Office: 37A Schweitzer Hall
117 Schweitzer Hall
University of Missouri
Columbia, MO 65211
|BS||Oklahoma State University||Stillwater, Okla.||Biochemistry/Computer Science|
|PhD||University of Illinois||Urbana-Champaign, Ill.||Biophysics|
Our laboratory investigates molecular workings of enzymes (and their partners) underlying lung disease, cancer, cardiovascular disease, and innate immunity. NMR-based structural studies in solution joined with biochemical and biophysical approaches help us figure out how the enzymes may work.
I. Structural and mechanistic features of matrix metalloproteinases (MMPs) in pericellular proteolysis
In innate immune responses to infection in lungs and elsewhere, macrophages employ MMP-7 MMP-12, and MMP-14 at its cell surfaces. Macrophages and these three proteases tend also to be active in older smokers with with COPD or arterial aneurysms, in tumors, in arterial plaques prone to rupture unto heart attack or stroke, and in damage after heart attack. Key molecular interactions of these three proteases are investigated in this lab include: (i) MMP-12 and -7 digestion of elastic fibrils enriched in lungs and arteries, (ii) MMP-12 and -14 digestion and binding of collagen triple helices that are ubiquitous throughout the body, (iii) MMP-12 and -7 interaction with membrane bilayer models of cell surfaces, and (iv) proMMP-7 activation by glycosaminoglycans found at cell surfaces. We have also contributed to mechanistic understanding of the blockage of representative MMP-3 by the inhibitory TIMP-1 protein.
II. Inner workings of enzyme that handles phosphosugars to support bacterial infectivity
Bacteria such as Pseudomonas aeruginosa (which lives in places from soils to lungs afflicted with COPD or cystic fibrosis) can encase themselves in sugar chains that promote infection and fend off attack by immune systems’ defenses in the lungs. The building blocks for the sugar chains are phosphorylated glucose or mannose. An enzyme named PMM/PGM (P for phospho, M for mannose, and G for glucose) moves a phosphoryl group from one end of the monosaccharide to the other. We have been using NMR to study how this enzyme’s catalysis may be connected to the enzyme’s movements, phosphorylation, and binding of phosphosugars. The > 460 residues of PMM/PGM have presented a rigorous challenge for NMR. The shape changes, ligand binding, and states of the enzyme have made for interesting observations on the transmission of changes across the enzyme.
III. Characterizing asthma in cat models in terms of its metabolic signature
Our third project connected to lung disease is meant to identify metabolic signatures of asthma, in order that asthma and its severity may one day be recognizable in cats and children sooner for more timely treatment. Using NMR, we are statistically recognizing patterns in NMR spectra of samples non-invasively collected (by Dr. Reinero’s lab here at MU) from cats that develop asthma.
Innovative styles of work:
We have introduced innovative approaches for greater insight when possible. For example, when trying to characterize protein-protein specificity without feasibility of structures of the complexes, we developed a successful new strategy called BINDSIght to discover the amino acid residues that tune the specificity of interaction (Palmier et al, 2010). BINDSIght combines (i) a more accurate way to map protein-protein interfaces by paramagnetic NMR that we introduced (Arumugam et al, 1998), with a bioinformatics approach, and our expedited way to compare the kinetics of mutant enzymes (Palmier & Van Doren, 2007). BINDSIght refers to bioinformatics and NMR discovery of specificity of interactions (Palmier et al, 2010).
We were also one of the first groups outside of NIH to refine an NMR structure of a protein and an RNA using residual dipolar couplings for greater accuracy (Leeper et al, 2002; Wu et al, 2000). We hope soon to demonstrate our new solution structural approach that we used to dock an MMP to a bilayer, and which is applicable to other peripheral membrane proteins (Koppisetti et al, in preparation).
A recurring theme in our studies of enzyme interactions with their partners is that remote parts of the protein often couple to the site of binding. That is, molecular recognition and control runs deeper than the active site. A few of our emerging insights are suggesting potential therapeutic and diagnostic strategies.
Xu J and Van Doren SR. Tracking Equilibrium and Non-equilibrium Shifts in Data with TREND. Biophysical J. 2017 Jan 24; 112(2): https://dx.doi.org/10.1016/j.bpj.2016.12.018.
Fulcher YG, Fotso M, Chang C-H, Rindt H, Reinero CL, Van Doren SR. Noninvasive Recognition and Biomarkers of Early Allergic Asthma in Cats using Multivariate Statistical Analysis of NMR Spectra of Exhaled Breath Condensate. PLoS One. 11(10):e0164394. doi:10.1371/journal.pone.0164394 (2016).
