Phylogenetic analysis of Cytochrome P450 Structures. Gowri Shankar, University of Sydney, Australia.

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1 Phylogenetic analysis of Cytochrome P450 Structures Gowri Shankar, University of Sydney, Australia.

2 Overview Introduction Cytochrome P Structures. Results. Conclusion. Future Work.

3 Aims How the structure of the cytochrome P450 changes Time Across species. Estimate the ages and functional Changes with structural changes. How the residues changes with time and its impact on structure and function of CYPs.

4

5 Introduction Cytochrome P450 (CYPs) - important element of oxidative metabolism Heme-containing monooxygenase proteins Responsible for oxidative metabolism of different endogenous and exogenous compounds 7 of the 57 known human P450s are responsible for more than 90% of the metabolism of all pharmaceuticals in current use Some of them display polymorphisms which can result in the poor metabolism pf drugs

6 Introduction They are found in almost all eukaryotes, prokaryotes, plants and even in hyperthermophilic archea. ~1000 genes/enzymes are avilable till date Divided into 70 different families. Classifications of families - based on nucleotide sequence similarity Enzymes with less than ~40% sequence identity are placed in different gene families

7 Cytochrome P450 --Structures CYP enzymes are membrane bound proteins, So difficult to crystallize. First crystal structure of P450 was solved in the year 1985, it was from pseudomonas putia with a resolution of 2.6 Å. After 2 decades, in 2000 the first mammalian P450 structure was determined. CYP proteins have large binding pockets accommodating all exogenous and endogenous substances. CYPs have 6 Substrate Binding Sites (SRS), enabling CYPs to assimilate a large number of compounds.

8 Cytochrome P450 --Structures

9 Cytochrome P Structures PDB ID Date Resolution Source 1nr6 12/08/ Oryctolagus cuniculus 1po5 7/10/ Oryctolagus cuniculus 1tqn 27/07/ Homo sapiens 1jpz 9/11/ Synthetic Pseudomonas putida 1izo 18/03/ Bacillus subtillis 1n97 25/02/ Thermus thermophilus 1cpt 26/11/ Pseudomonas Sp 1jfb 20/12/ Fusarium oxysporum 1odo 2/01/ Streptomyces coelictor 1eup 28/04/ Saccaropolyspora erythrea 1q5d 23/10/ Polyangium cellulosum 1h5z 3/10/ Mycobacterium tuberculosis 1io7 28/02/ Sulfolbus sulfataricus 1lfk 11/12/ Streptomyces coelictor 1dz4 20/07/ Pseudomonas putida

10 Method - Overview

11 Method Structural Analysis 15 structures were compared pair-wise using FATCAT (Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists) Alignment of one-to-one carbon atoms of each pair of protein structures. From FATCAT analysis FATCAT scores (Structural Similarity) Sequence Identity and Similarity

12 Methods Phylogenetic Analysis Sequences were aligned using Multiple Sequence Alignment. Aligned amino acids are subjected to tree building PAUP* - Maximum Parsimony PHYLIP using Maximum Likelihood method with molecular clock and Jones-Taylor-Thornton model of amino acid change. Evolutionary distances were calculated from the inferred trees.

13 Results SIMILAR Vs IDENTICAL AMINO ACID IDENTICAL SIMILAR Human with Rabbit Human with Archaea The amino acid similarity between CYPs is approximately double the sequence identity Property of the amino acid play an important role in structure- function than its identity.

14 Results FATCAT SCORE Vs EVOLUTIONARY DISTANCE 1500 Human with Rabbit DISTANCE Human with Archaea The structures are similar in most aspects, except at some positions, which are the functionality sites of these proteins. In SRS 1,6,2 there is little conserved sequences and structures. In SRS 3-5 there is a considerable similarity in the protein structures.

15 Observations The Heme binding are conserved and they exhibits a unique pattern. Significant conservation in SRS3-5. This conversation observed is in F/G helix region which forms the major binding region. The catalytic residues of CYPs are present in the helix region of the CYP proteins. The tyrosine residue in the catalytic site plays an important role in the catalysis because the Iron ion oxidises the tyrosine side chain and produces a tyrosyl free radical, which is essential for catalysis.

16 Observations Very few crystal structures available for the extensive study of this enzyme. Phylogenetic analysis gives an insight on the structural aspects of these proteins, evolution and structure-function relation. This paves the way to future research like mutational and modelling analysis.

17 Future Work Explore the binding sites of these proteins and how these binding sites of these proteins have changed with time. Mutational studies on these proteins and how the substrate acts on the mutational sites. Molecular Dynamics and Molecular Modeling of these proteins.

18 References Nelson et al., P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 6:1 42. Yuzhen Ye & Adam Godzik., Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics. 2: Swofford, D. L PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts. Felsenstein, J PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

19 Acknowledgment Prof. Michael Murray, Professor Pharmacogenomics, University of Sydney. Dr Michael Charleston, Lecturer Bioinformatics, University of Sydney. Dr. David Hibbs,, Lecturer Pharmaceutical Chemistry, University of Sydney.

20 Thank You

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