The Influence of Sequence Alignment Length of template on the Accuracy and Quality of Homology modelling: Human Cytochrome P450 2D6 (CYP2D6) case study

Elrashid Saleh Mahdi, Nurul Bahiyah Ahmad Khairudin, Habibah A. Wahab


Homology modelling is one of the important alternative techniques to X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy in structural determination of protein. CYP2D6 drug metabolizing enzymes have extensively studied prior to the successful determination of its 3D structure using X-ray crystallography. This study is one of the earlier works being carried out before the crystal structure was solved. The enzyme is polymorphic and more than 80 different alleles have been identified. The aim of this study is to identify possible criteria to improve the quality of 2D6 model. Four mammalian crystal structures CYP2C8, CYP2B4, CYP2C9 and CYP2C5 were selected from protein databank as template for CYP2D6 model. Multiple sequence alignment between the selected target and template was performed. Secondary structure prediction was generated using CYP2D6 sequence and the 3D models built based on each template. The quality of the models was evaluated using Ramachandran’s plot. The final models were superimposed with CYP2D6 crystal structure. The result shows that not only the sequence identity is important for the template selection but also the alignment length of sequence. The secondary structure prediction of CYP2D6 sequence was found significantly matched the secondary structure prediction of the 3D structures of CYP2D6 models. The stereochemical quality of CYP2D6 models were found adequately satisfied the Ramachandran.plot requirements and comparable to the stereochemical quality crystal structure proteins used as templates and CYP2D6 crystal structure. The criteria set shows that CYP2C8 is the better template for homology modelling of CYP2D6 since it has scored lower E-value and longer alignment length, high sequence identity provided by ClustalW . In addition the secondary structure prediction of the model better matched the consensus and satisfy the criteria of Ramachandran’s plot as well it retained lowest RMSD value from the crystal structure. The study concludes to that the length of the sequence alignment is a critical factor in template selection it is also shows the important primary and secondary structure prediction.

Keywords: Homology modelling, CYP2D6, CYP2C8, CYP2C9, CYP2B4, CYP2C5.


Homology modelling, CYP2D6, CYP2C8, CYP2C9, CYP2B4, CYP2C5.

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Kemp C, Maréchal J, Sutcliffe M. Progress in cytochrome P450 active site modeling. Archives of Biochemistry and Biophysics. 2005;433:361-368.

Kirton S, Baxter C, Sutcliffe M. Comparative modelling of cytochromes P450. Advanced drug delivery reviews. 2002;54:385-406.

Sánchez R. Advances in comparative protein-structure modelling. Current opinion in structural biology. 1997;7:206-214.

Kopp J, Schwede T. Automated protein structure homology modeling: a progress report. pgs 2004;5:405-416.

Hillisch A, Pineda L, Hilgenfeld R. Utility of homology models in the drug discovery process. Drug discovery today. 2004;9:659-669.

Ali A. Comparative protein modeling by satisfaction of spatial restraints. Molecular medicine today. 1995;1:270-277.

Hasler J, Estabrook R, Murray M, et al. Human cytochromes P450. Molecular Aspects of Medicine. 1999;20:1-137.

Nebert D, Russell D. Clinical importance of the cytochromes P450. The Lancet. 2002;360:1155-1162.

Nebert D, Dalton T: The role of cytochrome P450 enzymes in endogenous signalling pathways and environmental carcinogenesis. Nature Reviews Cancer. 2006;6:947-960.

Zanger U, Raimundo S, Eichelbaum M. Cytochrome P450 2D6: overview and update on pharmacology, genetics, biochemistry. Naunyn-Schmiedeberg's archives of pharmacology. 2004;369:23-37.

Ingelman-Sundberg M. Genetic polymorphisms of cytochrome P450 2D6 (CYP2D6): clinical consequences, evolutionary aspects and functional diversity. The Pharmacogenomics Journal. 2004;5:6-13.

Rowland P, Blaney FE, Smyth MG, et al. Crystal Structure of Human Cytochrome P450 2D6. Journal of Biological Chemistry. 2006;281:7614-7622.

de Groot M, Ackland M, Horne V, et al. Novel approach to predicting P450-mediated drug metabolism: development of a combined protein and pharmacophore model for CYP2D6. J Med Chem. 1999;42:1515-1524.

Lewis D. Homology modelling of human CYP2 family enzymes based on the CYP2C5 crystal structure. Xenobiotica. 2002;32:305-323.

Ito Y, Kondo H, Goldfarb P, Lewis D. Analysis of CYP2D6 substrate interactions by computational methods. Journal of Molecular Graphics and Modelling. 2008;26:947-956.

Bairoch A, Apweiler R. The SWISS-PROT protein sequence database: its relevance to human molecular medical research. Journal of molecular medicine. 1997;75:312-316.

Altschul S, Madden T, Schaffer A, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research. 1997;25:3389.

Williams P, Cosme J, Ward A, et al. Crystal structure of human cytochrome P450 2C9 with bound warfarin. Nature 2003;424:464-468.

Schoch GA, Yano JK, Wester MR, et al. Structure of Human Microsomal Cytochrome P450 2C8. Journal of Biological Chemistry. 2004;279:9497-9503.

Williams P, Cosme J, Sridhar V, et al. Microsomal cytochrome P450 2C5: comparison to microbial P450s and unique features. Journal of Inorganic Biochemistry. 2000;81:183-190.

Scott EE, White MA, He YA, et al. Structure of Mammalian Cytochrome P450 2B4 Complexed with 4-(4-Chlorophenyl)imidazole at 1.9-Ã… Resolution. Journal of Biological Chemistry. 2004;279:27294-27301.

Thompson JD, Higgins DG, Gibson TJ, Clustal W. improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res. 1994;22:4673-4680.

Krogh A, Larsson B, von Heijne G, Sonnhammer E. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of molecular biology. 2001;305:567-580.

Rost B. Review: protein secondary structure prediction continues to rise. Journal of Structural Biology. 2001;134:204-218.

Jones D: Protein secondary structure prediction based on position-specific scoring matrices. Journal of molecular biology. 1999;292:195-202.

Ceroni A, Frasconi P, Passerini A, Vullo A. A combination of support vector machines and bidirectional recurrent neural networks for protein secondary structure prediction. Lecture notes in computer science. 2003:142-153.

Fiser A, Do R, Šali A: Modeling of loops in protein structures. PRS 2000;9:1753-1773.

Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods in enzymology. 2003;374:461-491.

John B, Sali A. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic acids research. 2003;31:3982.

Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. Journal of molecular biology. 1993;234:779-815.

Laskowski R, MacArthur M, Moss D, Thornton J. PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography. 1993;26:283-291.

Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins-Structure Function and Genetics. 1995;23:566-579.

Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Structure, Function, and Genetics. 1991;9:56-68.

Notredame C, Higgins D, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of molecular biology. 2000;302:205-217.

Monné M, Nilsson I, Elofsson A, von Heijne G. Turns in transmembrane helices: determination of the minimal length of a “helical hairpin” and derivation of a fine-grained turn propensity scale. Journal of molecular biology. 1999;293:807-814.

Monné M, von Heijne G. Effects of ‘hydrophobic mismatch’on the location of transmembrane helices in the ER membrane. FEBS letters. 2001;496:96-100.

Sánchez R, Šali A. Advances in comparative protein-structure modelling. Current opinion in structural biology. 1997;7:206-214.

Kleywegt G, Jones T. Phi/psi-chology: Ramachandran revisited. Structure. 1996;4:1395-1400.


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