Madeline Shea, PhD

Portrait
Professor of Biochemistry

Contact Information

Primary Office: 4-450 BSB
Iowa City, 52242
Phone: 319-335-7885

Education

PhD, T.C. Jenkins Dept. of Biophysics, The Johns Hopkins University
BS, Chemistry, California Institute of Technology

Fellow, Dept. of Biology, The Johns Hopkins University

Education/Training Program Affiliations

Department of Biochemistry PhD, Interdisciplinary Graduate Program in Translational Biomedicine, Medical Scientist Training Program

Center, Program and Institute Affiliations

Center for Biocatalysis and Bioprocessing

Research Summary

This laboratory probes the linkage between cooperative ligand binding, conformational change and enzyme activation by calmodulin, a regulatory calcium- binding protein. Calmodulin is the primary eukaryotic intracellular calcium receptor and serves as a second messenger to regulate cellular responses to transient calcium fluxes. It is clinically relevant for human physiology and is also found in plants and fungi. Cooperative binding of calcium ions to calmodulin causes large conformational changes; these changes control the sites and extent of calmodulin activation of important cellular enzymes and structural proteins. In order to determine the states that are functionally significant in this complex network of interactions, it is necessary to develop and apply new methods to directly determine energetic and structural properties of calcium binding. Quantitative proteolytic footprinting and applications of multi-dimensional heteronuclear NMR are capable of monitoring individual residues or bonds during a titration representative of a cellular influx of calcium. These studies have shown that the two domains of calmodulin interact in different ways as calcium fills the four sites of the protein. X-ray crystallography is used to determine how the domains interact with peptides that represent CaM-binding motifs in target proteins. Calcium-dependent structural rearrangements of calmodulin also are monitored by changes in the fluorescence, circular dichroism and hydrodynamic properties. These combined approaches are aimed at elucidating molecular mechanisms of cooperativity in calmodulin by determining the differences in intrinsic binding affinity at the four calcium-binding sites of calmodulin and the extent and nature of inter- and intra-domain cooperativity. To dissect these interactions, we are studying the isolated domains of calmodulin and many mutants shown to have phenotypic effects on complexes of calmodulin with its target enzymes. Computational molecular modeling is used to visualize and calculate properties of these proteins and serves as a complement to the experimental studies of ligand- linked conformational change. The goal is to combine energetic and structural data to formulate models that will explain how synchronized changes in calcium levels modulate many diverse physiological processes.

Publications

Hovey, L., Fowler, C. A., Mahling, R., Lin, Z., Miller, M. S., Marx, D. C., Yoder, J. B., Kim, E. H., Tefft, K. M., Waite, B. C., Feldkamp, M. D., Yu, L. & Shea, M. A. (2017). Calcium triggers reversal of calmodulin on nested anti-parallel sites in the IQ motif of the neuronal voltage-dependent sodium channel Na<sub>V</sub>1.2.. Biophysical chemistry, 224, 1-19. DOI: 10.1016/j.bpc.2017.02.006.
[PubMed]

Marx, D., Yoder, J., Hovey, L., Weaver, L., Mahling, R., Lin, Z., Miller, M., Kim, E., Tefft, K., Martin, S., Klein, S., Dickinson, C. & Shea, M. (2017). Calmodulation of Nine Human Voltage-Gated Sodium Channels: Not all IQ Motifs Prefer Apo Calmodulin.

Sorensen, B., Faga, L., Newman, R., Song, L., Jaren, O. & Shea, M. (2017). Thermostability of Domain-Specific Calmodulin Mutants Defective in Ion Channel Regulation.

Fowler, C., Nunez-Hernandez, M., O'Donnell, S., Yu, L. & Shea, M. (2016). Backbone and Side-chain Resonance Assignments of 13C, 15N-(Ca2+)4-Clamodulin bound to 13C, 15N-Beta CalcineurinA CaMBD Peptide.

Mahling, R., Kilpatrick, A. & Shea, M. (2016). Backbone Resonance Assignments of Apo and Calcium-Saturated 13C, 15N-Calmodulin bound to Voltage-Gated Sodium Channel 13C, 15N-Nav1.2 IQ Motif Peptide.

