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Volumn 158, Issue 2-3, 2011, Pages 126-133

The effect of pH on PAMAM dendrimer-siRNA complexation - Endosomal considerations as determined by molecular dynamics simulation

Author keywords

Dendrimer; Endosome; Gene delivery; Molecular dynamics simulation; Proton sponge theory; siRNA

Indexed keywords

DENDRIMER; POLYAMIDOAMINE; SMALL INTERFERING RNA;

EID: 79960707221     PISSN: 03014622     EISSN: 18734200     Source Type: Journal    
DOI: 10.1016/j.bpc.2011.06.003     Document Type: Article
Times cited : (81)

References (66)
  • 1
    • 33745460260 scopus 로고    scopus 로고
    • Current status of polymeric gene delivery systems
    • DOI 10.1016/j.addr.2006.03.007, PII S0169409X06000500
    • T.G. Park, J.H. Jeong, and S.W. Kim Current status of polymeric gene delivery systems Adv. Drug Deliv. Rev. 58 4 2006 467 486 (Pubitemid 43949425)
    • (2006) Advanced Drug Delivery Reviews , vol.58 , Issue.4 , pp. 467-486
    • Park, T.G.1    Jeong, J.H.2    Kim, S.W.3
  • 2
    • 27244457081 scopus 로고    scopus 로고
    • Barriers to gene delivery using synthetic vectors
    • DOI 10.1016/S0065-2660(05)53002-5, PII S0065266005530025, Non-Viral Vectors for Gene Therapy, Second Edition: Part 1
    • M.L. Read, A. Logan, and L.W. Seymour Barriers to gene delivery using synthetic vectors Adv. Genet. 53 2005 19 46 (Pubitemid 43580681)
    • (2005) Advances in Genetics , vol.53 , pp. 19-46
    • Read, M.L.1    Logan, A.2    Seymour, L.W.3
  • 3
    • 0038205763 scopus 로고    scopus 로고
    • Polycation gene delivery systems: Escape from endosomes to cytosol
    • DOI 10.1211/002235703765951311
    • Y.W. Cho, J.D. Kim, and K. Park Polycation gene delivery systems: escape from endosomes to cytosol J. Pharm. Pharmacol. 55 6 2003 721 734 (Pubitemid 36752715)
    • (2003) Journal of Pharmacy and Pharmacology , vol.55 , Issue.6 , pp. 721-734
    • Cho, Y.W.1    Kim, J.-D.2    Park, K.3
  • 4
    • 78650476432 scopus 로고    scopus 로고
    • The proton sponge: A trick to enter cells the viruses did not exploit
    • J.P. Behr The proton sponge: a trick to enter cells the viruses did not exploit Chimia 51 1-2 1997 34 36
    • (1997) Chimia , vol.51 , Issue.12 , pp. 34-36
    • Behr, J.P.1
  • 5
    • 0242414440 scopus 로고    scopus 로고
    • Chloride accumulation and swelling in endosomes enhances DNA transfer by polyamine-DNA polyplexes
    • DOI 10.1074/jbc.M308643200
    • N.D. Sonawane, F.C. Szoka, and A.S. Verkman Chloride accumulation and swelling in endosomes enhances DNA transfer by polyamine-DNA polyplexes J. Biol. Chem. 278 45 2003 44826 44831 (Pubitemid 37377241)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.45 , pp. 44826-44831
    • Sonawane, N.D.1    Szoka Jr., F.C.2    Verkman, A.S.3
  • 6
    • 78651363162 scopus 로고    scopus 로고
    • Coarse-grained molecular simulation of interacting dendrimers
    • W.D. Tian, and Y.Q. Ma Coarse-grained molecular simulation of interacting dendrimers Soft Matter 7 2 2011 500 505
    • (2011) Soft Matter , vol.7 , Issue.2 , pp. 500-505
    • Tian, W.D.1    Ma, Y.Q.2
  • 7
    • 13444266498 scopus 로고    scopus 로고
    • Effect of solvent and pH on the structure of PAMAM dendrimers
