About

Rachel Klevit holds the WRF Endowed Chair in Biochemistry at the University of Washington. Her research focuses on biochemistry, with particular emphasis on understanding the molecular mechanisms underlying biological processes. As a professor, she contributes to the field through her expertise in biochemistry, advancing knowledge in this area and mentoring students and colleagues in related research endeavors.

Research topics

• Chemistry
• Biology
• Cell biology
• Biochemistry
• Biophysics
• Genetics
• Computational biology
• Physics
• Stereochemistry
• Medicine
• Business

Selected publications

• Correction: Toggle switch residues control allosteric transitions in bacterial adhesins by participating in a concerted repacking of the protein core

  PLoS Pathogens · 2026-02-02

  articleOpen access

  [This corrects the article DOI: 10.1371/journal.ppat.1009440.].

  PublisherOA PDFDOI

• The E3-ome gene-centric compendium reveals the human E3 ligase landscape

  Cell · 2026-03-20 · 5 citations

  articleOpen access

  To define and systematically characterize the human E3 ubiquitin ligase (E3) landscape, we generated the E3-ome, a compendium of E3s encoded by the human genome. The E3-ome integrates experimental data, bioinformatics, and published research, revealing 672 high-confidence E3s. We standardized E3 classifications to create a unified framework for annotation and comparative analysis. The E3-ome identified several previously unrecognized domains, motifs, E3 candidates, and relationships, expanding the diversity of E3s. Furthermore, the E3-ome mapped the spatial and physiological organization of E3s across human tissues and cell types, revealing context-dependent E3s. Genetic analyses identified disease-associated variants across the E3-ome, linking E3s to diverse human pathologies. Together, these analyses define the human E3 landscape at high resolution and deliver a foundational resource to drive mechanistic and therapeutic discovery.

  PublisherDOI

• Function within Disorder: Small heat shock proteins use different functional regions to chaperone tau aggregation

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-29

  articleOpen accessSenior author

  Abstract In numerous neurodegenerative diseases known collectively as tauopathies, the microtubule-associated protein tau forms fibrillar aggregates that are hallmarks of disease pathology. Tauopathies represent a substantial fraction of diseases associated with protein misfolding. Cellular chaperones known as small heat shock proteins (sHSPs) play a critical role in maintaining protein homeostasis by delaying the onset of protein aggregation. Two sHSPs, HSPB1 (Hsp27) and HSPB5 ( α B-crystallin), are constitutively expressed in brain and neurons. Here, we show that HSPB1 and HSPB5 delay tau aggregation in vitro through distinct mechanisms dictated by their disordered N-terminal regions (NTRs). HSPB1 inhibits tau aggregation under normal cellular conditions, whereas HSPB5 displays activity towards tau when activated by stress conditions such as pH acidosis. Using chimeric HSPB1/HSPB5 constructs in which small NTR subregions are swapped, we identify functional regions within the NTRs that modulate chaperone function for tau. The functional regions contain known sites of phosphorylation, suggesting that they are also control points that respond to cellular stress conditions. Our findings support an emerging model in which specific functional motifs within disordered regions of sHSPs govern activity and client engagement under normal and stress conditions. Broader Audience In many neurodegenerative diseases, the microtubule-associated protein tau forms fibrillar aggregates in the brain. Small heat shock proteins (sHSP) help prevent such aggregation, but their mechanisms of action remain enigmatic. We show HSPB1 and HSBP5, two sHSPs that are abundant and co-localize with tau, delay the onset of tau aggregation through distinct mechanisms. Each relies on specific small regions within their disordered N- terminal domains whose accessibility can be regulated by stress conditions and post- translational modifications.

