Research Themes:
Biomaterials and Regenerative Medicine
Molecular and Cellular Engineering
Systems, Synthetic and Quantitative Biology

Education

PhD (bioengineering), University of Washington, 2003
MS (applied mathematics), University of Washington, 2003
BA (molecular biology), Princeton University, 1987

Research Interests

• Mechanical regulation of reversible & nonfouling biomaterial adhesives
• Bacterial adhesion and biofilms
• Platelet adhesion and thrombosis

Contact Information

Department of Bioengineering
University of Washington
Box 355061
William H. Foege Building, Room N430P
Phone: 206-616-3947
Fax: 206-685-4434
E-mail
Web site: http://faculty.washington.edu/wendyt/index.html

Research Description

I am interested in understanding how proteins are mechanically regulated, with a particular emphasis on adhesion. Many proteins experience mechanical force from fluid flow, cytoskeletal forces, or other sources. This might be expected to weaken adhesion, by tearing the bound molecules away from each other, but we study situations where force or fluid flow enhances adhesion. In particular, we study catch bonds, which are biological receptor-ligand interactions that bind longer when you try to pull them apart. We study the biophysics of adhesive mechanics in order to understand and address related clinical problems and to design novel adhesive technologies.

One project in the lab involves studying a bacterial adhesive protein called FimH that forms catch-bonds. Bacteria binding through FimH will only bind firmly at high levels of fluid flow, and will roll across the surface or detach if the flow is stopped. FimH is expressed on most of our intestinal bacteria and is involved in urinary tract infections. One thrust of this research is to understand how bacteria use catch bonds to form biofilms in the presence of flowing bodily fluids. We hope to learn methods to prevent biofilms from forming on indwelling medical devices such as urinary catheters since this can lead to sepsis and death.

FimH catch-bonds have remarkable properties, lasting less than a second in the absence of mechanical force but surpassing the strength of biotin-streptavidin bonds at high force. This makes them the ultimate in reversible adhesion. Like a nanoscale locking seatbelt, they bind when needed but allow movement at other times. Their ligand, mannose, is ubiquitous in human tissues. We are thus pursuing a wide range of technological applications of FimH for microfluidics, nanotechnology, and biomaterials.

A second project involves thrombosis, or blood clots. Most mechanisms through which blood can clot do not function well at high shear stress, which is encountered in spurting wounds. One mechanism—binding of platelets to the blood protein von Willebrand Factor—not only works in this condition, but it actually requires high shear to be activated. We are seeking to understand the molecular basis of this shear activated thrombosis. Unfortunately, high shear is also encountered in advanced atheroschlerosis, where plaques restrict vessels, so this protective mechanism can cause blood clots in these vessels that in turn can cause a heart attack or stroke. We hope that understanding this mechanism will lead to minimally invasive ways to protect patients with atheroschlerosis from deadly blood clots.

We integrate computational and experimental tools for all of these projects. We use an atomic force microscope to apply force to single molecular bonds or macromolecular complexes. Molecular Dynamics simulations and Rosetta protein structure prediction allow an understanding of the structural basis of the observed behavior.  Genetic mutation of the proteins can link the structural simulations to the experiments. We also use microfluidics to see how cells or microparticles adhere in flow. Multi-scale simulations relate the nanoscale molecular properties to cellular or other microscale properties in our different experiments. For success in this interdisciplinary research, some group members do both simulations and experiments, while others do just one or the other and instead collaborate to enable integration of the two approaches.

Honors, Awards and Professional Activities

• 2007-2010: BMES Board of Directors
• 2007: American Heart Association National Scientist Development Grant
• 2007: National Science Foundation CAREER Award
• 1999-2003: Whitaker Foundation Graduate Fellowship

