Skip Navigation



PEDS Advance Access published online on June 15, 2006
Protein Engineering Design and Selection, doi:10.1093/protein/gzl012
This Article
Right arrow FREE Full Text (PDF) Freely available
Right arrow All Versions of this Article:
19/8/345    most recent
gzl012v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Baudry, J.
Right arrow Articles by Schuler, M. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Baudry, J.
Right arrow Articles by Schuler, M. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org
Received January 5, 2006
Accepted March 21, 2006

Article

Class-dependent sequence alignment strategy improves the structural and functional modeling of P450s

Jerome Baudry 1 4, Sanjeewa Rupasinghe 2 4, and Mary A. Schuler 2 *

1 School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
2 Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, 161 Edward R. Madigan Laboratory, Urbana, IL 61801, USA

* To whom correspondence should be addressed.
Mary A. Schuler, E-mail: maryschu{at}uiuc.edu


  Abstract

Different procedures for obtaining homology models for P450s are investigated using various sequence alignments sharing various levels of sequence identity with available P450 crystal structures. In this analysis, we have investigated how well homology modeling can reproduce known crystal structures as well as how effectively these homology models can be used to reproduce known ligand-binding modes. Homology models obtained from sequence alignments that discriminate between Class I and Class II P450s are significantly closer to the experimental crystal structures and more closely reproduce known ligand's binding modes, than those obtained using sequence alignments that combine Class I and Class II P450s. The quality of the models is slightly improved by constructing hybrid-structure models that model three of the most variable regions of P450s independently from the rest of the protein: the B region that includes SRS1, the FG region that includes SRS2 and SRS3 and the {beta}4 region that includes SRS6.

Keywords: Molecular modeling; cytochrome P450 monooxygenases; P450s.
4These authors contributed equally to the work.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Protein Eng Des SelHome page
A. Nayeem, S.-J. Chiang, S.-W. Liu, Y. Sun, L. You, and J. Basch
Engineering enzymes for improved catalytic efficiency: a computational study of site mutagenesis in epothilone-B hydroxylase
Protein Eng. Des. Sel., April 1, 2009; 22(4): 257 - 266.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
T.-L. Chiu, Z. Wen, S. G. Rupasinghe, and M. A. Schuler
Comparative molecular modeling of Anopheles gambiae CYP6Z1, a mosquito P450 capable of metabolizing DDT
PNAS, July 1, 2008; 105(26): 8855 - 8860.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. R. Berenbaum and A. R. Zangerl
Facing the Future of Plant-Insect Interaction Research: Le Retour a la "Raison d'Etre"
Plant Physiology, March 1, 2008; 146(3): 804 - 811.
[Full Text] [PDF]

Home page
 Protein Eng Des SelHome page
S. G. Rupasinghe, Z. Wen, T.-L. Chiu, and M. A. Schuler
Helicoverpa zea CYP6B8 and CYP321A1: different molecular solutions to the problem of metabolizing plant toxins and insecticides
Protein Eng. Des. Sel., December 6, 2007; (2007) gzm063v1.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
Z. Wen, S. Rupasinghe, G. Niu, M. R. Berenbaum, and M. A. Schuler
CYP6B1 and CYP6B3 of the Black Swallowtail (Papilio polyxenes): Adaptive Evolution through Subfunctionalization
Mol. Biol. Evol., December 1, 2006; 23(12): 2434 - 2443.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.