title: A combination of evolutionary trace method, molecular surface accessibility and hydrophobicity analysis to design a high hydrophobicity laccase.
abstract: Laccases are industrially attractive enzymes and their applications have expanded to the field of bioremediation. The challenge of today's biotechnology in enzymatic studies is to design enzymes that not only have a higher activity but are also more stable and could fit well with the condition requirements. Laccases are known to oxidize non-natural substrates like polycyclic aromatic hydrocarbons (PAHs). We suppose by increasing the hydrophobicity of laccase, it would increase the chance of the enzyme to meet the hydrophobic substrates in a contamination site, therefore increasing the bioremediation efficacy of PAHs from environment. In this attempt, the applications of evolutionary trace (ET), molecular surface accessibility and hydrophobicity analysis on laccase sequences and laccase's crystal structure (1KYA) are described for optimal design of an enzyme with higher hydrophobicity. Our analysis revealed that Q23A, Q45I, N141A, Q237V, N262L, N301V, N331A, Q360L and Q482A could be promising exchanges to be tested in mutagenesis experiments.
authors.affiliation: Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia. saharuddin@um.edu.my
authors.forename: Saharuddin Bin
authors.initials: SB
authors.lastname: Mohamad
authors.forename: Ai Ling
authors.initials: AL
authors.lastname: Ong
authors.forename: Raja Farhana
authors.initials: RF
authors.lastname: Khairuddin
authors.forename: Adiratna Mat
authors.initials: AM
authors.lastname: Ripen
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D001673:Biodegradation, Environmental; D003198:Computer Simulation; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000737:chemistry* / Q000235:genetics; D057927:Hydrophobic and Hydrophilic Interactions; D042845:Laccase / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D011084:Polycyclic Aromatic Hydrocarbons / Q000737:chemistry; D015202:Protein Engineering; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D013499:Surface Properties; D055454:Trametes / Q000201:enzymology
chemical_list: D005656:Fungal Proteins; D011084:Polycyclic Aromatic Hydrocarbons; D042845:Laccase