Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin

Freindorf, Marek; Shao, Yihan; Kong, Jing; Furlani, Thomas R.

doi:10.1016/j.jinorgbio.2007.11.006

Cited by 7 publications

(5 citation statements)

References 48 publications

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“…The geometric parameters in Figure 6 are in basic accord with the experimental data. 178 A recent DFT(B3LYP)/MM study of 3 with and without the reductase (putidaredoxin) by Freindorf et al 212 gave similar structural data and further showed that the Fe-S bond distance gets shorter upon binding of the reductase, to the proximal side of the active site. This bond shortening (by 0.05-0.10 Å) is accompanied by an increase of the stretching frequency of the Fe-S bond in qualitative accord with experimental findings.…”

Section: The Pentacoordinated Statesmentioning

confidence: 85%

P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations

et al. 2009

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Section: The Pentacoordinated Statesmentioning

confidence: 85%

P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations

et al. 2009

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“…The modified PDB file was then loaded into xleap and recombined with the previously prepared heme and M-IV models using the 2Y98 coordinates for all atoms. A covalent linkage was created from the heme iron to Cys 346 with a Fe-S bond length of 2.45 angstroms (21). The water distally coordinated to the heme iron was retained based on evidence found in the 2Y98 (MycG-M-IV) and 2YGX (MycG) crystallographic structures.…”

Section: Methodsmentioning

confidence: 99%

“…A covalent linkage was created from the heme iron to Cys 346 with a Fe−S bond length of 2.45 Å. 21 The water distally coordinated to the heme iron was retained on the basis of evidence found in the 2Y98 (MycG−M-IV) and 2YGX (MycG) crystallographic structures. The complex was solvated within a cubic periodic box with 90 Å edges, leaving a minimal 15 Å distance from the periodic boundary to the protein surface.…”

mentioning

confidence: 99%

Solution Conformations and Dynamics of Substrate-Bound Cytochrome P450 MycG

Tietz¹,

Podust

Sherman

et al. 2017

Biochemistry

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MycG is a P450 monoxygenase that catalyzes the sequential hydroxylation and epoxidation of mycinamicin IV (M-IV), the last two steps in the biosynthesis of mycinamicin II, a macrolide antibiotic isolated from M. griseorubida. The crystal structure of MycG with M-IV bound was previously determined, but showed the bound substrate in an orientation that did not rationalize the observed regiochemistry of M-IV hydroxylation. NMR paramagnetic relaxation enhancements (PRE) gave evidence for an orientation of M-IV in the MycG active site more compatible with the observed chemistry, but substrate-induced changes in the enzyme structure were not characterized. We now describe the use of amide 1H-15N residual dipolar couplings (RDCs) as experimental restraints in solvated “soft annealing” molecular dynamics simulations to generate solution structural ensembles of M-IV-bound MycG. Chemical shift perturbations, hydrogen-deuterium exchange and 15N relaxation behavior provide insight into dynamic and electronic perturbations in the MycG structure in response to M-IV binding. The solution and crystallographic structures are compared, and the possibility that the crystallographic orientation of bound M-IV represents an inhibitory mode is discussed.

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“…A covalent bond was created between the Fe atom at the coordination site of heme and the proximal cysteine, Cys 348, with a Fe-S distance of 2.45 Å, as computed by Freindorf et al33 using QM/MM. WAT 515 in the 3CPP structure (proposed to correspond to the K + bound between the B-B′ loop and B′ helix) was replaced with a potassium ion 34.…”

Section: Methodsmentioning

confidence: 99%

Structural and Dynamic Implications of an Effector-induced Backbone Amide cis–trans Isomerization in Cytochrome P450cam

Asciutto

Madura

Pochapsky

et al. 2009

Journal of Molecular Biology

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Experimental evidence has been provided for a functionally relevant cis-trans isomerization of the Ile 88-Pro 89 peptide bond in cytochrome P450cam (CYP101). The isomerization is proposed to be a key element of the structural reorganization leading to the catalytically competent form of CYP101 upon binding of the effector protein putidaredoxin (Pdx). A detailed comparison of the results of molecular dynamics simulations on the cis and trans conformations of substrate- and carbonmonoxy-bound ferrous CYP101 with sequence-specific Pdx-induced structural perturbations identified by nuclear magnetic resonance is presented, providing insight into the structural and dynamic consequences of the isomerization. The mechanical coupling between the Pdx binding site on the proximal face of CYP101 and the site of isomerization is described.

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Combined QM/MM calculations of active-site vibrations in binding process of P450cam to putidaredoxin

Abstract: Combined QM/MM calculations of the active-site of cytochorme P450cam have been performed before and after the binding of P450cam to putidaredoxin. The calculations were carried out for both a 5-coordinated and a 6-coordinated active

Cited by 7 publications

References 48 publications

P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations

P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations

Solution Conformations and Dynamics of Substrate-Bound Cytochrome P450 MycG

Structural and Dynamic Implications of an Effector-induced Backbone Amide cis–trans Isomerization in Cytochrome P450cam

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