VX hydrolysis by human serum paraoxonase 1: A comparison of experimental and computational results

PLoS ONE

Volumn 6, Issue 5, 2011, Pages

  Peterson, Matthew W ^a,b   Fairchild, Steven Z ^a   Otto, Tamara C ^c   Mohtashemi, Mojdeh ^a,d   Cerasoli, Douglas M ^c   Chang, Wenling E ^a,e  

^a MITRE CORPORATION   (United States)

^b Boston University   (United States)

^c US ARMY MEDICAL RESEARCH INSTITUTE OF CHEMICAL DEFENSE   (United States)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^e GEORGE MASON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARYLDIALKYLPHOSPHATASE 1; ARYLDIALKYLPHOSPHATASE; METHYLPHOSPHONOTHIOIC ACID S (2 DIISOPROPYLAMINOETHYL) O ETHYL ESTER; PHOSPHOROTHIOIC ACID DERIVATIVE; PON1 PROTEIN, HUMAN;

ARTICLE; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME BLOOD LEVEL; ENZYME STRUCTURE; HUMAN; MATHEMATICAL ANALYSIS; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PHASE TRANSITION; PREDICTION; PROTEIN HYDROLYSIS; QUANTUM MECHANICS; REACTION ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HYDROLYSIS; METABOLISM;

ARYLDIALKYLPHOSPHATASE; HUMANS; HYDROLYSIS; MODELS, MOLECULAR; ORGANOTHIOPHOSPHORUS COMPOUNDS;

EID: 79957836444     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020335     Document Type: Article

References (32)

1. Newmark J, (2007) Nerve agents. Neurologist 13: 20-32.
2. Cannard K, (2006) The acute treatment of nerve agent exposure. J Neurol Sci 249: 86-94.
3. Mackness B, Mackness M, Aviram M, Paragh G, Yeung DT, et al. (2008) Human Paraoxonase I: A Potential Bioscavenger of Organophosphorus Nerve Agents. In: Ridley A, Frampton J, editors. The Paraoxonases: Their Role in Disease Development and Xenobiotic Metabolism: Springer Netherlands pp. 151-170.
4. Kuo CL, La Du BN, (1998) Calcium binding by human and rabbit serum paraoxonases. Structural stability and enzymatic activity. Drug Metab Dispos 26: 653-660.
5. Yeung DT, Lenz DE, Cerasoli DM, (2005) Analysis of active-site amino-acid residues of human serum paraoxonase using competitive substrates. FEBS J 272: 2225-2230.
6. Rochu D, Chabriere E, Masson P, (2007) Human paraoxonase: a promising approach for pre-treatment and therapy of organophosphorus poisoning. Toxicology 233: 47-59.
7. Draganov DI, Teiber JF, Speelman A, Osawa Y, Sunahara R, et al. (2005) Human paraoxonases (PON1, PON2, and PON3) are lactonases with overlapping and distinct substrate specificities. J Lipid Res 46: 1239-1247.
8. Khersonsky O, Tawfik DS, (2005) Structure-reactivity studies of serum paraoxonase PON1 suggest that its native activity is lactonase. Biochemistry 44: 6371-6382.
9. Josse D, Lockridge O, Xie W, Bartels CF, Schopfer LM, et al. (2001) The active site of human paraoxonase (PON1). J Appl Toxicol 21 (Suppl 1): S7-11.
10. Yeung DT, Josse D, Nicholson JD, Khanal A, McAndrew CW, et al. (2004) Structure/function analyses of human serum paraoxonase (HuPON1) mutants designed from a DFPase-like homology model. Biochim Biophys Acta 1702: 67-77.
11. Sanan TT, Muthukrishnan S, Beck JM, Tao P, Hayes CJ, et al. Computational modeling of human paraoxonase 1: preparation of protein models, binding studies, and mechanistic insights. Journal of Physical Organic Chemistry 23: 357-369.
12. Fairchild SZ, Peterson MW, Hamza A, Zhan CG, Cerasoli DM, et al. (2011) Computational characterization of how the VX nerve agent binds human serum paraoxonase 1. J Mol Model Jan;17 (1): 97-109. Epub 2010 Apr 9.
13. Hu X, Jiang X, Lenz DE, Cerasoli DM, Wallqvist A, (2009) In silico analyses of substrate interactions with human serum paraoxonase 1. Proteins 75: 486-498.
14. Harel M, Brumshtein B, Meged R, Dvir H, Ravelli RB, et al. (2007) 3-D structure of serum paraoxonase 1 sheds light on its activity, stability, solubility and crystallizability. Arh Hig Rada Toksikol 58: 347-353.
15. Khersonsky O, Tawfik DS, (2006) The histidine 115-histidine 134 dyad mediates the lactonase activity of mammalian serum paraoxonases. J Biol Chem 281: 7649-7656.
16. Otto TC, Harsch CK, Yeung DT, Magliery TJ, Cerasoli DM, et al. (2009) Dramatic differences in organophosphorus hydrolase activity between human and chimeric recombinant mammalian paraoxonase-1 enzymes. Biochemistry 48: 10416-10422.
17. Tantillo DJ, Houk KN, (2002) Transition state docking: a probe for noncovalent catalysis in biological systems. Application to antibody-catalyzed ester hydrolysis. J Comput Chem 23: 84-95.
18. Rydberg P, Hansen SM, Kongsted J, Norrby P-O, Olsen L, et al. (2008) Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450. Journal of Chemical Theory and Computation 4: 673-681.
19. Zhang Y, (2009) I-TASSER: fully automated protein structure prediction in CASP8. Proteins 77 (Suppl 9): 100-113.
20. Zhang Y, (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9: 40.
21. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, et al. (2005) The Amber biomolecular simulation programs. J Comput Chem 26: 1668-1688.
22. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, et al. (2007) Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci Chapter 2: Unit 2 9.
23. Morris GM, Huey R, Olson AJ, (2008) Using AutoDock for ligand-receptor docking. Curr Protoc Bioinformatics Chapter 8: Unit 8 14.
24. Wang Q, Canutescu AA, Dunbrack RL Jr, (2008) SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. Nat Protoc 3: 1832-1847.
25. Weininger D, (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. Journal of Chemical Information and Computer Sciences 28: 31-36.
26. Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, et al. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65: 712-725.
27. AutoDockTools. 4.2 ed.
28. Gasteiger J, Marsili M, (1980) Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron 36: 3219-3228.
29. Fersht AR, (1985) Enzyme Structure and Mechanism. San Francisco Freeman.
30. Otto TC, Kasten SA, Kovaleva E, Liu Z, Buchman G, et al. (2010) Purification and characterization of functional human paraoxonase-1 expressed in Trichoplusia ni larvae. Chem Biol Interact 187: 388-392.
31. Jaguar. 7.7 ed. Portland, OR Shrodinger.
32. Jorgensen WL, Maxwell DS, Tirado-Rives J, (1996) Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. Journal of the American Chemical Society 118: 11225-11236.