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.)

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 Mar 22;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 Jan;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 Dec 1;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 Nov 24;112(47):14593-8. PMID: 26553992

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 Nov 17;112(46):14272-7. PMID: 26578772

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 Aug;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 Jun 30;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 Jul 14;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 Jul 17-24;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 Jul;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 Apr 7;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 Mar 30;.

McCaffrey JE, James ZM, Thomas DD. Optimization of bicelle lipid composition and temperature for EPR spectroscopy of aligned membranes. J Magn Reson. 2015 Jan;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 Nov 4;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 Mar 18;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 Jul 30;110(31):12507-8.

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).

David Thomas