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Molecular Modeling of Chemoreceptor:Ligand Interactions

  • Asuka A. Orr
  • Arul Jayaraman
  • Phanourios Tamamis
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1729)

Abstract

Docking algorithms have been widely used to elucidate ligand:receptor interactions that are important in biological function. Here, we introduce an in-house developed docking-refinement protocol that combines the following innovative features. (1) The use of multiple short molecular dynamics (MD) docking simulations, with residues within the binding pocket of the receptor unconstrained, so that the binding modes of the ligand in the binding pocket may be exhaustively examined. (2) The initial positioning of the ligand within the binding pocket based on complementary shape, and the use of both harmonic and quartic spherical potentials to constrain the ligand in the binding pocket during multiple short docking simulations. (3) The selection of the most probable binding modes generated by the short docking simulations using interaction energy calculations, as well as the subsequent application of all-atom MD simulations and physical-chemistry based free energy calculations to elucidate the most favorable binding mode of the ligand in complex with the receptor. In this chapter, we provide step-by-step instructions on how to computationally investigate the binding of small-molecule ligands to protein receptors by examining as control and test cases, respectively, the binding of l-serine and R-3,4-dihydroxymandelic acid (R-DHMA) to the Escherichia coli chemoreceptor Tsr. Similar computational strategies can be used for the molecular modeling of a series of ligand:protein receptor interactions.

Keywords

Chemoattractants 3,4-Dihydroxymandelic acid (DHMA) Chemoreceptor Tsr Molecular docking Molecular dynamics simulations 

Notes

Acknowledgments

We thank the Texas A&M High Performance Research Computing Facility for the use of the Ada supercomputing cluster, where all MD simulations and free energy calculations were performed. This study is supported by start-up funding from the Artie McFerrin Department of Chemical Engineering at Texas A&M University awarded to P.T. and the Texas A&M University Graduate Diversity Fellowship from the TAMU Office of Graduate and Professional Studies awarded to A.A.O.

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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Asuka A. Orr
    • 1
  • Arul Jayaraman
    • 1
  • Phanourios Tamamis
    • 1
  1. 1.Artie McFerrin Department of Chemical EngineeringTexas A&M UniversityCollege StationUSA

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