  PublisherOA PDFDOI

• Activation mechanism of small heat shock protein HSPB5 revealed by disease-associated mutants

  Proceedings of the National Academy of Sciences · 2025-05-16 · 9 citations

  articleOpen accessSenior authorCorresponding

  Found from bacteria to humans, small heat shock proteins (sHSPs) are the least understood protein chaperones. HSPB5 (or αB-crystallin) is among the most widely expressed of the 10 human sHSPs, including in muscle, brain, and eye lens where it is constitutively present at high levels. A high content of disorder in HSPB5 has stymied efforts to uncover how its structure gives rise to function. To uncover its mechanisms of action, we compared human HSPB5 and two disease-associated mutants, R120G and D109H. Expecting to learn how the mutations lead to loss of function, we found instead that the mutants are constitutively activated chaperones while wild-type HSPB5 can transition reversibly between nonactivated (low activity) and activated (high activity) states in response to changing conditions. Techniques that provide information regarding interactions and accessibility of disordered regions revealed that the disordered N-terminal regions (NTR) that are required for chaperone activity exist in a complicated interaction network within HSPB5 oligomers and are sequestered from solvent in nonactivated states. Either mutation or an activating pH change causes rearrangements in the network that expose parts of the NTR, making them more available to bind an aggregating client. Although beneficial in the short-term, failure of the mutants to adopt a state with lower activity and lower NTR accessibility leads to increased coaggregation propensity and, presumably, early cataract. The results support a model where chaperone activity and solubility are modulated through the quasi-ordered NTR and its multiple competing interactions.

  PublisherDOI

• Abstract 2672 Structural and Dynamical Studies of FimH Reveal Novel Mechanisms of Protein Inhibition

  Journal of Biological Chemistry · 2025-05-01

  articleOpen accessSenior author

  Bacterial adhesins are critical mediators of host-pathogen interactions, enabling bacteria to attach to host tissues and establish colonization. The adhesin FimH, located at the tip of type 1 pili in uropathogenic Escherichia coli (UPEC), is a key virulence factor in urinary tract infections (UTIs) and an important target for therapeutic intervention. With the rise in antimicrobial resistance, anti-adhesive strategies that block FimH-mediated adhesion are promising alternatives to antibiotics. FimH is characterized by substantial conformational flexibility, which is fundamental to its function and regulation.

  PublisherOA PDFDOI

• Small heat shock protein HSPB5 uses disorder to bind zinc with high affinity

  Journal of Biological Chemistry · 2025-12-10

  articleOpen accessSenior author

  Zinc is an essential metal that supports diverse cellular functions. Zinc exerts its biological activity through protein binding, serving as catalytic cofactors and structural stabilizers of many enzymes, transcription factors, and ubiquitin E3 ligases, among others. Despite total cellular zinc concentrations reaching hundreds of micromolar, free zinc levels are tightly buffered. Elevated free zinc promotes protein mismetalation and aggregation. While zinc is redox inert, its cysteine (Cys)-based protein ligands are readily oxidized. Oxidative modification of Cys leads to zinc dissociation and a rapid increase in free zinc. With ∼3000 proteins in the human zinc proteome, uncontrolled zinc release could be highly deleterious. Metallothioneins buffer zinc under basal conditions, but their resynthesis following oxidative inactivation occurs on the timescale of hours, raising the question of how free zinc is managed in the interim. Histidine, the second most prevalent zinc-coordinating residue, is resistant to oxidative modification. We characterized zinc binding by the small heat shock protein HSPB5 (αB-crystallin), a Cys-free, histidine-rich protein chaperone that responds to cellular stress and found (1) HSPB5 binds zinc with high affinity and rapid reversibility; (2) zinc binding requires the disordered HSPB5 N-terminal region; (3) zinc binding increases HSPB5 disorder; and (4) prolonged zinc exposure promotes formation of assemblies of oligomers crossbridged by zinc. We propose that HSPB5 has evolved specialized zinc-dependent properties distinct among human small HSPs, enabling it to function not only as a protein chaperone but also as a conditional zinc reservoir under oxidative stress.

  PublisherOA PDFDOI

• <i>De Novo</i> Design of Miniprotein Inhibitors of Bacterial Adhesins

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-18 · 1 citations

  preprintOpen access

  Abstract The rise of multidrug-resistant bacterial infections necessitates the discovery of novel antimicrobial strategies. Here, we show that protein design provides a generalizable means of generating new antimicrobials by neutralizing the function of bacterial adhesins, which are virulence factors critical in host-pathogen interactions. We de novo designed high-affinity miniprotein binders to FimH and Abp1D/Abp2D chaperone usher pili adhesins from uropathogenic Escherichia coli and Acinetobacter baumannii , respectively, which are implicated in mediating both uncomplicated and catheter-associated urinary tract infections (UTI) responsible for significant morbidity and mortality worldwide. The designed antagonists have high specificity and stability, disrupt bacterial recognition of host receptors, block biofilm formation, and are effective in treating and preventing uncomplicated and catheter-associated UTIs in vivo . Targeting virulence factors outside the cell membrane with protein design provides a rapid route to next-generation therapeutics that can disrupt pathogenesis and thus are capable of treating and preventing disease in an antibiotic-sparing manner.

