Molecular dynamics and ligand docking of a hinge region variant of South African HIV-1 subtype C protease
Tài liệu tham khảo
Joint United Nations Programme on HIV/AIDS (UNAIDS), 2016
Furfine, 1992, Two-step binding mechanism for HIV protease inhibitors, Biochemistry, 31, 7886, 10.1021/bi00149a020
Cullen, 1991, Human immunodeficiency virus as a prototypic complex retrovirus, J. Virol., 65, 1053, 10.1128/JVI.65.3.1053-1056.1991
Li, 1994, Inhibitors of HIV-1 transcription, Trends Microbiol., 2, 164, 10.1016/0966-842X(94)90666-1
Ali, 2010, Molecular basis for drug resistance in HIV-1 protease, Viruses, 2, 2509, 10.3390/v2112509
Wlodawer, 1998, Inhibitors of HIV-1 protease: a major success of structure-assisted drug design 1, Annu. Rev. Biophys. Biomol. Struct., 27, 249, 10.1146/annurev.biophys.27.1.249
Velázquez-Campoy, 2001, Catalytic efficiency and vitality of HIV-1 proteases from African viral subtypes, Proc. Natl. Acad. Sci. U. S. A., 98, 6062, 10.1073/pnas.111152698
Velazquez-Campoy, 2002, Amplification of the effects of drug resistance mutations by background polymorphisms in HIV-1 protease from African subtypes, Biochemistry, 41, 8613, 10.1021/bi020160i
Naicker, 2013, Structural insights into the South African HIV-1 subtype C protease: impact of hinge region dynamics and flap flexibility in drug resistance, J. Biomol. Struct. Dyn., 31, 1370, 10.1080/07391102.2012.736774
Gustchina, 1990, Comparison of inhibitor binding in HIV-1 protease and in non-viral aspartic proteases: the role of the flap, FEBS Lett., 269, 269, 10.1016/0014-5793(90)81171-J
Meiselbach, 2007, Insights into amprenavir resistance in E35D HIV-1 protease mutation from molecular dynamics and binding free-energy calculations, J. Mol. Model., 13, 297, 10.1007/s00894-006-0121-3
Liu, 2006, Mechanism of drug resistance revealed by the crystal structure of the unliganded HIV-1 protease with F53L mutation, J. Mol. Biol., 358, 1191, 10.1016/j.jmb.2006.02.076
Kuhn, 2014, Drug resistance among newly diagnosed HIV-infected children in the era of more efficacious antiretroviral prophylaxis, AIDS, 28, 1673, 10.1097/QAD.0000000000000261
Rhee, 2003, Human immunodeficiency virus reverse transcriptase and protease sequence database, Nucleic Acids Res., 31, 298, 10.1093/nar/gkg100
Kozisek, 2008, Ninety-nine is not enough: molecular characterization of inhibitor-resistant human immunodeficiency virus type 1 protease mutants with insertions in the flap region, J. Virol., 82, 5869, 10.1128/JVI.02325-07
Karthik, 2011, Dynamic flaps in HIV-1 protease adopt unique ordering at different stages in the catalytic cycle, Proteins Struct. Funct. Bioinf., 79, 1830, 10.1002/prot.23008
Hornak, 2006, HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations, Proc. Natl. Acad. Sci., 103, 915, 10.1073/pnas.0508452103
Trylska, 2007, HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics, Biophys. J., 92, 4179, 10.1529/biophysj.106.100560
Louis, 2011, The L76V drug resistance mutation decreases the dimer stability and rate of autoprocessing of HIV-1 protease by reducing internal hydrophobic contacts, Biochemistry, 50, 4786, 10.1021/bi200033z
Berman, 2000, The Protein Data Bank, Nucleic Acids Res., 28, 235, 10.1093/nar/28.1.235
Velazquez-Campoy, 2000, HIV-1 protease inhibitors: enthalpic versus entropic optimization of the binding affinity, Biochemistry, 39, 2201, 10.1021/bi992399d
Sievers, 2011, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol. Syst. Biol., 7, 539, 10.1038/msb.2011.75
