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.)

  • Nelson SED, Ha KN, Gopinath T, Exline MH, Mascioni A, Thomas DD, Veglia G. Effects of the Arg9Cys and Arg25Cys mutations on phospholamban's conformational equilibrium in membrane bilayers. Biochim Biophys Acta. 2018 Mar 2;1860(6):1335-1341. 
  • Ruff EF, Muretta JM, Thompson AR, Lake EW, Cyphers S, Albanese SK, Hanson SM, Behr JM, Thomas DD, Chodera JD, Levinson NM. A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation. Elife. 2018 Feb 21;7. 
  • Muretta JM, Reddy BJN, Scarabelli G, Thompson AF, Jariwala S, Major J, Venere M, Rich JN, Willard B, Thomas DD, Stumpff J, Grant BJ, Gross SP, Rosenfeld SS. A posttranslational modification of the mitotic kinesin Eg5 that enhances its mechanochemical coupling and alters its mitotic function. Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):E1779-E1788. 
  • Fealey ME, Binder BP, Uversky VN, Hinderliter A, Thomas DD. Structural Impact of Phosphorylation and Dielectric Constant Variation on Synaptotagmin's IDR. Biophys J. 2018 Feb 6;114(3):550-561. 
  • O'Rourke AR, Lindsay A, Tarpey MD, Yuen S, McCourt P, Nelson DM, Perrin BJ, Thomas DD, Spangenburg EE, Lowe DA, Ervasti JM. Impaired muscle relaxation and mitochondrial fission associated with genetic ablation of cytoplasmic actin isoforms. 
  • O'Rourke AR, Lindsay A, Tarpey MD, Yuen S, McCourt P, Nelson DM, Perrin BJ, Thomas DD, Spangenburg EE, Lowe DA, Ervasti JM. FEBS J. 2017 Dec 18. doi: 10.1111/febs.14367
  • Avery AW, Thomas DD, Hays TS. β-III-spectrin spinocerebellar ataxia type 5 mutation reveals a dominant cytoskeletal mechanism that underlies dendritic arborization.Proc Natl Acad Sci U S A. 2017;114(44):E9376-E9385.
  • Colson BA, Thompson AR, Espinoza-Fonseca LM, Thomas DD. Site-directed spectroscopy of cardiac myosin-binding protein C reveals effects of phosphorylation on protein structural dynamics. Proc Natl Acad Sci U S A. 2016;113(12):3233-8.
  • McCaffrey JE, James ZM, Svensson B, Binder BP, Thomas DD. A bifunctional spin label reports the structural topology of phospholamban in magnetically-aligned bicelles. J Magn Reson. 2016;262:50-6.
  • Muretta JM, Jun Y, Gross SP, Major J, Thomas DD, Rosenfeld SS. The structural kinetics of switch-1 and the neck linker explain the functions of kinesin-1 and Eg5. Proc Natl Acad Sci U S A. 2015;112(48):E6606-13.
  • Trivedi DV, Muretta JM, Swenson AM, Davis JP, Thomas DD, Yengo CM. Direct measurements of the coordination of lever arm swing and the catalytic cycle in myosin V. Proc Natl Acad Sci U S A. 2015;112(47):14593-8.
  • Muretta JM, Rohde JA, Johnsrud DO, Cornea S, Thomas DD. Direct real-time detection of the structural and biochemical events in the myosin power stroke. Proc Natl Acad Sci U S A. 2015;112(46):14272-7.
  • Oda T, Yang Y, Uchinoumi H, Thomas DD, Chen-Izu Y, Kato T, Yamamoto T, Yano M, Cornea RL, Bers DM. Oxidation of ryanodine receptor (RyR) and calmodulin enhance Ca release and pathologically alter, RyR structure and calmodulin affinity. J Mol Cell Cardiol. 2015;85:240-8.
  • Binder BP, Cornea S, Thompson AR, Moen RJ, Thomas DD. High-resolution helix orientation in actin-bound myosin determined with a bifunctional spin label. Proc Natl Acad Sci U S A. 2015;112(26):7972-7.
  • Espinoza-Fonseca LM, Alamo L, Pinto A, Thomas DD, Padrón R. Sequential myosin phosphorylation activates tarantula thick filament via a disorder-order transition. Mol Biosyst. 2015;11(8):2167-79.
  • Espinoza-Fonseca LM, Autry JM, Thomas DD. Sarcolipin and phospholamban inhibit the calcium pump by populating a similar metal ion-free intermediate state. Biochem Biophys Res Commun. 2015;463(1-2):37-41.
  • Iram SH, Gruber SJ, Raguimova ON, Thomas DD, Robia SL. ATP-binding cassette transporter structure changes detected by intramolecular fluorescence energy transfer for high-throughput screening. Mol Pharmacol. 2015;88(1):84-94.
