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VX hydrolysis by human serum paraoxonase 1: a comparison of experimental and computational results.

Peterson MW, Fairchild SZ, Otto TC, Mohtashemi M, Cerasoli DM, Chang WE - PLoS ONE (2011)

Bottom Line: The average Vina interaction energies for different clusters were compared to the experimentally determined activities of HuPON1 variants to determine which computational procedures best predict how well HuPON1 variants will hydrolyze VX.The analysis showed that only conformations which have the attacking hydroxyl group of VX(ts) coordinated by the sidechain oxygen of D269 have a significant correlation with experimental results.The results from this study can be used for further characterization of how HuPON1 hydrolyzes VX and design of HuPON1 variants with increased activity against VX.

View Article: PubMed Central - PubMed

Affiliation: The MITRE Corporation, Bedford, Massachusetts, United States of America.

ABSTRACT
Human Serum paraoxonase 1 (HuPON1) is an enzyme that has been shown to hydrolyze a variety of chemicals including the nerve agent VX. While wildtype HuPON1 does not exhibit sufficient activity against VX to be used as an in vivo countermeasure, it has been suggested that increasing HuPON1's organophosphorous hydrolase activity by one or two orders of magnitude would make the enzyme suitable for this purpose. The binding interaction between HuPON1 and VX has recently been modeled, but the mechanism for VX hydrolysis is still unknown. In this study, we created a transition state model for VX hydrolysis (VX(ts)) in water using quantum mechanical/molecular mechanical simulations, and docked the transition state model to 22 experimentally characterized HuPON1 variants using AutoDock Vina. The HuPON1-VX(ts) complexes were grouped by reaction mechanism using a novel clustering procedure. The average Vina interaction energies for different clusters were compared to the experimentally determined activities of HuPON1 variants to determine which computational procedures best predict how well HuPON1 variants will hydrolyze VX. The analysis showed that only conformations which have the attacking hydroxyl group of VX(ts) coordinated by the sidechain oxygen of D269 have a significant correlation with experimental results. The results from this study can be used for further characterization of how HuPON1 hydrolyzes VX and design of HuPON1 variants with increased activity against VX.

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Predicted binding conformation of WT HuPON1 and VXts(+) according to the D269-based hydrolysis mechanism.The specific binding method utilized the ITASSER/SMD structure of HuPON1 with ds = 1.25 Å and dt = 2.00 Å. The structure has been energy minimized in Jaguar [31] using the OPLS energy function [32] with distance constraints on the breaking P-S bond and the nascent O-P bond. A full water molecule was utilized as the nucleophilic group for proper charge modeling.
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pone-0020335-g004: Predicted binding conformation of WT HuPON1 and VXts(+) according to the D269-based hydrolysis mechanism.The specific binding method utilized the ITASSER/SMD structure of HuPON1 with ds = 1.25 Å and dt = 2.00 Å. The structure has been energy minimized in Jaguar [31] using the OPLS energy function [32] with distance constraints on the breaking P-S bond and the nascent O-P bond. A full water molecule was utilized as the nucleophilic group for proper charge modeling.

Mentions: Figure 4 illustrates some key features of the binding methods with significant correlations. Here, the VXts P(+) model is bound to the ITASSER/SMD structure of HuPON1 according to the D269-based hydrolysis mechanism. The attacking hydroxide ion has been converted to a full water for proper charge modeling, and the entire structure has been minimized using the OPLS molecular mechanical energy function with distance constraints on the breaking P-S bond and nascent O-P bond (to preserve the transition state geometry). The resulting structure illustrates many features that were predicted in previous binding studies with HuPON1 and VX. Specifically, the lone oxygen from VX is found to form a direct interaction with the HuPON1 active site calcium while the hydrophobic tail of VX points outward from the enzyme active site. Figure 4 also illustrates that the attacking water is oriented so its oxygen atom is near the phosphorus atom of VX and one of its hydrogen atoms is near a side-chain oxygen of D269. Interestingly, the water molecule's other hydrogen atom is found adjacent to a sidechain oxygen of residue E53. This raises the possibility that D269 and E53 may both help stabilize a water molecule while it attacks VX's phospho-sulfur bond, with each residue using one of its sidechain oxygen's to help stabilize a hydrogen on the attacking water molecule.


