European Biophysics Journal

, Volume 41, Issue 2, pp 241–248 | Cite as

Docking and molecular dynamics simulation studies on glycation-induced conformational changes of human paraoxonase 1

  • Ammara Saleem
  • S. Sikander Azam
  • Shamshad Zarina
Original Paper
First Online:
Received:
Revised:
Accepted:

Abstract

Human paraoxonase 1 (huPON1) is a calcium-dependent esterase responsible for hydrolysis of a wide variety of substrates including organophosphates, esters, lactones, and paraoxon. Although its natural substrate is unknown, the action of PON as an antioxidant is well documented. Because recent reports have suggested glycation may induce reduced PON activity in diabetes, we investigated the structural features of huPON1 and its glycated mutant by template-based modeling, docking, and molecular dynamics (MD) simulations. Our results corroborated the importance of the His115–His134 dyad in both the lactonase and paraoxonase activity of huPON1. Structural alterations in the glycated model reflected weak interactions between the docked substrate and the active site cleft. We also used MD simulation to gain insight into glycation-induced conformational changes of huPON1 and the implication of this on depleted enzymatic activity. The catalytic calcium found on the surface interacts with the side chain oxygen of residues, including Asn224, Asn270, Asn168, Asp269, and Glu53, and this interaction with the respective residues undergoes minor displacement on glycation. The root-mean-square fluctuation had high motional flexibility in the non-glycated model whereas the conformation of the glycated structure was comparatively stable. Our findings emphasize the consequence of glycation-induced alterations and their effect on overall enzymatic activity.

Keywords

Human paraoxonase 1 Paraoxon Lactones Molecular dynamics Glycation Structure prediction 
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Notes

Acknowledgments

Financial support provided by Higher Education Commission, Pakistan, (grant no. 20-752) is gratefully acknowledged. The authors are grateful to David M. Case and his team for providing the license for the Amber 10 software.

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Copyright information

© European Biophysical Societies' Association 2011

Authors and Affiliations

  • Ammara Saleem
    • 1
  • S. Sikander Azam
    • 1
    • 2
  • Shamshad Zarina
    • 1
  1. 1.National Center for ProteomicsUniversity of KarachiKarachiPakistan
  2. 2.National Center for BioinformaticsQuaid-i-Azam UniversityIslamabadPakistan

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