Department of Chemistry

Thomas Pochapsky

Thomas PochapskyProfessor of Chemistry and Biochemistry

Group website

Degrees

University of Illinois, PhD
University of Pittsburgh, BSc

Profile

Our research is directed towards an understanding of non-covalent interactions in chemical and biochemical systems. We employ a variety of techniques in our work, but nuclear magnetic resonance is our most important tool. NMR can be used to obtain structures of complex macromolecules and is sensitive to molecular dynamics over a wide range of time scales. Equally important is the ability of NMR to provide information concerning intermolecular interactions via nuclear Overhauser effects. Combining NMR with other experimental and computational methods, we are actively investigating the following areas:

  • Enzymes in the methionine salvage pathway: structure and function
  • Monooxygenase enzyme systems: structure and dynamics
  • Closed-shell ion pair structure and dynamics
  • Amino acid interaction free energies for protein folding simulations: experimental and theoretical considerations

 

Selected Publications

  • A dynamic understanding of cytochrome P450 structure and function through solution NMR. Pochapsky TC. Curr Opin Biotechnol. 2021 Jun;69:35-42.
  • The Metal Drives the Chemistry: Dual Functions of Acireductone Dioxygenase. Deshpande AR, Pochapsky TC, Ringe D. Chem Rev. 2017 Aug 9;117(15):10474-10501. 
  • Analysis of α-synuclein species enriched from cerebral cortex of humans with sporadic dementia with Lewy bodies. Sanderson JB, De S, Jiang H, Rovere M, Jin M, Zaccagnini L, Hays Watson A, De Boni L, Lagomarsino VN, Young-Pearse TL, Liu X, Pochapsky TC, Hyman BT, Dickson DW, Klenerman D, Selkoe DJ, Bartels T. Brain Commun. 2020;2(1):fcaa010.
  • Dual chemistry catalyzed by human acireductone dioxygenase. Deshpande AR, Pochapsky TC, Petsko GA, Ringe D. Protein Eng Des Sel. 2017 Mar 1;30(3):197-204. 
  • A Model for the Solution Structure of Human Fe(II)-Bound Acireductone Dioxygenase and Interactions with the Regulatory Domain of Matrix Metalloproteinase I (MMP-I). Liu X, Garber A, Ryan J, Deshpande A, Ringe D, Pochapsky TC. Biochemistry. 2020 Nov 10;59(44):4238-4249.
  • Substrate recognition by two different P450s: Evidence for conserved roles in a common fold. Tietz DR, Colthart AM, Sondej Pochapsky S, Pochapsky TC. Sci Rep. 2017 Oct 19;7(1):13581.
  • Some Surprising Implications of NMR-directed Simulations of Substrate Recognition and Binding by Cytochrome P450cam (CYP101A1). Asciutto EK, Pochapsky TC. J Mol Biol. 2018 Apr 27;430(9):1295-1310.
  • Human acireductone dioxygenase (HsARD), cancer and human health: Black hat, white hat or gray? Liu X, Pochapsky TC. Inorganics (Basel). 2019 Aug;7(8):101.
  • A new approach to understanding structure-function relationships in cytochromes P450 by targeting terpene metabolism in the wild. Wong NR, Liu X, Lloyd H, Colthart AM, Ferrazzoli AE, Cooper DL, Zhuang Y, Esquea P, Futcher J, Pochapsky TM, Matthews JM, Pochapsky TC.  J Inorg Biochem. 2018 Nov;188:96-101. 
  • NADH reduction of nitroaromatics as a probe for residual ferric form high-spin in a cytochrome P450. Pochapsky TC, Wong N, Zhuang Y, Futcher J, Pandelia ME, Teitz DR, Colthart AM. Biochim Biophys Acta Proteins Proteom. 2018 Jan;1866(1):126-133.
  • Detection of substrate-dependent conformational changes in the P450 fold by nuclear magnetic resonance. Colthart AM, Tietz DR, Ni Y, Friedman JL, Dang M, Pochapsky TC. Sci Rep. 6:22035 (2016).
  • Metal-Dependent Function of a Mammalian Acireductone Dioxygenase. Deshpande AR, Wagenpfeil K, Pochapsky TC, Petsko GA, Ringe D. Biochemistry. 55(9):1398-407 (2016).
  • From intrinsically disordered protein to context-dependent folding: The α-synuclein tetramer is teased out of hiding. Pochapsky TC. Proc Natl Acad Sci U S A. 112(31):9502-3 (2015).
  • Unfolding a molecular trefoil derived from a zwitterionic metallopeptide to form self-assembled nanostructures. Zhang Y, Zhou N, Shi J, Pochapsky SS, Pochapsky TC, Zhang B, Zhang X, Xu B. Nat Commun. 6:6165 (2015).