    • DOI 10.1021/ma049168l
    • P.K. Maiti, T. Cagin, S.T. Lin, and W.A. Goddard Effect of solvent and pH on the structure of PAMAM dendrimers Macromolecules 38 3 2005 979 991 (Pubitemid 40213137)
    • (2005) Macromolecules , vol.38 , Issue.3 , pp. 979-991
    • Maiti, P.K.1    Cagin, T.2    Lin, S.-T.3    Goddard III, W.A.4
  • 8
    • 56349113905 scopus 로고    scopus 로고
    • Release of cationic polymer-DNA complexes from the endosome: A theoretical investigation of the proton sponge hypothesis
    • S. Yang, and S. May Release of cationic polymer-DNA complexes from the endosome: a theoretical investigation of the proton sponge hypothesis J. Chem. Phys. 129 18 2008
    • (2008) J. Chem. Phys. , vol.129 , Issue.18
    • Yang, S.1    May, S.2
  • 9
    • 69949157316 scopus 로고    scopus 로고
    • Missing pieces in understanding the intracellular trafficking of polycation/DNA complexes
    • Y.Y. Won, R. Sharma, and S.F. Konieczny Missing pieces in understanding the intracellular trafficking of polycation/DNA complexes J. Control. Release 139 2 2009 88 93
    • (2009) J. Control. Release , vol.139 , Issue.2 , pp. 88-93
    • Won, Y.Y.1    Sharma, R.2    Konieczny, S.F.3
  • 10
    • 64149113037 scopus 로고    scopus 로고
    • Internally cationic polyamidoamine PAMAM-OH dendrimers for siRNA delivery: Effect of the degree of quaternization and cancer targeting
    • M.L. Patil, M. Zhang, O. Taratula, O.B. Garbuzenko, H.X. He, and T. Minko Internally cationic polyamidoamine PAMAM-OH dendrimers for siRNA delivery: effect of the degree of quaternization and cancer targeting Biomacromolecules 10 2 2009 258 266
    • (2009) Biomacromolecules , vol.10 , Issue.2 , pp. 258-266
    • Patil, M.L.1    Zhang, M.2    Taratula, O.3    Garbuzenko, O.B.4    He, H.X.5    Minko, T.6
  • 11
    • 35748935107 scopus 로고    scopus 로고
    • The advance of dendrimers - A versatile targeting-platform for gene/drug delivery
    • DOI 10.2174/138161207781757024
    • H.S. Parekh The advance of dendrimers-a versatile targeting platform for gene/drug delivery Curr. Pharm. Des. 13 27 2007 2837 2850 (Pubitemid 350138967)
    • (2007) Current Pharmaceutical Design , vol.13 , Issue.27 , pp. 2837-2850
    • Parekh, H.S.1
  • 12
    • 0032032440 scopus 로고    scopus 로고
    • Membrane permeabilization and efficient gene transfer by a peptide containing several histidines
    • DOI 10.1021/bc9701611
    • P. Midoux, A. Kichler, V. Boutin, J.C. Maurizot, and M. Monsigny Membrane permeabilization and efficient gene transfer by a peptide containing several histidines Bioconjug. Chem. 9 2 1998 260 267 (Pubitemid 28147145)
    • (1998) Bioconjugate Chemistry , vol.9 , Issue.2 , pp. 260-267
    • Midoux, P.1    Kichler, A.2    Boutin, V.3    Maurizot, J.-C.4    Monsigny, M.5
  • 13
    • 0033137012 scopus 로고    scopus 로고
    • Efficient gene transfer by histidylated polylysine/pDNA complexes
    • DOI 10.1021/bc9801070
    • P. Midoux, and M. Monsigny Efficient gene transfer by histidylated polylysine/pDNA complexes Bioconjug. Chem. 10 3 1999 406 411 (Pubitemid 29243322)
    • (1999) Bioconjugate Chemistry , vol.10 , Issue.3 , pp. 406-411
    • Midoux, P.1    Monsigny, M.2
