메뉴 건너뛰기




Volumn 5, Issue SUPPL. 3, 2008, Pages

DNA and lipid bilayers: Self-assembly and insertion

Author keywords

Coarse grain; DNA; Gene therapy; Molecular dynamics

Indexed keywords

BIOINFORMATICS; DNA; GENE THERAPY; LIPID BILAYERS; LIPIDS; SELF ASSEMBLY;

EID: 58749084517     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2008.0239.focus     Document Type: Article
Times cited : (64)

References (37)
  • 2
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar, I., Atilgan, A. R. & Erman, B. 1997 Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des. 2, 173-181. (doi:10.1016/S1359-0278(97)00024-2) (Pubitemid 127740467)
    • (1997) Folding and Design , vol.2 , Issue.3 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 3
    • 0346401967 scopus 로고    scopus 로고
    • Molecular dynamics study of a lipid-DNA complex
    • doi:10.1021/jp9927496
    • Bandyopadhyay, S., Tarek, M. & Klein, M. L. 1999 Molecular dynamics study of a lipid-DNA complex. J. Phys. Chem. B 103, 10075-10080. (doi:10.1021/jp9927496)
    • (1999) J. Phys. Chem. B , vol.103 , pp. 10075-10080
    • Bandyopadhyay, S.1    Tarek, M.2    Klein, M.L.3
  • 5
    • 0029633168 scopus 로고
    • GROMACS: A message-passing parallel molecular dynamics implementation
    • doi:10. 1016/0010-4655(95)00042-E
    • Berendsen, H. J. C., van der Spoel, D. & van Drunen, R. 1995 GROMACS: a message-passing parallel molecular dynamics implementation.Comput. Phys. Commun. 95, 43-56. (doi:10. 1016/0010-4655(95)00042-E)
    • (1995) Comput. Phys. Commun. , vol.95 , pp. 43-56
    • Berendsen, H.J.C.1    Van Der Spoel, D.2    Van Drunen, R.3
  • 6
    • 33644644163 scopus 로고    scopus 로고
    • Insertion and assembly of membrane proteins via simulation
    • DOI 10.1021/ja0569104
    • Bond, P. J. & Sansom, M. S. P. 2006 Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 128, 2697-2704. (doi:10.1021/ja0569104) (Pubitemid 43327948)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.8 , pp. 2697-2704
    • Bond, P.J.1    Sansom, M.S.P.2
  • 7
    • 33847242278 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of membrane proteins and peptides
    • doi:10.1016/j.jsb.2006.10.004
    • Bond, P.J., Holyoake, J., Ivetac, A., Khalid, S.&Sansom, M.S. 2007 Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J. Struct. Biol. 157, 593-605. (doi:10.1016/j.jsb.2006.10.004)
    • (2007) J. Struct. Biol. , vol.157 , pp. 593-605
    • Bond, P.J.1    Holyoake, J.2    Ivetac, A.3    Khalid, S.4    Sansom, M.S.5
  • 9
    • 3343005633 scopus 로고    scopus 로고
    • Differences and limits in estimates of persistence length for semi-flexible macromolecules
    • DOI 10.1016/j.polymer.2004.06.034, PII S0032386104006196
    • Cifra, P. 2004 Differences and limits in estimates of persistence length for semi-flexible macromolecules. Polymer 45, 5995-6002. (doi:10.1016/j.polymer. 2004.06.034) (Pubitemid 38993473)
    • (2004) Polymer , vol.45 , Issue.17 , pp. 5995-6002
    • Cifra, P.1
  • 10
    • 0033593503 scopus 로고    scopus 로고
    • Static curvature and flexibility measurements of DNA with microscopy. A simple renormalization method, its assessment by experiment and simulation
    • DOI 10.1006/jmbi.1998.2322
    • Cognet, J. A. H., Pakleza, C., Cherny, D., Delain, E. & Le Cam, E. 1999 Static curvature and flexibility measurements of DNA with microscopy. A simple renormalization method, its assessment by experiment and simulation. J. Mol. Biol. 285, 997-1009. (doi:10.1006/jmbi.1998.2322) (Pubitemid 29054312)
    • (1999) Journal of Molecular Biology , vol.285 , Issue.3 , pp. 997-1009
