pochapskyThomas C. Pochapsky, Ph.D.
Professor of Chemistry
Protein Structure

Ph.D., University of Illinois at Urbana-Champaign

Contact Information
Pochapsky Lab Home Page

Our group is interested in how biomolecules such as enzymes and proteins do their jobs.  Nature has had a very long time (4 billion years!) to come up with just the right combinations of sequence and fold to accomplish all of the biochemical tasks required by a living organism.  We don't have quite that long, so we use a variety of biophysical and molecular biological methods to try and tease out the details of protein structure and function.  Our aim is to be able to apply what we learn to such things as rational drug design and protein engineering.
Cytochrome P450 monooxygenases catalyze the selective oxidation of unactivated C-H and C-C bonds by molecular oxygen, and this activity is critical for diverse biological functions including steroid hormone biosynthesis, drug and xenobiotic metabolism and clearance, and pro-drug activation.  We are the first group to apply high-resolution NMR methods to understanding structure-activity relationships in the P450 superfamily.  NMR offers a unique perspective on these enzymes, as it allows atomic-resolution detail of the enzymes as they exist in solution.  The P450 reaction cycle is complicated, requiring multiple substrate binding, electron and proton transfer steps, with interactions between redox partners and effector molecules leading to poorly understood conformational changes.  We have identified critical (and previously unrecognized) conformational changes that occur during the course of the reaction cycle, and have pinpointed particular residues that are involved in those changes using NMR and mutagenesis.  We are currently using a combination of enzyme activity assays, site-directed mutagenesis and NMR to “evolve”  new P450 enzymes based on the well-understood cytochrome P450cam (Figure 1).  Our aim is to produce new enzymes that combine the efficiency and selectivity of the wild-type enzyme with modified substrate selectivity/product specificity.  We envision a family of enzymes, each with its own particular substrate/product combination, that can be used for environmentally friendly manufacturing of fine chemicals.

figure 1
Figure 1. Cytochrome P450cam

Selected Publications:

Deshpande AR, Wagenpfeil K, Pochapsky TC, Petsko GA and Ringe D (2016). "Metal-Dependent Function of a Mammalian Acireductone Dioxygenase." Biochemistry 55(9): 1398-1407.

Colthart AM, Tietz DR, Ni Y, Friedman JL, Dang M and Pochapsky TC (2016). "Detection of substrate-dependent conformational changes in the P450 fold by nuclear magnetic resonance." Sci Rep 2016 Feb 25;6:22035. .

Pochapsky TC (2015). "From intrinsically disordered protein to context-dependent folding: The alpha-synuclein tetramer is teased out of hiding." Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):9502-3

Zhang Y, Zhou N, Shi J, Pochapsky SS, Pochapsky TC, Zhang B, Zhang X and Xu B(2015). "Unfolding a molecular trefoil derived from a zwitterionic metallopeptide to form self-assembled nanostructures." Nat Commun. 2015 Feb 19;6:6165.

Pochapsky TC (2014). "Examining how enzymes self-organize in a membrane." Proc Natl Acad Sci USA. 2014 Mar 11;111(10):3659-60.

Gurry T, Ullman O, Fisher CK, Perovic I, Pochapsky T and Stultz CM (2013). "The dynamic structure of alpha-synuclein multimers." J Am Chem Soc. 2013 Mar 13;135(10):3865-72

Li S, Tietz DR, Rutaganira FU, Kells PM, Anzai Y, Kato F, Pochapsky TC, Sherman DH and Podust LM (2012). "Substrate Recognition by the Multifunctional Cytochrome P450 MycG in Mycinamicin Hydroxylation and Epoxidation Reactions." J Biol Chem 287(45): 37880-37890.

Asciutto EK, Young MJ, Madura J, Pochapsky SS and Pochapsky TC (2012). "Solution Structural Ensembles of Substrate-Free Cytochrome P450(cam)." Biochemistry 51(16): 3383-3393.

Wang W, Perovic I, Chittuluru J, Kaganovich A, Nguyen LT, Liao J, Auclair JR, Johnson D, Landeru A, Simorellis AK, Ju S, Cookson MR, Asturias FJ, Agar JN, Webb BN, Kang C, Ringe D, Petsko GA, Pochapsky TC and Hoang QQ (2011). "A soluble alpha-synuclein construct forms a dynamic tetramer." Proc Natl Acad Sci U S A 108(43): 17797-17802.

