|BS||Biochemistry/Computer Science||Oklahoma State University||Stillwater, Okla.|
|PhD||Biophysics||University of Illinois||Urbana-Champaign, Ill.|
Structural biology: Biomolecular recognition, protein structure and dynamics by NMR, software to analyze NMR spectra and cardiac MRI
Biomolecular Recognition and Analysis of Spectra and Imaging are the passions of the laboratory. The molecular recognition events are germane to movements of tumor cells, innate immunity in mammals, and synthesis of oils in plants. Magnetic resonance supplies the NMR spectra and MR imaging of our investigations. Our innovative software approaches enrich and expedite analyses of enzyme-partner interactions, drug discovery, cardiac MR imaging, and pulmonary disease.
Molecular recognition by enzymes
We love to learn how enzymes interact with companion biomolecules. NMR is our favorite information-rich strategy, and can capture fluctuations in the interactions and structures. Other techniques extend the insights.
We probed collagen and elastin interactions with enzymes that digest them called MMPs (short for matrix metallproteinases; Palmier et al., 2010, JBC; Fulcher et al., 2011, Biochemistry; Zhao et al., 2015, Structure). Unexpectedly, two of three intertwined chains of the collagen triple-helix fitted into the narrow part of an MMP active site (Prior et al., 2016, JBC).
We docked an inhibitory protein called TIMP-1 to an MMP (Arumugam et al., 2003, Biochemistry) and were surprised to learn that conformational entropy gain in TIMP-1 upon binding contributes to the high affinity (Arumugam et al., 2003, JMB).
We located where the chaperone from a tumor virus binds the chaperone Hsc70 factor (Garimella et al., 2006, Biochemistry), and found the “business end” of the viral chaperone to be dynamic (Berjanskii et al., 2002, JMB).
Enzyme interactions with dynamic partners from cell surfaces
Peripheral associations with lipid bilayers
We discovered dual modes of bilayer binding by proteolytic enzymes MMP-12 (Koppisetti et al., 2014, Nat. Comms.), proMMP-7 (Prior et al., 2015, Structure), and MT1-MMP (Marcink et al., 2019, Structure). The movie shows an example of the MT1-MMP bound to a nanodisc. Anionic lipids trigger membrane insertion and reorientation of proMMP-7. Bilayered micelles triggered allosteric maturation of proMMP-7 to MMP-7, unless prevented.
Binding and activation by sulfated carbohydrates from cell surfaces
We captured the dynamic associations of polyanionic carbohydrates known as glycosaminoglycans (GAGs) with two basic regions of proMMP-7 (Fulcher et al., 2017, Structure). GAG chain lengths of 16+ sugar units make GAG-triggered maturation of proMMP-7 efficient, conditions which create elongated, heterogeneous assemblies (Fulcher et al., 2014, ACS Chem. Biol.). GAGs enhance the proteolytic velocity of MMP-7 and link it to growth factors and receptors that it releases from cell surfaces.
Larger enzymes and their internal interactions via NMR
The enzyme that starts the synthesis of fatty acids, acetyl-CoA carboxylase or ACCase, is highly regulated and relevant to the oil content of oilseed crops. With Jay Thelen’s lab, we are uncovering in part how its subunits called BADCs slow down ACCase activity in chloroplasts.
Bacterial phosphohexomutases move a phosphoryl group across a 6-carbon sugar, in the course of making carbohydrates at cell surfaces, such as virulence factors. We reported the mobility of domain 4 and mixed phosphorylation of a 52 kDa bacterial PGM/PMM, together with collaborator Lesa Beamer (Sarma et al., 2012). Phosphorylation of the active site closes the cleft a little while phosphosugar binding closes it fully. Both phosphorylation and binding have almost globally stabilizing effects on the enzyme (Xu et al., 2015, Biophys. J.; Xu et al., 2017, Sci. Rep.).
Peptide interactions that communicate across proteins
FHA domains bind phosphoThr peptides in signaling. We identified phosphoThr peptides from receptor-like kinases recognized by the FHA domain from the kinase-associated phosphatase in plant cell membranes (Ding et al., 2007, Biochemistry). One peptide widely rigidified this FHA domain, analogously to phosphoTyr peptide effects on the SH2 and PTB domains (Ding et al., 2005, Biochemistry).
In MMP-12, we discovered that peptidic inhibitors trigger conformational change propagating through the catalytic domain (Bhaskaran et al., 2007, JMB).
Intriguingly, remote binding of elastin fragments to distant exosites of MMP-12 enhanced proteolytic digestion of elastin (Fulcher et al., 2011, Biochemistry).
We surmise that molecular recognition can run deep and wide.
More efficient analysis and collection, especially from magnetic resonance
We enjoy making data interpretation more efficient and accurate where we can.
Software acceleration of fitting of NMR spectra, MRI movies, and enzyme kinetics
Our TREND software packages derive the main changes spanning series of NMR spectra or frames of MRI scans.
NMR. TREND NMR quickly finds and fits binding isotherms in all chemical exchange regimes (Xu and Van Doren, 2016 Anal. Chem; 2017 Biophys. J., 2018 Meth. Enzym.). This hastens and generalizes the analysis of titrations detected by 2D NMR spectra. A simple example is illustrated here.
