메뉴 건너뛰기




Volumn 974, Issue 1-3, 2011, Pages 122-132

Comparative structural studies of T-20 analogues using molecular dynamics

Author keywords

Turn; CLASICO; Hydrogen bond; Molecular dynamics; NMR; T 20

Indexed keywords


EID: 84555218343     PISSN: 2210271X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.comptc.2011.07.024     Document Type: Article
Times cited : (4)

References (37)
  • 2
    • 0038187684 scopus 로고    scopus 로고
    • Novel therapies based on mechanisms of HIV-1 cell entry
    • Kilby J.M., Eron J.J. Novel therapies based on mechanisms of HIV-1 cell entry. N. Engl. J. Med. 2003, 348:2228-2238.
    • (2003) N. Engl. J. Med. , vol.348 , pp. 2228-2238
    • Kilby, J.M.1    Eron, J.J.2
  • 4
    • 0030002637 scopus 로고    scopus 로고
    • HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G protein coupled receptor
    • Feng Y., Broder C.C., Kennedy P.E., Berger E.A. HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G protein coupled receptor. Science 1996, 272:872-877.
    • (1996) Science , vol.272 , pp. 872-877
    • Feng, Y.1    Broder, C.C.2    Kennedy, P.E.3    Berger, E.A.4
  • 5
    • 0037381269 scopus 로고    scopus 로고
    • The structural biology of type I viral membrane fusion
    • Colman P.M., Lawrence M.C. The structural biology of type I viral membrane fusion. Nat. Rev. Mol. Cell Biol. 2003, 4:309-319.
    • (2003) Nat. Rev. Mol. Cell Biol. , vol.4 , pp. 309-319
    • Colman, P.M.1    Lawrence, M.C.2
  • 6
    • 0036223198 scopus 로고    scopus 로고
    • Peptide and non-peptide HIV fusion inhibitors
    • Jiang S., Zhao Q., Debnath A.K. Peptide and non-peptide HIV fusion inhibitors. Curr. Pharm. Des. 2002, 8:563-580.
    • (2002) Curr. Pharm. Des. , vol.8 , pp. 563-580
    • Jiang, S.1    Zhao, Q.2    Debnath, A.K.3
  • 9
    • 0035701421 scopus 로고    scopus 로고
    • A potent cross-clade neutralizing human monoclonal antibody against a novel epitope on gp41 of human immunodeficiency virus type 1
    • Stiegler G., Kunert R., Purtscher M., Wolbank S., Voglauer R., Steindl F., Katinger H. A potent cross-clade neutralizing human monoclonal antibody against a novel epitope on gp41 of human immunodeficiency virus type 1. AIDS Res. Hum. Retroviruses 2001, 17:1757-1765.
    • (2001) AIDS Res. Hum. Retroviruses , vol.17 , pp. 1757-1765
    • Stiegler, G.1    Kunert, R.2    Purtscher, M.3    Wolbank, S.4    Voglauer, R.5    Steindl, F.6    Katinger, H.7
  • 11
    • 8844228894 scopus 로고    scopus 로고
    • HIV fusion inhibitor peptide T-1249 is able to insert or adsorb to lipidic bilayers. Putative correlation with improved efficiency
    • Veiga A.S., Santos N.C., Loura L.M.S., Fedorov A., Castanho M.A. HIV fusion inhibitor peptide T-1249 is able to insert or adsorb to lipidic bilayers. Putative correlation with improved efficiency. J. Am. Chem. Soc. 2004, 126:14758-14763.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 14758-14763
    • Veiga, A.S.1    Santos, N.C.2    Loura, L.M.S.3    Fedorov, A.4    Castanho, M.A.5
  • 12
    • 1642494594 scopus 로고    scopus 로고
    • Putative role of membranes in the HIV fusion inhibitor enfuvirtide mode of action at the molecular level
    • Veiga S., Henriques S., Santos N.C., Castanho M. Putative role of membranes in the HIV fusion inhibitor enfuvirtide mode of action at the molecular level. Biochem. J. 2004, 377:107-110.
    • (2004) Biochem. J. , vol.377 , pp. 107-110
    • Veiga, S.1    Henriques, S.2    Santos, N.C.3    Castanho, M.4
  • 13
    • 0037230970 scopus 로고    scopus 로고
    • Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation
    • Wang T., Wade R.C. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins: Struct. Funct. Bioinf. 2003, 50:158-169.
    • (2003) Proteins: Struct. Funct. Bioinf. , vol.50 , pp. 158-169
    • Wang, T.1    Wade, R.C.2
  • 14
    • 0036234027 scopus 로고    scopus 로고
    • Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water
    • Xia B., Tsui B., Case D., Dyson H., Wright P. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water. J. Biomol. 2002, 22:317-331.
    • (2002) J. Biomol. , vol.22 , pp. 317-331
    • Xia, B.1    Tsui, B.2    Case, D.3    Dyson, H.4    Wright, P.5
  • 15
    • 84961985307 scopus 로고    scopus 로고
    • Development of a Generalized Born model parameterization for proteins and nucleic acids
