Related ArticlesSome Surprising Implications of NMR-directed Simulations of Substrate Recognition and Binding by Cytochrome P450cam (CYP101A1).
J Mol Biol. 2018 04 27;430(9):1295-1310
Authors: Asciutto EK, Pochapsky TC
Abstract
Cytochrome P450cam (CYP101A1) catalyzes the stereospecific 5-exo hydroxylation of d-camphor by molecular oxygen. Previously, residual dipolar couplings measured for backbone amide 1H-15N correlations in both substrate-free and bound forms of CYP101A1 were used as restraints in soft annealing molecular dynamic simulations in order to identify average conformations of the enzyme with and without substrate bound. Multiple substrate-dependent conformational changes remote from the enzyme active site were identified, and site-directed mutagenesis and activity assays confirmed the importance of these changes in substrate recognition. The current work makes use of perturbation response scanning (PRS) and umbrella sampling molecular dynamic of the residual dipolar coupling-derived CYP101A1 structures to probe the roles of remote structural features in enforcing the regio- and stereospecific nature of the hydroxylation reaction catalyzed by CYP101A1. An improper dihedral angle ? was defined and used to maintain substrate orientation in the CYP101A1 active site, and it was observed that different values of ? result in different PRS response maps. Umbrella sampling methods show that the free energy of the system is sensitive to ?, and bound substrate forms an important mechanical link in the transmission of mechanical coupling through the enzyme structure. Finally, a qualitative approach to interpreting PRS maps in terms of the roles of secondary structural features is proposed.
[NMR paper] The Structure of the Cytochrome P450cam-Putidaredoxin Complex Determined by Paramagnetic NMR Spectroscopy and Crystallography.
The Structure of the Cytochrome P450cam-Putidaredoxin Complex Determined by Paramagnetic NMR Spectroscopy and Crystallography.
The Structure of the Cytochrome P450cam-Putidaredoxin Complex Determined by Paramagnetic NMR Spectroscopy and Crystallography.
J Mol Biol. 2013 Jul 12;
Authors: Hiruma Y, Hass MA, Kikui Y, Liu WM, Olmez B, Skinner SP, Blok A, Kloosterman A, Koteishi H, Lohr F, Schwalbe H, Nojiri M, Ubbink M
Abstract
Cytochrome P450cam catalyzes the hydroxylation of camphor in a complex process involving two electron transfers from...
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[NMR paper] Substrate-Modulated Cytochrome P450 17A1 and Cytochrome b5 Interactions Revealed by NMR.
Substrate-Modulated Cytochrome P450 17A1 and Cytochrome b5 Interactions Revealed by NMR.
Related Articles Substrate-Modulated Cytochrome P450 17A1 and Cytochrome b5 Interactions Revealed by NMR.
J Biol Chem. 2013 Apr 25;
Authors: Estrada DF, Laurence JS, Scott EE
Abstract
The membrane heme protein cytochrome b5 (b5) can enhance, inhibit, or have no effect on cytochrome P450 (P450) catalysis, depending on the specific P450, substrate, and reaction conditions, but the structural basis remains unclear. Herein the interactions between the...
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Transient Enzyme–Substrate Recognition Monitored by Real-Time NMR
Transient Enzyme–Substrate Recognition Monitored by Real-Time NMR
Caroline Haupt, Rica Patzschke, Ulrich Weininger, Stefan Gro?ger, Michael Kovermann and Jochen Balbach
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja2010048/aop/images/medium/ja-2011-010048_0002.gif
Journal of the American Chemical Society
DOI: 10.1021/ja2010048
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/nknzYbs0FNE
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NMR structure of CaBP1 in a Ca(2+) -bound closed state: Implications for target recognition.
NMR structure of CaBP1 in a Ca(2+) -bound closed state: Implications for target recognition.
NMR structure of CaBP1 in a Ca(2+) -bound closed state: Implications for target recognition.
Protein Sci. 2011 May 23;
Authors: Park S, Li C, Ames JB
Calcium binding protein 1 (CaBP1), a neuron-specific member of the calmodulin (CaM) superfamily, regulates the Ca(2+) dependent activity of inositol 1,4,5-triphosphate receptors (InsP3Rs) and various voltage-gated Ca(2+) channels. Here we present the NMR structure of full-length CaBP1 with Ca(2+) bound at the...
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Targeting Bacterial Membranes: Identification of Pseudomonas aeruginosa D-Arabinose-5P Isomerase and NMR Characterisation of its Substrate Recognition and Binding Properties.
Targeting Bacterial Membranes: Identification of Pseudomonas aeruginosa D-Arabinose-5P Isomerase and NMR Characterisation of its Substrate Recognition and Binding Properties.
Targeting Bacterial Membranes: Identification of Pseudomonas aeruginosa D-Arabinose-5P Isomerase and NMR Characterisation of its Substrate Recognition and Binding Properties.
Chembiochem. 2011 Feb 17;
Authors: Airoldi C, Sommaruga S, Merlo S, Sperandeo P, Cipolla L, Polissi A, Nicotra F
The identification and characterisation of Pseudomonas aeruginosa KdsD (Pa-KdsD), a...
[NMR paper] Substrate recognition by the Lyn protein-tyrosine kinase. NMR structure of the immuno
Substrate recognition by the Lyn protein-tyrosine kinase. NMR structure of the immunoreceptor tyrosine-based activation motif signaling region of the B cell antigen receptor.
Related Articles Substrate recognition by the Lyn protein-tyrosine kinase. NMR structure of the immunoreceptor tyrosine-based activation motif signaling region of the B cell antigen receptor.
J Biol Chem. 2000 May 26;275(21):16174-82
Authors: Gaul BS, Harrison ML, Geahlen RL, Burton RA, Post CB
The immunoreceptor tyrosine-based activation motif (ITAM) plays a central role...
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[NMR paper] The substrate binding site of human liver cytochrome P450 2C9: an NMR study.
The substrate binding site of human liver cytochrome P450 2C9: an NMR study.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles The substrate binding site of human liver cytochrome P450 2C9: an NMR study.
Biochemistry. 1997 Oct 21;36(42):12672-82
Authors: Poli-Scaife S, Attias R, Dansette PM, Mansuy D
Purified recombinant human liver cytochrome P450 2C9 was produced, from expression of the corresponding cDNA in yeast, in quantities large enough for UV-visible and 1H NMR experiments. Its...
Some Surprising Implications of NMR-directed Simulations of Substrate Recognition and Binding by Cytochrome P450cam (CYP101A1).
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