title: Conformational variability of organophosphorus hydrolase upon soman and paraoxon binding.
abstract: The bacterial enzyme organophosphorus hydrolase (OPH) exhibits both catalytic and substrate promiscuity. It hydrolyzes bonds in a variety of phosphotriester (P-O), phosphonothioate (P-S), phosphofluoridate (P-F), and phosphonocyanate (F-CN) compounds. However, its catalytic efficiency varies markedly for different substrates, limiting the broad-range application of OPH as catalyst in the bioremediation of pesticides and chemical war agents. In the present study, pK(a) calculations and multiple explicit-solvent molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of OPH bound to two substrates hydrolyzed with very distinct catalytic efficiencies: the nerve agent soman (O-pinacolylmethylphosphonofluoridate) and the pesticide paraoxon (diethyl p-nitrophenyl phosphate). pK(a) calculations for the substrate-bound and unbound enzyme showed a significant pK(a) shift from standard values (ΔpK(a) = ±3 units) for residues His254 and Arg275. MD simulations of protonated His254 revealed a dynamic hydrogen bond network connecting the catalytic residue Asp301 via His254 to Asp232, Asp233, Arg275, and Asp235, and is consistent with a previously postulated proton relay mechanism to ferry protons away from the active site with substrates that do not require activation of the leaving group. Hydrogen bonds between Asp301 and His254 were persistent in the OPH-paraoxon complex but not in the OPH-soman one, suggesting a potential role for such interaction in the more efficient hydrolysis of paraoxon over soman by OPH. These results are in line with previous mutational studies of residue His254, which led to an increase of the catalytic efficiency of OPH over soman yet decreased its efficiency for paraoxon. In addition, comparative analysis of the molecular trajectories for OPH bound to soman and paraoxon suggests that binding of the latter facilitates the conformational transition of OPH from the open to the closed substate promoting a tighter binding of paraoxon.
authors.affiliation: Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21949-900, Brazil.
authors.forename: Diego E B
authors.initials: DE
authors.lastname: Gomes
authors.forename: Roberto D
authors.initials: RD
authors.lastname: Lins
authors.forename: Pedro G
authors.initials: PG
authors.lastname: Pascutti
authors.forename: Chenghong
authors.initials: C
authors.lastname: Lei
authors.forename: Thereza A
authors.initials: TA
authors.lastname: Soares
mesh_terms: D043303:Aryldialkylphosphatase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001419:Bacteria / Q000201:enzymology; D006860:Hydrogen Bonding; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009154:Mutation; D010261:Paraoxon / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D012999:Soman / Q000737:chemistry / Q000378:metabolism*
chemical_list: D012999:Soman; D043303:Aryldialkylphosphatase; D010261:Paraoxon
references.citation: J Chem Theory Comput. 2008 Mar;4(3):435-47
references.pmid: 26620784
references.citation: Nanotechnology. 2008 Mar 26;19(12):125102
references.pmid: 21817721
references.citation: Bioinformatics. 1998;14(6):523-8
references.pmid: 9694991
references.citation: J Am Chem Soc. 2003 Jul 30;125(30):8990-1
references.pmid: 15369336
references.citation: J Biol Chem. 1992 Jul 5;267(19):13278-83
references.pmid: 1320014
references.citation: J Mol Biol. 2008 Feb 1;375(5):1189-96
references.pmid: 18082180
references.citation: J Phys Chem B. 2010 Jan 14;114(1):531-40
references.pmid: 19938866
references.citation: Curr Opin Struct Biol. 2011 Feb;21(1):62-7
references.pmid: 21109422
references.citation: Biochemistry. 2004 May 18;43(19):5707-15
references.pmid: 15134445
references.citation: Adv Enzymol Relat Areas Mol Biol. 2000;74:51-93
references.pmid: 10800593
references.citation: J Am Chem Soc. 2003 Jun 25;125(25):7526-7
references.pmid: 12812487
references.citation: Eur Biophys J. 2005 Jun;34(4):273-84
references.pmid: 15803330
references.citation: Nat Chem Biol. 2009 Nov;5(11):789-96
references.pmid: 19841628
