O2 migration pathways are not conserved across proteins of a similar fold.
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.
Cohen
Jordi
J
Beckman Institute, University of Illinois, Urbana, Illinois, USA.
Schulten
Klaus
K
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*
D010940:Plant Proteins; D011506:Proteins; D005914:Globins; D010100:Oxygen
Nat Struct Biol. 1994 Apr;1(4):226-9
7656050
J Biol Chem. 2001 Mar 23;276(12):9093-100
11084036
Annu Rev Biochem. 1979;48:327-86
382987
Biophys J. 2004 Jun;86(6):3855-62
15189882
Proteins. 1996 Apr;24(4):433-8
9162944
Proc Natl Acad Sci U S A. 1995 May 9;92(10):4224-8
7753786
Trends Cardiovasc Med. 2003 Apr;13(3):111-6
12691675
Protein Sci. 2001 Oct;10(10):1927-35
11567083
Biochemistry. 1997 Sep 30;36(39):11909-17
9305984
Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11704-9
16085709
J Biol Chem. 2001 Feb 16;276(7):5177-88
11018046
Biochemistry. 1984 Jun 19;23(13):2849-57
6466620
Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):5998-6002
15067128
Curr Opin Biotechnol. 2004 Aug;15(4):343-8
15358002
Trends Biotechnol. 2000 Dec;18(12):506-11
11102662
Nat Struct Biol. 1997 Jul;4(7):523-6
9228943
Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):735-40
11136228
Proteins. 2002 Oct 1;49(1):49-60
12211015
J Biol Chem. 1992 Nov 5;267(31):22022-34
1429552
Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2058-63
10681426
Biochemistry. 2001 Nov 20;40(46):13802-15
11705369
Proteins. 1991;10(1):70-80
2062829
J Biol Chem. 2005 Nov 18;280(46):38740-55
16155005
J Comput Chem. 2005 Dec;26(16):1781-802
16222654
Science. 2003 Jun 20;300(5627):1944-7
12817148
Biophys J. 1999 Oct;77(4):2153-74
10512835
Bioessays. 2004 Apr;26(4):422-33
15057940
J Mol Biol. 1966 Oct 28;21(1):199-202
5969763
Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2370-4
11226246
J Mol Biol. 2001 Jun 22;309(5):1153-64
11399085
J Mol Biol. 1995 Aug 4;251(1):104-15
7643380
Structure. 2005 Sep;13(9):1321-9
16154089
Biophys J. 2005 Jul;89(1):465-74
15849248
Biochemistry. 1975 Dec 2;14(24):5355-73
1191643
J Biol Chem. 2005 Jun 24;280(25):23791-6
15849358
J Mol Biol. 1979 Jan 25;127(3):309-38
430568
J Struct Biol. 2004 Sep;147(3):223-34
15450292
Biochim Biophys Acta. 1997 Aug 15;1341(1):1-13
9300804
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
8744570
J Phys Chem B. 1998 Apr 30;102(18):3586-616
24889800
Physiol Rev. 2001 Apr;81(2):569-628
11274340
Nature. 2000 Mar 9;404(6774):205-8
10724176
Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):8704-9
12847289
Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11617-21
15289603
J Exp Biol. 2003 Jun;206(Pt 12):2011-20
12756283
J Mol Biol. 1997 Mar 14;266(5):1032-42
9086279
J Mol Biol. 1994 Nov 18;244(1):86-99
7966324
Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15330-4
15489270
J Mol Biol. 1979 Aug 15;132(3):343-68
533895
J Struct Biol. 2007 Mar;157(3):534-44
17306562
J Biol Chem. 2007 Jun 15;282(24):17767-76
17409383
J Mol Biol. 2004 Nov 26;344(3):599-607
15533431
Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):12825-31
9788999
Biophys J. 2006 Sep 1;91(5):1844-57
16751246
Biochemistry. 2003 Dec 30;42(51):15148-57
14690425
FEBS Lett. 1994 Sep 19;352(1):63-6
7925944
J Mol Biol. 1989 Feb 5;205(3):529-44
2926816
J Biol Chem. 1988 Feb 5;263(4):1803-13
3338995
Biochemistry. 1996 Jan 30;35(4):1125-36
8573567
J Biol Chem. 2005 Jul 29;280(30):27477-80
15932877
EMBO Rep. 2001 Aug;2(8):674-9
11493595
Science. 1996 Dec 6;274(5293):1726-9
8939867