    • Cognet, J.A.H.1    Pakleza, C.2    Cherny, D.3    Delain, E.4    Cam, E.L.5
  • 12
    • 1642503835 scopus 로고    scopus 로고
    • Cationic lipid-DNA complexes for gene therapy: Understanding the relationship between complex structure and gene delivery pathways at the molecular level
    • DOI 10.2174/0929867043456160
    • Ewert, K., Slack, N. L., Ahmad, A., Evans, H. M., Lin, A. J., Samuel, C. E. & Safinya, C. R. 2004 Cationic lipid-DNA complexes for gene therapy: understanding the relationship between complex structure and gene delivery pathways at the molecular level. Curr. Med. Chem. 11, 133-149. (doi:10.2174/0929867043456160) (Pubitemid 38128841)
    • (2004) Current Medicinal Chemistry , vol.11 , Issue.2 , pp. 133-149
    • Ewert, K.1    Slack, N.L.2    Ahmad, A.3    Evans, H.M.4    Lin, A.J.5    Samuel, C.E.6    Safinya, C.R.7
  • 13
    • 34247555456 scopus 로고    scopus 로고
    • Computational and analytical modeling of cationic lipid-DNA complexes
    • DOI 10.1529/biophysj.106.096990
    • Farago, O. & Gronbech-Jensen, N. 2007 Computational and analytical modeling of cationic lipid-DNA complexes. Biophys. J. 92, 3228-3240. (doi:10.1529/biophysj.106. 096990) (Pubitemid 46684582)
    • (2007) Biophysical Journal , vol.92 , Issue.9 , pp. 3228-3240
    • Farago, O.1    Gronbech-Jensen, N.2
  • 14
    • 32644460458 scopus 로고    scopus 로고
    • Mesoscale computer modeling of Lipid-DNA complexes for gene therapy
    • DOI 10.1103/PhysRevLett.96.018102
    • Farago, O., Gronbech-Jensen, N. & Pincus, P. 2006 Mesoscale computer modeling of lipid-DNA complexes for gene therapy. Phys. Rev. Lett. 96, 018102. (doi:10.1103/PhysRevLett.96.018102) (Pubitemid 43248410)
    • (2006) Physical Review Letters , vol.96 , Issue.1 , pp. 018102
    • Farago, O.1    Gronbech-Jensen, N.2    Pincus, P.3
  • 16
    • 29344446842 scopus 로고    scopus 로고
    • Pore formation coupled to ion transport through lipid membranes as induced by transmembrane ionic charge imbalance: Atomistic molecular dynamics study
    • DOI 10.1021/ja053129n
    • Gurtovenko, A. A. & Vattulainen, I. 2005 Pore formation coupled to ion transport through lipid membranes as induced by transmembrane ionic charge imbalance: atomistic molecular dynamics study. J. Am. Chem. Soc. 127, 17570-17571. (doi:10.1021/ja053129n) (Pubitemid 43003349)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.50 , pp. 17570-17571
    • Gurtovenko, A.A.1    Vattulainen, I.2
  • 17
    • 0023746243 scopus 로고
    • Flexibility of DNA
    • doi:10.1146/annurev.bb.17.060188.001405
    • Hagerman, P. J. 1988 Flexibility of DNA. Ann. Rev. Biophys. Biophys. Chem. 17, 265-286. (doi:10.1146/annurev.bb.17. 060188.001405)
    • (1988) Ann. Rev. Biophys. Biophys. Chem. , vol.17 , pp. 265-286
    • Hagerman, P.J.1
  • 18
    • 0029878720 scopus 로고    scopus 로고
    • VMD: Visual molecular dynamics
    • DOI 10.1016/0263-7855(96)00018-5
    • Humphrey, W., Dalke, A. & Schulten, K. 1996 VMD-visual molecular dynamics. J. Mol. Graph. Model. 14, 33-38. (doi:10.1016/0263-7855(96)00018-5) (Pubitemid 26152973)
    • (1996) Journal of Molecular Graphics , vol.14 , Issue.1 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 19
    • 0032479572 scopus 로고    scopus 로고
    • An inverted hexagonal phase of cationic liposome-DNA complexes related to DNA release and delivery
    • DOI 10.1126/science.281.5373.78
    • Koltover, I., Salditt, T., Radler, J. O. & Safinya, C. R. 1998 An inverted hexagonal phase of cationic liposome-DNA complexes related to DNA release and delivery. Science 281, 78-81. (doi:10.1126/science.281.5373.78) (Pubitemid 28354046)