  • 15
    • 33847112468 scopus 로고    scopus 로고
    • Optimising histidine rich peptides for efficient DNA delivery in the presence of serum
    • DOI 10.1016/j.jconrel.2006.12.004, PII S0168365906007012
    • A.J. Mason, C. Leborgne, G. Moulay, A. Martinez, O. Danos, B. Bechinger, and A. Kichler Optimising histidine rich peptides for efficient DNA delivery in the presence of serum J. Control. Release 118 1 2007 95 104 (Pubitemid 46283102)
    • (2007) Journal of Controlled Release , vol.118 , Issue.1 , pp. 95-104
    • Mason, A.J.1    Leborgne, C.2    Moulay, G.3    Martinez, A.4    Danos, O.5    Bechinger, B.6    Kichler, A.7
  • 16
    • 34247577622 scopus 로고    scopus 로고
    • Carboxymethyl poly(L-histidine) as a new pH-sensitive polypeptide at endosomal/lysosomal pH
    • DOI 10.1002/pat.890
    • S. Asayama, H. Kato, H. Kawakami, and S. Nagaoka Carboxymethyl poly(L-histidine) as a new pH-sensitive polypeptide at endosomal/lysosomal pH Polym. Adv. Technol. 18 4 2007 329 333 (Pubitemid 46672034)
    • (2007) Polymers for Advanced Technologies , vol.18 , Issue.4 , pp. 329-333
    • Asayama, S.1    Kato, H.2    Kawakami, H.3    Nagaoka, S.4
  • 17
    • 33846810138 scopus 로고    scopus 로고
    • Comparison of the endocytic properties of linear and branched PEIs, and cationic PAMAM dendrimers in B16f10 melanoma cells
    • DOI 10.1016/j.jconrel.2006.10.020, PII S0168365906005761
    • F.P. Seib, A.T. Jones, and R. Duncan Comparison of the endocytic properties of linear and branched PEIs, and cationic PAMAM dendrimers in B16f10 melanoma cells J. Control. Release 117 3 2007 291 300 (Pubitemid 46216575)
    • (2007) Journal of Controlled Release , vol.117 , Issue.3 , pp. 291-300
    • Seib, F.P.1    Jones, A.T.2    Duncan, R.3
  • 18
    • 77950358992 scopus 로고    scopus 로고
    • Investigation of DNA spectral conformational changes and polymer buffering capacity in relation to transfection efficiency of DNA/polymer complexes
    • J.Y. Cherng Investigation of DNA spectral conformational changes and polymer buffering capacity in relation to transfection efficiency of DNA/polymer complexes J. Pharm. Pharm. Sci. 12 3 2009 346 356
    • (2009) J. Pharm. Pharm. Sci. , vol.12 , Issue.3 , pp. 346-356
    • Cherng, J.Y.1
  • 19
    • 19744372388 scopus 로고    scopus 로고
    • Exploring polyethylenimine-mediated DNA transfection and the proton sponge hypothesis
    • DOI 10.1002/jgm.696
    • A. Akinc, M. Thomas, A.M. Klibanov, and R. Langer Exploring polyethylenimine-mediated DNA transfection and the proton sponge hypothesis J. Gene Med. 7 5 2005 657 663 (Pubitemid 40744532)
    • (2005) Journal of Gene Medicine , vol.7 , Issue.5 , pp. 657-663
    • Akinc, A.1    Thomas, M.2    Klibanov, A.M.3    Langer, R.4
  • 20
    • 0034688198 scopus 로고    scopus 로고
    • Design of imidazole-containing endosomolytic biopolymers for gene delivery
    • DOI 10.1002/(SICI)1097-0290(20000120)67:2<217::AID-BIT11>3.0.CO;2-Q
    • D.W. Pack, D. Putnam, and R. Langer Design of imidazole-containing endosomolytic biopolymers for gene delivery Biotechnol. Bioeng. 67 2 2000 217 223 (Pubitemid 30029783)
    • (2000) Biotechnology and Bioengineering , vol.67 , Issue.2 , pp. 217-223
