메뉴 건너뛰기




Volumn 47, Issue 5, 2010, Pages 982-990

Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants

Author keywords

Epitope; HIV 1; p17; Pairwise decomposition; Single chain Fv

Indexed keywords

ASPARAGINE; EPITOPE; HISTIDINE; LEUCINE; LYSINE; MATRIX PROTEIN; MATRIX PROTEIN P17; METHIONINE; MUTANT PROTEIN; SINGLE CHAIN FRAGMENT VARIABLE ANTIBODY; UNCLASSIFIED DRUG;

EID: 74849100500     PISSN: 01615890     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molimm.2009.11.021     Document Type: Article
Times cited : (25)

References (42)
  • 2
    • 51749110001 scopus 로고    scopus 로고
    • Structure and dynamics of the anti-AMCV scFv(F8): effects of selected mutations on the antigen combining site
    • Arcangeli C., Cantale C., Galeffi P., and Rosato V. Structure and dynamics of the anti-AMCV scFv(F8): effects of selected mutations on the antigen combining site. J. Struct. Biol. 164 (2008) 119-133
    • (2008) J. Struct. Biol. , vol.164 , pp. 119-133
    • Arcangeli, C.1    Cantale, C.2    Galeffi, P.3    Rosato, V.4
  • 3
    • 0032112137 scopus 로고    scopus 로고
    • Prediction of binding constants of protein-ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs
    • Bohm H.J. Prediction of binding constants of protein-ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J. Comput. Aided Mol. Des. 12 (1998) 309-323
    • (1998) J. Comput. Aided Mol. Des. , vol.12 , pp. 309-323
    • Bohm, H.J.1
  • 5
    • 2942720886 scopus 로고    scopus 로고
    • HIV-1 assembly and maturation
    • Bukrinskaya A.G. HIV-1 assembly and maturation. Arch. Virol. 149 (2004) 1067-1082
    • (2004) Arch. Virol. , vol.149 , pp. 1067-1082
    • Bukrinskaya, A.G.1
  • 8
    • 0033405041 scopus 로고    scopus 로고
    • Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7
    • Chong L.T., Duan Y., Wang L., Massova I., and Kollman P.A. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 14330-14335
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 14330-14335
    • Chong, L.T.1    Duan, Y.2    Wang, L.3    Massova, I.4    Kollman, P.A.5
  • 9
    • 33846823909 scopus 로고
    • Particle mesh Ewald: an N log(N) method for Ewald sums in large systems
    • Darden T., York D., and Pedersen L. Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 10
    • 41949118164 scopus 로고    scopus 로고
    • A scFv antibody fragment as a therapeutic candidate to neutralize a broad diversity of human IFN-alpha subtypes
    • Depetris M., Casalis P., Kratje R., Etcheverrigaray M., and Oggero M. A scFv antibody fragment as a therapeutic candidate to neutralize a broad diversity of human IFN-alpha subtypes. J. Immunol. Methods 334 (2008) 104-113
    • (2008) J. Immunol. Methods , vol.334 , pp. 104-113
    • Depetris, M.1    Casalis, P.2    Kratje, R.3    Etcheverrigaray, M.4    Oggero, M.5
  • 12
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule database
    • Ewing T.J.A., Makino S., Skillman A.G., and Kuntz I.D. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule database. J. Comput. Aided Mol. Des. 15 (2001) 411-428
    • (2001) J. Comput. Aided Mol. Des. , vol.15 , pp. 411-428
    • Ewing, T.J.A.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 14
    • 0001491955 scopus 로고    scopus 로고
    • Hybrid quantum mechanical/molecular mechanical simulations: an alternative avenue to solvent effects in organic chemistry
    • Gao J. Hybrid quantum mechanical/molecular mechanical simulations: an alternative avenue to solvent effects in organic chemistry. Acc. Chem. Res. 29 (1996) 298-305
    • (1996) Acc. Chem. Res. , vol.29 , pp. 298-305
    • Gao, J.1
  • 15
