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In Silico Biology 10, 0010 (2010); ©2009, Bioinformation Systems e.V.  



A combination of evolutionary trace method, molecular surface accessibility and hydrophobicity analysis to design a high hydrophobicity laccase

Saharuddin Bin Mohamad1*, Ai Ling Ong2, Raja Farhana Khairuddin3 and Adiratna Mat Ripen4

1 Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
2Multimedia University, Jalan Ayer Keroh Lama, 75450 Melaka, Malaysia
3Department of Biology, Faculty of Science and Technology, Universiti Pendidikan Sultan Idris, 35900 Tanjong Malim, Perak
4Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia

* Corresponding author
   Email: saharuddin@um.edu.my


Edited by E. Wingender; received June 13, 2009; revised October 18, 2009; accepted November 02, 2009; published March 14, 2010


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.


Keywords: laccase, evolutionary trace (ET) analysis, enzymatic bioremediation, hydrophobicity, polycyclic aromatic hydrocarbons (PAHs)