Molecular modelling and quantum biochemistry computations of a naturally occurring bioremediation enzyme: Alkane hydroxylase from Pseudomonas putida P1

• Published in: Journal of molecular graphics & modelling 2017-10, Vol.77, p.232-239
• Main Authors: de Sousa, B.G., Oliveira, J.I.N., Albuquerque, E.L., Fulco, U.L., Amaro, V.E., Blaha, C.A.G.
• Format: Article
• Language: English
• Subjects: 3-D homology modelling; Alkane hydroxylase; Alkanes - chemistry; Binding energy; Biodegradation, Environmental; Cytochrome P-450 CYP4A - chemistry; Models, Molecular; Octanes - chemistry; Pseudomonas putida - enzymology; Pseudomonas putida P1; Quantum chemistry approach; Quantum Theory
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2017.08.021

[Display omitted] •Through the 3-D homology modelling it was possible to predict the atomic structural arrangement of AlkB enzyme in the cytoplasmic region.•We detected the preferred position of the octane molecule in Cytosolic Binding Pocket, namely the AlkB_P1one.•Ala53, Trp55, Val15 and Tyr339 of AlkBenzyme are involved with the octane/uptake, octanol/exit, and the 1-octyne/up take molecule. Many species of bacteria involved in degradation of n-alkanes have an important constitutional metabolic enzyme, the alkane hydroxylase called AlkB, specialized in the conversion of hydrocarbons molecules that can be used as carbon and/or energy source. This enzyme plays an important role in the microbial degradation of oil, chlorinated hydrocarbons, fuel additives, and many other compounds. A number of these enzymes has been biochemically characterized in detail because the potential of alkane hydroxylases to catalyse high added-value reactions is widely recognized. Nevertheless, the industrial and process bioremediation application of them is restricted, owing to their complex biochemistry, challenging process requirements, and the limited number of their three-dimensional structures. Furthermore, AlkB has great potential as biocatalysts for selective transformation of a wide range of chemically inert unreactive alkanes into reactive chemical precursors that can be used as tools for bioremediation and bioprocesses. Aiming to understand the possible ways the AlkB enzyme Pseudomonas putida P1 interacts with octane, octanol and 1-octyne, we consider its suitable biochemical structure taking into account a 3-D homology modelling. Besides, by using a quantum chemistry computational model based on the density functional theory (DFT), we determine possible protein-substrate interaction regions measured by means of its binding energy simulated throughout the Molecular Fractionation with Conjugated Caps (MFCC) approach.