title: Transition States and transition state analogue interactions with enzymes.
abstract: Enzymatic transition states have lifetimes of a few femtoseconds (fs). Computational analysis of enzyme motions leading to transition state formation suggests that local catalytic site motions on the fs time scale provide the mechanism to locate transition states. An experimental test of protein fs motion and its relation to transition state formation can be provided by isotopically heavy proteins. Heavy enzymes have predictable mass-altered bond vibration states without altered electrostatic properties, according to the Born-Oppenheimer approximation. On-enzyme chemistry is slowed in most heavy proteins, consistent with altered protein bond frequencies slowing the search for the transition state. In other heavy enzymes, structural changes involved in reactant binding and release are also influenced. Slow protein motions associated with substrate binding and catalytic site preorganization are essential to allow the subsequent fs motions to locate the transition state and to facilitate the efficient release of products. In the catalytically competent geometry, local groups move in stochastic atomic motion on the fs time scale, within transition state-accessible conformations created by slower protein motions. The fs time scale for the transition state motions does not permit thermodynamic equilibrium between the transition state and stable enzyme states. Isotopically heavy enzymes provide a diagnostic tool for fast coupled protein motions to transition state formation and mass-dependent conformational changes. The binding of transition state analogue inhibitors is the opposite in catalytic time scale to formation of the transition state but is related by similar geometries of the enzyme-transition state and enzyme-inhibitor interactions. While enzymatic transition states have lifetimes as short as 10(-15) s, transition state analogues can bind tightly to enzymes with release rates greater than 10(3) s. Tight-binding transition state analogues stabilize the rare but evolved enzymatic geometry to form the transition state. Evolution to efficient catalysis optimized this geometry and its stabilization by a transition state mimic results in tight binding. Release rates of transition state analogues are orders of magnitude slower than product release in normal catalytic function. During catalysis, product release is facilitated by altered chemistry. Compared to the weak associations found in Michaelis complexes, transition state analogues involve strong interactions related to those in the transition state. Optimum binding of transition state analogues occurs when the complex retains the system motions intrinsic to transition state formation. Conserved dynamic motion retains the entropic components of inhibitor complexes, improving the thermodynamics of analogue binding.
authors.affiliation: Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States.
authors.forename: Vern L
authors.initials: VL
authors.lastname: Schramm
mesh_terms: D055162:Biocatalysis; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008968:Molecular Conformation; D013816:Thermodynamics
chemical_list: D004798:Enzymes
references.citation: J Am Chem Soc. 2014 Jul 23;136(29):10349-60
references.pmid: 24977791
references.citation: Nature. 1969 Aug 16;223(5207):704-5
references.pmid: 4979456
references.citation: Top Curr Chem. 2013;337:189-208
references.pmid: 23508766
references.citation: Chem Biol. 2013 Feb 21;20(2):212-22
references.pmid: 23438750
references.citation: Biochem J. 2002 Jan 1;361(Pt 1):1-25
references.pmid: 11743878
references.citation: Mol Phys. 2012 May 10;110(9-10):531-536
references.pmid: 22942460
references.citation: Biochemistry. 2012 Aug 14;51(32):6476-86
references.pmid: 22775299
references.citation: Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):4805-12
references.pmid: 20212140
references.citation: Biochemistry. 2013 Mar 26;52(12):2012-20
references.pmid: 23240765
references.citation: J Phys Chem Lett. 2012 Dec 6;3(23):3538-3544
references.pmid: 24496053
references.citation: Curr Opin Chem Biol. 2014 Aug;21:11-8
references.pmid: 24709164
references.citation: J Am Chem Soc. 2012 Jan 25;134(3):1468-70
references.pmid: 22239413
references.citation: Proc Natl Acad Sci U S A. 2013 Oct 8;110(41):16344-9
references.pmid: 24065822
references.citation: Nat Chem Biol. 2009 Apr;5(4):251-7
references.pmid: 19270684
references.citation: Biochemistry. 2009 Apr 28;48(16):3658-68
references.pmid: 19191546
references.citation: Nature. 1991 Mar 14;350(6314):121-4
references.pmid: 2005961
references.citation: J Phys Chem B. 2010 Dec 16;114(49):16263-72
references.pmid: 20936808
references.citation: J Biol Chem. 2014 Oct 31;289(44):30198-204
references.pmid: 25210030
references.citation: J Am Chem Soc. 2005 Oct 12;127(40):13822-31
references.pmid: 16201803
references.citation: J Phys Chem A. 2006 Jan 19;110(2):463-72
references.pmid: 16405318
references.citation: J Chem Phys. 2004 Oct 1;121(13):6442-7
references.pmid: 15446943
references.citation: Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15341-5
references.pmid: 15494437
references.citation: J Am Chem Soc. 2013 Feb 20;135(7):2512-7
references.pmid: 23373704
references.citation: Chem Biol. 2009 Sep 25;16(9):971-9
references.pmid: 19778725
references.citation: J Am Chem Soc. 2014 Jun 11;136(23):8333-41
references.pmid: 24820793
references.citation: Mol Microbiol. 2011 Jan;79(1):7-20
references.pmid: 21166890
references.citation: J Am Chem Soc. 2013 Feb 20;135(7):2509-11
references.pmid: 23373756
references.citation: Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16543-8
references.pmid: 18946041
references.citation: J Biol Chem. 2011 Jun 3;286(22):19392-8
references.pmid: 21489995
references.citation: Nature. 2007 Dec 13;450(7172):964-72
references.pmid: 18075575
references.citation: J Am Chem Soc. 2011 Dec 7;133(48):19358-61
references.pmid: 22059645
references.citation: Biochemistry. 2004 Feb 17;43(6):1458-68
references.pmid: 14769022
references.citation: Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):18661-5
references.pmid: 22065757
references.citation: Annu Rev Phys Chem. 2002;53:291-318
references.pmid: 11972010
references.citation: Biochemistry. 1986 Jul 15;25(14):4132-40
references.pmid: 3741845
references.citation: Biochemistry. 2009 Jun 16;48(23):5226-38
references.pmid: 19425594
references.citation: J Phys Chem A. 2013 Aug 15;117(32):7107-13
references.pmid: 23441954
references.citation: Biochemistry. 2010 Mar 9;49(9):2058-67
references.pmid: 20108972
references.citation: Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):15991-6
references.pmid: 24043827
references.citation: Biochemistry. 2014 Mar 25;53(11):1849-57
references.pmid: 24576110
references.citation: J Phys Chem B. 2013 Aug 22;117(33):9591-7
references.pmid: 23895500
references.citation: Curr Opin Chem Biol. 2010 Oct;14(5):636-43
references.pmid: 20822946