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

Marek Freindorf, Yihan Shao, Jing Kong, Thomas R. Furlani
2008 Journal of Inorganic Biochemistry  
Combined QM/MM calculations of the active-site of cytochorme P450cam have been performed before and after the binding of P450cam to putidaredoxin.  ...  An experimentally observed increase in the Fe-S stretching frequency that occurs after cytochrome P450cam binds to putidaredoxin, has been reproduced in our study.  ...  Acknowledgments The authors gratefully acknowledge support of NIH grants R44GM65617 and R44GM073408.  ... 
doi:10.1016/j.jinorgbio.2007.11.006 pmid:18180042 pmcid:PMC2292843 fatcat:dmvuyu2gq5ce5lr6c5begej7ti

Structure and function of the cytochrome P450 peroxygenase enzymes

Andrew W. Munro, Kirsty J. McLean, Job L. Grant, Thomas M. Makris
2018 Biochemical Society Transactions  
The cytochromes P450a brief introduction The cytochromes P450 (P450s, CYPs) were the first group of enzymes to be classified as a 'superfamily' through bioinformatics studies performed by Nebert et al.  ...  The cytochromes P450 (P450s or CYPs) constitute a large heme enzyme superfamily, members of which catalyze the oxidative transformation of a wide range of organic substrates, and whose functions are crucial  ...  The nature of this abstraction, combined with structural and functional analogy to the well-studied CYP152 hydroxylases BS β and SP α that exhibit significant steady-state 2 H kinetic isotope effects (  ... 
doi:10.1042/bst20170218 pmid:29432141 pmcid:PMC5818669 fatcat:kn24sj624fbatfykdvckmkea5i

Quantum Mechanics/Molecular Mechanics Studies on the Relative Reactivities of Compound I and II in Cytochrome P450 Enzymes

Verònica Postils, Maud Saint-André, Amy Timmins, Xiao-Xi Li, Yong Wang, Josep Luis, Miquel Solà, Sam de Visser
2018 International Journal of Molecular Sciences  
of cytochrome P450 enzymes.  ...  To illustrate the size and shape of the substrate binding pocket in P450 isozymes, we show in Figure 1 the crystal structure extracts of protein databank (pdb) files for P450cam (2CPP pdb [17]), P450BM3  ...  of international mobility of Sorbonne Universities as well as from an Erasmus+ exchange scholarship to MStA.  ... 
doi:10.3390/ijms19071974 pmid:29986417 pmcid:PMC6073316 fatcat:3gt2tknkcbbjrcantlxkaajsnm

The mystery of cytochrome P450 Compound I

Christiane Jung
2011 Biochimica et Biophysica Acta - Proteins and Proteomics  
There is a need for improved experimental approaches, detection techniques, and theoretical simulations for future studies of cytochrome P450 Compound I.  ...  It will be discussed what was known and suggested in the years before 1984, the year when Klaus Ruckpaul's first book about cytochrome P450 appeared, and compared with recent approaches and studies to  ...  Acknowledgments The diverse studies on cytochrome P450 were funded by the Deutsche Forschungsgemeinschaft grants Ju229/4-(1-3), Ju229/5-1, Sk35/3-(3-5) to C. Jung; Le 812/2-1 to F.  ... 
doi:10.1016/j.bbapap.2010.06.007 pmid:20558327 fatcat:tn4lmgb4r5gonm4ghsjvvmengu

Heme Enzyme Structure and Function

Thomas L. Poulos
2014 Chemical Reviews  
A recent combination of crystallography and QM/MM calculations have provided the most recent details (Fig. 42 ). 354 Cleavage of the O-O bond results in the addition of the distal O atom to the porphyrin  ...  Pooling these results together with additional QM/MM calculations 376 leads to the mechanism shown in Fig. 44C.  ... 
doi:10.1021/cr400415k pmid:24400737 pmcid:PMC3981943 fatcat:7cedgjeexzhwjnxwzdow675vjy

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

Eliana K. Asciutto, Jeffry D. Madura, Susan Sondej Pochapsky, Bo OuYang, Thomas C. Pochapsky
2009 Journal of Molecular Biology  
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).  ...  The mechanical coupling between the Pdx binding site on the proximal face of CYP101 and the site of isomerization is described.  ...  Acknowledgments This work was supported in part by a grant from the National Institutes of Health, GM44191 (T.C.P).  ... 
doi:10.1016/j.jmb.2009.03.046 pmid:19327368 pmcid:PMC2799046 fatcat:3sp6qy5htrfyjpb2wdfudogkle

Electron Transfer from Cytochrome P450 Reductase to Cytochrome P450: Towards a Structural and Dynamic Understanding [article]

Goutam Mukherjee, Prajwal P Nandekar, Rebecca C. Wade
2020 bioRxiv   pre-print
We find that upon binding to CPR, the CYP 1A1 catalytic domain becomes less embedded in the membrane and reorients, indicating that CPR may affect ligand passage between the membrane and the CYP active  ...  Despite the constraints imposed by membrane binding, we identify several arrangements of CPR around CYP 1A1 that are compatible with ET.  ...  of the substrate, possibly due to realignment of the heme in the mutant. 65 The I458P mutation had a smaller and opposite effect to the I458V mutation. 65 From a QM/MM study of CYP 3A4, it was concluded  ... 
doi:10.1101/2020.06.12.149112 fatcat:bfsdskt2mbetlipvwtyqap4y3m

An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase

Goutam Mukherjee, Prajwal P. Nandekar, Rebecca C. Wade
2021 Communications Biology  
We find that upon binding to CPR, the CYP 1A1 catalytic domain becomes less embedded in the membrane and reorients, indicating that CPR may affect ligand passage to the CYP active site.  ...  Despite the constraints imposed by membrane binding, we identify several arrangements of CPR around CYP 1A1 that are compatible with ET.  ...  fellowship to G.M.) for support.  ... 
doi:10.1038/s42003-020-01568-y pmid:33420418 fatcat:k6kmmj7nz5gopi2zg24hy62ghi

A computational study of the substrate conversion and selective inhibition of aldosterone synthase [article]

Roumen, L (Luc), Hermans, JJRM (Rob), Hilbers, PAJ (Peter)
2008
A computational study of the substrate conversion and selective inhibition of aldosterone synthase.  ...  Eindhoven: Technische Universiteit Eindhoven. https://doi.org/10.6100/IR637195 A Computational Study of the Substrate Conversion and Selective Inhibition of Aldosterone Synthase The cover illustrates my  ...  Ishimura, "Putidaredoxin-cytochrome P450cam interaction", J. Inorg. Biochem., 2001, 83, 4, 255-260 12 O.  ... 
doi:10.6100/ir637195 fatcat:a2v7hcatunahdgzo7aukx63exa