    • 0043245780 scopus 로고    scopus 로고
    • Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
    • Gohlke H., Kiel C., and Case D. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J. Mol. Biol. 330 (2003) 891-913
    • (2003) J. Mol. Biol. , vol.330 , pp. 891-913
    • Gohlke, H.1    Kiel, C.2    Case, D.3
  • 16
    • 0037198807 scopus 로고    scopus 로고
    • Predictions of binding of a diverse set of ligands to gelatinase-A by a combination of molecular dynamics and continuum solvent models
    • Hou T., Guo S., and Xu X. Predictions of binding of a diverse set of ligands to gelatinase-A by a combination of molecular dynamics and continuum solvent models. J. Phys. Chem. B 106 (2002) 5527-5535
    • (2002) J. Phys. Chem. B , vol.106 , pp. 5527-5535
    • Hou, T.1    Guo, S.2    Xu, X.3
  • 17
    • 39049111013 scopus 로고    scopus 로고
    • Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain
    • Hou T., Zhang W., Case D.A., and Wang W. Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain. J. Mol. Biol. 376 (2008) 1201-1214
    • (2008) J. Mol. Biol. , vol.376 , pp. 1201-1214
    • Hou, T.1    Zhang, W.2    Case, D.A.3    Wang, W.4
  • 18
    • 59849085800 scopus 로고    scopus 로고
    • A scFv antibody-based immunoaffinity chromatography column for clean-up of bisphenol A-contaminated water samples
    • Inui H., Takehara A., Doi F., Nishi K., Takai M., Miyake S., and Ohkawa H. A scFv antibody-based immunoaffinity chromatography column for clean-up of bisphenol A-contaminated water samples. J. Agric. Food. Chem. 57 (2009) 353-358
    • (2009) J. Agric. Food. Chem. , vol.57 , pp. 353-358
    • Inui, H.1    Takehara, A.2    Doi, F.3    Nishi, K.4    Takai, M.5    Miyake, S.6    Ohkawa, H.7
  • 19
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G., Willett P., Glen R.C., Leach A.R., and Taylor R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267 (1997) 727-748
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 20
    • 74849132038 scopus 로고    scopus 로고
    • Yale University, New Haven, CT
    • Jorgensen W.L. BOSS 3. 6 (1996), Yale University, New Haven, CT
    • (1996) BOSS 3. 6
    • Jorgensen, W.L.1
  • 22
    • 7044239742 scopus 로고
    • Free energy calculations: applications to chemical and biochemical phenomena
    • Kollman P.A. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93 (1993) 2395-2417
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.A.1
  • 26
    • 0032233055 scopus 로고    scopus 로고
    • Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects
    • Levy R.M., and Gallicchio E. Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Annu. Rev. Phys. Chem. 49 (1998) 531-567
    • (1998) Annu. Rev. Phys. Chem. , vol.49 , pp. 531-567
    • Levy, R.M.1    Gallicchio, E.2
  • 27
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris G.M., Goodsell D.S., Halliday R., Huey R., Hart W.E., Belew R.K., and Olson A.J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19 (1998) 1639-1662
    • (1998) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olson, A.J.7
  • 28
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: a simplified potential approach
    • Muegge I., and Martin Y.C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem. 42 (1999) 791-804
    • (1999) J. Med. Chem. , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 32
    • 33748809530 scopus 로고    scopus 로고
    • The change of the scFv into the Fab format improves the stability and in vivo toxin neutralization capacity of recombinant antibodies