    • Dominy B., Brooks C.L. Development of a Generalized Born model parameterization for proteins and nucleic acids. J. Phys. Chem. 1999, 103:3765-3773.
    • (1999) J. Phys. Chem. , vol.103 , pp. 3765-3773
    • Dominy, B.1    Brooks, C.L.2
  • 16
    • 84555164130 scopus 로고    scopus 로고
    • Protein molecular dynamics with the generalized Born/ACE solvent model
    • Calimet N., Schaefer M., Simonson T. Protein molecular dynamics with the generalized Born/ACE solvent model. J. Mol. Graph. Model. 2001, 19:136-145.
    • (2001) J. Mol. Graph. Model. , vol.19 , pp. 136-145
    • Calimet, N.1    Schaefer, M.2    Simonson, T.3
  • 17
    • 0025283002 scopus 로고
    • Electrostatic interactions in macromolecules: theory and applications
    • Sharp K.A., Honig B. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 1990, 19:301-332.
    • (1990) Annu. Rev. Biophys. Biophys. Chem. , vol.19 , pp. 301-332
    • Sharp, K.A.1    Honig, B.2
  • 18
    • 38549181424 scopus 로고    scopus 로고
    • Development of a heterogeneous dielectric generalized Born model for the implicit modeling of membrane environments
    • Royal Society of Chemistry, Cambridge, UK, K. Naidoo (Ed.)
    • Feig M., Tanizaki S. Development of a heterogeneous dielectric generalized Born model for the implicit modeling of membrane environments. Modelling Molecular Structure and Reactivity in Biological Systems 2006, 141-150. Royal Society of Chemistry, Cambridge, UK. K. Naidoo (Ed.).
    • (2006) Modelling Molecular Structure and Reactivity in Biological Systems , pp. 141-150
    • Feig, M.1    Tanizaki, S.2
  • 19
    • 0036708447 scopus 로고    scopus 로고
    • Bridging implicit and explicit solvent approaches for membrane electrostatics
    • Lin J.-H., Baker N.A., McCammon J.A. Bridging implicit and explicit solvent approaches for membrane electrostatics. Biophys. J. 2002, 83:1374-1379.
    • (2002) Biophys. J. , vol.83 , pp. 1374-1379
    • Lin, J.-H.1    Baker, N.A.2    McCammon, J.A.3
  • 20
    • 0030735981 scopus 로고    scopus 로고
    • Influence of the membrane potential on the free energy of an intrinsic protein
    • Roux B. Influence of the membrane potential on the free energy of an intrinsic protein. Biophys. J. 1997, 73:2980-2989.
    • (1997) Biophys. J. , vol.73 , pp. 2980-2989
    • Roux, B.1
  • 21
    • 0032536194 scopus 로고    scopus 로고
    • Group additive contributions to the alcohol-induced alpha-helix formation of melittin: implication for the mechanism of the alcohol effects on proteins
    • Hirota N., Mizuno K., Goto Y. Group additive contributions to the alcohol-induced alpha-helix formation of melittin: implication for the mechanism of the alcohol effects on proteins. J. Mol. Biol. 1998, 275:365-378.
    • (1998) J. Mol. Biol. , vol.275 , pp. 365-378
    • Hirota, N.1    Mizuno, K.2    Goto, Y.3
  • 22
    • 0033595582 scopus 로고    scopus 로고
    • Clustering of fluorine-substituted alcohols as a factor responsible for their marked effects on proteins and peptides
    • Hong D., Hoshino M., Kuboi R., Goto Y. Clustering of fluorine-substituted alcohols as a factor responsible for their marked effects on proteins and peptides. J. Am. Chem. Soc. 1999, 121:8427-8433.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 8427-8433
    • Hong, D.1    Hoshino, M.2    Kuboi, R.3    Goto, Y.4
  • 23
    • 0842333152 scopus 로고    scopus 로고
    • Implicit solvation based on generalized Born theory in different dielectric environments
    • Feig M., Im W., Brooks C.L. Implicit solvation based on generalized Born theory in different dielectric environments. J. Chem. Phys. 2004, 120:903-911.
    • (2004) J. Chem. Phys. , vol.120 , pp. 903-911
    • Feig, M.1    Im, W.2    Brooks, C.L.3
  • 24
    • 22944441922 scopus 로고    scopus 로고
    • Incorporating variable dielectric environments into the generalized Born model
    • Sigalov G., Scheffel P., Onufriev A. Incorporating variable dielectric environments into the generalized Born model. J. Chem. Phys. 2005, 122:94511-94515.
    • (2005) J. Chem. Phys. , vol.122 , pp. 94511-94515
    • Sigalov, G.1    Scheffel, P.2    Onufriev, A.3
  • 25
    • 1842479952 scopus 로고    scopus 로고
    • Exploring protein native states and large-scale conformational changes with a modified generalized Born model
