title: Many local motions cooperate to produce the adenylate kinase conformational transition.
abstract: Conformational transitions are functionally important in many proteins. In the enzyme adenylate kinase (AK), two small domains (LID and NMP) close over the larger CORE domain; the reverse (opening) motion limits the rate of catalytic turnover. Here, using double-well Gō simulations of Escherichia coli AK, we elaborate on previous investigations of the AK transition mechanism by characterizing the contributions of rigid-body (Cartesian), backbone dihedral, and contact motions to transition-state (TS) properties. In addition, we compare an apo simulation to a pseudo-ligand-bound simulation to reveal insights into allostery. In Cartesian space, LID closure precedes NMP closure in the bound simulation, consistent with prior coarse-grained models of the AK transition. However, NMP-first closure is preferred in the apo simulation. In backbone dihedral space, we find that, as expected, backbone fluctuations are reduced in the O/C transition in parts of all three domains. Among these "quenching" residues, most in the CORE, especially residues 11-13, are rigidified in the TS of the bound simulation, while residues 42-44 in the NMP are flexible in the TS. In contact space, in both apo and bound simulations, one nucleus of closed-state contacts includes parts of the NMP and CORE; CORE-LID contacts are absent in the TS of the apo simulation but formed in the TS of the bound simulation. From these results, we predict mutations that will perturb the opening and/or closing transition rates by changing the entropy of dihedrals and/or the enthalpy of contacts. Furthermore, regarding allostery, the fully closed structure is populated in the apo simulation, but our contact results imply that ligand binding shifts the preferred O/C transition pathway, thus precluding a simple conformational selection mechanism. Finally, the analytical approach and the insights derived from this work may inform the rational design of flexibility and allostery in proteins.
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Daily
authors.forename: George N
authors.initials: GN
authors.lastname: Phillips
authors.forename: Qiang
authors.initials: Q
authors.lastname: Cui
mesh_terms: D000263:Adenylate Kinase / Q000737:chemistry* / Q000378:metabolism; D000494:Allosteric Regulation; D003198:Computer Simulation; D004926:Escherichia coli / Q000737:chemistry / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation
chemical_list: D029968:Escherichia coli Proteins; D000263:Adenylate Kinase
references.citation: Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12570-5
references.pmid: 14566052
references.citation: Nat Chem Biol. 2009 Nov;5(11):789-96
references.pmid: 19841628
references.citation: J Mol Biol. 2007 Mar 9;366(5):1661-71
references.pmid: 17217965
references.citation: J Chem Phys. 2004 Jun 15;120(23):10880-9
references.pmid: 15268118
references.citation: Annu Rev Phys Chem. 1997;48:545-600
references.pmid: 9348663
references.citation: J Am Chem Soc. 2005 Jun 29;127(25):9167-76
references.pmid: 15969595
references.citation: J Mol Biol. 2003 Nov 21;334(2):309-25
references.pmid: 14607121
references.citation: J Am Chem Soc. 2007 Aug 22;129(33):10261-8
references.pmid: 17655236
references.citation: Nature. 2007 Dec 6;450(7171):838-44
references.pmid: 18026086
references.citation: J Mol Biol. 1990 Jun 20;213(4):627-30
references.pmid: 2162964
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11844-9
references.pmid: 16877541
references.citation: Biophys J. 2007 Aug 1;93(3):920-9
references.pmid: 17483178
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3023-8
references.pmid: 19204278
references.citation: J Phys Chem B. 2009 Feb 12;113(6):1662-72
references.pmid: 19159290
references.citation: Int J Mol Sci. 2009 Mar;10(3):889-905
references.pmid: 19399227
references.citation: Science. 2001 Mar 23;291(5512):2429-33
references.pmid: 11264542
references.citation: Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):16984-9
references.pmid: 19805185
references.citation: Proc Natl Acad Sci U S A. 2006 Feb 14;103(7):2132-7
references.pmid: 16452168
references.citation: Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18496-501
references.pmid: 18000050
references.citation: Biochemistry. 2009 Mar 10;48(9):1911-27
references.pmid: 19219996
references.citation: J Mol Biol. 1992 Apr 5;224(3):771-82
references.pmid: 1569556
references.citation: Biophys J. 2007 Dec 1;93(11):3820-7
references.pmid: 17704146
references.citation: J Mol Biol. 2005 Sep 30;352(4):807-22
references.pmid: 16139299
references.citation: J Chem Phys. 2004 Jan 8;120(2):516-23
references.pmid: 15267886
references.citation: Protein Sci. 2008 Aug;17(8):1295-307
references.pmid: 18560010
references.citation: Biophys J. 2010 Mar 17;98(6):L15-7
references.pmid: 20303846
references.citation: Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2104-9
references.pmid: 19190183
references.citation: Proc Natl Acad Sci U S A. 1958 Feb;44(2):98-104
references.pmid: 16590179
references.citation: Nature. 2007 Dec 6;450(7171):913-6
references.pmid: 18026087
references.citation: J Comput Chem. 2009 Jul 30;30(10):1545-614
references.pmid: 19444816
references.citation: Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13643-8
references.pmid: 17699616
references.citation: J Mol Biol. 1963 Apr;6:306-29
references.pmid: 13936070
references.citation: PLoS Comput Biol. 2008 Apr 11;4(4):e1000060
references.pmid: 18404207
references.citation: Nature. 1989 Jul 13;340(6229):122-6
references.pmid: 2739734
references.citation: J Mol Biol. 2009 Nov 20;394(1):160-76
references.pmid: 19751742
references.citation: Proteins. 2006 Jun 1;63(4):846-67
references.pmid: 16475196
references.citation: Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):18055-60
references.pmid: 17989222
references.citation: Nat Chem Biol. 2008 Aug;4(8):474-82
references.pmid: 18641628
references.citation: PLoS Comput Biol. 2008 Mar 28;4(3):e1000047
references.pmid: 18369437
references.citation: Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13829-34
references.pmid: 18772387
references.citation: Structure. 1996 Feb 15;4(2):147-56
references.pmid: 8805521
references.citation: Proc Natl Acad Sci U S A. 2005 May 10;102(19):6732-7
references.pmid: 15814618
references.citation: Protein Sci. 2002 Oct;11(10):2351-61
references.pmid: 12237457
references.citation: J Am Chem Soc. 2008 Apr 9;130(14):4772-83
references.pmid: 18338887
references.citation: Proc Natl Acad Sci U S A. 2004 Jan 13;101(2):511-6
references.pmid: 14694192
references.citation: Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18908-13
references.pmid: 16354836
references.citation: PLoS Comput Biol. 2009 Feb;5(2):e1000293
references.pmid: 19229311
references.citation: Biophys J. 2007 Dec 1;93(11):3860-71
references.pmid: 17704151
references.citation: Structure. 2005 Dec;13(12):1755-63
references.pmid: 16338404
references.citation: Nat Struct Mol Biol. 2004 Oct;11(10):945-9
references.pmid: 15334070
references.citation: J Mol Biol. 1965 May;12:88-118
references.pmid: 14343300