Feldkamp, M. D., Gakhar, L., Pandey, N. & Shea, M. A. (2015). Opposing orientations of the anti-psychotic drug trifluoperazine selected by alternate conformations of M144 in calmodulin.. Proteins, 83(5), 989-96. DOI: 10.1002/prot.24781.
[PubMed]

Wang, X., Boyken, S. E., Hu, J., Xu, X., Rimer, R. P., Shea, M. A., Shaw, A. S., Andreotti, A. H. & Huang, Y. H. (2014). Calmodulin and PI(3,4,5)P3 cooperatively bind to the Itk pleckstrin homology domain to promote efficient calcium signaling and IL-17A production. Sci. Signal, 7, 337. DOI: 10.1126/scisignal.2005147.
[PubMed]

Newman, R. A., Sorensen, B. R., Kilpatrick, A. M. & Shea, M. A. (2014). Calcium-dependent energetics of calmodulin domain interactions with regulatory regions of the Ryanodine Receptor Type 1 (RyR1). Biophys Chem, 193-194, 35-49. DOI: 10.1016/j.bpc.2014.07.004.
[PubMed]

O'Donnell, S. E., Yu, L., Fowler, C. A. & Shea, M. A. (2011). Recognition of ß-calcineurin by the domains of calmodulin: thermodynamic and structural evidence for distinct roles. Proteins, 79(3), 765-86.
[PubMed]

Shea, M. A., Correia, J. J. & Brenowitz, M. D. (2011). Introduction: twenty five years of the Gibbs Conference on Biothermodynamics. Biophysical Chemistry, 159(1), 1-5.
[PubMed]

Evans, T. I., Hell, J. W. & Shea, M. A. (2011). Thermodynamic linkage between calmodulin domains binding calcium and contiguous sites in the C-terminal tail of Ca(V)1.2. Biophysical Chemistry, 159(1), 172-87.
[PubMed]

Feldkamp, M. D., Yu, L. & Shea, M. A. (2011). Structural and energetic determinants of apo calmodulin binding to the IQ motif of the Na(V)1.2 voltage-dependent sodium channel. Structure (London, England: 1993), 19(5), 733-47.
[PubMed]

Feldkamp, M. D., O'Donnell, S. E., Yu, L. & Shea, M. A. (2010). Allosteric effects of the antipsychotic drug trifluoperazine on the energetics of calcium binding by calmodulin. Proteins, 78(10), 2265-82.
[PubMed]

Evans, T. I., Shea, M. A. (2009). Energetics of calmodulin domain interactions with the calmodulin binding domain of CaMKII. Proteins, 76(1), 47-61.
[PubMed]

O'Donnell, S. E., Newman, R. A., Witt, T. J., Hultman, R., Froehlig, J. R., Christensen, A. P. & Shea, M. A. (2009). Thermodynamics and conformational change governing domain-domain interactions of calmodulin. Methods in Enzymology, 466, 503-26.
[PubMed]

Theoharis, N. T., Sorensen, B. R., Theisen-Toupal, J. & Shea, M. A. (2008). The neuronal voltage-dependent sodium channel type II IQ motif lowers the calcium affinity of the C-domain of calmodulin. Biochemistry, 47(1), 112-23.
[PubMed]

Newman, R. A., Van Scyoc, W. S., Sorensen, B. R., Jaren, O. R. & Shea, M. A. (2008). Interdomain cooperativity of calmodulin bound to melittin preferentially increases calcium affinity of sites I and II. Proteins, 71(4), 1792-812.
[PubMed]

Erickson, J. R., Joiner, M. L., Guan, X., Kutschke, W., Yang, J., Oddis, C. V., Bartlett, R. K., Lowe, J. S., O'Donnell, S. E., Aykin-Burns, N., Zimmerman, M. C., Zimmerman, K., Ham, A. J., Weiss, R. M., Spitz, D. R., Shea, M. A., Colbran, R. J., Mohler, P. J. & Anderson, M. E. (2008). A dynamic pathway for calcium-independent activation of CaMKII by methionine oxidation. Cell, 133(3), 462-74.
[PubMed]

Li, Q., Cooper, J. J., Altwerger, G. H., Feldkamp, M. D., Shea, M. A. & Price, D. H. (2007). HEXIM1 is a promiscuous double-stranded RNA-binding protein and interacts with RNAs in addition to 7SK in cultured cells. Nucleic acids research, 35(8), 2503-12.
[PubMed]

Merrill, M. A., Malik, Z., Akyol, Z., Bartos, J. A., Leonard, A. S., Hudmon, A., Shea, M. A. & Hell, J. W. (2007). Displacement of alpha-actinin from the NMDA receptor NR1 C0 domain By Ca2+/calmodulin promotes CaMKII binding. Biochemistry, 46(29), 8485-97.
[PubMed]

Ataman, Z. A., Gakhar, L., Sorensen, B. R., Hell, J. W. & Shea, M. A. (2007). The NMDA receptor NR1 C1 region bound to calmodulin: structural insights into functional differences between homologous domains. Structure (London, England : 1993), 15(12), 1603-17.
[PubMed]

Ross, J., Laws, W. & Shea, M. (2006). Intrinsic fluorescence in protein structure analysis. Protein Structures: Methods in Protein Structure and Structure Analysis: Luinescence Spectroscopy and Circular Dichroism, Nova Science Publishers, Inc (NY), 55-72.