Friedman EJ, Wang HX, Jiang K, Perovic I, Deshpande A, Pochapsky TC, Temple BR, Hicks SN, Harden TK, Jones AM (2011). "ACI-reductone dioxygenase 1 (ARD1) is an effector of the heterotrimeric G protein beta subunit in Arabidopsis." J Biol Chem. 2011 Aug 26;286(34):30107-18.

Asciutto EK, Dang M, Pochapsky SS, Madura JD, Pochapsky TC (2011). "Experimentally restrained molecular dynamics simulations for characterizing the open states of cytochrome P450cam." Biochemistry. 2011 Mar 15;50(10):1664-71.

Dang M, Pochapsky SS, Pochapsky TC (2011). "Spring-loading the active site of cytochrome P450cam." Metallomics. 2011 Apr 1;3(4):339-43.

Pochapsky TC, Kazanis S, Dang M (2010). "Conformational plasticity and structure/function relationships in cytochromes P450." Antioxid Redox Signal. 2010 Oct;13(8):1273-96.

Pochapsky SS, Dang M, OuYang B, Simorellis AK, Pochapsky TC (2009). "Redox-dependent dynamics in cytochrome P450cam." Biochemistry. 2009 May 26;48(20):4254-61.

Asciutto EK, Madura JD, Pochapsky SS, OuYang B, Pochapsky TC (2009). "Structural and dynamic implications of an effector-induced backbone amide cis-trans isomerization in cytochrome P450cam. " J Mol Biol. 2009 May 15;388(4):801-14.

Zhang W, Pochapsky SS, Pochapsky TC, Jain NU (2008). "Solution NMR structure of putidaredoxin-cytochrome P450cam complex via a combined residual dipolar coupling-spin labeling approach suggests a role for Trp106 of putidaredoxin in complex formation." J Mol Biol. 2008 Dec 12;384(2):349-63.

OuYang B, Pochapsky SS, Dang M, and Pochapsky TC (2008). "A Functional Proline Switch in Cytochrome P450cam." Structure. 2008 May 7;16(5).

OuYang B, Pochapsky SS, Pagani GM, Pochapsky TC (2006). "Specific effects of potassium ion binding on wild-type and L358P cytochrome P450cam." Biochemistry. 2006 Dec 5;45(48):14379-88 .

Ju T, Goldsmith RB, Chai SC, Maroney MJ, Pochapsky SS, Pochapsky TC. (2006). "One protein, two enzymes revisited: a structural entropy switch interconverts the two isoforms of acireductone dioxygenase." J Mol Biol. 2006 Nov 3;363(4):823-34.

Rui L, Pochapsky SS, Pochapsky TC. (2006). "Comparison of the complexes formed by cytochrome P450cam with cytochrome b5 and putidaredoxin, two effectors of camphor hydroxylase activity." Biochemistry. 2006 Mar 28;45(12):3887-97..

Pochapsky TC, Pochapsky SS, Ju T, Hoefler C, Liang J. (2006). "A refined model for the structure of acireductone dioxygenase from Klebsiella ATCC 8724 incorporating residual dipolar couplings." J Biomol NMR. 2006 Feb;34(2):117-27.

Sauter M, Lorbiecke R, Ouyang B, Pochapsky TC, Rzewuski G. (2005). "The immediate-early ethylene response gene OsARD1 encodes an acireductone dioxygenase involved in recycling of the ethylene precursor S-adenosylmethionine." Plant J. 2005 Dec;44(5):718-29.

Wei JY, Pochapsky TC and Pochapsky SS (2005). "Detection of a High-Barrier Conformational Change in the Active Site of Cytochrome P450cam upon Binding of Putidaredoxin." Journal of the American Chemical Society, 127: 6974-6976.

Zhang Y, Heinsen MH, Kostic M, Pagani GM, Riera TV, Perovic I, Hedstrom L, Snider BB, Pochapsky TC (2004). "Analogs of 1-phosphonooxy-2,2-dihydroxy-3-oxo-5-(methylthio)pentane, an acyclic intermediate in the methionine salvage pathway: a new preparation and characterization of activity with E1 enolase/phosphatase from Klebsiella oxytoca." Bioorg Med Chem. 12:3847-55.