Selected Publications

• Kidd BA, Baker D*, and Thomas WE* “Computation of Conformational Coupling in Allosteric Proteins” in press, PLoS computational Biology
• Thomas, WE*. Mechanochemistry of receptor-ligand bonds. Current Opinion in Structural Biology (2009)
• Sokurenko EV*, Vogel V, Thomas WE. Catch-Bond Mechanism of Force-Enhanced Adhesion: Counterintuitive, Elusive, but … Widespread? Cell Host and Microbe 4 p 314-323 (2008)
• Nilsson, L. M., Thomas, W. E., Sokurenko, E. V., Vogel*, V. Beyond induced-fit receptor-ligand interactions: structural changes that can significantly extend bond lifetimes. Structure 16 p. 1047-58 (2008)
• Ronald LS, Yakovenko O, Yazvenko N, Chattopadhyay S, Aprikian P, Thomas WE, Sokurenko EV*. Adaptive mutations in the signal peptide of the type 1 fimbrial adhesin of uropathogenic Escherichia coli PNAS 105 p. 10937-42 (2008)
• Thomas WE. Catch Bonds in Adhesion. Ann Rev. Biomed Eng 10: p 39-57 (2008)
• Thomas WE. Vogel, V. and Sokurenko, E. Biophysics of Catch Bonds. Annual Review of Biophysics 37: p 399-416 (2008)
• Yakovenko O, Sharma S, Forero M, Tchesnokova V, Aprikian P, Kidd B, Mach A, Vogel V, Thomas WE. FimH forms catch bonds that are enhanced by mechanical force due to allosteric regulation. J Biol Chem 283(17) p 11596-605 (2008)
• Tchesnokova V, Aprikian P, Yakovenko O, LaRock, C, Kidd B, Vogel V, Thomas W, and Sokurenko E. Integrin-like allosteric properties of the catch-bond forming FimH adhesin of E. coli. J Biol Chem 283(12) p 7823-33 (2008)
• Korotkova N, Yang Y, Le Trong I, Cota E, Demeler B, Marchant J, Thomasn WE, Stenkamp RE, Moseley SL and Matthews S, Binding of Dr adhesins of Escherichia coli to carcinoembryonic antigen triggers receptor dissociation. Molecular Microbiology 67(2) p 420-434 (2008)
• Aprikian P, Tchesnokova V, Kidd B, Yakovenko O, Yarov-Yarovoy V, et al. 2007. Interdomain Interaction in the FimH Adhesin of Escherichia coli Regulates the Affinity to Mannose. J Biol Chem 282: 23437-46
• Anderson, B., A. Ding, L. Nilsson, K. Kusuma, V. Tchesnokova, V. Vogel, E. Sokurenko, and W.E. Thomas, " Weak Rolling Adhesion Enhances Bacterial Surface Colonization ". J. Bac. 189(5): 1794-802.(2007)
• Thomas, W.E. , "Understanding the Counterintuitive Phenomenon of Catch Bonds". Current Nanotechnology. (in press)
• Thomas, W.E. , "For catch bonds, it all hinges on the interdomain region". J Cell Biol. 2006 174(7): 911-3.
• Forero, M., O. Yakovenko, E.V. Sokurenko, W.E. Thomas, and V. Vogel, "Uncoiling Mechanics of Escherichia coli Type I Fimbriae Are Optimized for Catch Bonds". PLoS Biol 2006. 4(9): 1509-1516.
• Nilsson, L.M., W.E. Thomas, E.V. Sokurenko, and V. Vogel, Elevated Shear Stress Protects Escherichia coli Cells Adhering to Surfaces via Catch Bonds from Detachment by Soluble Inhibitors. Appl Environ Microbiol, 2006. 72(4): p. 3005-10.
• Nilsson, L., W.E. Thomas, E. Trintchina, V. Vogel, and E.V. Sokurenko “Catch bond-mediated adhesion without a shear threshold: trimannose versus monomannose interactions with the FimH adhesin of Escherichia coli.” . J Biol Chem 2006. 84(24) 16656-63.
• Thomas, W.E ., M. Forero, O. Yakovenko, L. Nilsson, P. Vicini, E.V. Sokurenko, and V. Vogel, Catch Bond Model Derived from Allostery Explains Force-Activated Bacterial Adhesion. Biophys J, 2006. 90(3): p. 753-64.
• Pereverzev, Y.V., O.V. Prezhdo, W.E. Thomas, and E.V. Sokurenko, Distinctive features of the biological catch bond in the jump-ramp force regime predicted by the two-pathway model. Phys Rev E Stat Nonlin Soft Matter Phys, 2005. 72(1 Pt 1): p. 010903.
• Pereverzev, Y., O.V. Prezhdo, M. Forero, E. Sokurenko, and W.E. Thomas, The Two-Pathway Model for the Catch-Slip Transition in Biological Adhesion. Biophys J, 2005. 89(3): p. 1446-1454.
• Thomas, W.E ., L. Nilsson, M. Forero, E.V. Sokurenko, and V. Vogel, “'Stick-and-roll' bacterial adhesion mediated by catch-bonds” Molecular Microbiology, 2004. 53: p. 1545
• M. Forero , W. E. Thomas, C. Bland, L. Nilsson, E.V. Sokurenko, and V. Vogel, “A Catch-Bond Based Smart Nano-Adhesive Sensitive to Shear Stress” Nano Letters 2004 , 4(9); p. 1593-1597
• Thomas, W.E ., E. Trintchina, M. Forero, V. Vogel, and E.V. Sokurenko, “Bacterial adhesion to target cells enhanced by shear force” Cell, 2002. 109(7): p. 913-23
• Krammer, A., D. Craig, W.E. Thomas, K. Schulten, and V. Vogel, “A structural model for force regulated integrin binding to fibronectin's RGD-synergy site” Matrix Biol, 2002. 21(2): p. 139-147
• Vogel, V., W.E. Thomas, D.W. Craig, A. Krammer, and G. Baneyx, “Structural insights into the mechanical regulation of molecular recognition sites” Trends Biotechnol, 2001. 19(10): p. 416-23
• Thomas, W.E . and J.A. Glomset, “Affinity purification and catalytic properties of a soluble, Ca2+-independent, diacylglycerol kinase” Biochemistry, 1999. 38(11): p. 3320-6
• Thomas, W.E . and J.A. Glomset, “Multiple factors influence the binding of a soluble, Ca2+-independent, diacylglycerol kinase to unilamellar phosphoglyceride vesicles” Biochemistry, 1999. 38(11): p. 3310-9