    • Quintero-Hernandez V., Juarez-Gonzalez V.R., Ortiz-Leon M., Sanchez R., Possani L.D., and Becerril B. The change of the scFv into the Fab format improves the stability and in vivo toxin neutralization capacity of recombinant antibodies. Mol. Immunol. 44 (2007) 1307-1315
    • (2007) Mol. Immunol. , vol.44 , pp. 1307-1315
    • Quintero-Hernandez, V.1    Juarez-Gonzalez, V.R.2    Ortiz-Leon, M.3    Sanchez, R.4    Possani, L.D.5    Becerril, B.6
  • 33
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey M., Kramer B., Lengauer T., and Klebe G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 261 (1996) 470-489
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 34
    • 41449093106 scopus 로고    scopus 로고
    • Engineering peptide linkers for scFv immunosensors
    • Shen Z., Yan H., Zhang Y., Mernaugh R.L., and Zeng X. Engineering peptide linkers for scFv immunosensors. Anal. Chem. 80 (2008) 1910-1917
    • (2008) Anal. Chem. , vol.80 , pp. 1910-1917
    • Shen, Z.1    Yan, H.2    Zhang, Y.3    Mernaugh, R.L.4    Zeng, X.5
  • 35
    • 33751158897 scopus 로고
    • Modeling solvent in biomolecular systems
    • Smith P.E., and Pettitt B.M. Modeling solvent in biomolecular systems. J. Phys. Chem. 98 (1994) 9700-9711
    • (1994) J. Phys. Chem. , vol.98 , pp. 9700-9711
    • Smith, P.E.1    Pettitt, B.M.2
  • 36
    • 22544471858 scopus 로고    scopus 로고
    • Intrabodies as drug discovery tools and therapeutics
    • Stocks M. Intrabodies as drug discovery tools and therapeutics. Curr. Opin. Chem. Biol. 9 (2005) 359-365
    • (2005) Curr. Opin. Chem. Biol. , vol.9 , pp. 359-365
    • Stocks, M.1
  • 37
    • 0032169344 scopus 로고    scopus 로고
    • cDNA encoding a single-chain antibody to HIV p17 with cytoplasmic or nuclear retention signals inhibits HIV-1 replication
    • Tewari D., Goldstein S.L., Notkins A.L., and Zhou P. cDNA encoding a single-chain antibody to HIV p17 with cytoplasmic or nuclear retention signals inhibits HIV-1 replication. J. Immunol. 161 (1998) 2642-2647
    • (1998) J. Immunol. , vol.161 , pp. 2642-2647
    • Tewari, D.1    Goldstein, S.L.2    Notkins, A.L.3    Zhou, P.4
  • 38
    • 11744256643 scopus 로고
    • Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent
    • Tomasi J., and Persico M. Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent. Chem. Rev. 94 (1994) 2027-2094
    • (1994) Chem. Rev. , vol.94 , pp. 2027-2094
    • Tomasi, J.1    Persico, M.2
  • 39
    • 0034701222 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acids with a generalized Born solvation model
    • Tsui V., and Case D.A. Molecular dynamics simulations of nucleic acids with a generalized Born solvation model. J. Am. Chem. Soc. 122 (2000) 2489-2498
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2489-2498
    • Tsui, V.1    Case, D.A.2
  • 41
    • 36448995495 scopus 로고    scopus 로고
    • Treatment of acute myeloid leukemia by directly targeting both leukemia stem cells and oncogenic molecule with specific scFv-immunolipoplexes as a deliverer
    • Wang G.P., Qi Z.H., and Chen F.P. Treatment of acute myeloid leukemia by directly targeting both leukemia stem cells and oncogenic molecule with specific scFv-immunolipoplexes as a deliverer. Med. Hypotheses 70 (2008) 122-127
    • (2008) Med. Hypotheses , vol.70 , pp. 122-127
    • Wang, G.P.1    Qi, Z.H.2    Chen, F.P.3
  • 42
    • 0343005873 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation
    • Weber W., Hünenberger P., and McCammon J. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation. J. Phys. Chem. B 104 (2000) 3668-4575
    • (2000) J. Phys. Chem. B , vol.104 , pp. 3668-4575
    • Weber, W.1    Hünenberger, P.2    McCammon, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.