    • Pack, D.W.1    Putnam, D.2    Langer, R.3
  • 21
    • 0037778991 scopus 로고    scopus 로고
    • High transfection efficiency of poly(4-vinylimidazole) as a new gene carrier
    • J.E. Ihm, K.O. Han, I.K. Han, K.D. Ahn, D.K. Han, and C.S. Cho High transfection efficiency of poly(4-vinylimidazole) as a new gene carrier Bioconjug. Chem. 14 4 2003 707 708
    • (2003) Bioconjug. Chem. , vol.14 , Issue.4 , pp. 707-708
    • Ihm, J.E.1    Han, K.O.2    Han, I.K.3    Ahn, K.D.4    Han, D.K.5    Cho, C.S.6
  • 22
    • 68549130637 scopus 로고    scopus 로고
    • Chemical vectors for gene delivery: A current review on polymers, peptides and lipids containing histidine or imidazole as nucleic acids carriers
    • P. Midoux, C. Pichon, J.J. Yaouanc, and P.A. Jaffres Chemical vectors for gene delivery: a current review on polymers, peptides and lipids containing histidine or imidazole as nucleic acids carriers Brit. J. Pharmacol. 157 2 2009 166 178
    • (2009) Brit. J. Pharmacol. , vol.157 , Issue.2 , pp. 166-178
    • Midoux, P.1    Pichon, C.2    Yaouanc, J.J.3    Jaffres, P.A.4
  • 23
    • 33846164122 scopus 로고    scopus 로고
    • Structure and dynamics of DNA-dendrimer complexation: Role of counterions, water, and base pair sequence
    • DOI 10.1021/nl061609m
    • P.K. Maiti, and B. Bagchi Structure and dynamics of DNA-dendrimer complexation: role of counterions, water, and base pair sequence Nano Lett. 6 11 2006 2478 2485 (Pubitemid 46076936)
    • (2006) Nano Letters , vol.6 , Issue.11 , pp. 2478-2485
    • Maiti, P.K.1    Bagchi, B.2
  • 24
    • 0037104623 scopus 로고    scopus 로고
    • Single-stranded DNA condensed with poly-L-lysine results in nanometric particles that are significantly smaller, more stable in physiological ionic strength fluids and afford higher efficiency of gene delivery than their double-stranded counterparts
    • DOI 10.1016/S0304-4165(02)00276-3, PII S0304416502002763
    • M. Molas, R. Bartrons, and J.C. Perales Single-stranded DNA condensed with poly-L-lysine results in nanometric particles that are significantly smaller, more stable in physiological ionic strength fluids and afford higher efficiency of gene delivery than their double-stranded counterparts Biochim. Biophys. Acta-Gen. Subj. 1572 1 2002 37 44 (Pubitemid 35223054)
    • (2002) Biochimica et Biophysica Acta - General Subjects , vol.1572 , Issue.1 , pp. 37-44
    • Molas, M.1    Bartrons, R.2    Perales, J.C.3
  • 25
    • 0027655718 scopus 로고
    • Polyamidoamine cascade polymers mediate efficient transfection of cells in culture
    • J. Haensler, and F.C. Szoka Polyamidoamine cascade polymers mediate efficient transfection of cells in culture Bioconjug. Chem. 4 5 1993 372 379
    • (1993) Bioconjug. Chem. , vol.4 , Issue.5 , pp. 372-379
    • Haensler, J.1    Szoka, F.C.2
  • 26
    • 79955919831 scopus 로고    scopus 로고
    • Low-generation asymmetric dendrimers exhibit minimal toxicity and effectively complex DNA
    • 10.1002/psc.1347
    • N.S.R.J. Shah, and H.S. Parekh Low-generation asymmetric dendrimers exhibit minimal toxicity and effectively complex DNA J. Pept. Sci. 2011 10.1002/psc.1347
    • (2011) J. Pept. Sci.