VanScyoc, W. S., Newman, R. A., Sorensen, B. R. & Shea, M. A. (2006). Calcium binding to calmodulin mutants having domain-specific effects on the regulation of ion channels. Biochemistry, 45(48), 14311-24.
[PubMed]

Akyol, Z., Bartos, J. A., Merrill, M. A., Faga, L. A., Jaren, O. R., Shea, M. A. & Hell, J. W. (2004). Apo-calmodulin binds with its C-terminal domain to the N-methyl-D-aspartate receptor NR1 C0 region. The Journal of Biological Chemistry, 279(3), 2166-75.
[PubMed]

Hines, R., Sorensen, B. R., Shea, M. A. & Maury, W. (2004). PU.1 binding to ets motifs within the equine infectious anemia virus long terminal repeat (LTR) enhancer: regulation of LTR activity and virus replication in macrophages. Journal of Virology, 78(7), 3407-18.
[PubMed]

Wang, B., Martin, S. R., Newman, R. A., Hamilton, S. L., Shea, M. A., Bayley, P. M. & Beckingham, K. M. (2004). Biochemical properties of V91G calmodulin: A calmodulin point mutation that deregulates muscle contraction in Drosophila. Protein science : a publication of the Protein Society, 13(12), 3285-97.
[PubMed]

Faga, L. A., Sorensen, B. R., VanScyoc, W. S. & Shea, M. A. (2003). Basic interdomain boundary residues in calmodulin decrease calcium affinity of sites I and II by stabilizing helix-helix interactions. Proteins, 50(3), 381-91.
[PubMed]

Jaren, O. R., Kranz, J. K., Sorensen, B. R., Wand, A. J. & Shea, M. A. (2002). Calcium-induced conformational switching of Paramecium calmodulin provides evidence for domain coupling. Biochemistry, 41(48), 14158-66.
[PubMed]

Sorensen, B. R., Faga, L. A., Hultman, R. & Shea, M. A. (2002). An interdomain linker increases the thermostability and decreases the calcium affinity of the calmodulin N-domain. Biochemistry, 41(1), 15-20.
[PubMed]

Xiong, L. W., Newman, R. A., Rodney, G. G., Thomas, O., Zhang, J. Z., Persechini, A., Shea, M. A. & Hamilton, S. L. (2002). Lobe-dependent regulation of ryanodine receptor type 1 by calmodulin. The Journal of Biological Chemistry, 277(43), 40862-70.
[PubMed]

VanScyoc, W. S., Sorensen, B. R., Rusinova, E., Laws, W. R., Ross, J. B. & Shea, M. A. (2002). Calcium binding to calmodulin mutants monitored by domain-specific intrinsic phenylalanine and tyrosine fluorescence. Biophysical Journal, 83(5), 2767-80.
[PubMed]

Leonard, A. S., Bayer, K. U., Merrill, M. A., Lim, I. A., Shea, M. A., Schulman, H. & Hell, J. W. (2002). Regulation of calcium/calmodulin-dependent protein kinase II docking to N-methyl-D-aspartate receptors by calcium/calmodulin and alpha-actinin. The Journal of Biological Chemistry, 277(50), 48441-8.
[PubMed]

Sorensen, B. R., Eppel, J. T. & Shea, M. A. (2001). Paramecium calmodulin mutants defective in ion channel regulation associate with melittin in the absence of calcium but require it for tertiary collapse. Biochemistry, 40(4), 896-903.
[PubMed]

Sun, H., Yin, D., Coffeen, L. A., Shea, M. A. & Squier, T. C. (2001). Mutation of Tyr138 disrupts the structural coupling between the opposing domains in vertebrate calmodulin. Biochemistry, 40(32), 9605-17.
[PubMed]

VanScyoc, W. S., Shea, M. A. (2001). Phenylalanine fluorescence studies of calcium binding to N-domain fragments of Paramecium calmodulin mutants show increased calcium affinity correlates with increased disorder. Protein science : a publication of the Protein Society, 10(9), 1758-68.
[PubMed]

