User:Yuan-Ping Pang/Sandbox 1: Difference between revisions

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[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]
[http://www.proteopedia.org/wiki/images/2/22/Hab1.pdb Download the coordinates of Model 1 (Hab1.pdb, PDB format)]


[http://www.proteopedia.org/wiki/index.php/Image:Hab2.pdb Download the coordinates of Model 2 (Hab2.pdb, PDB format)]
[http://www.proteopedia.org/wiki/images/f/f7/Hab2.pdb Download the coordinates of Model 2 (Hab2.pdb, PDB format)]


[http://www.proteopedia.org/wiki/index.php/Image:Hab3.pdb Download the coordinates of Model 3 (Hab3.pdb, PDB format)]
[http://www.proteopedia.org/wiki/index.php/Image:Hab3.pdb Download the coordinates of Model 3 (Hab3.pdb, PDB format)]

Revision as of 03:52, 10 March 2010

Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.


Model: Botulinum Neurotoxin Serotype A Endopeptidase Liganded with a Small-Molecule Inhibitor HAB

Botulinum neurotoxin serotype A (BoNTA) causes botulism[1][2]. Small-molecule inhibitors of BoNTA endopeptidase (BoNTAe) are sought in our laboratories as potential antidotes to antagonize the extracellular or intracellular BoNTA[3][4][5]. HAB is one such inhibitor that exhibits nanomolar potency in inhibiting BoNTAe (to be published). Multiple molecular dynamics simulations of HAB•BoNTAe (20 10-ns-long simulations) suggest that one functional group of HAB is highly flexible or intrinsically disordered; the percentages of the top three most-populated conformations of the complex (Models 1-3) are 21%, 13% and 12%, respectively. To evaluate the computational methods, the coordinates of the three models were released before the forthcoming crystal structure of HAB•BoNTAe. Only 33% of the heavy atoms of HAB are provided in the released models[6]. The full structure of HAB will be released upon manuscript acceptance[7].

Download the coordinates of Model 1 (Hab1.pdb, PDB format)

Download the coordinates of Model 2 (Hab2.pdb, PDB format)

Download the coordinates of Model 3 (Hab3.pdb, PDB format)

References & Notes

  1. ↑ Botulism in the United States - a clinical and epidemiologic review, Ann Intern Med 129:221-228 (1998)
  2. ↑ Botulinum toxin as a biological weapon: medical and public health management, JAMA 285:1059-1070 (2001)
  3. ↑ Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, Bioorg Med Chem 14:395-408 (2006) reprint
  4. ↑ Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A, PLoS ONE 2:e761 (2007) reprint
  5. ↑ Potent new small-molecule inhibitor of botulinum neurotoxin serotype A endopeptidase developed by synthesis-based computer-aided molecular design, PLoS ONE 4:e7730 (2009) reprint
  6. ↑ The models of HAB•BoNTAe were released at Mayo Research Protein Structure Prediction on March 5, 2010.
  7. ↑ This author thanks Professor Joel L. Sussman and his colleagues for their creation and maintenance of PROTEOPEDIA that permits archiving computational models of macromolecular structures and assessment of protein structure prediction made prior to experimental structures.
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