    • Shah, N.S.R.J.1    Parekh, H.S.2
  • 28
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • DOI 10.1021/ar000033j
    • P.A. Kollman, I. Massova, C. Reyes, B. Kuhn, S.H. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, and T.E. Cheatham Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models Acc. Chem. Res. 33 12 2000 889 897 (Pubitemid 32056774)
    • (2000) Accounts of Chemical Research , vol.33 , Issue.12 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5    Chong, L.6    Lee, M.7    Lee, T.8    Duan, Y.9    Wang, W.10    Donini, O.11
  • 29
    • 84961980685 scopus 로고    scopus 로고
    • Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
    • B. Kuhn, and P.A. Kollman Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models J. Med. Chem. 43 20 2000 3786 3791
    • (2000) J. Med. Chem. , vol.43 , Issue.20 , pp. 3786-3791
    • Kuhn, B.1    Kollman, P.A.2
  • 30
    • 0034212858 scopus 로고    scopus 로고
    • Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece
    • M.R. Lee, Y. Duan, and P.A. Kollman Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece Proteins-Struct. Funct. Genet. 39 4 2000 309 316 (Pubitemid 30414169)
    • (2000) Proteins: Structure, Function and Genetics , vol.39 , Issue.4 , pp. 309-316
    • Lee, M.R.1    Duan, Y.2    Kollman, P.A.3
  • 31
    • 0034084991 scopus 로고    scopus 로고
    • Combined molecular mechanical and continuum solvent approach (MM- PBSA/GBSA) to predict ligand binding
    • DOI 10.1023/A:1008763014207
    • I. Massova, and P.A. Kollman Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding Perspect. Drug Discov. Des. 18 2000 113 135 (Pubitemid 30191024)
    • (2000) Perspectives in Drug Discovery and Design , vol.18 , pp. 113-135
    • Massova, I.1    Kollman, P.A.2
  • 32
    • 0034646574 scopus 로고    scopus 로고
    • Structure and thermodynamics of RNA-protein binding: Using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change
    • C.M. Reyes, and P.A. Kollman Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change J. Mol. Biol. 297 5 2000 1145 1158
    • (2000) J. Mol. Biol. , vol.297 , Issue.5 , pp. 1145-1158
    • Reyes, C.M.1    Kollman, P.A.2
  • 35
    • 0029633186 scopus 로고
    • AMBER, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
    • D.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross, T.E. Cheatham, S. Debolt, D. Ferguson, G. Seibel, and P. Kollman AMBER, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules Comput. Phys. Commun. 91 1-3 1995 1 41
    • (1995) Comput. Phys. Commun. , vol.91 , Issue.13 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham, T.E.5    Debolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.9
  • 36
    • 27544455180 scopus 로고    scopus 로고
    • RNA interference against human papillomavirus oncogenes in cervical cancer cells results in increased sensitivity to cisplatin
    • DOI 10.1124/mol.105.014191
    • L.N. Putral, M.J. Bywater, W. Gu, N.A. Saunders, B.G. Gabrielli, G.R. Leggatt, and N.A. McMillan RNA interference against human papillomavirus oncogenes in cervical cancer cells results in increased sensitivity to cisplatin Mol. Pharmacol. 68 5 2005 1311 1319 (Pubitemid 41539987)
    • (2005) Molecular Pharmacology , vol.68 , Issue.5 , pp. 1311-1319
    • Putral, L.N.1    Bywater, M.J.2    Gu, W.3    Saunders, N.A.4    Gabrielli, B.G.5    Leggatt, G.R.6    McMillan, N.A.J.7
  • 37
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • J.M. Wang, P. Cieplak, and P.A. Kollman How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21 12 2000 1049 1074
    • (2000) J. Comput. Chem. , vol.21 , Issue.12 , pp. 1049-1074
    • Wang, J.M.1    Cieplak, P.2    Kollman, P.A.3
  • 38
    • 11144347566 scopus 로고    scopus 로고
    • Erratum: Development and testing of a general amber force field (Journal of Computational Chemistry (2004) 25 (1157))
    • DOI 10.1002/jcc.20145
    • J.M. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, and D.A. Case Development and testing of a general amber force field (vol 25, pg 1157-1174, 2004) J. Comput. Chem. 26 1 2005 114 (Pubitemid 40021628)
