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Related Experiment Videos

Structural and conformational changes concomitant with the E1-E2 transition in H(+)K(+)-ATPase: a comparative protein

P Hima Bindu1, G Madhavi Sastry, U Suryanarayana Murty

  • 1Molecular Modelling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Hyderabad 500007, India.

Biochemical and Biophysical Research Communications
|June 5, 2004
PubMed
Summary

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Comparative modeling of gastric H(+)K(+)-ATPase shows E1-E2 transitions cause major tertiary structural changes, particularly in cytoplasmic and transmembrane regions. Activity retention is linked to buried side chain areas in key residues.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biophysics

Background:

  • The gastric H(+)K(+)-ATPase (proton pump) is crucial for digestion.
  • Understanding its conformational changes is key to drug development.
  • Previous studies hinted at structural rearrangements during ion transport.

Purpose of the Study:

  • To investigate the structural dynamics of gastric H(+)K(+)-ATPase during the E1-E2 conformational transition.
  • To identify key regions and residues involved in these structural changes.
  • To correlate structural alterations with enzyme activity and ion binding specificity.

Main Methods:

  • Comparative molecular modeling of conserved regions of the gastric H(+)K(+)-ATPase.
  • Analysis of tertiary and secondary structural deviations during the E1-E2 transition.

Related Experiment Videos

  • Calculation of buried side chain areas for inhibitor-binding residues.
  • Site-directed mutagenesis simulations (in silico) of transmembrane helix 6 (TM6) residues.
  • Assessment of residue side chain exposure to polar atoms.

    • Main Results:

    • The E1-E2 transition significantly alters tertiary structure while preserving secondary structure.
    • Residues 516-530 (cytoplasmic) and TM10 (transmembrane) exhibit maximum tertiary structural changes.
    • Residues 249-304 show the largest secondary structural deviations.
    • Cys-815 and Cys-323 have smaller buried side chain areas in the E1 conformation.
    • In silico mutation of TM6 residues demonstrates a correlation between buried side chain area and enzyme activity.
    • Specific residues (E345, D826, V340, A341, V343, E822) show conformational specificity for ion binding.

    Conclusions:

    • The E1-E2 conformational transition of gastric H(+)K(+)-ATPase involves substantial tertiary structural rearrangements.
    • Specific cytoplasmic and transmembrane regions are hotspots for these structural changes.
    • Buried side chain area is a critical factor for enzyme activity and inhibitor binding.
    • Structural modeling provides insights into the mechanism of ion binding specificity.