) J. Comput. Chem , vol.4 , pp. 187-217
    • Brooks, B.R.1    Bruccoleri, R.E.2    Olafson, B.D.3    States, D.J.4    Swaminathan, S.5
  • 23
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. 1985. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 31:1695-1697.
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 24
    • 36449007836 scopus 로고
    • Constant-pressure molecular-dynamics simulation: The Langevin piston method
    • Feller, S. E., Y. H. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant-pressure molecular-dynamics simulation: the Langevin piston method. J. Chem. Phys. 103:4613-4621.
    • (1995) J. Chem. Phys , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3    Brooks, B.R.4
  • 25
    • 33646170214 scopus 로고    scopus 로고
    • Simulation-based methods for interpreting x-ray data from lipid bilayers
    • Klauda, J. B., N. Kucerka, B. R. Brooks, R. W. Pastor, and J. F. Nagle. 2006. Simulation-based methods for interpreting x-ray data from lipid bilayers. Biophys. J. 90:2796-2807.
    • (2006) Biophys. J , vol.90 , pp. 2796-2807
    • Klauda, J.B.1    Kucerka, N.2    Brooks, B.R.3    Pastor, R.W.4    Nagle, J.F.5
  • 26
    • 28444481767 scopus 로고    scopus 로고
    • A molecular dynamics study of the response of lipid bilayers and monolayers to trehalose
    • Skibinsky, A., R. M. Venable, and R. W. Pastor. 2005. A molecular dynamics study of the response of lipid bilayers and monolayers to trehalose. Biophys. J. 89:4111-4121.
    • (2005) Biophys. J , vol.89 , pp. 4111-4121
    • Skibinsky, A.1    Venable, R.M.2    Pastor, R.W.3
  • 27
    • 0036229927 scopus 로고    scopus 로고
    • Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions
    • Dolan, E. A., R. M. Venable, R. W. Pastor, and B. R. Brooks. 2002. Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions. Biophys. J. 82:2317-2325.
    • (2002) Biophys. J , vol.82 , pp. 2317-2325
    • Dolan, E.A.1    Venable, R.M.2    Pastor, R.W.3    Brooks, B.R.4
  • 28
    • 0032536098 scopus 로고    scopus 로고
    • Oligomerization of protegrin-1 in the presence of DPC micelles. A proton high-resolution NMR study
    • Roumestand, C., V. Louis, A. Aumelas, G. Grassy, B. Calas, et al. 1998. Oligomerization of protegrin-1 in the presence of DPC micelles. A proton high-resolution NMR study. FEBS Lett. 421:263-267.
    • (1998) FEBS Lett , vol.421 , pp. 263-267
    • Roumestand, C.1    Louis, V.2    Aumelas, A.3    Grassy, G.4    Calas, B.5
  • 29
    • 66449133930 scopus 로고    scopus 로고
    • β-hairpin restraint potentials for calculations of potentials of mean force as a function of β-hairpin tilt, rotation, and distance
    • Lee, J., S. Ham, and W. Im. 2009. β-hairpin restraint potentials for calculations of potentials of mean force as a function of β-hairpin tilt, rotation, and distance. J. Comput. Chem. 30:1334-1343.
    • (2009) J. Comput. Chem , vol.30 , pp. 1334-1343
    • Lee, J.1    Ham, S.2    Im, W.3
  • 30
    • 40749090459 scopus 로고    scopus 로고
    • Transmembrane helix tilting: Insights from calculating the potential of mean force
    • Lee, J., and W. Im. 2008. Transmembrane helix tilting: insights from calculating the potential of mean force. Phys. Rev. Lett. 100:018103.
    • (2008) Phys. Rev. Lett , vol.100 , pp. 018103
    • Lee, J.1    Im, W.2
  • 31
    • 22144486884 scopus 로고    scopus 로고
    • Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles
    • Kucerka, N., Y. Liu, N. Chu, H. I. Petrache, S. Tristram-Nagle, et al. 2005. Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles. Biophys. J. 88:2626-2637.
    • (2005) Biophys. J , vol.88 , pp. 2626-2637
    • Kucerka, N.1    Liu, Y.2    Chu, N.3    Petrache, H.I.4    Tristram-Nagle, S.5
  • 32
    • 34247225571 scopus 로고    scopus 로고
    • Hydration of POPC bilayers studied by H-1-PFG-MAS-NOESY and neutron diffraction
    • Gawrisch, K., H. C. Gaede, M. Mihailescu, and S. H. White. 2007. Hydration of POPC bilayers studied by H-1-PFG-MAS-NOESY and neutron diffraction. Eur. Biophys. J. 36:281-291.