    • (2005) Journal of Computational Chemistry , vol.26 , Issue.1 , pp. 114
    • Wang, J.1    Wolf, R.M.2    Caldwell, J.W.3    Kollman, P.A.4    Case, D.A.5
  • 39
    • 33846823909 scopus 로고
    • Particle mesh Ewald - An n.log(n) method for Ewald sums in large systems
    • T. Darden, D. York, and L. Pedersen Particle mesh Ewald - an n.log(n) method for Ewald sums in large systems J. Chem. Phys. 98 12 1993 10089 10092
    • (1993) J. Chem. Phys. , vol.98 , Issue.12 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 41
    • 0031334264 scopus 로고    scopus 로고
    • Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program
    • M.F. Crowley, T.A. Darden, T.E. Cheatham, and D.W. Deerfield Adventures in improving the scaling and accuracy of a parallel molecular dynamics program J. Supercomput. 11 3 1997 255 278 (Pubitemid 127507287)
    • (1997) Journal of Supercomputing , vol.11 , Issue.3 , pp. 255-278
    • Crowley, M.F.1    Darden, T.A.2    Cheatham III, T.E.3    Deerfield II, D.W.4
  • 43
    • 0034506266 scopus 로고    scopus 로고
    • Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions
    • DOI 10.1063/1.1324708
    • A. Toukmaji, C. Sagui, J. Board, and T. Darden Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions J. Chem. Phys. 113 24 2000 10913 10927 (Pubitemid 32087579)
    • (2000) Journal of Chemical Physics , vol.113 , Issue.24 , pp. 10913-10927
    • Toukmaji, A.1    Sagui, C.2    Board, J.3    Darden, T.4
  • 44
    • 0942288583 scopus 로고    scopus 로고
    • Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations
    • C. Sagui, L.G. Pedersen, and T.A. Darden Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations J. Chem. Phys. 120 1 2004 73 87
    • (2004) J. Chem. Phys. , vol.120 , Issue.1 , pp. 73-87
    • Sagui, C.1    Pedersen, L.G.2    Darden, T.A.3
  • 48
    • 33646940952 scopus 로고
    • Numerical-integration of Cartesian equations of motion of a system with constrains - Molecular dynamics of n-alkanes
    • J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical-integration of Cartesian equations of motion of a system with constrains - molecular dynamics of n-alkanes J. Comput. Phys. 23 3 1977 327 341
    • (1977) J. Comput. Phys. , vol.23 , Issue.3 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 49
    • 58149163268 scopus 로고    scopus 로고
    • A vulnerability in popular molecular dynamics packages concerning Langevin and Andersen dynamics
    • D.S. Cerutti, R. Duke, P.L. Freddolino, H. Fan, and T.P. Lybrand A vulnerability in popular molecular dynamics packages concerning Langevin and Andersen dynamics J. Chem. Theory Comput. 4 10 2008 1669 1680
    • (2008) J. Chem. Theory Comput. , vol.4 , Issue.10 , pp. 1669-1680
    • Cerutti, D.S.1    Duke, R.2    Freddolino, P.L.3    Fan, H.4    Lybrand, T.P.5
  • 51
    • 0242509772 scopus 로고    scopus 로고
    • Self-guided Langevin dynamics simulation method
    • X.W. Wu, and B.R. Brooks Self-guided Langevin dynamics simulation method Chem. Phys. Lett. 381 3-4 2003 512 518
    • (2003) Chem. Phys. Lett. , vol.381 , Issue.34 , pp. 512-518
    • Wu, X.W.1    Brooks, B.R.2
  • 52
    • 0036771626 scopus 로고    scopus 로고
    • Accelerated Poisson-Boltzmann calculations for static and dynamic systems
    • DOI 10.1002/jcc.10120
    • R. Luo, L. David, and M.K. Gilson Accelerated Poisson-Boltzmann calculations for static and dynamic systems J. Comput. Chem. 23 13 2002 1244 1253 (Pubitemid 35009216)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.13 , pp. 1244-1253
    • Luo, R.1    David, L.2    Gilson, M.K.3
  • 53
    • 0347410858 scopus 로고    scopus 로고
    • A Poisson-Boltzmann dynamics method with nonperiodic boundary condition
    • Q. Lu, and R. Luo A Poisson-Boltzmann dynamics method with nonperiodic boundary condition J. Chem. Phys. 119 21 2003 11035 11047
    • (2003) J. Chem. Phys. , vol.119 , Issue.21 , pp. 11035-11047
    • Lu, Q.1    Luo, R.2
