Kylie J. Walters, Ph.D.

Senior Investigator

Center for Structural Biology


Bldg. 538/Room 167
Frederick, MD 21702


Research Topics

The Walters lab studies the structural and mechanistic basis of ubiquitin signaling events, proteasome function, and protein quality control. We use an interdisciplinary approach that merges functional cell-based assays with a variety of biophysical and structural biology techniques to define the mechanistic underpinnings of how protein lifetimes are regulated in cells. We have helped to identify the mechanisms of substrate recognition by the proteasome, identifying Rpn1 and Rpn13 as substrate receptors that bind to ubiquitin chains directly and to the shuttle factors that deliver ubiquitinated substrates to the proteasome. By using NMR spectroscopy, we have solved structures of these receptors complexed with ubiquitin chains and shuttle factors. We have also used cryoelectron microscopy to study ubiquitin chain binding to the 26S proteasome.

We discovered that Rpn13 is targeted in its ubiquitin-binding domain by cell permeable molecules that restrict cancer cell proliferation. We generated CRISPR cell lines that have revealed the importance of Rpn13 at the proteasome and its requirement for triggered apoptosis by these small molecules. Small molecules that inhibit the catalytic core particle of the proteasome are approved for treatment of hematological cancers and the targeting of Rpn13 is expected to function synergistically with these core particle inhibitors. We are further developing other Rpn13-targeting molecules by using structure-based drug design methods.

In a related project, we recently identified a binding site for the E3 ubiquitin ligase E6AP/UBE3A at the proteasome in substrate receptor Rpn10. This functional domain is the first found at the proteasome to recruit ubiquitination machinery. E6AP is targeted by the human papilloma virus E6 oncoprotein leading to degradation of tumor suppressor p53 and its dysfunction is also associated with prostate cancer, Angelman syndrome, and autism spectrum disorders. We continue to study the role of E6AP at the proteasome as well as other protein-protein interactions in the ubiquitin-proteasome pathway to understand the determinants of protein targeting for degradation as well as the mechanistic features that go awry in these pathways during carcinogenesis and neurological disorders.


Dr. Walters’ training in the field of biophysics began as an undergraduate at Wesleyan University, where she obtained HHMI funding to apply NMR methods to study the dynamic properties of DNA under the supervision of Dr. Irina Russu. She then obtained a Ph.D. in Biophysics from Harvard University, where with Dr. Gerhard Wagner, she developed and used methods to study protein structure, dynamics, and interaction mechanisms. As an American Cancer Society Postdoctoral Fellow with Dr. Peter Howley in the Pathology Department at Harvard Medical School, she began to apply structural biology methods to study the ubiquitin-proteasome pathway. In 2002, Dr. Walters joined the University of Minnesota as an Assistant Professor and was promoted to Associate Professor with tenure in 2008. During this time, Dr. Walters was selected for an American Cancer Society Research Scholar award for her work in protein quality control. In 2013, she moved to the Center for Cancer Research as a Senior Investigator, where she runs a vibrant research program that aims to apply basic science discoveries to translational benefit in the clinic. She has been awarded an NIH Director’s Award, NIH OD Honor Award, NCI Champions-Leading Diversity Award, and CCR top scientific advance. She currently serves on the CCR Science Board, Editorial Board of PLOS Biology, Advisory Board for the journal Structure, and has served as Guest Editor for PNAS and Current Opinions in Structural Biology.

Selected Publications

  1. Buel GR, Chen X, Chari R, O'Neill MJ, Ebelle DL, Jenkins C, Sridharan V, Tarasov SG, Tarasova NI, Andresson T, Walters KJ. Structure of E3 ligase E6AP with a proteasome-binding site provided by substrate receptor hRpn10. Nat Commun. 2020;11(1):1291.
  2. Lu X, Ebelle DL, Matsuo H, Walters KJ. An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure. Structure. 2020;28(5):495-506.e3.
  3. Chen X, Dorris Z, Shi D, Huang RK, Khant H, Fox T, de Val N, Williams D, Zhang P, Walters KJ. Cryo-EM Reveals Unanchored M1-Ubiquitin Chain Binding at hRpn11 of the 26S Proteasome. Structure. 2020;28(11):1206-1217.e4.
  4. Lu X, Nowicka U, Sridharan V, Liu F, Randles L, Hymel D, Dyba M, Tarasov SG, Tarasova NI, Zhao XZ, Hamazaki J, Murata S, Burke TR Jr, Walters KJ. Structure of the Rpn13-Rpn2 complex provides insights for Rpn13 and Uch37 as anticancer targets. Nat Commun. 2017;8:15540.
  5. Shi Y, Chen X, Elsasser S, Stocks BB, Tian G, Lee BH, Shi Y, Zhang N, de Poot SA, Tuebing F, Sun S, Vannoy J, Tarasov SG, Engen JR, Finley D, Walters KJ. Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome. Science. 2016;351(6275).

Related Scientific Focus Areas

This page was last updated on Tuesday, March 26, 2024