Skip to main content

Advertisement

SpringerLink
Log in

Molecular Dynamics Study on the Unbinding of HBY 097 in the K103N Mutant RT

  • Published:
Monatshefte für Chemie - Chemical Monthly Aims and scope Submit manuscript

Summary.

The structural rearrangement due to the unbinding of HBY 097 in K103N mutant HIV-1 reverse transcriptase (RT) was studied using two nanosecond molecular dynamics simulations. The simulations showed the dynamics of an open or upright position of the p66 thumb subdomain moving to a closed configuration together with the dynamic correction of protein residues around the non-nucleoside inhibitor binding pocket (NNIBP) and its putative entrance.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • LA Kohlstaedt J Wang JM Friedman PA Rice TA Steitz (1992) Science 256 1783 Occurrence Handle10.1126/science.1377403 Occurrence Handle1:CAS:528:DyaK38Xls1Kmur8%3D

    Article  CAS  Google Scholar 

  • A Jacobo-Molina AD Clark SuffixJr RL Williams RG Nanni P Clark AL Ferris SH Hughes E Arnold (1991) Proc Natl Acad Sci USA 88 10895 Occurrence Handle10.1073/pnas.88.23.10895 Occurrence Handle1:CAS:528:DyaK38XitlSltbg%3D

    Article  CAS  Google Scholar 

  • C Tantillo J Ding A Jacobo-Molina RG Nanni BL Boyer SH Hughes R Pauwels K Andries PA Janssen E Arnold (1994) J Mol Biol 243 369 Occurrence Handle10.1006/jmbi.1994.1665 Occurrence Handle1:CAS:528:DyaK2cXmvFWrt7k%3D

    Article  CAS  Google Scholar 

  • J Ding K Das C Tantillo W Zhang AD Clark SuffixJr S Jessen X Lu Y Hsiou A Jacobo-Molina K Andries R Pauwels H Moereels L Koymans PAJ Janssen RH Smith SuffixJr Koepke M Kroeger CJ Michejda SH Hughes E Arnold (1995) Structure 3 365 Occurrence Handle10.1016/S0969-2126(01)00168-X Occurrence Handle1:CAS:528:DyaK2MXltFGju70%3D

    Article  CAS  Google Scholar 

  • DW Rodgers SJ Gamblin BA Harris S Ray JS Culp B Hellmig DJ Woolf C Debouck SC Harrison (1995) Proc Natl Acad Sci USA 92 1222 Occurrence Handle10.1073/pnas.92.4.1222 Occurrence Handle1:CAS:528:DyaK2MXjslegsbY%3D

    Article  CAS  Google Scholar 

  • HM Bermann J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne (2000) Nucleic Acids Res 28 235 Occurrence Handle10.1093/nar/28.1.235

    Article  Google Scholar 

  • J Ding K Das H Moereels L Koymans K Andries PA Janssen SH Hughes E Arnold (1995) Nat Struct Biol 2 407 Occurrence Handle10.1038/nsb0595-407 Occurrence Handle1:CAS:528:DyaK2MXlsFKltrY%3D

    Article  CAS  Google Scholar 

  • J Wang SJ Smerdon J Jager LA Kohlstaedt PA Rice JM Friedman TA Steitz (1994) Proc Natl Acad Sci USA 91 7242 Occurrence Handle10.1073/pnas.91.15.7242 Occurrence Handle1:CAS:528:DyaK2cXlvF2gur0%3D

    Article  CAS  Google Scholar 

  • J Ren RM Esnouf E Garman D Somers C Ross I Kirby J Keeling G Darby Y Jones D Stuart D Stammers (1995) Nat Struct Biol 2 293 Occurrence Handle10.1038/nsb0495-293 Occurrence Handle1:CAS:528:DyaK2MXkvVKmtLk%3D