    • (1998) Science , vol.281 , Issue.5373 , pp. 78-81
    • Koltover, I.1    Salditt, T.2    Radler, J.O.3    Safinya, C.R.4
  • 20
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • DOI 10.1007/S008940100045
    • Lindahl, E., Hess, B. & van der Spoel, D. 2001 GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7, 306-317. (Pubitemid 36153547)
    • (2001) Journal of Molecular Modeling , vol.7 , Issue.8 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 21
    • 1642485164 scopus 로고    scopus 로고
    • Coarse grained model for semiquantitative lipid simulations
    • doi:10.1021/jp036508g
    • Marrink, S. J., de Vries, A. H. & Mark, A. E. 2004 Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B 108, 750-760. (doi:10.1021/jp036508g)
    • (2004) J. Phys. Chem. B , vol.108 , pp. 750-760
    • Marrink, S.J.1    De Vries, A.H.2    Mark, A.E.3
  • 22
    • 0034671291 scopus 로고    scopus 로고
    • DNA structure: What's in charge?
    • DOI 10.1006/jmbi.2000.4167
    • McConnell, K. J. & Beveridge, D. L. 2000 DNA structure: what's in charge? J. Mol. Biol. 304, 803-820. (doi:10.1006/jmbi.2000.4167) (Pubitemid 32047084)
    • (2000) Journal of Molecular Biology , vol.304 , Issue.5 , pp. 803-820
    • McConnell, K.J.1    Beveridge, D.L.2
  • 25
    • 0031036238 scopus 로고    scopus 로고
    • Structure of DNA-cationic liposome complexes: DNA intercalation in multilamellar membranes in distinct interhelical packing regimes
    • DOI 10.1126/science.275.5301.810
    • Radler, J. O., Koltover, I., Salditt, T. & Safinya, C. R. 1997 Structure of DNA-cationic liposome complexes: DNA intercalation in multilamellar membranes in distinct interhelical packing regimes. Science 275, 810-814. (doi:10.1126/science.275.5301.810) (Pubitemid 27074877)
    • (1997) Science , vol.275 , Issue.5301 , pp. 810-814
    • Radler, J.O.1    Koltover, I.2    Salditt, T.3    Safinya, C.R.4
  • 26
    • 34249325178 scopus 로고    scopus 로고
    • Aggregation and vesiculation of membrane proteins by curvature-mediated interactions
    • DOI 10.1038/nature05840, PII NATURE05840
    • Reynwar, B. J., Illya, G., Harmandaris, V. A., Muller, M. M., Kremer, K. & Deserno, M. 2007 Aggregation and vesiculation of membrane proteins by curvature-mediated interactions. Nature 447, 461-464. (doi:10.1038/nature 05840) (Pubitemid 46816743)
    • (2007) Nature , vol.447 , Issue.7143 , pp. 461-464
    • Reynwar, B.J.1    Illya, G.2    Harmandaris, V.A.3    Muller, M.M.4    Kremer, K.5    Deserno, M.6
  • 27
    • 4143138536 scopus 로고    scopus 로고
    • Exploring the counterion atmosphere around DNA: What can be learned from molecular dynamics simulations?
    • DOI 10.1529/biophysj.104.040451
    • Rueda, M., Cubero, E., Laughton, C. A. & Orozco, M. 2004 Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations? Biophys. J. 87, 800-811. (doi:10.1529/biophysj.104.040451) (Pubitemid 39095063)
    • (2004) Biophysical Journal , vol.87 , Issue.2 , pp. 800-811
    • Rueda, M.1    Cubero, E.2    Laughton, C.A.3    Orozco, M.4
  • 28
    • 0035425499 scopus 로고    scopus 로고
    • Structures of lipid-DNA complexes: Supramolecular assembly and gene delivery
    • DOI 10.1016/S0959-440X(00)00230-X
    • Safinya, C. R. 2001 Structures of lipid-DNA complexes: supramolecular assembly and gene delivery. Curr. Opin. Struct. Biol. 11, 440-448. (doi:10.1016/S0959-440X(00) 00230-X) (Pubitemid 32728495)
    • (2001) Current Opinion in Structural Biology , vol.11 , Issue.4 , pp. 440-448
