title: Conformational freedom in tight binding enzymatic transition-state analogues.
abstract: Transition-state analogues of bacterial 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases (MTANs) disrupt quorum-sensing pathways in Escherichia coli and Vibrio cholerae, demonstrating the potential to limit pathogenicity without placing bacteria under intense selective pressure that leads to antibiotic resistance. Despite the similarity of the crystal structures of E. coli MTAN (EcMTAN) and V. cholerae MTAN (VcMTAN) bound to DADMe-Immucillin-A transition-state (TS) analogues, EcMTAN demonstrates femtomolar affinity for BuT-DADMe-Immucillin-A (BDIA) whereas VcMTAN possesses only picomolar affinity. Protein dynamic interactions are therefore implicated in this inhibitor affinity difference. We conducted molecular dynamics simulations of both EcMTAN and VcMTAN in complex with BDIA to explore differences in protein dynamic architecture. Simulations revealed that electrostatic and hydrophobic interactions with BDIA are similar for both enzymes and thus unlikely to account for the difference in inhibitor affinity. The EcMTAN-BDIA complex reveals a greater flexibility and conformational freedom of catalytically important atoms. We propose that conserved motions related to the EcMTAN transition state correlate with the increased affinity of BDIA for EcMTAN. Transition-state analogues permitting protein motion related to formation of the transition state are better mimics of the enzymatic transition state and can bind more tightly than those immobilizing catalytic site dynamics.
authors.affiliation: Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Motley
authors.forename: Vern L
authors.initials: VL
authors.lastname: Schramm
authors.forename: Steven D
authors.initials: SD
authors.lastname: Schwartz
mesh_terms: D000225:Adenine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D000241:Adenosine / Q000031:analogs & derivatives; D001419:Bacteria / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D020134:Catalytic Domain; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D009699:N-Glycosyl Hydrolases / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011759:Pyrrolidines / Q000737:chemistry / Q000378:metabolism; D014734:Vibrio cholerae / Q000201:enzymology*
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D011759:Pyrrolidines; D009699:N-Glycosyl Hydrolases; C505576:5'-methylthioadenosine nucleosidase, E coli; D000225:Adenine; D000241:Adenosine; C517546:galidesivir
references.citation: Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12253-8
references.pmid: 17640885
references.citation: J Am Chem Soc. 2004 Dec 8;126(48):15720-9
references.pmid: 15571394
references.citation: Biochemistry. 2012 Sep 4;51(35):6892-4
references.pmid: 22891633
references.citation: J Biol Chem. 2005 May 6;280(18):18265-73
references.pmid: 15749708
references.citation: Biochemistry. 2005 Sep 6;44(35):11647-59
references.pmid: 16128565
references.citation: J Phys Chem B. 2010 Dec 16;114(49):16263-72
references.pmid: 20936808
references.citation: Nat Chem Biol. 2009 Apr;5(4):251-7
references.pmid: 19270684
references.citation: J Comput Chem. 2010 Mar;31(4):671-90
references.pmid: 19575467
references.citation: Protein Sci. 1998 Mar;7(3):649-66
references.pmid: 9541397
references.citation: J Comput Chem. 2009 Jul 30;30(10):1545-614
references.pmid: 19444816
references.citation: ACS Chem Biol. 2007 Nov 20;2(11):725-34
references.pmid: 18030989
references.citation: Nat Chem Biol. 2009 Aug;5(8):543-50
references.pmid: 19620995
references.citation: Biochemistry. 2004 Jan 13;43(1):9-18
references.pmid: 14705926
references.citation: Arch Biochem Biophys. 2005 Jan 1;433(1):13-26
references.pmid: 15581562
references.citation: Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16543-8
references.pmid: 18946041
references.citation: Nature. 1969 Aug 16;223(5207):704-5
references.pmid: 4979456
references.citation: J Biol Chem. 2005 May 6;280(18):18274-82
references.pmid: 15746096
references.citation: FEBS J. 2008 Jan;275(1):1-21
references.pmid: 18034855