MRI. The TREND approach can separate cardiac motion from breathing motion (Xu and Van Doren, 2017, Biophysical J.). In the movie of the 4-chamber scan, the cardiac motion is in the left panel and the breathing motion in the right panel. We are working with Drs. Thomen and Altes in Radiology toward the vision of sick patients being able to breathe freely in cardiac MRI exams in the future. See publicity at:
Notable Honors and Service
- PDB-101 Molecule of the Month (Sept. 2019) feature on Nanodiscs highlights our nanodisc-MT-MMP1 coordinates (PDB: 6clz)
- Distinguished Researcher Award, CAFNR, University of Missouri, 2015
- Faculty of 1000, Structural Biology, Experimental Biophysical Methods, 2008-2014
- Director of Graduate Education, 2005-2010
- Sigma Xi Excellence in Graduate Research Mentoring, MU chapter, 2006
- American Cancer Society Research Scholar, 2003
Marcink TC, Simoncic JA, An B, Knapinska AM, Fulcher YG, Akkaladevi N, Fields GB, Van Doren SR. (2019). MT1-MMP Binds Membranes by Opposite Tips of Its β Propeller to Position It for Pericellular Proteolysis. Structure. 27(2):281-292.e6. doi: 10.1016/j.str.2018.10.008. [PubMed]
Xu J, Van Doren SR. (2018). Affinities and Comparisons of Enzyme States by Principal Component Analysis of NMR Spectra, Automated using TREND Software. Methods Enzymol. 607:217-240. doi: 10.1016/bs.mie.2018.05.016. [PubMed]
Stiers KM, Xu J, Lee Y, Addison ZR, Van Doren SR, Beamer LJ. (2017). Phosphorylation-Dependent Effects on the Structural Flexibility of Phosphoglucosamine Mutase from Bacillus anthracis. ACS Omega. 2(11):8445-8452. doi: 10.1021/acsomega.7b01490. eCollection 2017 Nov 30. [PubMed]
Xu J, Sarma AVS, Wei Y, Beamer LJ, Van Doren SR. (2017). Multiple Ligand-Bound States of a Phosphohexomutase Revealed by Principal Component Analysis of NMR Peak Shifts. Sci Rep. 7(1):5343. doi: 10.1038/s41598-017-05557-w. [PubMed]
Fulcher YG, Prior SH, Masuko S, Li L, Pu D, Zhang F, Linhardt RJ, Van Doren SR. (2017). Glycan Activation of a Sheddase: Electrostatic Recognition between Heparin and proMMP-7. Structure. 25(7):1100-1110.e5. doi: 10.1016/j.str.2017.05.019. [PubMed]
Van Doren SR, Marcink TC, Koppisetti RK, Jurkevich A, Fulcher YG. (2017). Peripheral membrane associations of matrix metalloproteinases. Biochim Biophys Acta Mol Cell Res. 1864(11 Pt A):1964-1973. doi: 10.1016/j.bbamcr.2017.04.013. Review. [PubMed]
Marcink TC, Koppisetti RK, Fulcher YG, Van Doren SR. (2017). Mapping Lipid Bilayer Recognition Sites of Metalloproteinases and Other Prospective Peripheral Membrane Proteins. Methods Mol Biol. 1579:61-86. doi: 10.1007/978-1-4939-6863-3_5. [PubMed]
Fulcher YG, Fotso M, Chang CH, Rindt H, Reinero CR, Van Doren SR. (2016). 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. eCollection 2016. [PubMed]
Prior SH, Byrne TS, Tokmina-Roszyk D, Fields GB, Van Doren SR. (2016). Path to Collagenolysis: COLLAGEN V TRIPLE-HELIX MODEL BOUND PRODUCTIVELY AND IN ENCOUNTERS BY MATRIX METALLOPROTEINASE-12. J Biol Chem. 291(15):7888-901. doi: 10.1074/jbc.M115.703124. [PubMed]
Prior SH, Fulcher YG, Koppisetti RK, Jurkevich A, Van Doren SR. (2015). Charge-Triggered Membrane Insertion of Matrix Metalloproteinase-7, Supporter of Innate Immunity and Tumors. Structure. 23(11):2099-110. doi: 10.1016/j.str.2015.08.013. [PubMed]
Zhao Y, Marcink TC, Sanganna Gari RR, Marsh BP, King GM, Stawikowska R, Fields GB, Van Doren SR. (2015). Transient collagen triple helix binding to a key metalloproteinase in invasion and development. Structure. 23(2):257-69. doi: 10.1016/j.str.2014.11.021. [PubMed]
Xu J, Lee Y, Beamer LJ, Van Doren SR. (2015). Phosphorylation in the catalytic cleft stabilizes and attracts domains of a phosphohexomutase. Biophys J. 108(2):325-37. doi: 10.1016/j.bpj.2014.12.003. [PubMed]
NSF / MCB 1716688. A New Paradigm for Regulation of De Novo Fatty Acid Synthesis in Plants (Thelen, PI; Bates & Van Doren, coIs). 8/17 – 8/20
American Heart Association 19IPLOI34760520. Quantifying Cardiac Motion Abnormalities on MR Exams using Principal Component Analysis. (Van Doren, PI; Thomen, Flors Blasco, & Altes, coIs). 7/19 – 6/21
Hirshberg Foundation for Pancreatic Cancer Research. Early-Stage Drug Discovery Targeting a Marker of Pancreatic Cancer and its Metastasis. (Van Doren, PI; Brekken, co-I—UT Southwestern).
Coulter Translational Partnership at MU. HeartSpeed for Fast Cardiac MR Exams with Freedom to Breathe. (Van Doren, PI; Thomen & Altes, coIs). 7/18 – 6/20
MU Research Council URC-19-059. Early Stage Anti-Cancer Drug Screening: New Strategy to Block a Key Enzyme. 11/18 – 4/20