About

David Thomas, PhD, is the William F. Dietrich Professor at the University of Minnesota Medical School. His laboratory studies fundamental molecular motions and interactions responsible for cellular movement, with the goal of understanding the molecular bases of muscle disorders and devising novel therapies based on these discoveries. The research employs a multidisciplinary approach, utilizing techniques such as physiology, enzyme kinetics, molecular genetics, peptide synthesis, and computer simulation, with a particular emphasis on site-directed spectroscopic probes. These probes, including spin labels, fluorescent dyes, phosphorescent dyes, or isotopes, are attached to muscle proteins in solution or in cells, allowing magnetic resonance or optical spectroscopy to directly detect the motions of force-generating proteins like actin and myosin, as well as membrane ion pumps and channels involved in muscle excitation and relaxation. His research involves several types of muscle, with an increasing focus on the heart. A key direction of his work is to use principles of structural biophysics to design new molecular therapies for heart failure. This ambitious and high-risk endeavor is supported by a unique combination of technologies, insights, and collaborations. The lab's advances have led to the creation of Photonic Pharma LLC, a company aimed at commercializing discoveries in drug development.

Research topics

• Biology
• Chemistry
• Biophysics
• Biochemistry
• Cell biology
• Computational biology
• Genetics
• Physics
• Computer Science
• Bioinformatics
• Endocrinology
• Medicine
• Acoustics
• Internal medicine

Selected publications

• BPS2025 - Live-cell FRET biosensors for high-throughput screening targeting the SERCA2a-DWORF complex

  Biophysical Journal · 2025-02-01

  articleSenior author
  PublisherDOI

• Myosin relaxation states in skeletal muscle fibers of rats and mice: Effects of sex and adiposity

  Physiological Reports · 2025-04-01

  articleOpen access

  Myosin disordered- and super-relaxed states (DRX and SRX, respectively) in skeletal muscle fibers are hypothesized to play key roles in thermogenesis and basal metabolic energy expenditure, raising potential for novel therapeutic targets for obesity and other metabolic diseases. Limited studies have investigated relationships between body composition or biological sex and myosin relaxed states. Using fluorescence-based single-nucleotide turnover, we report quantitative relationships of diet-induced adiposity and sex with biochemical parameters of myosin relaxed states of rodent muscle fibers. Our main findings were: (1) adiposity had minimal to no effect on parameters of relaxed myosin states measured in fibers from rats and mice, (2) fibers from female rats and mice had 10%-20% shorter SRX lifetimes than those from males (p ≤ 0.035), (3) in rats, females had shorter DRX lifetimes than males, and (4) myosin heavy chain isoform had negligible impact on parameters of relaxed myosin states. We conclude that skeletal muscle energy utilization during rest, as measured by myosin ATPase, is affected minimally by adiposity, but differs by sex. Continued exploration of the metabolic implications of myosin transitioning between SRX and DRX will provide further understanding of muscle thermogenesis and whole-body metabolism; in so doing, sex as a biological factor should be considered.

  PublisherOA PDFDOI

• A FRET assay to monitor different structural states of human β-cardiac myosin including the interacting-heads motif

  Proceedings of the National Academy of Sciences · 2025-08-20 · 8 citations

  articleOpen access

  In cardiac muscle, myosin molecules exist in multiple structural states as they transit through their ATPase cycle, including an off-cycle resting or OFF-state with their catalytic heads in a folded structure known as the interacting-heads motif (IHM). The blocked head configuration (BHC) of the IHM is unusual because its light chain binding region is held in an exaggerated prestroke angle stabilized by interactions with its own S2 tail. An additional partial OFF-state, where the second head of the IHM is not folded back onto the blocked head, has been proposed, which still has the blocked head interacting with S2. Many mutations in the human β-cardiac myosin gene that cause hypertrophic cardiomyopathy are thought to destabilize (decrease the population of) the OFF-states. The effects of pathogenic mutations on the folded back structural states are often studied using indirect assays, including a single-ATP turnover assay that detects the biochemical state of myosin functionally. Here, we use a fluorescence resonance energy transfer (FRET) based sensor for direct quantification in solution of the myosin BHC state. Using the FRET sensor, we provide evidence that the myosin tail acts as an activator of the recovery stroke transition after ATP binding to poststroke state apomyosin and that BHC formation is rapid after ATP binding and depends on formation of the prestroke state. We propose that the positively charged loop 2 of the prestroke state head interacts with the Ring 2 cluster of negatively charged residues on the S2 tail to form a preBHC state that facilitates BHC state formation.