  PublisherOA PDFDOI

• Author response: Force transmission through the inner kinetochore is enhanced by centromeric DNA sequences

  2025-02-21

  peer-reviewOpen access

  Previously, we reconstituted a minimal functional kinetochore from recombinant S. cerevisiae proteins that was capable of transmitting force from dynamic microtubules to nucleosomes containing the centromere-specific histone variant Cse4 (). This work revealed two paths of force transmission through the inner kinetochore: through Mif2 and through the Okp1/Ame1 complex (OA). Here, using a chimeric DNA sequence that contains crucial centromere-determining elements of the budding yeast point centromere, we demonstrate that the presence of centromeric DNA sequences in Cse4-containing nucleosomes significantly strengthens OA-mediated linkages. Our findings indicate that centromeric sequences are important for the transmission of microtubule-based forces to the chromosome.

  PublisherDOI

• Mapping Hydrogen Migration Thresholds for Site-Specific HDX-MS

  Molecular & Cellular Proteomics · 2025-10-10 · 2 citations

  articleOpen access

  A long-standing limitation of Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) has been the difficulty in accurately measuring amide exchange with single amide resolution. Excitation of peptides or proteins during ionization, ion transmission, or collisional activation rapidly induces intermolecular hydrogen migration, leading to a loss of the deuterium-labeled state; a term commonly known as "scrambling." Electron-based fragmentation methods in conjunction with gentle ion transmission settings can minimize scrambling but often not completely. Levels of scrambling have been shown to vary with ion transmission settings, peptide charge, and size, but the general properties that govern the susceptibility of peptides to scrambling are not well understood. Furthermore, it remains unclear whether scrambling is generally a global process or if local scrambling networks commonly exist within peptides. Here, we examine a panel of peptides using gentle electron transfer dissociation and map the activation thresholds of scrambling to define a relationship between peptide charge density and scrambling propensity. This study suggests that by and large, the scrambling process has a single activation threshold and involves all exchangeable sites within a peptide. For some peptides, the activation energy required for scrambling is surprisingly close to that of amide bond dissociation.

  PublisherDOI

• Rigorous Analysis of Multimodal HDX-MS Spectra

  Journal of the American Society for Mass Spectrometry · 2025-01-21 · 20 citations

  article

  An inherent strength of hydrogen/deuterium exchange coupled to mass spectrometry (HDX-MS) is its ability to detect the presence of multiple conformational states of a protein, which often manifest as multimodal isotopic envelopes. However, the statistical considerations for accurate analysis of multimodal spectra have yet to be established. Here we outline an unrestrained binomial distribution fitting approach with the corresponding statistical tests to accurately detect and, when possible, deconvolute isotopic distributions that contain multiple subpopulations. The algorithms have been incorporated into an updated version of the freely available software, HX-Express, and validated using known mixtures of peptides deuterated to varying degrees. This approach presents a readily accessible tool to fit and interpret bimodal and trimodal behavior in HDX-MS data for mixed populations, EX1 kinetics, and pulse labeling data.

  PublisherDOI

Recent grants

• NIH Grant R01GM046701

  NIH · $568k · 1998

• NIH Grant S10RR019133

  NIH · $1.0M · 2006

• NIH Grant R01GM055369

  NIH · $686k · 2001

• NIH Grant R01CA079953

  NIH · $3.0M · 2009

• NIH Grant P01GM032681

  NIH · $10.8M · 1998

Frequent coauthors

• Peter S. Brzović

  University of Washington

  48 shared

• E. Bruce Waygood

  University of Saskatchewan

  45 shared

• Ponni Rajagopal

  University of Washington

  44 shared

• David E. Wemmer

  QB3

  27 shared

• Michael R. Levitt

  North Shore University Hospital

  25 shared

• C. Radloff

  25 shared

• James C. Mathies

  Harvard University

  25 shared

• Shirley K. DeSimone

  25 shared