Shea, M. A., Sorensen, B. R., Pedigo, S. & Verhoeven, A. S. (2000). Proteolytic footprinting titrations for estimating ligand-binding constants and detecting pathways of conformational switching of calmodulin. Methods in enzymology, 323, 254-301.
[PubMed]

Jaren, O. R., Harmon, S., Chen, A. F. & Shea, M. A. (2000). Paramecium calmodulin mutants defective in ion channel regulation can bind calcium and undergo calcium-induced conformational switching. Biochemistry, 39(23), 6881-90.
[PubMed]

Sorensen, B. R., Shea, M. A. (1998). Interactions between domains of apo calmodulin alter calcium binding and stability. Biochemistry, 37(12), 4244-53.
[PubMed]

Sorensen, B. R., Shea, M. A. (1996). Calcium binding decreases the stokes radius of calmodulin and mutants R74A, R90A, and R90G. Biophysical journal, 71(6), 3407-20.
[PubMed]

Shea, M. A., Verhoeven, A. S. & Pedigo, S. (1996). Calcium-induced interactions of calmodulin domains revealed by quantitative thrombin footprinting of Arg37 and Arg106. Biochemistry, 35(9), 2943-57.
[PubMed]

Pedigo, S., Shea, M. A. (1995). Quantitative endoproteinase GluC footprinting of cooperative Ca2+ binding to calmodulin: proteolytic susceptibility of E31 and E87 indicates interdomain interactions. Biochemistry, 34(4), 1179-96.
[PubMed]

Pedigo, S., Shea, M. A. (1995). Discontinuous equilibrium titrations of cooperative calcium binding to calmodulin monitored by 1-D 1H-nuclear magnetic resonance spectroscopy. Biochemistry, 34(33), 10676-89.
[PubMed]

Daugherty, M. A., Shea, M. A. & Ackers, G. K. (1994). Bohr effects of the partially-ligated (CN-met) intermediates of hemoglobin as probed by quaternary assembly. Biochemistry, 33(34), 10345-57.
[PubMed]

Koblan, K. S., Bain, D. L., Beckett, D., Shea, M. A. & Ackers, G. K. (1992). Analysis of site-specific interaction parameters in protein-DNA complexes. Methods in enzymology, 210, 405-25.
[PubMed]

Daugherty, M. A., Shea, M. A., Johnson, J. A., LiCata, V. J., Turner, G. J. & Ackers, G. K. (1991). Identification of the intermediate allosteric species in human hemoglobin reveals a molecular code for cooperative switching. Proceedings of the National Academy of Sciences of the United States of America, 88(4), 1110-4.
[PubMed]

Perrella, M., Benazzi, L., Shea, M. A. & Ackers, G. K. (1990). Subunit hybridization studies of partially ligated cyanomethemoglobins using a cryogenic method. Evidence for three allosteric states. Biophysical chemistry, 35(1), 97-103.
[PubMed]

Brenowitz, M., Senear, D. F., Shea, M. A. & Ackers, G. K. (1986). Quantitative DNase footprint titration: a method for studying protein-DNA interactions. Methods in Enzymology, 130(part K), 132-81.
[PubMed]

Brenowitz, M., Senear, D. F., Shea, M. A. & Ackers, G. K. (1986). Footprint titrations yield valid thermodynamic isotherms. Proceedings of the National Academy of Sciences of the United States of America, 83(22), 8462-6.
[PubMed]

Senear, D. F., Brenowitz, M., Shea, M. A. & Ackers, G. K. (1986). Energetics of cooperative protein-DNA interactions: comparison between quantitative deoxyribonuclease footprint titration and filter binding. Biochemistry, 25(23), 7344-54.
[PubMed]

Shea, M. A., Ackers, G. K. (1985). The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. Journal of Molecular Biology, 181(2), 211-30.
[PubMed]

Shea, M. A., Ackers,, G. K. (1983). Dynamics of gene regulation in the QR/OL control system of bacteriophage lambda. Mobility and Recognition in Cell Biology, Walter de Gruyter, Berlin, 328-343.

Ackers, G. K., Shea, M. A. & Smith, F. R. (1983). Free energy coupling within macromolecules. The chemical work of ligand binding at the individual sites in co-operative systems. Journal of Molecular Biology, 170(1), 223-42.
[PubMed]

Ackers, G. K., Johnson, A. D. & Shea, M. A. (1982). Quantitative model for gene regulation by lambda phage repressor. Proceedings of the National Academy of Sciences of the United States of America, 79(4), 1129-33.
[PubMed]