Kaitlin Schaefer
Assistant ProfessorDownloadHi-Res Photo
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Microbial Pathogenesis
295 Congress Ave, BCMM 345/443
New Haven, CT 06519
United States
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Assistant Professor
Biography
Katie is an assistant professor in the Department of Microbial Pathogenesis at the Yale School of Medicine. Her research integrates chemistry, chemical biology, proteomics, structural biology, and microbiology. Katie studied with Suzanne Walker and Daniel Kahne, earning her Ph.D. in Chemistry and Chemical Biology at Harvard. In her Ph.D. training, she focused on the bacterial cell surface, which requires complex glycan assembly. She then completed her postdoctoral training with Jim Wells at UCSF, leveraging chemical biology to develop new proteomic methods.
As an enthusiastic and curiosity-driven scientist, Katie is excited to bring her interdisciplinary approaches to her lab and explore how human:microbe communities interact in human health. Outside of the lab, you may catch her running around New Haven, exploring the New England foliage with her baby, or sampling local bakeries.
Last Updated on September 20, 2025.
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Microbial Pathogenesis
Assistant ProfessorPrimary
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Overview
chemical biology; proteomics; human:microbe interactions; glycan:protein interactions; membrane biochemistry; immunology; microbiology.
ORCID
0000-0003-4825-1389- View Lab Website
Schaefer Lab
Research at a Glance
Publications Timeline
A big-picture view of Kaitlin Schaefer's research output by year.
18Publications
2,130Citations
Publications
2025
Hypoxia Induces Extensive Protein and Proteolytic Remodeling of the Cell Surface in Pancreatic Adenocarcinoma (PDAC) Cell Lines
Lui I, Schaefer K, Kirkemo L, Zhou J, Perera R, Leung K, Wells J. Hypoxia Induces Extensive Protein and Proteolytic Remodeling of the Cell Surface in Pancreatic Adenocarcinoma (PDAC) Cell Lines. Journal Of Proteome Research 2025, 24: 2791-2800. PMID: 40312771, PMCID: PMC12161487, DOI: 10.1021/acs.jproteome.4c01037.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsProteolytic remodelingCell surfacePancreatic ductal adenocarcinomaCell linesCell surface proteinsUpregulation of proteinsCellular response to hypoxiaN-terminomicsTumor microenvironmentCellular processesPancreatic ductal adenocarcinoma cell linesSurface proteinsShed proteinsMetabolic processesMolecular eventsTissue developmentCellular adhesionProteinMass spectrometry technologyCancer progressionHypoxia regulationHypoxia-induced alterationsProteolysisResponse to hypoxiaTherapeutic targetEngineered Proteins and Chemical Tools to Probe the Cell Surface Proteome
Leung K, Schaefer K, Lin Z, Yao Z, Wells J. Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome. Chemical Reviews 2025, 125: 4069-4110. PMID: 40178992, PMCID: PMC12022999, DOI: 10.1021/acs.chemrev.4c00554.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsProximity labeling proteomicsCell surface proteomeSurface proteomeTarget discoveryProximity labeling techniquesProtein-protein interactionsPost-translational modificationsMembrane protein complexesCell surface glycosylationCell surface proteinsPeptide MHC complexesExtracellular post-translational modificationDisease-associated changesLabeling proteomicsProtein complexesProteome levelProteomic approachSurface glycosylationEngineered proteinsSurfaceomeProteolytic remodelingSurface proteinsProteomicsFunctional importanceCell surface
2024
Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells
Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney D, Palar A, Sali A, Wells J. Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Science 2024, 385: eadl5763. PMID: 39024454, DOI: 10.1126/science.adl5763.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsProximity labeling proteomicsProtein neighborhoodsOncogenic epidermal growth factor receptorProximity labelingAlphaFold-MultimerLabeling radiusLabeling proteomicsProtein networkCell surfaceEpidermal growth factor receptorVisible light illuminationGrowth factor receptorPhoto-probesFactor receptorEosin YCellsLight illuminationInteractome
2022
Direct Identification of Proteolytic Cleavages on Living Cells Using a Glycan-Tethered Peptide Ligase
Schaefer K, Lui I, Byrnes J, Kang E, Zhou J, Weeks A, Wells J. Direct Identification of Proteolytic Cleavages on Living Cells Using a Glycan-Tethered Peptide Ligase. ACS Central Science 2022, 8: 1447-1456. PMID: 36313159, PMCID: PMC9615116, DOI: 10.1021/acscentsci.2c00899.Peer-Reviewed Original ResearchCitationsAltmetricConceptsNeo-N-terminiProteolytic cleavageN-terminomicsPeptide ligaseN-terminal nucleophileRemodeling of proteinsLiving cellsCell surface proteinsSurface of living cellsCancer cell growthCell-cell interactionsMalignant cell phenotypeExtracellular proteasesCleavage siteCellular contextSignaling proteinsMembrane proteinsProteomic approachProteomic analysisProteomic studiesSurface proteinsCell growthCell typesProteinLigase
2020
Lipoteichoic acid polymer length is determined by competition between free starter units
Hesser A, Schaefer K, Lee W, Walker S. Lipoteichoic acid polymer length is determined by competition between free starter units. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 29669-29676. PMID: 33172991, PMCID: PMC7703640, DOI: 10.1073/pnas.2008929117.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsStarter unitGram-positive bacteriaLipoteichoic acidAlternative starter unitsLipoteichoic acid synthaseLipoteichoic acid polymersPolymer lengthCarbohydrate polymersAnionic glycopolymersDiglucosyl diacylglycerolLipid anchorAcid synthaseExtracellular leafletBiological functionsCell growthReconstituted systemBinding sitesLtaSPhosphatidylglycerolCell membraneStructural diversityBacteriaShort polymersPolymerEnzymeStructure and reconstitution of a hydrolase complex that may release peptidoglycan from the membrane after polymerization
Schaefer K, Owens T, Page J, Santiago M, Kahne D, Walker S. Structure and reconstitution of a hydrolase complex that may release peptidoglycan from the membrane after polymerization. Nature Microbiology 2020, 6: 34-43. PMID: 33168989, PMCID: PMC7755832, DOI: 10.1038/s41564-020-00808-5.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsMature peptidoglycanLipid IIMembrane proteinsPolytopic membrane proteinsPeptidoglycan cell wallCell wall assemblyCell wall hydrolasesCaaX proteasesGlycan strandsCell wall matrixNascent peptidoglycanMembrane-anchoredTransmembrane helicesPeptidoglycan strandsPeptidoglycanPeptidoglycan polymerCell wallProtein scaffoldHydrolaseWall assemblyWall matrixBacteriaActive siteProteinMembraneAn ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike
Schoof M, Faust B, Saunders R, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle C, Puchades C, Azumaya C, Kratochvil H, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen H, Chio C, Merz G, Thompson M, Diwanji D, Schaefer K, Anand A, Dobzinski N, Zha B, Simoneau C, Leon K, White K, Chio U, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith A, Rizo A, Moss F, Brilot A, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill A, Nock S, Liu Y, Krogan N, Ralston C, Swaney D, García-Sastre A, Ott M, Vignuzzi M, Walter P, Manglik A, Azumaya C, Puchades C, Sun M, Braxton J, Brilot A, Gupta M, Li F, Lopez K, Melo A, Merz G, Moss F, Paulino J, Pospiech T, Pourmal S, Rizo A, Smith A, Thomas P, Wang F, Yu Z, Dickinson