    Article  CAS  Google Scholar 

  • K Das J Ding Y Hsiou AD Clark SuffixJr H Moereels L Koymans K Andries R Pauwels PA Janssen PL Boyer P Clark RH Smith SuffixJr Smith MB Kroeger CJ Michejda SH Hughes E Arnold (1996) J Mol Biol 264 1085 Occurrence Handle10.1006/jmbi.1996.0698 Occurrence Handle1:CAS:528:DyaK2sXmvVyr

    Article  CAS  Google Scholar 

  • Y Hsiou J Ding K Das AD Clark SuffixJr SH Hughes E Arnold (1996) Structure 4 853 Occurrence Handle10.1016/S0969-2126(96)00091-3 Occurrence Handle1:CAS:528:DyaK28Xks1Sgsrs%3D

    Article  CAS  Google Scholar 

  • Y Hsiou J Ding K Das AD Clark SuffixJr PL Boyer P Lewi PA Janssen JP Kleim M Rosner SH Hughes E Arnold (2001) J Mol Biol 309 437 Occurrence Handle10.1006/jmbi.2001.4648 Occurrence Handle1:CAS:528:DC%2BD3MXjslansro%3D

    Article  CAS  Google Scholar 

  • JA Mc Cammon BR Gelin M Karplus (1977) Nature 267 585 Occurrence Handle10.1038/267585a0 Occurrence Handle1:CAS:528:DyaE2sXlsVOgsbg%3D

    Article  CAS  Google Scholar 

  • Y Duan PA Kollman (1998) Science 282 740 Occurrence Handle10.1126/science.282.5389.740 Occurrence Handle1:CAS:528:DyaK1cXmvFOqtb0%3D

    Article  CAS  Google Scholar 

  • T Hansson C Oostenbrink WF van Gunsteren (2002) Curr Opin Struc Biol 12 190 Occurrence Handle10.1016/S0959-440X(02)00308-1 Occurrence Handle1:CAS:528:DC%2BD38XivVals7o%3D

    Article  CAS  Google Scholar 

  • MAL Eriksson J Pitera PA Kollman (1999) J Med Chem 42 868 Occurrence Handle10.1021/jm980277y Occurrence Handle1:CAS:528:DyaK1MXhs1WnsL0%3D

    Article  CAS  Google Scholar 

  • P Weinzinger S Hannongbua P Wolschann (2005) J Enzym Inhib Med Chem 20 129 Occurrence Handle10.1080/14756360400020520 Occurrence Handle1:CAS:528:DC%2BD2MXjvVOksbs%3D

    Article  CAS  Google Scholar 

  • J Wang P Morin W Wang PA Kollman (2001) J Med Chem 123 5221 Occurrence Handle1:CAS:528:DC%2BD3MXjtlyqtrc%3D

    CAS  Google Scholar 

  • L Shen J Shen X Luo F Cheng Y Xu K Chen E Arnold J Ding H Jiang (2003) Biophys J 84 3547 Occurrence Handle1:CAS:528:DC%2BD3sXksVKgu7g%3D Occurrence Handle10.1016/S0006-3495(03)75088-7

    Article  CAS  Google Scholar 

  • Z Zhou M Madrid JD Evanseck JD Madura (2005) J Am Chem Soc 127 17253 Occurrence Handle10.1021/ja053973d Occurrence Handle1:CAS:528:DC%2BD2MXht1WltL7I

    Article  CAS  Google Scholar 

  • RH Smith SuffixJr WL Jorgensen J Tirado-Rives ML Lamb PAJ Janssen CJ Michejda MBK Smith (1998) J Med Chem 41 5272 Occurrence Handle10.1021/jm9804174 Occurrence Handle1:CAS:528:DyaK1cXnsFKnsbk%3D

    Article  CAS  Google Scholar 

  • J Ding K Das Y Hsiou SG Sarafianos AD Clark SuffixJr A Jacobo-Molina C Tantillo SH Hughes E Arnold (1998) J Mol Biol 284 1095 Occurrence Handle10.1006/jmbi.1998.2208 Occurrence Handle1:CAS:528:DyaK1MXivFCiuw%3D%3D

