User:Basya
Design of Novel Semisynthetic Metalloenzyme from Thermolysin
Mohd Basyaruddin Abdul Rahman*1, Ahmad Haniff Jaafar1, Mahiran Basri1, Raja Noor Zaliha Raja Abdul Rahman2, Abu Bakar Salleh2 and Habibah Abdul Wahab3 1Department of Chemistry, Faculty of Science, 2Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. 3Laborotary of Biocrystallography and Bioinformatic Structure, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia. Email: basya@science.upm.edu.my
Background Initial applications of biocatalysis involved the used of naturally occurring enzyme. With new challenges in green chemical reaction, biocatalyst that shed the light is metalloenzyme, which function as enzyme and contain metal that are tightly attached and always isolated with the protein [1]. In recent years, enzyme engineering has proven to be an invaluable tool for elucidating biocatalytic mechanisms as well as producing enzymes for industrial purposes. Approaches developed for in vivo chemical modification and in silico computational methods promise to increase the scope and have already been used successfully to alter existing protein so that they have better stability and functionality [2]. This task might be good to address in designing a new biocatalyst with improved properties.
Methods The AutoDock programme 3.05 was employed in order to identify the binding conformations of the ligands and the metal ions and to perform docking using Lamarckian Genetic Algorithm (LGA) [3]. The coordinate of thermolysin-substrate free structure coded as 1KEI was taken from Brookhaven Protein Data Bank (PDB).
Results The predicted KEI-ligand complexes with the lowest final docked energy for PSE and PHN were -6.71 kcal/mol at pocket 45 and -6.60 kcal/mol at pocket 47, respectively. Non-covalent interactions of hydrogen bond and hydrophobic interaction between protein and ligands established the final conformation. Analysis on finding the most favorable metal ions to dock onto each complex found that Mg2+ was docked onto KEI-PSE45 complex with final docked energy of -1.09 kcal/mol and performed four interactions with the PSE ligand. Meanwhile, Ca2+ represented the best metal ions to dock to the KEI-PHN47 complex with final docked energy of -4.12 kcal/mol and performed three interactions with the nearby residues.
Conclusions An important branch of novel protein design is through engineering and design of new metal-binding sites into native proteins. By employing in silico approach of molecular docking, screening of putative ligand for possible interactions may enhance the discovery of novel semisynthetic enzyme and lead to a new protein function. Finally, the framework which was introduced for the experiment may be a competent method for screening potential metal ions in this in vivo route.
References [1] R Davies, H Kuang, D Qi, A Mazhary, E Mayaan and M Distefeno: Artificial Metalloenzymes Based on Protein Cavities: Exploring the Effect of Altering the Metal Ligand Attachment Position by Site Directed Mutagenesis. J.Bioorg. Med. Chem. 1999, 9: 79-84. [2] MB Abdul Rahman, A Misran, H Abdul Wahab, RNZ Abdul Rahman, AB Salleh and M Basri: Screening and Docking of Chemical Ligands onto Pocket Cavities of Protease for Designing a Biocatalyst. Biocatal. Biotransform. 2005, 23: 211-216. [3] GM Morris, DS Goodsell, RS Halliday, R Huey, WE Hart, RK Belew and AJ Olson: Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19: 1639-1662.