    • (2007) Eur. Biophys. J , vol.36 , pp. 281-291
    • Gawrisch, K.1    Gaede, H.C.2    Mihailescu, M.3    White, S.H.4
  • 33
    • 44649087026 scopus 로고    scopus 로고
    • Application of solid-state NMR restraint potentials in membrane protein modeling
    • Lee, J., J. Chen, C. L. Brooks, 3rd, and W. Im. 2008. Application of solid-state NMR restraint potentials in membrane protein modeling. J. Magn. Reson. 193:68-76.
    • (2008) J. Magn. Reson , vol.193 , pp. 68-76
    • Lee, J.1    Chen, J.2    Brooks 3rd, C.L.3    Im, W.4
  • 34
    • 26444593282 scopus 로고    scopus 로고
    • Intermolecular packing and alignment in an ordered β-hairpin antimicrobial peptide aggregate from 2D solid-state NMR
    • Tang, M., A. J. Waring, and M. Hong. 2005. Intermolecular packing and alignment in an ordered β-hairpin antimicrobial peptide aggregate from 2D solid-state NMR. J. Am. Chem. Soc. 127:13919-13927.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 13919-13927
    • Tang, M.1    Waring, A.J.2    Hong, M.3
  • 35
    • 0037159195 scopus 로고    scopus 로고
    • Lai, J. R., B. R. Huck, B. Weisblum, and S. H. Gellman. 2002. Design of non-cysteine-containing antimicrobial β-hairpins: structure-activity relationship studies with linear protegrin-1 analogues. Biochemistry. 41:12835-12842.
    • Lai, J. R., B. R. Huck, B. Weisblum, and S. H. Gellman. 2002. Design of non-cysteine-containing antimicrobial β-hairpins: structure-activity relationship studies with linear protegrin-1 analogues. Biochemistry. 41:12835-12842.
  • 36
  • 37
    • 0029886161 scopus 로고    scopus 로고
    • Synthesis and solution structure of the antimicrobial peptide protegrin-1
    • Aumelas, A., M. Mangoni, C. Roumestand, L. Chiche, E. Despaux, et al. 1996. Synthesis and solution structure of the antimicrobial peptide protegrin-1. Eur. J. Biochem. 237:575-583.
    • (1996) Eur. J. Biochem , vol.237 , pp. 575-583
    • Aumelas, A.1    Mangoni, M.2    Roumestand, C.3    Chiche, L.4    Despaux, E.5
  • 38
    • 0345276804 scopus 로고    scopus 로고
    • Immobilization and aggregation of the antimicrobial peptide protegrin-1 in lipid bilayers investigated by solid-state NMR
    • Buffy, J. J., A. J. Waring, R. I. Lehrer, and M. Hong. 2003. Immobilization and aggregation of the antimicrobial peptide protegrin-1 in lipid bilayers investigated by solid-state NMR. Biochemistry. 42:13725-13734.
    • (2003) Biochemistry , vol.42 , pp. 13725-13734
    • Buffy, J.J.1    Waring, A.J.2    Lehrer, R.I.3    Hong, M.4
  • 39
    • 50649121583 scopus 로고    scopus 로고
    • Solution structure of the integral human membrane protein VDAC-1 in detergent micelles
    • Hiller, S., R. G. Garces, T. J. Malia, V. Y. Orekhov, M. Colombini, et al. 2008. Solution structure of the integral human membrane protein VDAC-1 in detergent micelles. Science. 321:1206-1210.
    • (2008) Science , vol.321 , pp. 1206-1210
    • Hiller, S.1    Garces, R.G.2    Malia, T.J.3    Orekhov, V.Y.4    Colombini, M.5
  • 40
    • 35048820105 scopus 로고    scopus 로고
    • Phosphate-mediated arginine insertion into lipidmembranes and pore formation by a cationicmembrane peptide from solid-state NMR
    • Tang, M., A. J. Waring, and M. Hong. 2007. Phosphate-mediated arginine insertion into lipidmembranes and pore formation by a cationicmembrane peptide from solid-state NMR. J. Am. Chem. Soc. 129:11438-11446.
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 11438-11446
    • Tang, M.1    Waring, A.J.2    Hong, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.