title: O2 migration pathways are not conserved across proteins of a similar fold.
abstract: Recent advances in computational biology have made it possible to map the complete network and energy profile of gas migration pathways inside proteins. Although networks of O(2) pathways have already been characterized for a small number of proteins, the general properties and locations of these pathways have not been previously compared between proteins. In this study, maps of the O(2) pathways inside 12 monomeric globins were computed. It is found that, despite the conserved tertiary structure fold of the studied globins, the shape and topology of O(2) pathway networks exhibit a large variability between different globins, except when two globins are nearly identical. The locations of the O(2) pathways are, however, found to be correlated with the location of large hydrophobic residues, and a similar correlation is observed in two unrelated protein families: monomeric globins and copper-containing amine oxidases. The results have implications for the evolution of gas pathways in proteins and for protein engineering applications involving modifications of these pathways.
authors: Beckman Institute, University of Illinois, Urbana, Illinois, USA.
authors: Jordi
authors: J
authors: Cohen
authors: Klaus
authors: K
authors: Schulten
mesh_terms: D000818:Animals; D001703:Biophysics / Q000379:methods; D003198:Computer Simulation; D030562:Databases, Protein; D005914:Globins / Q000737:chemistry; D006801:Humans; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D010100:Oxygen / Q000737:chemistry*; D010940:Plant Proteins / Q000737:chemistry; D015202:Protein Engineering / Q000379:methods*; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D010940:Plant Proteins; D011506:Proteins; D005914:Globins; D010100:Oxygen
references: Nat Struct Biol. 1994 Apr;1(4):226-9
references: 7656050
references: J Biol Chem. 2001 Mar 23;276(12):9093-100
references: 11084036
references: Annu Rev Biochem. 1979;48:327-86
references: 382987
references: Biophys J. 2004 Jun;86(6):3855-62
references: 15189882
references: Proteins. 1996 Apr;24(4):433-8
references: 9162944
references: Proc Natl Acad Sci U S A. 1995 May 9;92(10):4224-8
references: 7753786
references: Trends Cardiovasc Med. 2003 Apr;13(3):111-6
references: 12691675
references: Protein Sci. 2001 Oct;10(10):1927-35
references: 11567083
references: Biochemistry. 1997 Sep 30;36(39):11909-17
references: 9305984
references: Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11704-9
references: 16085709
references: J Biol Chem. 2001 Feb 16;276(7):5177-88
references: 11018046
references: Biochemistry. 1984 Jun 19;23(13):2849-57
references: 6466620
references: Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):5998-6002
references: 15067128
references: Curr Opin Biotechnol. 2004 Aug;15(4):343-8
references: 15358002
references: Trends Biotechnol. 2000 Dec;18(12):506-11
references: 11102662
references: Nat Struct Biol. 1997 Jul;4(7):523-6
references: 9228943
references: Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):735-40
references: 11136228
references: Proteins. 2002 Oct 1;49(1):49-60
references: 12211015
references: J Biol Chem. 1992 Nov 5;267(31):22022-34
references: 1429552
references: Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2058-63
references: 10681426
references: Biochemistry. 2001 Nov 20;40(46):13802-15
references: 11705369
references: Proteins. 1991;10(1):70-80
references: 2062829
references: J Biol Chem. 2005 Nov 18;280(46):38740-55
references: 16155005
references: J Comput Chem. 2005 Dec;26(16):1781-802
references: 16222654
references: Science. 2003 Jun 20;300(5627):1944-7
references: 12817148
references: Biophys J. 1999 Oct;77(4):2153-74
references: 10512835
references: Bioessays. 2004 Apr;26(4):422-33
references: 15057940
references: J Mol Biol. 1966 Oct 28;21(1):199-202
references: 5969763
references: Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2370-4
references: 11226246
references: J Mol Biol. 2001 Jun 22;309(5):1153-64
references: 11399085
references: J Mol Biol. 1995 Aug 4;251(1):104-15
references: 7643380
references: Structure. 2005 Sep;13(9):1321-9
references: 16154089
references: Biophys J. 2005 Jul;89(1):465-74
references: 15849248
references: Biochemistry. 1975 Dec 2;14(24):5355-73
references: 1191643
references: J Biol Chem. 2005 Jun 24;280(25):23791-6
references: 15849358
references: J Mol Biol. 1979 Jan 25;127(3):309-38
references: 430568
references: J Struct Biol. 2004 Sep;147(3):223-34
references: 15450292
references: Biochim Biophys Acta. 1997 Aug 15;1341(1):1-13
references: 9300804
references: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references: 8744570
references: J Phys Chem B. 1998 Apr 30;102(18):3586-616
references: 24889800
references: Physiol Rev. 2001 Apr;81(2):569-628
references: 11274340
references: Nature. 2000 Mar 9;404(6774):205-8
references: 10724176
references: Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):8704-9
references: 12847289
references: Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11617-21
references: 15289603
references: J Exp Biol. 2003 Jun;206(Pt 12):2011-20
references: 12756283
references: J Mol Biol. 1997 Mar 14;266(5):1032-42
references: 9086279
references: J Mol Biol. 1994 Nov 18;244(1):86-99
references: 7966324
references: Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15330-4
references: 15489270
references: J Mol Biol. 1979 Aug 15;132(3):343-68
references: 533895
references: J Struct Biol. 2007 Mar;157(3):534-44
references: 17306562
references: J Biol Chem. 2007 Jun 15;282(24):17767-76
references: 17409383
references: J Mol Biol. 2004 Nov 26;344(3):599-607
references: 15533431
references: Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):12825-31
references: 9788999
references: Biophys J. 2006 Sep 1;91(5):1844-57
references: 16751246
references: Biochemistry. 2003 Dec 30;42(51):15148-57
references: 14690425
references: FEBS Lett. 1994 Sep 19;352(1):63-6
references: 7925944
references: J Mol Biol. 1989 Feb 5;205(3):529-44
references: 2926816
references: J Biol Chem. 1988 Feb 5;263(4):1803-13
references: 3338995
references: Biochemistry. 1996 Jan 30;35(4):1125-36
references: 8573567
references: J Biol Chem. 2005 Jul 29;280(30):27477-80
references: 15932877
references: EMBO Rep. 2001 Aug;2(8):674-9
references: 11493595
references: Science. 1996 Dec 6;274(5293):1726-9
references: 8939867