Quantum cluster size and solvent polarity effects on the geometries and Mössbauer properties of the active site model for ribonucleotide reductase intermediate X: a density functional theory study.
In studying the properties of metalloproteins using ab initio quantum mechanical methods, one has to focus on the calculations on the active site. The bulk protein and solvent environment is often neglected, or is treated as a continuum dielectric medium with a certain dielectric constant. The size of the quantum cluster of the active site chosen for calculations can vary by including only the first-shell ligands which are directly bound to the metal centers, or including also the second-shell residues which are adjacent to and normally have H-bonding interactions with the first-shell ligands, or by including also further hydrogen bonding residues. It is not well understood how the size of the quantum cluster and the value of the dielectric constant chosen for the calculations will influence the calculated properties. In this paper, we have studied three models (A, B, and C) of different sizes for the active site of the ribonucleotide reductase intermediate X, using density functional theory (DFT) OPBE functional with broken-symmetry methodology. Each model is studied in gas-phase and in the conductor-like screening (COSMO) solvation model with different dielectric constants ε = 4, 10, 20, and 80, respectively. All the calculated Fe-ligand geometries, Heisenberg J coupling constants, and the Mössbauer isomer shifts, quadrupole splittings, and the (57)Fe, (1)H, and (17)O hyperfine tensors are compared. We find that the calculated isomer shifts are very stable. They are virtually unchanged with respect to the size of the cluster and the dielectric constant of the environment. On the other hand, certain Fe-ligand distances are sensitive to both the size of the cluster and the value of ε. ε = 4, which is normally used for the protein environment, appears too small when studying the diiron active site geometry with only the first-shell ligands as seen by comparisons with larger models.
Han
Wen-Ge
WG
Department of Molecular Biology, TPC-15, The Scripps Research Institute, La Jolla, CA 92037, USA.
Noodleman
Louis
L
J Am Chem Soc. 2003 Sep 17;125(37):11200-1
16220933
Structure. 1996 Sep 15;4(9):1053-64
8805591
Chem Rev. 2004 Feb;104(2):459-508
14871132
Inorg Chem. 1997 Mar 12;36(6):1198-1217
11669688
J Mol Biol. 1982 May 25;157(3):571-5
7120403
J Am Chem Soc. 2008 Nov 12;130(45):15022-7
18937466
Biophys J. 2000 Sep;79(3):1610-20
10969021
J Am Chem Soc. 2005 Nov 16;127(45):15778-90
16277521
J Am Chem Soc. 2008 Nov 12;130(45):15002-21
18928258
J Am Chem Soc. 2003 Feb 19;125(7):1923-36
12580620
J Comput Chem. 2006 Sep;27(12):1292-306
16786546
Biochemistry. 2008 Dec 30;47(52):13736-44
19061340
Chem Rev. 1999 Aug 11;99(8):2161-2200
11849023
Biophys J. 2007 Mar 15;92(6):2041-53
17172297
Biochemistry. 2008 Aug 19;47(33):8477-84
18656954
J Mol Biol. 1985 Jan 20;181(2):323-6
2984434
Inorg Chem. 2003 Apr 21;42(8):2751-8
12691585
Q Rev Biophys. 2003 Feb;36(1):91-145
12643044
Biophys J. 1998 Apr;74(4):1744-53
9545037
Inorg Chem. 1999 Jun 14;38(12):2880-2889
11671034
Biochemistry. 1996 Jun 18;35(24):7819-33
8672483
Science. 1991 Jul 19;253(5017):292-8
1650033
Phys Rev B Condens Matter. 1992 Sep 15;46(11):6671-6687
10002368
J Biomol Struct Dyn. 1999 Apr;16(5):1019-32
10333172
Chem Rev. 1996 Nov 7;96(7):2625-2658
11848839
J Am Chem Soc. 2004 Mar 3;126(8):2613-22
14982471
Chem Biol. 1995 Dec;2(12):793-801
8807812
Chem Rev. 2000 Nov 8;100(11):4187-4226
11749344
J Am Chem Soc. 2002 Aug 28;124(34):10225-35
12188687
Protein Sci. 2008 May;17(5):833-45
18369193
J Phys Chem. 1972 Oct 12;76(21):2987-94
5073361
J Mol Biol. 1993 Jul 5;232(1):123-64
8331655
Inorg Chem. 2004 Jan 26;43(2):613-21
14731023
J Inorg Biochem. 2006 Apr;100(4):771-9
16504298
Inorg Chem. 2008 Jul 21;47(14):6162-72
18578487
Biophys J. 2002 Jun;82(6):3289-304
12023252
Inorganica Chim Acta. 2008 Mar 3;361(4):973-986
19262682
Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11146-51
18678891
Phys Rev Lett. 2001 Aug 6;87(6):062701
11497826
J Mol Biol. 1997 Jul 18;270(3):520-34
9237916
Inorg Chem. 2008 Apr 21;47(8):2975-86
18366153
J Phys Chem B. 2005 Aug 18;109(32):15645-50
16852982
Inorg Chem. 2006 Oct 16;45(21):8533-42
17029364
Phys Rev Lett. 1996 Oct 28;77(18):3865-3868
10062328
Biochemistry. 2009 Feb 10;48(5):1056-66
19138102
Proc Natl Acad Sci U S A. 1989 Aug;86(15):5820-4
2762299
Biochemistry. 1990 Nov 6;29(44):10219-25
2271649
Cell Mol Life Sci. 1998 Jul;54(7):684-95
9711234