    Article  CAS  Google Scholar 

  • VW Byrnes EA Emini WA Schleif JH Condra CL Schneider WJ Long JA Wolfgang DJ Graham L Gotlib AJ Schlabach BS Wolanski OM Blahy JC Quintero A Rhodes E Roth DL Titus VV Sardana (1994) Antimicrob Agents Chemother 38 1404 Occurrence Handle1:CAS:528:DyaK2cXlt1ClsbY%3D

    CAS  Google Scholar 

  • DD Richman (1993) Antimicrob Agents Chemother 37 1207 Occurrence Handle1:CAS:528:DyaK3sXks1aht7Y%3D

    CAS  Google Scholar 

  • E de Clercq (1998) Antiviral Research 38 153 Occurrence Handle10.1016/S0166-3542(98)00025-4 Occurrence Handle1:CAS:528:DyaK1cXksVyrsr4%3D

    Article  CAS  Google Scholar 

  • H Rübsamen-Waigmann E Huguenel A Shah A Paessens HJ Ruoff H von Briesen A Immelmann U Dietrich MA Wainberg (1999) Antiviral Research 42 15 Occurrence Handle10.1016/S0166-3542(99)00010-8

    Article  Google Scholar 

  • JP Kleim M Winters A Dunkler JR Suarez G Riess I Winkler J Balzarini D Oette TC Merigan (1999) J Infect Dis 179 709 Occurrence Handle10.1086/314633 Occurrence Handle1:CAS:528:DyaK1MXhvVKktrk%3D

    Article  CAS  Google Scholar 

  • K Das SG Sarafianos AD Clark SuffixJr PL Boyer SH Hughes E Arnold (2007) J Mol Biol 365 77 Occurrence Handle10.1016/j.jmb.2006.08.097 Occurrence Handle1:CAS:528:DC%2BD28Xht1KnsrnI

    Article  CAS  Google Scholar 

  • Garner J, Deadman J, Rhodes D, Griffith R, Keller PA (2007) J Mol Graph Model (doi: 10.1016/j.jmgm.2006.11.004)

  • JP Kleim R Bender R Kirsch C Meichsner A Paessens M Rosner H Rubsamen-Waigmann R Kaiser M Wichers KE Schneweis (1995) Antimicrob Agents Chemother 39 2253 Occurrence Handle1:CAS:528:DyaK2MXotlOgsrw%3D

    CAS  Google Scholar 

  • J Balzarini H Pelemans G Riess M Roesner I Winkler E de Clercq JP Kleim (1998) Biochem Pharmacol 55 617 Occurrence Handle10.1016/S0006-2952(97)00506-6 Occurrence Handle1:CAS:528:DyaK1cXnvVantw%3D%3D

    Article  CAS  Google Scholar 

  • Case DA, Pearlman DA, Caldwell JW, Cheatham III TE, Wang J, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Gohlke H, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner PK, Kollman PA (2002) AMBER7, University of California, San Francisco

  • Molecular Simulations Inc. (2000) WebLab ViewerPro 4.0, Molecular Simulations Inc., San Diego

Download references

Author information

Authors and Affiliations

  1. Department of Common and Graduate Studies, Sirindhorn International Institute of Technology (SIIT), Thammasat University, Pathum Thani, Thailand

    Luckhana Lawtrakul

  2. Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand

    Supa Hannongbua

Authors
  1. Luckhana Lawtrakul
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Supa Hannongbua
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Luckhana Lawtrakul.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lawtrakul, L., Hannongbua, S. Molecular Dynamics Study on the Unbinding of HBY 097 in the K103N Mutant RT . Monatsh. Chem. 138, 1029–1034 (2007). https://doi.org/10.1007/s00706-007-0704-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00706-007-0704-4

Search

Navigation