Molecular basis of P450 OleTJE: an investigation of substrate binding mechanism and major pathways.
Cytochrome P450 OleTJEhas attracted much attention for its ability to catalyze the decarboxylation of long chain fatty acids to generate alkenes, which are not only biofuel molecule, but also can be used broadly for making lubricants, polymers and detergents. In this study, the molecular basis of the binding mechanism of P450 OleTJEfor arachidic acid, myristic acid, and caprylic acid was investigated by utilizing conventional molecular dynamics simulation and binding free energy calculations. Moreover, random acceleration molecular dynamics (RAMD) simulations were performed to uncover the most probable access/egress channels for different fatty acids. The predicted binding free energy shows an order of arachidic acid < myristic acid < caprylic acid. Key residues interacting with three substrates and residues specifically binding to one of them were identified. The RAMD results suggest the most likely channel for arachidic acid, myristic acid, and caprylic acid are 2e/2b, 2a and 2f/2a, respectively. It is suggested that the reaction is easier to carry out in myristic acid bound system than those in arachidic acid and caprylic acid bound system based on the distance of Hβ atom of substrate relative to P450 OleTJECompound I states. This study provided novel insight to understand the substrate preference mechanism of P450 OleTJEand valuable information for rational enzyme design for short chain fatty acid decarboxylation.
Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China.
Juan
http://orcid.org/0000-0001-5993-4949
J
Du
Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China.
Lin
L
Liu
Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China.
Li Zhong
LZ
Guo
College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China.
Xiao Jun
XJ
Yao
Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China. yjming888@126.com.
Jian Ming
JM
Yang
D002210:Caprylates / Q000737:chemistry*; D002384:Catalysis; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry*; D004537:Eicosanoic Acids / Q000737:chemistry*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D019814:Myristic Acid / Q000737:chemistry*; D010084:Oxidation-Reduction; D011485:Protein Binding; D011487:Protein Conformation; D015398:Signal Transduction; D013379:Substrate Specificity; D013816:Thermodynamics
D002210:Caprylates; D004537:Eicosanoic Acids; D019814:Myristic Acid; D003577:Cytochrome P-450 Enzyme System; C031492:octanoic acid; C094477:arachidic acid
Access/egress channels; Decarboxylation; Fatty acid; MM-GB/PBSA; Molecular dynamics simulation; P450 OleTJE; Random acceleration molecular dynamics simulation