title: Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies.
abstract: The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the calculations. The effects of the local protein environment were accounted for by including the five nearest surrounding residues in the calculated systems. The specific role of histidine-64 in the distal pocket was examined in more detail in this study than in other studies in the literature. Although the present calculated results do not change the previous conclusion that the hydrogen bonding by the distal histidine-64 residue plays a major role in the O2/CO discrimination by Mb, more details about the interaction between the protein environment and the bound ligand have been revealed in this study by comparing the binding energies of AB to a porphyrin and the various myoglobins. The changes in the experimental binding energies from one system to another are well reproduced by the calculations. Without constraints on the residues in geometry optimization, the dispersion correction is necessary, since it improves the calculated structures and energetic results significantly.
authors: Department of Chemistry, Jackson State University, Jackson, MS 39217, USA.
authors: Meng-Sheng
authors: MS
authors: Liao
authors: Ming-Ju
authors: MJ
authors: Huang
authors: John D
authors: JD
authors: Watts
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites; D002248:Carbon Monoxide / Q000737:chemistry*; D006418:Heme / Q000737:chemistry*; D006639:Histidine / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D009211:Myoglobin / Q000737:chemistry* / Q000235:genetics; D010100:Oxygen / Q000737:chemistry*; D011485:Protein Binding; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D008024:Ligands; D009211:Myoglobin; D006418:Heme; D006639:Histidine; D002248:Carbon Monoxide; D010100:Oxygen
references: Biochemistry. 2003 May 6;42(17):4896-903
references: 12718530
references: Mol Phys. 2011 Aug 20;109(16):2035-2048
references: 22228914
references: Phys Rev B Condens Matter. 1986 Jun 15;33(12):8822-8824
references: 9938299
references: J Biol Inorg Chem. 1999 Feb;4(1):99-110
references: 10499107
references: J Comput Chem. 2011 May;32(7):1456-65
references: 21370243
references: J Mol Biol. 1986 Nov 5;192(1):133-54
references: 3820301
references: J Mol Biol. 1991 Jul 20;220(2):381-99
references: 1856864
references: Nature. 1981 Jul 2;292(5818):81-2
references: 7278969
references: J Biol Chem. 1989 Feb 25;264(6):3057-60
references: 2644279
references: J Phys Chem Lett. 2012 Jun 7;3(11):1448-52
references: 26285620
references: Science. 1995 Aug 18;269(5226):962-6
references: 7638619
references: J Phys Chem B. 2007 Feb 1;111(4):841-52
references: 17249828
references: Phys Rev Lett. 1996 Oct 28;77(18):3865-3868
references: 10062328
references: J Phys Chem B. 2007 Jun 28;111(25):7384-91
references: 17547444
references: J Chem Theory Comput. 2010 Jul 13;6(7):2040-4
references: 26615933
references: J Am Chem Soc. 1986 Apr 1;108(9):2196-204
references: 22175559
references: Biochemistry. 1998 Nov 10;37(45):15896-907
references: 9843395
references: Acc Chem Res. 2001 Feb;34(2):137-44
references: 11263872
references: Phys Chem Chem Phys. 2008 Nov 28;10(44):6615-20
references: 18989472
references: Biophys J. 1999 Oct;77(4):2153-74
references: 10512835
references: Phys Chem Chem Phys. 2009 Jun 7;11(21):4365-74
references: 19458840
references: Biophys J. 2001 Jul;81(1):435-45
references: 11423426
references: J Chem Theory Comput. 2011 Nov 8;7(11):3567-77
references: 26598255
references: J Phys Chem A. 2010 Sep 9;114(35):9554-69
references: 20712371
references: J Chem Phys. 2005 Jan 1;122(1):14103
references: 15638638
references: J Phys Chem B. 2005 Feb 24;109(7):3065-70
references: 16851321
references: Phys Rev B Condens Matter. 1988 Jan 15;37(2):785-789
references: 9944570
references: J Comput Chem. 2006 Nov 30;27(15):1787-99
references: 16955487
references: Phys Chem Chem Phys. 2006 Jun 28;8(24):2831-40
references: 16775638
references: Chem Rev. 2010 Sep 8;110(9):5023-63
references: 20486691
references: Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10354-8
references: 10962034
references: J Inorg Biochem. 2005 Apr;99(4):949-58
references: 15811512
references: J Comput Chem. 2004 Sep;25(12):1463-73
references: 15224390
references: Biophys J. 2000 Jan;78(1):93-100
references: 10620276
references: J Chem Phys. 2010 Apr 21;132(15):154104
references: 20423165
references: Proc Natl Acad Sci U S A. 1976 Oct;73(10):3333-7
references: 1068445
references: Biochemistry. 2004 May 25;43(20):6241-52
references: 15147208
references: J Phys Chem A. 2008 Nov 20;112(46):11824-32
references: 18942804
references: Phys Rev A Gen Phys. 1988 Sep 15;38(6):3098-3100
references: 9900728
references: J Mol Biol. 1993 Nov 5;234(1):140-55
references: 8230194
references: J Biol Chem. 2002 Mar 1;277(9):7509-19
references: 11744723
references: Science. 1999 Apr 16;284(5413):473-6
references: 10205052
references: J Phys Chem A. 2006 Sep 21;110(37):10656-68
references: 16970354
references: J Inorg Biochem. 2002 Jul 25;91(1):101-15
references: 12121767
references: J Chem Theory Comput. 2009 Apr 14;5(4):719-27
references: 26609577
references: J Am Chem Soc. 2008 Nov 5;130(44):14778-90
references: 18847206
references: Biophys J. 2006 Feb 15;90(4):L27-9
references: 16387767