Department of Biological Science

Biological Science Faculty Member

Laboratory Home Page

Professor
Ph.D., The Scripps Research Institute, 2002
Graduate Faculty Status

Research and Professional Interests:

What is the relationship between a molecule's structure and its activity in the cell? I am interested in understanding the structure/function relationships driving two pathways: the transformation of a gene into a protein and sulfur metabolism. The two projects in my laboratory are not related topically, but are united in approach. In studying the progression of information from a gene to a protein include, we aim to answer how ribosomes are assembled into functional units. In studying the biochemical basis for sulfur metabolism, we aim to discover how  electrons move from the reductase subunit to the active site of the central sulfur metabolic enzyme sulfite reductase and how sulfite reductase' essential metallic cofactor are synthesized. I use x-ray crystallography and high resoltuion single-particle cryogenic electron microscopy (cryo-EM) to probe across resolutions so I can link atomic resolution details, macromolecular assemblies, and cellular activity.

The lab uses a combination of x-ray crystallography and cryo-EM to determine the structure and function of these important biomolecules.

Selected Publications:

Murray DT, Weiss KL, Stanley CB, Nagy G, Stroupe ME. Small-angle neutron scattering solution structures of NADPH-dependent sulfite reductase. J Struct Biol. 2021 Jun;213(2):107724. doi: 10.1016/j.jsb.2021.107724. Epub 2021 Mar 13. PMID: 33722582.

J. Rai, M. D. Parker, H. Huang, S. Choy, H. Ghalei, M. C. Johnson, K. Karbstein, M. E. Stroupe. An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7. RNA. 2021 Feb;27(2):221-233. https://doi.org/10.1261/rna.077610.120. Epub 2020 Nov 20. PMID: 33219089

J. M. Pennington, M. Kemp, L. McGarry, Y. Chen, M. E. Stroupe. Siroheme synthase orients substrates for dehydrogenase and chelatase activities in a common active site. Nat Commun. 2020 Feb 13;11(1):864. https://doi.org/10.1038/s41467-020-14722-1. 

Tavolieri, A. M., Murray, D. T., Askenasy, I., Pennington, J. M., McGarry, L., Stanley, C. B., & Stroupe, M. E. (2019). NADPH-Dependent  Sulfite Reductase Flavorprotein Adopts an Extended Conformation Unique to this Diflavin Reductase. J. Struct. Biol., 205, 170-179. Retrieved from https://doi.org/10.1016/j.jsb.2019.01.001

Askenasy, I., Murray, D. T., Andrews, R. M., Uversky, V. N., He, H. & Stroupe, M. E. (2018). Structure-Function Relationships in the Oligomeric NADPH-Dependent Assimilatory Sulfite Reductase. Biochemistry, 57, 3764-3772. Retrieved from https://doi.org/10.1021/acs.biochem.8b00446

Cepeda, M. R., McGarry, L., Pennington, J. M., Krystek, J., & Stroupe, M. E. (2018). The role of extended Fe₄S₄ cluster ligands in mediating sulfite reductase hemoprotein activity. Biochimi Biophys Acta Proteins Proteom., 1866, 933-940. Retrieved from https://doi.org/10.1016/j.bbapap.2018.05.013

Stroupe, M. E., & Warren, M. J. (2017). Siroheme assembly and insertion to Nitrite and Sulfite Reductase. In
Johnson, M. K, & Scott, RA. . (Eds.), Encyclopedia of Inorganic and Bioinorganic Chemistry: Metalloprotein Site Assembly. Chichester. Retrieved from http://dx.doi.org/10.1002/9781119951438.eibc2487

Johnson, M. C., Sena-Velez, M., Washburn, B. K., Platt, G. N., Lu, S., Brewer, T. E., Lynn, J. S., Stroupe, M. E., & Jones, K. M. (2017). Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome. J. Struct. Biol, 200, 343-359. Retrieved from http://dx.doi.org/10.1016/j.jsb.2017.08.005