    • Safinya, C.R.1
  • 29
    • 0029119568 scopus 로고
    • RasMol: Biomole-cular graphics for all
    • doi:10.1016/S0968-0004(00)89080-5
    • Sayle, R. A. & Milner-White, E. J. 1995 RasMol: biomole-cular graphics for all. Trends Biochem. Sci. 20, 374-376. (doi:10.1016/S0968-0004(00) 89080-5)
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 374-376
    • Sayle, R.A.1    Milner-White, E.J.2
  • 30
    • 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., Bond, P. J., Ivetac, A., Chetwynd, A. P., Khalid, S. & Sansom, M. S. 2008 Coarse-grained MD simulations of membrane protein-bilayer self-assembly structure. Structure 16, 621-630. (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
  • 32
    • 33644893631 scopus 로고    scopus 로고
    • Coarse grained protein-lipid model with application to lipoprotein particles
    • doi:10.1021/jp0550816
    • Shih, A. Y., Arkhipov, A., Freddolino, P. L. & Schulten, K. 2006 Coarse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B 110, 3674-3684. (doi:10.1021/jp0550816)
    • (2006) J. Phys. Chem. B , vol.110 , pp. 3674-3684
    • Shih, A.Y.1    Arkhipov, A.2    Freddolino, P.L.3    Schulten, K.4
  • 33
    • 22244452943 scopus 로고    scopus 로고
    • Membrane electroporation: A molecular dynamics simulation
    • DOI 10.1529/biophysj.104.050617
    • Tarek, M. 2005 Membrane electroporation: a molecular dynamics simulation. Biophys. J. 88, 4045-4053. (doi:10. 1529/biophysj.104.050617) (Pubitemid 40991116)
    • (2005) Biophysical Journal , vol.88 , Issue.6 , pp. 4045-4053
    • Tarek, M.1
  • 34
    • 17444405896 scopus 로고    scopus 로고
    • A coarse-grained model for double-helix molecules in solution: Spontaneous helix formation and equilibrium properties
    • DOI 10.1063/1.1869417, 124906
    • Tepper, H. L. & Voth, G. A. 2005 A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties. J. Chem. Phys. 122, 124 906. (doi:10.1063/1.1869417) (Pubitemid 40537498)
    • (2005) Journal of Chemical Physics , vol.122 , Issue.12 , pp. 1-11
    • Tepper, H.L.1    Voth, G.A.2
  • 35
    • 4043179941 scopus 로고    scopus 로고
    • DNA and its counterions: A molecular dynamics study
    • DOI 10.1093/nar/gkh765
    • Varnai, P. & Zakrzewska, K. 2004 DNA and its counterions: a molecular dynamics study. Nucleic Acids Res. 32, 4269-4280. (doi:10.1093/nar/gkh765) (Pubitemid 39232299)
    • (2004) Nucleic Acids Research , vol.32 , Issue.14 , pp. 4269-4280
    • Varnai, P.1    Zakrzewska, K.2
  • 36
    • 33750980984 scopus 로고    scopus 로고
    • Mesoscopic models of biological membranes
    • DOI 10.1016/j.physrep.2006.07.006, PII S0370157306003309
    • Venturoli, M., Maddalena Sperotto, M., Kranenburg, M. & Smit, B. 2006 Mesoscopic models of biological membranes. Phys. Rep. 437, 1-54. (doi:10.1016/j.physrep.2006.07.006) (Pubitemid 44739752)
    • (2006) Physics Reports , vol.437 , Issue.1-2 , pp. 1-54
    • Venturoli, M.1    Maddalena Sperotto, M.2    Kranenburg, M.3    Smit, B.4
  • 37
    • 0000153330 scopus 로고    scopus 로고
    • Thermotropic phase behavior of cationic lipid-DNA complexes compared to binary lipid mixtures
    • Zantl, R., Baicu, L., Artzner, F., Sprenger, I., Rapp, G. & Rädler, J. O. 1999 Thermotropic phase behavior of cationic lipid-DNA complexes compared to binary lipid mixtures. J. Phys. Chem. 103, 10 300-10 310.
    • (1999) J. Phys. Chem. , vol.103 , pp. 10300-10310
    • Zantl, R.1    Baicu, L.2    Artzner, F.3    Sprenger, I.4    Rapp, G.5    Rädler, J.O.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.