Arnold, 2006, Structural bioinformatics The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling, 22, 195
Biasini, 2014, SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information, 42, 252
Laskowski, 1996, AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR, J. Biomol. NMR, 8, 477, 10.1007/BF00228148
Laskowski, 1993, PROCHECK: a program to check the stereochemical quality of protein structures, J. Appl. Crystallogr., 26, 283, 10.1107/S0021889892009944
Louis, 1991, Autoprocessing of the HIV-1 protease using purified wild-type and mutated fusion proteins expressed at high levels in Escherichia coli, Eur. J. Biochem., 199, 361, 10.1111/j.1432-1033.1991.tb16132.x
Abraham, 2015, GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers, SoftwareX, 1–2, 19, 10.1016/j.softx.2015.06.001
Lange, 2010, Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR Data, Biophys. J., 99, 647, 10.1016/j.bpj.2010.04.062
Hornak, 2006, Comparison of multiple amber force fields and development of improved protein backbone parameters, Proteins Struct. Funct. Genet., 65, 712, 10.1002/prot.21123
Darden, 1993, Particle mesh Ewald: an N⋅log(N) method for Ewald sums in large systems, J. Chem. Phys., 98, 10089, 10.1063/1.464397
Okumura, 2007, Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles, J. Chem. Phys., 126, 84103, 10.1063/1.2434972
Berendsen, 1995, GROMACS: a message-passing parallel molecular dynamics implementation, Comput. Phys. Commun., 91, 43, 10.1016/0010-4655(95)00042-E
Pettersen, 2004, UCSF Chimera-A visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084
Skjaerven, 2013, vol. 2014, 1
Grant, 2006, Bio3d: an R package for the comparative analysis of protein structures, Bioinformatics, 22, 2695, 10.1093/bioinformatics/btl461
Skjaerven, 2014, Integrating protein structural dynamics and evolutionary analysis with Bio3D, BMC Bioinf., 15, 399, 10.1186/s12859-014-0399-6
Klepeis, 2009, Long-timescale molecular dynamics simulations of protein structure and function, Curr. Opin. Struct. Biol., 19, 120, 10.1016/j.sbi.2009.03.004
Lobanov, 2008, Radius of gyration is indicator of compactness of protein structure, Mol. Biol. (Mosk.), 42, 701, 10.1134/S0026893308040195
Amadei, 1993, Essential dynamics of proteins, Proteins Struct. Funct. Genet., 17, 412, 10.1002/prot.340170408
Haider, 2008, Molecular dynamics and principal components analysis of human telomeric quadruplex multimers, Biophys. J., 95, 296, 10.1529/biophysj.107.120501
Perryman, 2004, HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs, Protein Sci., 13, 1108, 10.1110/ps.03468904
Scott, 2000, Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance, Structure, 8, 1259, 10.1016/S0969-2126(00)00537-2
Freedberg, 2002, Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations, Protein Sci., 11, 221, 10.1110/ps.33202
Kumar, 2002, Close-range electrostatic interactions in proteins, ChemBioChem, 3, 604, 10.1002/1439-7633(20020703)3:7<604::AID-CBIC604>3.0.CO;2-X
Huang, 2014, The role of select subtype polymorphisms on HIV-1 protease conformational sampling and dynamics, J. Biol. Chem., 289, 17203, 10.1074/jbc.M114.571836
Ahmed, 2013, Comparison of the molecular dynamics and calculated binding free energies for nine FDA-approved HIV-1 PR drugs against subtype B and C-SA HIV PR, Chem. Biol. Drug Des., 81, 208, 10.1111/cbdd.12063
Du, 2016, Insights into protein–ligand interactions: mechanisms, models, and methods, Int. J. Mol. Sci., 17, 144, 10.3390/ijms17020144
