title: Protein collective motions coupled to ligand migration in myoglobin.
abstract: Ligand migration processes inside myoglobin and protein dynamics coupled to the migration were theoretically investigated with molecular dynamics simulations. Based on a linear response theory, we identified protein motions coupled to the transient migration of ligand, carbon monoxide (CO), through channels. The result indicates that the coupled protein motions involve collective motions extended over the entire protein correlated with local gating motions at the channels. Protein motions, coupled to opening of a channel from the distal pocket to a neighboring xenon site, were found to share the collective motion with experimentally observed protein motions coupled to a doming motion of the heme Fe atom upon photodissociation of the ligand. Analysis based on generalized Langevin dynamics elucidated slow and diffusive features of the protein response motions. Remarkably small transmission coefficients for rates of the CO migrations through myoglobin were found, suggesting that the CO migration dynamics are characterized as motions governed by the protein dynamics involving the collective motions, rather than as thermally activated transitions across energy barriers of well-structured channels.
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto Japan.
authors.forename: Yasutaka
authors.initials: Y
authors.lastname: Nishihara
authors.forename: Shigeki
authors.initials: S
authors.lastname: Kato
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Hayashi
mesh_terms: D000818:Animals; D001665:Binding Sites; D001696:Biomechanical Phenomena; D002248:Carbon Monoxide / Q000378:metabolism*; D017276:Friction; D006736:Horses; D007700:Kinetics; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009038:Motion; D009211:Myoglobin / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D013816:Thermodynamics; D013997:Time Factors; D014978:Xenon / Q000378:metabolism
chemical_list: D008024:Ligands; D009211:Myoglobin; D014978:Xenon; D002248:Carbon Monoxide
references.citation: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references.pmid: 8744570
references.citation: Proc Natl Acad Sci U S A. 2008 Jun 24;105(25):8619-24
references.pmid: 18562286
references.citation: Phys Rev Lett. 2005 Feb 25;94(7):078102
references.pmid: 15783858
references.citation: Science. 1991 Dec 13;254(5038):1598-603
references.pmid: 1749933
references.citation: Biophys Chem. 2004 Apr 1;109(1):41-58
references.pmid: 15059658
references.citation: Biochemistry. 1991 Apr 23;30(16):3988-4001
references.pmid: 2018767
references.citation: Proteins. 2008 May 15;71(3):1231-6
references.pmid: 18041761
references.citation: Biochemistry. 1988 May 31;27(11):4049-60
references.pmid: 3415972
references.citation: Biochemistry. 1984 Jun 19;23(13):2849-57
references.pmid: 6466620
references.citation: Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15330-4
references.pmid: 15489270
references.citation: Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9627-32
references.pmid: 17517618
references.citation: J Chem Phys. 2007 Oct 7;127(13):135101
references.pmid: 17919054
references.citation: J Phys Chem B. 2005 Sep 8;109(35):16911-7
references.pmid: 16853152
references.citation: Biochemistry. 2001 Nov 20;40(46):13802-15
references.pmid: 11705369
references.citation: Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):5998-6002
references.pmid: 15067128
references.citation: J Struct Biol. 2004 Sep;147(3):235-46
references.pmid: 15450293
references.citation: Nature. 2000 Feb 24;403(6772):921-3
references.pmid: 10706294
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9204-9
references.pmid: 18599444
references.citation: Protein Sci. 1994 Jun;3(6):936-43
references.pmid: 7520795
references.citation: Nature. 2000 Mar 9;404(6774):205-8
references.pmid: 10724176
references.citation: J Am Chem Soc. 2004 Sep 29;126(38):11877-88
references.pmid: 15382923
references.citation: Chemphyschem. 2004 Nov 12;5(11):1710-8
references.pmid: 15580931
references.citation: Biophys J. 2004 Jun;86(6):3855-62
references.pmid: 15189882
references.citation: J Am Chem Soc. 2001 May 9;123(18):4286-94
references.pmid: 11457195
references.citation: Science. 1999 Apr 16;284(5413):473-6
references.pmid: 10205052
references.citation: Annu Rev Phys Chem. 1991;42:581-614
references.pmid: 1747193
references.citation: Biophys J. 2006 Sep 1;91(5):1844-57
references.pmid: 16751246
references.citation: Proc Natl Acad Sci U S A. 2001 May 22;98(11):6110-5
references.pmid: 11344263