  PublisherOA PDFDOI

• Large-scale high-throughput screen for cardiac ryanodine receptor targeted therapeutics

  Journal of Biological Chemistry · 2025-11-20 · 1 citations

  articleOpen access

  <h2>Abstract</h2> In high-throughput screening (HTS) assays using fluorescence lifetime (FLT)-detected FRET, we have identified compounds that allosterically modulate the pathologically leaky ryanodine receptor (RyR) calcium release channels. These compounds may prevent or reduce the elevated Ca²⁺ that fuels arrhythmia, heart failure, and age-related neurodegeneration. RyRs are responsible for intracellular Ca²⁺ release from endoplasmic/sarcoplasmic reticulum (ER/SR). The resulting [Ca²⁺] pulse is a signal for many cellular processes, whereas sustained elevated [Ca²⁺] is pathologic. Our FRET-based HTS detects the pathology-linked RyR leaky state by monitoring binding of the accessory protein calmodulin and the DPc10 peptide (corresponding to RyR2 residues 2460–2495) known to perturb inter-domain interactions within RyR2. Under conditions mimicking a pathological state, we have screened a 50,000-compound chemical library to identify small-molecule modulators of RyR2 in cardiac SR membranes. This screen yielded 603 compounds that reproducibly altered FRET. Based on FRET response profiles that align with therapeutic potential, 83 of those most promising compounds were purchased and validated by FRET dose response evaluation. Focusing on ten chemical scaffolds that desirably increase A-CaM binding, six representative compounds reduced RyR2 activity as measured by [³H]ryanodine binding. Ca²⁺ dynamics in HEK293 cells expressing human RyR2 or in cardiomyocytes highlighted the isoxazole group of hits as potentially therapeutic by targeting the pathological RyR2 leak state.

  PublisherOA PDFDOI

• Tyrosine-Mediated Static and Dynamic Quenching of a Receptor Tyrosine Kinase Biosensor Reveals Inhibitor Binding Modes and Kinase Conformations

  ACS Chemical Biology · 2025-06-19

  articleOpen access

  Conformational changes triggered by kinase inhibitors are a major factor driving specificity and efficacy, but few scalable methods exist for differentiating induced conformations and binding modes. Using the receptor tyrosine kinase MET, we show that three classes of inhibitors can be distinguished by their contrasting effects on static and dynamic quenching of a fluorescent dye attached to the activation loop. Quenching is mediated by tyrosine residues on the flexible activation loop, and inhibitor binding induces order in the loop, sequestering the tyrosines and differentially suppressing static and dynamic quenching in a manner that is dependent on the induced structural state. Type I MET inhibitors have a large static and moderate dynamic component, type II inhibitors have only a static component, and active-state-selective inhibitors relieve both components to similar extents. These distinct dequenching signatures allow the straightforward detection of each binding mode by using parallel steady-state and time-resolved fluorescence measurements. We show that this technique can be applied to rapidly assess the effects of resistance mutations on inhibitor binding and can report on the chemical interactions and conformational changes that drive these effects. Conservation of the three activation loop tyrosine residues across many receptor tyrosine kinases suggests that this approach has broad utility.

  PublisherDOI

• Aurora A binds to the transactivation domain of c-Myc and recognizes the phosphorylated N-terminal degron motif

  Biochemical Journal · 2025-04-01 · 1 citations

  articleOpen access

  The oncoprotein c-Myc is overexpressed or mutated in a large fraction of human cancers. The stability of c-Myc is controlled by phosphorylation of T58 and S62 within a conserved degron motif in the N-terminal transactivation domain, which triggers recruitment of the SCF ubiquitin ligase. The kinase Aurora A (AurA) has been shown to bind to both c-Myc and its paralog N-Myc and to promote their stability by interfering with ubiquitination and degradation. Here we show, using NMR and FRET experiments, that AurA binds to c-Myc through several discrete interactions spanning 145 residues within its transactivation domain. AurA binding to c-Myc is enhanced by phosphorylation of the T58/S62 degron, demonstrating that the kinase recognizes the pool of c-Myc that has been marked for degradation by the ubiquitin proteasome pathway. Although AurA binds to segments of c-Myc flanking the degron, it does not appear to form extensive interactions with the phosphorylated degron itself, potentially leaving it accessible on the AurA surface. These observations establish a foundation for understanding the role of AurA in regulating c-Myc ubiquitination and degradation.