VX hydrolysis by human serum paraoxonase 1: a comparison of experimental and computational results.

Peterson MW, Fairchild SZ, Otto TC, Mohtashemi M, Cerasoli DM, Chang WE - PLoS ONE (2011)

Predicted binding conformation of WT HuPON1 and VXts(+) according to the D269-based hydrolysis mechanism.The specific binding method utilized the ITASSER/SMD structure of HuPON1 with ds = 1.25 Å and dt = 2.00 Å. The structure has been energy minimized in Jaguar [31] using the OPLS energy function [32] with distance constraints on the breaking P-S bond and the nascent O-P bond. A full water molecule was utilized as the nucleophilic group for proper charge modeling.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105050&req=5

pone-0020335-g004: Predicted binding conformation of WT HuPON1 and VXts(+) according to the D269-based hydrolysis mechanism.The specific binding method utilized the ITASSER/SMD structure of HuPON1 with ds = 1.25 Å and dt = 2.00 Å. The structure has been energy minimized in Jaguar [31] using the OPLS energy function [32] with distance constraints on the breaking P-S bond and the nascent O-P bond. A full water molecule was utilized as the nucleophilic group for proper charge modeling.
Mentions: Figure 4 illustrates some key features of the binding methods with significant correlations. Here, the VXts P(+) model is bound to the ITASSER/SMD structure of HuPON1 according to the D269-based hydrolysis mechanism. The attacking hydroxide ion has been converted to a full water for proper charge modeling, and the entire structure has been minimized using the OPLS molecular mechanical energy function with distance constraints on the breaking P-S bond and nascent O-P bond (to preserve the transition state geometry). The resulting structure illustrates many features that were predicted in previous binding studies with HuPON1 and VX. Specifically, the lone oxygen from VX is found to form a direct interaction with the HuPON1 active site calcium while the hydrophobic tail of VX points outward from the enzyme active site. Figure 4 also illustrates that the attacking water is oriented so its oxygen atom is near the phosphorus atom of VX and one of its hydrogen atoms is near a side-chain oxygen of D269. Interestingly, the water molecule's other hydrogen atom is found adjacent to a sidechain oxygen of residue E53. This raises the possibility that D269 and E53 may both help stabilize a water molecule while it attacks VX's phospho-sulfur bond, with each residue using one of its sidechain oxygen's to help stabilize a hydrogen on the attacking water molecule.

Bottom Line: The average Vina interaction energies for different clusters were compared to the experimentally determined activities of HuPON1 variants to determine which computational procedures best predict how well HuPON1 variants will hydrolyze VX.The analysis showed that only conformations which have the attacking hydroxyl group of VX(ts) coordinated by the sidechain oxygen of D269 have a significant correlation with experimental results.The results from this study can be used for further characterization of how HuPON1 hydrolyzes VX and design of HuPON1 variants with increased activity against VX.

View Article: PubMed Central - PubMed

Affiliation: The MITRE Corporation, Bedford, Massachusetts, United States of America.

ABSTRACT
Human Serum paraoxonase 1 (HuPON1) is an enzyme that has been shown to hydrolyze a variety of chemicals including the nerve agent VX. While wildtype HuPON1 does not exhibit sufficient activity against VX to be used as an in vivo countermeasure, it has been suggested that increasing HuPON1's organophosphorous hydrolase activity by one or two orders of magnitude would make the enzyme suitable for this purpose. The binding interaction between HuPON1 and VX has recently been modeled, but the mechanism for VX hydrolysis is still unknown. In this study, we created a transition state model for VX hydrolysis (VX(ts)) in water using quantum mechanical/molecular mechanical simulations, and docked the transition state model to 22 experimentally characterized HuPON1 variants using AutoDock Vina. The HuPON1-VX(ts) complexes were grouped by reaction mechanism using a novel clustering procedure. The average Vina interaction energies for different clusters were compared to the experimentally determined activities of HuPON1 variants to determine which computational procedures best predict how well HuPON1 variants will hydrolyze VX. The analysis showed that only conformations which have the attacking hydroxyl group of VX(ts) coordinated by the sidechain oxygen of D269 have a significant correlation with experimental results. The results from this study can be used for further characterization of how HuPON1 hydrolyzes VX and design of HuPON1 variants with increased activity against VX.

Show MeSH