Primary Citation PubMed: 15115397
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Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design.
(2008) Nucleic Acids Res 36
PubMed: 18676450 | PubMedCentral: PMC2528191 | DOI: 10.1093/nar/gkn464
( B ) Typical 1B1-RT/NNRTI residues involved in crystal packing (pdb code: 1S9E).
Publication Year: 2008
Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering.
(2014) J Chem Theory Comput 10
PubMed: 24803853 | PubMedCentral: PMC3985685 | DOI: 10.1021/ct400989x
21 , 22 , 24 , 26 Briefly, the initial coordinates of the complexes were identical to those used in Bollini et al., 26 being constructed from the 1S9E PDB file 27 using the MCPRO ( 17 ) and BOMB ( 1 )... software.
Publication Year: 2014
PubMed ID is not available.
Published in 2015
Additional time-dependent molecular dynamics simulations of the isolated fingers/palm domains starting from a structure that includes palm loop residues 219–230 (1S9E, green), the p51∆... L monomer in which palm loop residues from the 1DLO p66 subunit have been added back (4KSE, red), or the p51∆PL monomer taken to include the first 236 residues (corresponding to residues 1–249, since the construct is missing residues 219–230) (4KSE, black).
( B ) Ribbon diagram of the RT heterodimer structure (pdb: 1S9E, Das et al., 2004 ).
Das K , Clark AD , Lewi PJ , Heeres J , De Jonge MR , Koymans LM , Vinkers HM , Daeyaert F , Ludovici DW , Kukla MJ , De Corte B , Kavash RW , Ho CY , Ye H , Lichtenstein MA , Andries K , Pauwels R , Boyer PL , Clark P , Hughes SH , Janssen PA , Arnold E , 2004 , Crystal structure of HIV-1 reverse transcriptase (RT) in complex with Janssen-R129385 , http://www.rcsb.org/pdb/explore/explore.do?structureId=1S9E , Publicly available at RCSB Protein Data Bank (1S9E).
Analogous simulations starting with the monomer structure (pdb: 4KSE) or with the p51 subunit of an RT-inhibitor complex containing the missing loop residues (pdb: 1S9E) produced qualitatively similar results, with the most significant variation related to the time at which the transition to the more extended conformation occurs ( Figure 3—figure supplement 1 ).
Similar calculations were also performed starting with a p51 subunit of a structure that included the palm loop residues, pdb: 1S9E ( Das et al., 2004 ), and starting with the monomer, pdb: 4KSE ( Zheng et al., 2014 ).
Publication Year: 2015
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