    • Onufriev A., Bashford D., Case D.A. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins: Struct. Funct. Bioinf. 2004, 55:383-394.
    • (2004) Proteins: Struct. Funct. Bioinf. , vol.55 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 26
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still W.C., Tempczyk A., Hawley R.C., Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 1990, 12:6127-6129.
    • (1990) J. Am. Chem. Soc. , vol.12 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 27
    • 41949100049 scopus 로고    scopus 로고
    • Recent advances in implicit solvent based methods for biomolecular simulations
    • Chen J., Brooks C.L., Khandogin J. Recent advances in implicit solvent based methods for biomolecular simulations. Curr. Opin. Struct. Biol. 2008, 18:140-148.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 140-148
    • Chen, J.1    Brooks, C.L.2    Khandogin, J.3
  • 28
    • 0002098417 scopus 로고    scopus 로고
    • The development/application of a 'minimalist' organic/biochemical molecular mechanics force field using a combination of ab initio calculations and experimental data
    • Kollman P.A., Dixon R., Cornell W., Fox T., Chipot C., Pohorille A. The development/application of a 'minimalist' organic/biochemical molecular mechanics force field using a combination of ab initio calculations and experimental data. Comp. Simul. Biomol. Syst. 1997, 3:83-96.
    • (1997) Comp. Simul. Biomol. Syst. , vol.3 , pp. 83-96
    • Kollman, P.A.1    Dixon, R.2    Cornell, W.3    Fox, T.4    Chipot, C.5    Pohorille, A.6
  • 29
    • 0141704162 scopus 로고    scopus 로고
    • Free energy landscape of protein folding in water: explicit vs. implicit solvent
    • Zhou R. Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins: Struct. Funct. Bioinf. 2003, 53:148-161.
    • (2003) Proteins: Struct. Funct. Bioinf. , vol.53 , pp. 148-161
    • Zhou, R.1
  • 30
    • 33847723384 scopus 로고    scopus 로고
    • Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit salvation
    • Roe D.R., Okur A., Wickstrom L., Hornak V., Simmerling C. Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit salvation. J. Phys. Chem. B 2007, 111:1846-1857.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 1846-1857
    • Roe, D.R.1    Okur, A.2    Wickstrom, L.3    Hornak, V.4    Simmerling, C.5
  • 31
    • 46749105987 scopus 로고    scopus 로고
    • A test on peptide stability of AMBER force fields with implicit salvation
    • Shell M.S., Ritterson R., Dill K.A. A test on peptide stability of AMBER force fields with implicit salvation. J. Phys. Chem. B 2008, 11:26878-26886.
    • (2008) J. Phys. Chem. B , vol.11 , pp. 26878-26886
    • Shell, M.S.1    Ritterson, R.2    Dill, K.A.3
  • 32
    • 84555200133 scopus 로고    scopus 로고
    • LaFargaCPL: CLASTERIT: Project Info.
    • LaFargaCPL: CLASTERIT: Project Info, http://devel.cpl.upc.edu/clasterit.
  • 33
    • 9244219576 scopus 로고    scopus 로고
    • Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics
    • Corcho F., Canto J., Perez J.J. Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics. J. Comp. Chem. 2004, 25:1937-1952.
    • (2004) J. Comp. Chem. , vol.25 , pp. 1937-1952
    • Corcho, F.1    Canto, J.2    Perez, J.J.3
  • 35
    • 84952104504 scopus 로고
    • An analysis of the accuracy of Langevin and molecular-dynamics algorithms
    • Pastor R.W., Brooks B.R., Szabo A. An analysis of the accuracy of Langevin and molecular-dynamics algorithms. Mol. Phys. 1988, 65:1409-1419.
    • (1988) Mol. Phys. , vol.65 , pp. 1409-1419
    • Pastor, R.W.1    Brooks, B.R.2    Szabo, A.3
  • 36
    • 84944178665 scopus 로고
    • Hierarchical grouping to optimize an objective function
    • Jr Ward J.H. Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc. 1963, 58:236-244.
    • (1963) J. Am. Stat. Assoc. , vol.58 , pp. 236-244
    • Jr Ward, J.H.1
  • 37
    • 0017435119 scopus 로고
    • Conformational analysis of 20 naturally occurring amino-acid residues using ECEPP
    • Zimmerman S.S., Pottle M.S., Nemethy G., Scheraga H.A. Conformational analysis of 20 naturally occurring amino-acid residues using ECEPP. Macromolecules 1977, 10:1-9.
    • (1977) Macromolecules , vol.10 , pp. 1-9
    • Zimmerman, S.S.1    Pottle, M.S.2    Nemethy, G.3    Scheraga, H.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.