Kostic M., Bernhardt R, Pochapsky TC. (2003) "A conserved histidine in vertebrate-type ferredoxins is critical for redox-dependent dynamics." Biochemistry. 42:8171-82.

Pochapsky SS, Pochapsky TC, Wei JW. (2003). "A model for effector activity in a highly specific biological electron transfer complex: the cytochrome P450(cam)-putidaredoxin couple." Biochemistry. 42:5649-56.

Pochapsky TC, Pochapsky SS, Ju T, Mo H, Al-Mjeni F, Maroney MJ. (2002). "Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae." Nat Struct Biol. 9:966-72.

Kostic M, Pochapsky TC, Pochapsky SS. (2002). "Rapid Recycle 13C, 15N and 13C, 13C' Heteronuclear and Homonuclear Multiple Quantum Coherence Detection for Resonance Assignments in Paramagnetic Proteins: Example of Ni+2-Containing Acireductone Dioxygenase (ARD)." J. Am. Chem. Soc., 124(31):9054-9055.

Kostic M, Pochapsky SS, Pochapsky TC, Obenauer J, Mo H, Pagani GM and Pejchal R (2002). "Comparison of functional domains in vertebrate-type ferredoxins." Biochemistry 41: 5978-5989.

Al-Mjeni F, Ju T, Pochapsky TC, and Maroney MJ (2002). "XAS Investigation of the Structure and Function of Ni in Acireductone Dioxygenase." Biochemistry 41: 6761-6769.

Mukhopadhyay R, Wong LL, Lo KK, Pochapsky T and Hill HA. "A Molecular Level Study of Complex Formation between Putidaredoxin and Cytochrome P450 by Scanning Tunneling Microscopy." (2002) Physical Chemistry Chemical Physics 641-646.

Pochapsky TC and Pochapsky SS. (2001). "Nuclear magnetic resonance as a tool in drug discovery, metabolism and disposition." Curr. Top. Med. Chem. 1: 427-441.

Pochapsky TC, Kostic M, Jain N, Pejchal R (2001). "Redox-dependent conformational selection in a Cys4Fe2S2 ferredoxin." Biochemistry 19: 5602-5614.

Dai Y, Pochapsky TC and Abeles RH. (2001). "Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae." Biochemistry, 40: 6379-6387

Pochapsky TC and Hofstetter C (2000) "BF4- as a probe for ion pair solution structure using interionic one- and two-dimensional 19F{1H} NOEs." Magn. Reson. Chem. 38: 90-94.

Pereira de Araujo AF, Pochapsky TC, Joughin B (1999). "Thermodynamics of interactions between amino acid side chains: experimental differentiation of aromatic-aromatic, aromatic-aliphatic, and aliphatic-aliphatic side-chain interactions in water." Biophys J. 76: 2319-28.

Mo H, Pochapsky SS, Pochapsky TC (1999). "A model for the solution structure of oxidized terpredoxin, a Fe2S2 ferredoxin from Pseudomonas." Biochemistry. 38: 5666-75.

Pochapsky TC, Jain NU, Kuti M, Lyons TA, Heymont J (1999). "A refined model for the solution structure of oxidized putidaredoxin." Biochemistry. 38: 4681-90.

Jain NU, Pochapsky TC. (1999). "A new assignment strategy for the hyperfine-shifted 13C and 15N resonances in Fe2S2 ferredoxins." Biochem Biophys Res Commun. 258: 54-9.

Arico-Muendel CC, Patera A, Pochapsky TC, Kuti M, Wolfson AJ. (1999). "Solution structure and dynamics of a serpin reactive site loop using interleukin 1beta as a presentation scaffold." Protein Eng. 12:189-202.

Mo H, Dai Y, Pochapsky SS, Pochapsky TC. (1999). "1H, 13C and 15N NMR assignments for a carbon monoxide generating metalloenzyme from Klebsiella pneumoniae." J Biomol NMR. 14: 287-8.

Pochapsky TC. (1999). "Designed molecular recognition: A commentary on possible design elements." Enantiomer 4: 437-444.

Pochapsky TC, Hofstetter C and Wilkinson PS. (1999). "NMR structure determination of ion pairs derived from quinine: A model for templating in asymmetric phase transfer reductions by BH4- with implications for rational design of phase transfer catalysts." J. Org. Chem. 64: 8794-8800.


Last update: June 9. 2016.
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