David D. Thomas, Ph.D. Professor, Department of Biochemistry, Molecular Biology, and Biophysics E-mail: ddt@umn.edu

Research Interests:

Researchers in the Thomas laboratory use spectroscopic probes to study the role of protein structure and dynamics in physiological processes, particularly in muscle fibers and membranes. Site-directed mutagenesis and cell culture techniques are used to attach spectroscopic molecular probes to study selected components within intact and functional molecular assemblies. This laboratory is unique in its combination of state-of-the-art instrumentation and expertise in both magnetic resonance (EPR and NMR) and optical (laser) spectroscopy and imaging (fluorescence, phosphorescence, luminescence).

In the muscle fiber studies, mechanical, biochemical, and spectroscopic experiments are used to correlate the functional state of a muscle fiber with the orientation and motion of specifically labeled proteins (myosin or actin), thus providing direct tests for models of the mechanism of force generation. The main membrane system studied is the calcium pump of sarcoplasmic reticulum. Spectroscopic probes are used to determine which molecular structures and motions are essential for active calcium transport and its regulation, particularly in the heart, where phospholamban plays a crucial role in regulation. Some projects are focused on the fundamental biophysics of normal muscle; other projects are applied to specific medical problems, such as aging or inherited muscle disease or molecular therapeutic design. Workers in the laboratory include undergraduate students, postdoctoral fellows, and graduate students associated with Biochemistry, Biophysics, Biomedical Engineering, and Neuroscience programs.

Selected Publications:

(For a comprehensive list of recent publications, refer to PubMed, a service provided by the National Library of Medicine.)

James, Z., JE McCaffrey, KD Torgersen, CB Karim, and DD Thomas. 2012. Oligomeric interactions in calcium transport regulation probed by electron paramagnetic resonance. Biophys J in press.

Colson, BA, SJ Gruber, and DD Thomas. 2012. Structural dynamics of muscle protein phosphorylation. J Muscle Res Cell Motil in press.

Cornea, RL, SJ Gruber, EL Lockamy, JM Muretta, D Jin, J Chen, R Dahl, T Bartfai, KM Zsebo, GD Gillispie, and DD Thomas. 2012. High-throughput FRET assay yields allosteric SERCA activators. J Biomol Screen in press.

Hou, Z, S Hu, DJ Blackwell, TD Miller, DD Thomas, and SL Robia. 2012. Two-color calcium pump reveals closure of the cytoplasmic headpiece with calcium binding. PLoS One in press.

Guhathakurta, P, E Prochniewicz, JM Muretta, and David D. Thomas. 2012. Allosteric effects within the catalytic domain of Dictyostelium myosin in interaction with actin and nucleotide. J Muscle Res Cell Motil in press.

Valley, CC, JD Perlmutter, AR Braun, AK Lewis, CB Karim, DD Thomas, JR Brody, and JN Sachs. 2012. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces Death Receptor 5 networks that are highly organized. J Biol Chem 287:21265-21278.

Lin, AY, E Prochniewicz, DM Henderson,, B Li, JM Ervasti, and DD Thomas. 2012. Impacts of dystrophin and utrophin domains on actin structural dynamics: implications for therapeutic design. J Mol Biol 420:87-98.

Gruber, SJ, S Haydon, and DD Thomas. 2012. Phospholamban mutants compete with wild type for SERCA binding in HEK Cells. Biochem Biophys Res Commun 420:236-240.

Li, J, ZM James, X Dong, CB Karim, and DD Thomas. 2012. Structural and functional dynamics of an integral membrane protein complex modulated by lipid headgroup charge. J Mol Biol 418:379-389.

Ablorh, NA, T Miller, F Nitu, SJ Gruber, CB Karim, and DD Thomas. 2011. Accurate quantitation of phospholamban phosphorylation by immunoblot. Anal Biochem 425:68-75.

Henderson, DM, AY Lin, DD Thomas, and JM Ervasti. 2012. The carboxy-terminal third of dystrophin enhances actin binding activity. J Mol Biol 416:414–424.

Mello, R, and DD Thomas. 2012. Three distinct actin-attached structural states of myosin in muscle fibers. Biophys J 102:1088–1096.

Karon, BS, C van Buskirk, E Jaben, JD Hoyer, and DD Thomas. 2011. Temporal sequence of major biochemical events during blood bank storage of packed red blood cells. Blood Transfus published online.