  • Espinoza-Fonseca LM, Autry JM, Ramírez-Salinas GL, Thomas DD. Atomic-level mechanisms for phospholamban regulation of the calcium pump. Biophys J. 2015;108(7):1697-708.
  • Guhathakurta P, Prochniewicz E, Thomas DD. Amplitude of the actomyosin power stroke depends strongly on the isoform of the myosin essential light chain. Proc Natl Acad Sci U S A. 2015;112(15):4660-5
  • McCaffrey JE, James ZM, Thomas DD. Optimization of bicelle lipid composition and temperature for EPR spectroscopy of aligned membranes. J Magn Reson. 2015;250:71-5.
  • Svensson B, Oda T, Nitu FR, Yang Y, Cornea I, Chen-Izu Y, Fessenden JD, Bers DM, Thomas DD, Cornea RL. FRET-based trilateration of probes bound within functional ryanodine receptors. Biophys J. 2014;107(9):2037-48.
  • Lewis AK, James ZM, McCaffrey JE, Braun AR, Karim CB, Thomas DD, Sachs JN. Open and closed conformations of the isolated transmembrane domain of death receptor 5 support a new model of activation. Biophys J. 2014;106(6):L21-4.
  • Muretta JM, Thomas DD. Mutation that causes hypertrophic cardiomyopathy increases force production in human β-cardiac myosin. Proc Natl Acad Sci U S A. 2013;110(31):12507-8.
  • Colson BA, Gruber SJ, Thomas DD. 2012. Structural dynamics of muscle protein phosphorylation. J Muscle Res Cell Motil. 2012; 33(6): 419–429.
  • Hou Z, Hu Z, Blackwell DJ, Miller TD, Thomas DD, Robia SL. Two-color calcium pump reveals closure of the cytoplasmic headpiece with calcium binding. PLoS One. 2012;7(7):e40369.
  • Valley, CC, Perlmutter JD, Braun AR, Lewis AK, Karim CB,Thomas DD, Brody JR, Sachs JN. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces Death Receptor 5 networks that are highly organized. J Biol Chem. 2012;287:21265-21278.
  • Lin, AY, Prochniewicz E, HendersonDM, Li B, Ervasti JM, DD Thomas. Impacts of dystrophin and utrophin domains on actin structural dynamics: implications for therapeutic design. J Mol Biol 2012;420:87-98.
  • Gruber, SJ, Haydon S, Thomas DD. Phospholamban mutants compete with wild type for SERCA binding in HEK Cells. Biochem Biophys Res Commun 2012;420:236-240.
  • Li, J, James, Dong X, Karim, Thomas DD. Structural and functional dynamics of an integral membrane protein complex modulated by lipid headgroup charge. J Mol Biol 2012;418:379-389..
  • Henderson, DM, Lin AY, Thomas DD, Ervasti JM. The carboxy-terminal third of dystrophin enhances actin binding activity. J Mol Biol 2012;416:414–424.
  • Mello R, Thomas DD. Three distinct actin-attached structural states of myosin in muscle fibers. Biophys J. 2012;102:1088–1096.
  • Klein, JC, Moen RJ, Smith EA, Titus MA, Thomas DD. Structural and functional impact of site-directed methionine oxidation in myosin. Biochemistry 2011;50:10318–10327.
  • Espinoza-Fonseca LM, Thomas DD. Atomic-level characterization of the activation mechanism of SERCA by calcium. PLoS One 2011;6:e26936.
  • Prochniewicz, E, A Pierre, BR McCullough, HF Chin, W Cao, LP Saunders, DD Thomas, and EM De La Cruz. Actin filament dynamics in the actomyosin VI complex is regulated allosterically by calcium-calmodulin light chain. J Mol Biol 2011;413:584-92.
  • Moen RJ, Johnsrud DO, Thomas DD, Titus MA. Characterization of a myosin VII MyTH/FERM domain. J Mol Biol. 2011;413(1):17-23.
  • 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;108(31):12729-33..
  • Autry JM, Rubin JE, Pietrini SD, Winters DL, Robia SL, Thomas DD. Oligomeric interactions of sarcolipin and the Ca-ATPase. J Biol Chem. 2011;286(36):31697-706.
  • 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;416(1):27-38.
  • 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;408(3):388-92.
  • 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;408(4):755-65.
  • 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;108:1891-6.

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).

David Thomas