Johnson, M. C., Ghalei, H., Doxtader, K. A., Karbstein, K., & Stroupe, M. E. (2017). Structural Heterogeneity in Pre-40S Ribosomes. Structure, 25, 329-340. Retrieved from http://dx.doi.org/10.1016/j.str.2016.12

Khoshnevis, S., Askenasy, I., Johnson, M. C., Dattolo, M. D., Young-Erdos, C. L., Stroupe, M. E., & Karbstein, K. (2016.) The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation. PLoS Biology. Retrieved from: http://dx.doi.org/10.1371/journal.pbio.1002480

Johnson, M. C., Tatum, K. B., Lynn, J. S., Brewer, T. E., Washburn, B. K., Stroupe, M. E., & Jones, K. M. (2015). Sinorhizobium meliloti phage ΦM9 defines a new group of T4-superfamily phages with unusual genomic features, but a common T=16 capsid. Journal of Virology, 10945-10958. Retrieved from http://dx.doi.org/10.1128/JVI.01353-15

Askenasy, I., Pennington, J. M., Tao, Y., Marshall, A. G., Young, N. L., Sheng, W., & Stroupe, M. E. (2015). The N-terminal Domain of Escherichia coli Assimilatory NADPH-Sulfite Reductase Hemoprotein Is an Oligomerization Domain that Mediates Holoenzyme Assembly. Journal of Biological Chemistry, 290, 15. Retrieved from http://dx.doi.org/10.1074/jbc.M115.662379

Ghalei, H., Schaub, F., Doherty, J., Roush, W. R., Cleveland, J. J., Stroupe, M. E., & Karbstein, K. (2015). Hrr25/CK1δ-directed release of Ltv1 from pre-40S ribosomes is necessary for ribosome assembly and cell growth. The Journal of Cell Biology, 208, 745-759. Retrieved from http://dx.doi.org/10.1083/jcb.201409056

Kopylov, M., Bass, H. W., & Stroupe, M. E. (2015). Identification and characterization of a plant G-quadruplex-binding protein encoded by the maize (Zea mays L.) nucleoside diphosphate kinase1 gene, ZmNDPK1. Biochemistry, 54, 1743-1757. Retrieved from http://dx.doi.org/10.1021/bi501284g

Andorf, C. M., Kopylov, M., Dobbs, D., Koch, K. E., Stroupe, M. E., Lawrence, C. J., & Bass, H. W. (2014). G-Quadruplex (G4) Motifs in the Maize (Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status, Hypoxia, Low Sugar, and Nutrient Deprivation. J Genet Genomics, 12, 627-647. Retrieved from http://dx.doi.org/10.1016/j.jgg.2014.10.004 

Brewer, T., Stroupe, M. E., & Jones, K. M. (2014). The genome, proteome and phylogenetic analysis of Sinorhizobium meliloti phage ΦM12, the founder of a new group of T4-superfamily phages. Virology, 450-451, 84-97. Retrieved from http://dx.doi.org/10.1016/j.virol.2013.1

Stroupe, M. E., Brewer, T., Sousa, D. R., & Jones, K. M. (2014). The structure of Sinorhizobium meliloti phage ΦM12, which has a novel T=19l triangulation number and is the founder of a new group of T4-superfamily phages. Virology, 450-451, 205-212. Retrieved from http://dx.doi.org/10.1016/j.virol.2013.1

Sousa, D. R., Stagg, S. M., & Stroupe, M. E. (2013). Cryo-EM structures of the actin:tropomyosin filament reveal the mechanism for the transition from C- to M-state. J Mol Biol, 425(22), 4544-55. Retrieved from http://dx.doi.org/10.1016/j.jmb.2013.08.020

Smith, K. W., & Stroupe, M. E. (2012). Mutational analysis of sulfite reductase hemoprotein reveals the mechanism for coordinated electron and proton transfer. Biochemistry, 51(49), 9857-68. Retrieved from http://dx.doi.org/10.1021/bi300947a

Graduate Students: