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Insight into the redox partner interaction mechanism in cytochrome P450BM-3 using molecular dynamics simulations
Article first published online: 18 DEC 2013
Copyright © 2013 Wiley Periodicals, Inc.
Volume 101, Issue 3, pages 197–209, March 2014
How to Cite
Verma, R., Schwaneberg, U. and Roccatano, D. (2014), Insight into the redox partner interaction mechanism in cytochrome P450BM-3 using molecular dynamics simulations. Biopolymers, 101: 197–209. doi: 10.1002/bip.22301
- Issue published online: 18 DEC 2013
- Article first published online: 18 DEC 2013
- Accepted manuscript online: 10 JUN 2013 03:43AM EST
- Manuscript Accepted: 30 MAY 2013
- Manuscript Received: 21 MAR 2013
- European Union seventh framework program (OXYGREEN) . Grant Number: 212281
Additional Supporting Information may be found in the online version of this article.
Figure S1: Secondary structure per residue calculated by DSSP4 along the trajectory as a function of time for the HEME and FMN domains a) in solution and b) complex simulation. Color code represents different secondary structures.
Figure S2: Minimum distance between water molecules and the HEME iron as a function of time (the trajectories have been sampled every 100 ps) in solution (in red color) and the complex (in black color) simulation.
Figure S3: Minimum distance between the heavy atoms of the FMN isoalloxazine ring and the HEME cofactor as a function of time. Red color horizontal line shows the distance observed in the crystal structure.5
Figure S4: The distribution of distance along different FMN/HEME ET pathways identified during the complex simulation.
Figure S5: The cumulative sum of the relative positional fluctuation (RPF) of the first 50 eigenvectors of A and F chains in the isolated domain and the complex simulation. In the AF chain, the first 50 eigenvectors account for 80.45 % of the total RPF with 25.96 % contribution by the first eigenvector. The A chain has 79.28 % and 86.77 % cumulative RPF with 27.19 % and 48.54 % contribution by the first eigenvector in the complex and the isolated domain simulation, respectively. For The F chain, the cumulative RPF of the first 50 eigenvectors was 90.96 % and 89.19 % with 33.98 % and 35.02 % RPF of the first eigenvector in the complex and isolated domain simulations.…
Figure S6: The components for the (a) first, (b) second and (c) third eigenvectors of the AF chain (cyan color), and A and F chains in the complex (black color) simulation. The green vertical line separates the HEME and FMN domains. Horizontal bars, in the blue and orange color represent helices (labeled) and beta sheets, respectively. The regions involved in the cofactor binding are represented by horizontal bars in purple color.
Figure S7: RMSF of the protein backbone atoms along the first, second and third eigenvectors after projecting the trajectory on the corresponding eigenvector of the AF chain in the complex simulation in (a), (b) and (c), respectively. The 10 sequential frames represent the extension of the fluctuations in trajectories along the eigenvectors. The first extreme conformation is shown in green color and last extreme in violet color. Other conformations of the HEME and FMN domains are in sky blue and tan color, respectively. Helices and loops are labeled. N and C indicate the N- and C-terminus of the protein (labeled in red color).
Table S1: Partial charge on the HEME cofactor with the ferric iron1–3
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