title: The effect of conformational variability of phosphotriesterase upon N-acyl-L-homoserine lactone and paraoxon binding: insights from molecular dynamics studies.
abstract: The organophosphorous hydrolase (PTE) from Brevundimonas diminuta is capable of degrading extremely toxic organophosphorous compounds with a high catalytic turnover and broad substrate specificity. Although the natural substrate for PTE is unknown, its loop remodeling (loop 7-2/H254R) led to the emergence of a homoserine lactonase (HSL) activity that is undetectable in PTE (kcat/km values of up to 2 × 10(4)), with only a minor decrease in PTE paraoxonase activity. In this study, homology modeling and molecular dynamics simulations have been undertaken seeking to explain the reason for the substrate specificity for the wild-type and the loop 7-2/H254R variant. The cavity volume estimated results showed that the active pocket of the variant was almost two fold larger than that of the wild-type (WT) enzyme. pKa calculations for the enzyme (the WT and the variant) showed a significant pKa shift from WT standard values (ΔpKa = 3.5 units) for the His254 residue (in the Arg254 variant). Molecular dynamics simulations indicated that the displacement of loops 6 and 7 over the active site in loop 7-2/H254R variant is useful for N-acyl-L-homoserine lactone (C4-HSL) with a large aliphatic chain to site in the channels easily. Thence the expanding of the active pocket is beneficial to C4-HSL binding and has a little effect on paraoxon binding. Our results provide a new theoretical contribution of loop remodeling to the rapid divergence of new enzyme functions.
authors.forename: Dongling
authors.initials: D
authors.lastname: Zhan
authors.forename: Zhenhuan
authors.initials: Z
authors.lastname: Zhou
authors.forename: Shanshan
authors.initials: S
authors.lastname: Guan
authors.affiliation: Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130023, China. weiweihan@jlu.edu.cn.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Han
mesh_terms: D015107:4-Butyrolactone / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D000595:Amino Acid Sequence; D001665:Binding Sites; D006860:Hydrogen Bonding; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010261:Paraoxon / Q000737:chemistry* / Q000378:metabolism; D044345:Phosphoric Triester Hydrolases / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D015203:Reproducibility of Results; D016415:Sequence Alignment; D013379:Substrate Specificity
chemical_list: C088386:homoserine lactone; D044345:Phosphoric Triester Hydrolases; D015107:4-Butyrolactone; D010261:Paraoxon