Klein, JC, RJ Moen, EA Smith, MA Titus, and DD Thomas. 2011. Structural and functional impact of site-directed methionine oxidation in myosin. Biochemistry 50:10318–10327.

Espinoza-Fonseca, LM, and DD Thomas. 2011. Atomic-level characterization of the activation mechanism of SERCA by calcium. PLoS One 6:e26936.

Prochniewicz, E, A Pierre, BR McCullough, HF Chin, W Cao, LP Saunders, DD Thomas, and EM De La Cruz. 2011. Actin filament dynamics in the actomyosin VI complex is regulated allosterically by calcium-calmodulin light chain. J Mol Biol 413:584-92.

Moen RJ, Johnsrud DO, Thomas DD, Titus MA. Characterization of a myosin VII MyTH/FERM domain. J Mol Biol. 2011 Oct 14;413(1):17-23. Epub 2011 Aug 22.

Lin AY, Prochniewicz E, James ZM, Svensson B, Thomas DD. Large-scale opening of utrophin's tandem calponin homology (CH) domains upon actin binding by an induced-fit mechanism. Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12729-33. Epub 2011 Jul 18.

Autry JM, Rubin JE, Pietrini SD, Winters DL, Robia SL, Thomas DD. Oligomeric interactions of sarcolipin and the Ca-ATPase. J Biol Chem. 2011 Sep 9;286(36):31697-706. Epub 2011 Jul 7.

Wilson DJ, Shi C, Duckworth BP, Muretta JM, Manjunatha U, Sham YY, Thomas DD, Aldrich CC. A continuous fluorescence displacement assay for BioA: an enzyme involved in biotin biosynthesis. Anal Biochem. 2011 Sep 1;416(1):27-38. Epub 2011 May 8.

Lockamy EL, Cornea RL, Karim CB, Thomas DD. Functional and physical competition between phospholamban and its mutants provides insight into the molecular mechanism of gene therapy for heart failure. Biochem Biophys Res Commun. 2011 May 13;408(3):388-92. Epub 2011 Apr 12.

Gustavsson M, Traaseth NJ, Karim CB, Lockamy EL, Thomas DD, Veglia G. Lipid-mediated folding/unfolding of phospholamban as a regulatory mechanism for the sarcoplasmic reticulum Ca2+-ATPase. J Mol Biol. 2011 May 13;408(4):755-65. Epub 2011 Mar 17.

Nesmelov YE, Agafonov RV, Negrashov IV, Blakely SE, Titus MA, Thomas DD. Structural kinetics of myosin by transient time-resolved FRET. Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1891-6. Epub 2011 Jan 18.

Muretta JM, Kyrychenko A, Ladokhin AS, Kast DJ, Gillispie GD, Thomas DD. High-performance time-resolved fluorescence by direct waveform recording. Rev Sci Instrum. 2010 Oct;81(10):103101.

Cornea RL, Nitu FR, Samsó M, Thomas DD, Fruen BR. Mapping the ryanodine receptor FK506-binding protein subunit using fluorescence resonance energy transfer. J Biol Chem. 2010 Jun 18;285(25):19219-26. Epub 2010 Apr 19.

Kast D, Espinoza-Fonseca LM, Yi C, Thomas DD. Phosphorylation-induced structural changes in smooth muscle myosin regulatory light chain. Proc Natl Acad Sci U S A. 2010 May 4;107(18):8207-12. Epub 2010 Apr 19.

Current Graduate Students:

Simon Gruber (Biochemistry)

Suzanne Haydon (Biochemistry)

Zach James (Biochemistry)

David Kast (Biochemistry)

Yun Lin (MD/PhD)

Elizabeth Lockamy (Biochemistry)

Jesse McCaffrey (Physics)

Ryan Mello (Biophysics)

Rebecca Moen (Biochemistry)

Former Graduate Students:

Jack Grinband (Ph.D. 2002, Neuroscience, Univesity of Minnesota).

John Stamm (Biochemistry).

Josh Baker (Biochemistry).

Min Zhao (Chemistry).

Ming Li (Biochemistry).

John Voss (Biochemistry).

Brad Karon (Neuroscience).

Scott Lewis (Neuroscience).

Leslie LaConte (Biochemistry).

Wendy Smith (Biochemistry).

Tara Kirby (Biochemistry).

Diane Eschliman (Biophysical Sciences).

Ben Mueller (MD/PhD).

Jack Surek (Biochemistry).

Jennifer Klein (Biochemistry).

David Kast (Physics).

Brian Wiczer (Biochemistry).