  • 54
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • B. Honig, and A. Nicholls Classical electrostatics in biology and chemistry Science (New York, N.Y) 268 5214 1995 1144 1149
    • (1995) Science (New York, N.Y) , vol.268 , Issue.5214 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 55
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • W.C. Still, A. Tempczyk, R.C. Hawley, and T. Hendrickson Semianalytical treatment of solvation for molecular mechanics and dynamics J. Am. Chem. Soc. 112 16 1990 6127 6129
    • (1990) J. Am. Chem. Soc. , vol.112 , Issue.16 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 56
    • 0000043930 scopus 로고    scopus 로고
    • Solvation free energy of biomacromolecules: Parameters for a modified generalized born model consistent with the AMBER force field
    • B. Jayaram, D. Sprous, and D.L. Beveridge Solvation free energy of biomacromolecules: parameters for a modified generalized born model consistent with the AMBER force field J. Phys. Chem. B 102 47 1998 9571 9576 (Pubitemid 128611876)
    • (1998) Journal of Physical Chemistry B , vol.102 , Issue.47 , pp. 9571-9576
    • Jayaram, B.1    Sprous, D.2    Beveridge, D.L.3
  • 57
    • 84961981091 scopus 로고    scopus 로고
    • Implicit solvation models: Equilibria, structure, spectra, and dynamics
    • C.J. Cramer, and D.G. Truhlar Implicit solvation models: equilibria, structure, spectra, and dynamics Chem. Rev. 99 8 1999 2161 2200 (Pubitemid 129585183)
    • (1999) Chemical Reviews , vol.99 , Issue.8 , pp. 2161-2200
    • Cramer, C.J.1    Truhlar, D.G.2
  • 58
    • 0033654297 scopus 로고    scopus 로고
    • Generalized born models of macromolecular solvation effects
    • D. Bashford, and D.A. Case Generalized born models of macromolecular solvation effects Annu. Rev. Phys. Chem. 51 2000 129 152
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 129-152
    • Bashford, D.1    Case, D.A.2
  • 59
    • 20644449471 scopus 로고    scopus 로고
    • Modification of the generalized Born model suitable for macromolecules
    • A. Onufriev, D. Bashford, and D.A. Case Modification of the generalized Born model suitable for macromolecules J. Phys. Chem. B 104 15 2000 3712 3720
    • (2000) J. Phys. Chem. B , vol.104 , Issue.15 , pp. 3712-3720
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 63
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free-energies using macroscopic solvent models
    • D. Sitkoff, K.A. Sharp, and B. Honig Accurate calculation of hydration free-energies using macroscopic solvent models J. Phys. Chem-Us. 98 7 1994 1978 1988
    • (1994) J. Phys. Chem-Us. , vol.98 , Issue.7 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 64
    • 0000538815 scopus 로고
    • Analytical molecular-surface calculation
    • OCT
    • M.L. Connolly Analytical molecular-surface calculation J. Appl. Crystallogr. 16 OCT 1983 548 558
    • (1983) J. Appl. Crystallogr. , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 65
    • 77954694522 scopus 로고    scopus 로고
    • Structure, dynamics, and energetics of siRNA-cationic vector complexation: A molecular dynamics study
    • D. Ouyang, H. Zhang, D.P. Herten, H.S. Parekh, and S.C. Smith Structure, dynamics, and energetics of siRNA-cationic vector complexation: a molecular dynamics study J. Phys. Chem. B 114 28 2010 9220 9230
    • (2010) J. Phys. Chem. B , vol.114 , Issue.28 , pp. 9220-9230
    • Ouyang, D.1    Zhang, H.2    Herten, D.P.3    Parekh, H.S.4    Smith, S.C.5
  • 66
    • 77749280012 scopus 로고    scopus 로고
    • Ability to Adapt: Different generations of PAMAM dendrimers show different behaviors in binding siRNA
    • G.M. Pavan, L. Albertazzi, and A. Danani Ability to Adapt: Different generations of PAMAM dendrimers show different behaviors in binding siRNA J. Phys. Chem. B114 8 2010 2667 2675
    • (2010) J. Phys. Chem. , vol.114 B , Issue.8 , pp. 2667-2675
    • Pavan, G.M.1    Albertazzi, L.2    Danani, A.3


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