title: Are transversion mutations better? A Mutagenesis Assistant Program analysis on P450 BM-3 heme domain.
abstract: Directed evolution represents a versatile tool to tailor enzyme properties to needs in industrial applications and to understand structure-function relationships. Genetic diversity is commonly generated using error-prone PCR. Exploration of sequence space by random mutagenesis strongly favors transitions when enzyme-based mutagenesis methods are employed (Wong, T. S., Zhurina, D., Schwaneberg, U., Comb. Chem. High Throughput Screen. 2006, 9, 271-288). The genetic code has been organized in a manner that limits chemical diversity when a single transition mutation occurs in a codon (Wong, T. S., Roccatano, D., Schwaneberg, U., Biocatal. Biotransformation 2006, in press). Are transitions more beneficial than transversions for adapting biocatalysts to non-natural process conditions? In a statistical analysis performed with the Mutagenesis Assistant Program (MAP), we compared the consequences of transition and transversion bias on amino acid substitution patterns of the P450 BM-3 heme domain. For the analysis, we used a recently introduced benchmarking system consisting of a protein structure indicator, an amino acid diversity indicator with a codon diversity coefficient, and a chemical diversity indicator. A detailed analysis for the P450 BM-3 heme domain showed that an ideal transversion bias generates more diverse amino acid substitution patterns with a significantly different chemical composition than an ideal transition bias. Emphasis is given on the theoretical analysis with a brief discussion on potential implication of transition and transversion bias in directed evolution experiments.
authors.affiliation: International University Bremen, School of Engineering and Science, Bremen, Germany.
authors.forename: Tuck Seng
authors.initials: TS
authors.lastname: Wong
authors.forename: Danilo
authors.initials: D
authors.lastname: Roccatano
authors.forename: Ulrich
authors.initials: U
authors.lastname: Schwaneberg
mesh_terms: D000465:Algorithms; D019943:Amino Acid Substitution / Q000235:genetics; D003198:Computer Simulation; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry* / Q000235:genetics*; D019143:Evolution, Molecular; D006418:Heme / Q000737:chemistry / Q000235:genetics; D008956:Models, Chemical; D008957:Models, Genetic; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed / Q000379:methods*; D009154:Mutation; D017434:Protein Structure, Tertiary; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D006418:Heme; D003577:Cytochrome P-450 Enzyme System