Effect of pH on the structure and function of pyruvate dehydrogenase kinase 3: Combined spectroscopic and MD simulation studies

Saleha Anwar, Rajiv K. Kar, Md Anzarul Haque, Rashmi Dahiya, Preeti Gupta, Asimul Islam, Faizan Ahmad, Md Imtaiyaz Hassan

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Pyruvate dehydrogenase kinase-3 (PDK3) plays important role in the glucose metabolism and is associated with cancer progression, and thus being considered as an attractive target for cancer therapy. In this study, we employed spectroscopic techniques to study the structural and conformational changes in the PDK3 at varying pH conditions ranging from pH 2.0 to 12.0. UV/Vis, fluorescence and circular dichroism spectroscopic measurements revealed that PDK3 maintains its native-like structure (both secondary and tertiary) in the alkaline conditions (pH 7.0–12.0). However, a significant loss in the structure was observed under acidic conditions (pH 2.0–6.0). The propensity of aggregate formation at pH 4.0 was estimated by thioflavin T fluorescence measurements. To further complement structural data, kinase activity assay was performed, and maximum activity of PDK3 was observed at pH 7.0–8.0 range; whereas, its activity was lost under acidic pH. To further see conformational changes at atomistic level we have performed all-atom molecular dynamics at different pH conditions for 150 ns. A well defined correlation was observed between experimental and computational studies. This work highlights the significance of structural dependence of pH for wide implications in protein-protein interaction, biological function and drug design procedures.

Original languageEnglish (US)
Pages (from-to)768-777
Number of pages10
JournalInternational Journal of Biological Macromolecules
StatePublished - Mar 15 2020
Externally publishedYes


  • Cancer therapy
  • Glucose homeostasis
  • Kinase activity assay
  • MD simulation
  • Protein conformation
  • Protein folding
  • Pyruvate dehydrogenase kinase

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology
  • Biochemistry


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