  PublisherDOI

• BPS2025 - SERCA2a-targeted drugs for treatment of heart failure: Medicinal chemistry development of a compound identified via high-throughput screening

  Biophysical Journal · 2025-02-01

  articleSenior author
  PublisherDOI

• Development of activators for SERCA2a for heart failure treatments

  European Journal of Medicinal Chemistry · 2025-11-29

  articleOpen accessCorresponding
  PublisherOA PDFDOI

• ISMRM Open Science Initiative for Perfusion Imaging (OSIPI): Composite Python Library for ASL Image Processing

  Proceedings on CD-ROM - International Society for Magnetic Resonance in Medicine. Scientific Meeting and Exhibition/Proceedings of the International Society for Magnetic Resonance in Medicine, Scientific Meeting and Exhibition · 2025-09-16

  article

  Motivation: The ISMRM-Open Science Initiative for Perfusion Imaging (OSIPI) aims to facilitate collaboration, reproducibility, and transparency in perfusion imaging research by providing a shared platform for tools and methodologies. Goal(s): To develop an open-source library of functions and scripts for Arterial Spin Labeled (ASL) imaging preprocessing and analysis. Approach: We harmonized the code collected during our first roadmap into a Python library, PyASL, supporting both human and preclinical brain data. Results: PyASL currently includes two human data pipelines, two preclinical data pipelines, a deep learning-based denoising function, and a command line utility integration. Each function is fully documented for user reference. Impact: PyASL provides unified, open-source functions that enable researchers to apply standardized methods across studies, enhancing reproducibility and transparency. It also reduces redundant development, allowing scientists to focus on addressing new challenges in ASL perfusion imaging.

  PublisherDOI

• Kinetics insight into the roles of the N- and C-lobes of calmodulin in RyR1 channel regulation

  Journal of Biological Chemistry · 2025-02-02 · 1 citations

  articleOpen access

  Calmodulin (CaM) activates the skeletal muscle Ca²⁺ release channel (ryanodine receptor, RyR1) at nanomolar Ca²⁺ and inhibits it at micromolar Ca²⁺. CaM conversion from RyR1 activator to inhibitor is due to structural changes induced by Ca²⁺ binding at CaM's two lobes. However, it remains unclear which lobe provides the switch for this conversion. Here, we attached the environment-sensitive fluorophore acrylodan (Acr) at either lobe of intact CaM or lobe-specific Ca²⁺-sensitive CaM mutants, and monitored the effects of Ca²⁺ binding <i>via</i> the fluorescence change of free or RyR1-bound ^AcrCaM. Using steady state measurements, we found that Ca²⁺ binding to free CaM causes a dramatic structural change in the N-lobe, but only a slight effect on the C-lobe of the Ca²⁺-sensitive lobe-specific mutants, in addition to the previously known higher Ca²⁺ affinity at the C-lobe <i>versus</i> the N-lobe. Using stopped-flow measurements, we found ∼30x faster Ca²⁺ dissociation from the N- <i>versus</i> C-lobe, and ∼20x slower Ca²⁺ association to the N-lobe <i>versus</i> C-lobe. These Ca²⁺ binding properties hold for the CaM/RyR1 complex, and Ca²⁺ affinity is enhanced at the CaM C-lobe but decreased at the N-lobe by RyR1 binding. We propose that fast Ca²⁺-binding at the C-lobe of CaM initiates its inhibition to RyR1 at high [Ca²⁺], while slow Ca²⁺ binding to the N-lobe is necessary for timely enhancement of the inhibitory effect. The dysregulation of RyR1 by M124Q-CaM may be explained by the lower Ca²⁺ affinity <i>versus</i> WT-CaM, as suggested by both steady-state and transient kinetics results.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R03RR004300

  NIH · $32k · 1989

• Minnesota Muscle Training Program

  NIH · $9.0M · 2001–2027

• REU Site: Internship in Supercomputing for Physical Sciences

  NSF · $150k · 2008–2011

• Minnesota Muscle Training Program

  NIH · $319k · 2001–2027

• NIH Grant R01AR063007

  NIH · $1.3M · 2017

Frequent coauthors

• Răzvan L. Cornea

  University of Minnesota

  140 shared

• Joseph M. Autry

  University of Minnesota

  91 shared

• Larry R. Jones

  University of California, Davis

  84 shared

• Christine B. Karim

  University of Minnesota

  72 shared

• Ewa Próchniewicz

  University of Minnesota

  70 shared

• L. Michel Espinoza‐Fonseca

  University of Michigan–Ann Arbor

  69 shared

• Joseph M. Muretta

  University of Minnesota

  63 shared

• Bengt Svensson

  University of Minnesota

  61 shared

Education

• Postdoctoral, Biophysics (L. Stryer)

  Stanford University

  1979

• Postdoctoral, Biophysics (J. Gergely)

  Harvard University

  1977

• PhD, Biophysics (H. McConnell)

  Stanford University

  1975

• BS, Physics

  Stanford University

  1971

Awards & honors

• Dr. James E. Rubin Medical Memorial Award
• Graduating Medical Student Research Award
• Veneziale-Steer Award
• Dr. Marvin and Hadassah Bacaner Research Awards
• Schmidt Steer Award