references.citation: J Am Chem Soc. 2002 Sep 25;124(38):11242-3
references.pmid: 12236718
references.citation: Crit Care Clin. 1997 Oct;13(4):923-42
references.pmid: 9330846
references.citation: Annu Rev Biophys Biomol Struct. 2003;32:69-92
references.pmid: 12471064
references.citation: J Comput Chem. 2009 Nov 30;30(15):2388-401
references.pmid: 19353598
references.citation: Nature. 2004 Jul 29;430(6999):586-90
references.pmid: 15282609
references.citation: Biochemistry. 1989 May 30;28(11):4650-5
references.pmid: 2548585
references.citation: Biochemistry. 2001 Feb 6;40(5):1332-9
references.pmid: 11170460
references.citation: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references.pmid: 8744570
references.citation: Science. 2006 Sep 15;313(5793):1638-42
references.pmid: 16973882
references.citation: Biochem J. 2004 Jun 15;380(Pt 3):627-33
references.pmid: 15018612
references.citation: J Environ Qual. 2007 Jan 09;36(1):233-8
references.pmid: 17215231
references.citation: Biochemistry. 1991 Jul 30;30(30):7438-44
references.pmid: 1649628
references.citation: J Biol Chem. 1989 Nov 25;264(33):19659-65
references.pmid: 2555328
references.citation: Science. 2006 Sep 15;313(5793):1586-7
references.pmid: 16973868
references.citation: Neurology. 1992 May;42(5):946-50
references.pmid: 1315942
references.citation: Biochemistry. 1988 Mar 8;27(5):1591-7
references.pmid: 2835095
references.citation: Toxicol Appl Pharmacol. 1984 Jan;72(1):61-74
references.pmid: 6710485
references.citation: J Biomol NMR. 2004 Dec;30(4):407-22
references.pmid: 15630561
references.citation: Nature. 2005 Nov 3;438(7064):117-21
references.pmid: 16267559
references.citation: J Biochem Toxicol. 1988 Winter;3:235-59
references.pmid: 3236334
references.citation: Protein Eng Des Sel. 2008 Jun;21(6):405-12
references.pmid: 18434422
references.citation: Bioorg Med Chem. 2001 Aug;9(8):2083-91
references.pmid: 11504644
references.citation: Proteins. 2008 Nov 15;73(3):765-83
references.pmid: 18498103
references.citation: Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21631-6
references.pmid: 19966226
references.citation: Biochemistry. 1999 Mar 9;38(10):2866-72
references.pmid: 10074338
references.citation: Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12562-6
references.pmid: 12271136
references.citation: Biochemistry. 2001 Mar 6;40(9):2712-22
references.pmid: 11258882
references.citation: J Chem Theory Comput. 2007 Jul;3(4):1569-79
references.pmid: 26633227
references.citation: Biochemistry. 2001 Feb 6;40(5):1325-31
references.pmid: 11170459
references.citation: Biochemistry. 2007 Mar 20;46(11):3435-42
references.pmid: 17315951
references.citation: Curr Opin Struct Biol. 2009 Feb;19(1):31-8
references.pmid: 19157855
references.citation: Front Biosci. 2004 May 01;9:1082-99
references.pmid: 14977531
references.citation: Science. 2011 Apr 8;332(6026):234-8
references.pmid: 21474759
references.citation: Protein Sci. 2003 Feb;12(2):313-26
references.pmid: 12538895
references.citation: Biochem Biophys Res Commun. 2000 Dec 20;279(2):516-9
references.pmid: 11118318
references.citation: Phys Rev Lett. 2008 Jan 18;100(2):020603
references.pmid: 18232845
references.citation: Toxicol Sci. 1998 Jan;41(1):8-20
references.pmid: 9520337
references.citation: Biochemistry. 1993 Sep 7;32(35):9148-55
references.pmid: 8396425
references.citation: J Appl Toxicol. 1998 Nov-Dec;18(6):393-408
references.pmid: 9840747
references.citation: Curr Opin Microbiol. 2002 Jun;5(3):288-95
references.pmid: 12057683
references.citation: Experientia. 1990 Jul 15;46(7):729-31
references.pmid: 2164956
references.citation: Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1373-8
references.pmid: 20080605
references.citation: Science. 2006 Apr 14;312(5771):224-8
references.pmid: 16614210
references.citation: Biochemistry. 2007 Nov 20;46(46):13352-69
references.pmid: 17966992
references.citation: Rev Neurol. 2004 Oct 16-31;39(8):739-47
references.pmid: 15514903
references.citation: J Biol Chem. 2000 Sep 29;275(39):30556-60
references.pmid: 10871616
references.citation: Annu Rev Biochem. 2006;75:519-41
references.pmid: 16756501