Xu J, Van Doren SR. Binding Isotherms and Time Courses Readily from Magnetic Resonance. Anal Chem. 2016 Aug 16; 88(16):8172-8.
Prior SH, Byrne TS, Tokmina-Roszyk D, Fields GB, Van Doren SR. Path to Collagenolysis: Collagen V Triplex-Helix Bound Productively and in Encounters by Matrix Metalloproteinase-12. J. Biol. Chem. 291(15):7888-7901. doi:10.1074/jbc.M115.703124 (PDB:2N8R) (2016).
Prior SH, Fulcher YG, Koppisetti RK, Jurkevic A, Van Doren SR. Charge-Triggered Membrane Insertion of Matrix Metalloproteinase-7, Supporter of Innate Immunity and Tumors. Structure. 23(11):2099-2110. doi:10.1016/j.str/2015.08.013 (PDB:2MZE, 2MZH, 2MZI) (2015).
Zhao Y, Marcink TM, Stawikowska R, Sanganna Gari RR, Marsh BP, King GM, Fields GB, Van Doren SR. Transient Collagen Triple Helix Binding to a Key Metalloproteinase in Invasion and Development. Structure. 23(2):257-269. doi:10.1016/j.str.2014.11.021 (PDB:2MQS) (2015).
Xu J, Lee Y, Beamer LJ and Van Doren SR. Phosphorylation in the Catalytic Cleft Stabilizes and Attracts Domains of Phosphohexomutase. Biophysical J. 108(2):325-337 (2015).
Van Doren, SR. Matrix metalloproteinase interactions with collagen and elastin. Matrix Biology. 44-46:224-231. doi:10.1016/j.bpj.2014.12.003 (2015).
Koppisetti R, Fulcher YG, Jurkevic A, Prior SH, Xu J, Lenoir M, Overduin M, and Van Doren SR. (2014) Ambidextrous Binding of Cell and Membrane Bilayers by Soluble Matrix Metalloproteinase-12. Nature Commun. 5: 5552. DOI: 10.1038/ncomms6552 (PDB: 2MLR, 2MLS)
Yan G. Fulcher, Raghavendar Reddy Sanganna Gari, Nathan C. Frey Fuming Zhang, Robert J. Linhardt, Gavin M. King and Steven R. Van Doren. Heparinoids Activate a Protease, Secreted by Mucosa and Tumors, via Tethering Supplemented by Allostery. ACS Chem. Biol. 2014 Feb 4. dx.doi.org/10.1021/cb400898t.
Sarma AV, Anbanandam A, Kelm A, Mehra-Chaudhary R, Wei Y, Qin P, Lee Y, Berjanskii MV, Mick JA, Beamer LJ, Van Doren SR. Solution NMR of a 463-residue phosphohexomutase: domain 4 mobility, substates, and phosphoryl transfer defect. Biochemistry. 2012 Jan 24;51(3):807-19. doi: 10.1021/bi201609n. Epub 2012 Jan 17.
Fulcher YG, Van Doren SR. Remote exosites of the catalytic domain of matrix metalloproteinase-12 enhance elastin degradation. Biochemistry. 2011 Nov 8;50(44):9488-99. doi: 10.1021/bi2009807. Epub 2011 Oct 11.
Palmier MO, Fulcher YG, Bhaskaran R, Duong VQ, Fields GB, Van Doren SR. NMR and bioinformatics discovery of exosites that tune metalloelastase specificity for solubilized elastin and collagen triple helices. J Biol Chem. 2010 Oct 1;285(40):30918-30. doi: 10.1074/jbc.M110.136903. Epub 2010 Jul 27.
Liang X, Arunima A, Zhao Y, Bhaskaran R, Shende A, Byrnes T, Fleeks J, Palmier MO, Van Doren SR. Apparent Tradeoff of Higher Activity in MMP-12 for Enhanced Stability and Flexibility in MMP-3. Biophysical Journal 99 (1):273-283 (2010).
Research areas: Structural biology: NMR investigations of protein structure, dynamics and protein-protein interactions, particularly proteins important in inflammatory diseases.
How to apply:
Electronic submission is encouraged, e-mail to email@example.com
Applicants should send CV and names of two references to:
Dr. Steven R. Van Doren
117 Schweitzer Hall
University of Missouri
Columbia, MO 65211