M, Nguyen H, Asarnow D, Campbell M, Chio C, Chio U, Diwanji D, Faust B, Gupta M, Hoppe N, Jin M, Li J, Liu Y, Merz G, Sangwan S, Tsui T, Trenker R, Trinidad D, Tse E, Zhang K, Zhou F, Herrera N, Kratochvil H, Schulze-Gahmen U, Thompson M, Young I, Biel J, Deshpande I, Liu X, Billesbølle C, Nowotny C, Smith A, Zhao J, Bowen A, Hoppe N, Li Y, Nguyen P, Safari M, Schaefer K, Whitis N, Moritz M, Owens T, Diallo A, Kim K, Peters J, Titus E, Chen J, Doan L, Flores S, Lam V, Li Y, Lo M, Thwin A, Wankowicz S, Zhang Y, Bulkley D, Joves A, Joves A, McKay L, Tabios M, Rosenberg O, Verba K, Agard D, Cheng Y, Fraser J, Frost A, Jura N, Kortemme T, Krogan N, Manglik A, Southworth D, Stroud R. An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science 2020, 370: 1473-1479. PMID: 33154106, PMCID: PMC7857409, DOI: 10.1126/science.abe3255.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsAngiotensin-converting enzyme 2Structure-guided designCell receptor angiotensin-converting enzyme 2Host cell receptor angiotensin-converting enzyme 2Binds angiotensin-converting enzyme 2Receptor angiotensin-converting enzyme 2Cryo-electron microscopyReceptor-binding domainBinding domainFemtomolar affinityHost cellsInactive conformationSynthetic nanobodiesNanobody sequencesCryo-EMSpike proteinSARS-CoV-2 infectionNanobodiesAffinity maturationAirway epitheliaEnzyme 2Severe acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Trivalent nanobodyRespiratory syndrome coronavirus 2Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms
Gordon D, Hiatt J, Bouhaddou M, Rezelj V, Ulferts S, Braberg H, Jureka A, Obernier K, Guo J, Batra J, Kaake R, Weckstein A, Owens T, Gupta M, Pourmal S, Titus E, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O’Meara M, Tummino T, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney D, Fabius J, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas K, Naing Z, Pulido E, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero M, Burke D, Koh C, Vallet T, Silvas J, Azumaya C, Billesbølle C, Brilot A, Campbell M, Diallo A, Dickinson M, Diwanji D, Herrera N, Hoppe N, Kratochvil H, Liu Y, Merz G, Moritz M, Nguyen H, Nowotny C, Puchades C, Rizo A, Schulze-Gahmen U, Smith A, Sun M, Young I, Zhao J, Asarnow D, Biel J, Bowen A, Braxton J, Chen J, Chio C, Chio U, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam V, Li F, Li J, Li Y, Li Y, Liu X, Lo M, Lopez K, Melo A, Moss F, Nguyen P, Paulino J, Pawar K, Peters J, Pospiech T, Safari M, Sangwan S, Schaefer K, Thomas P, Thwin A, Trenker R, Tse E, Tsui T, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, Hodder A, Shun-Shion A, Williams D, White K, Rosales R, Kehrer T, Miorin L, Moreno E, Patel A, Rihn S, Khalid M, Vallejo-Gracia A, Fozouni P, Simoneau C, Roth T, Wu D, Karim M, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie C, Elliott M, Brown F, Burness K, Reid E, Dorward M, Johnson C, Wilkinson S, Geyer A, Giesel D, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough K, Lind A, Klesh R, Hemphill K, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard K, Sali A, Agard D, Cheng Y, Fraser J, Frost A, Jura N, Kortemme T, Manglik A, Southworth D, Stroud R, Alessi D, Davies P, Frieman M, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat K, García-Sastre A, Rassen J, Grosse R, Rosenberg O, Verba K, Basler C, Vignuzzi M, Peden A, Beltrao P, Krogan N, Owens T, Gupta M, Pourmal S, Titus E, Azumaya C, Billesbølle C, Brilot A, Campbell M, Diallo A, Dickinson M, Diwanji D, Herrera N, Hoppe N, Kratochvil H, Liu Y, Merz G, Moritz M, Nguyen H, Nowotny C, Puchades C, Rizo A, Schulze-Gahmen U, Smith A, Sun M, Young I, Zhao J, Asarnow D, Biel J, Bowen A, Braxton J, Chen J, Chio C, Chio U, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam V, Li F, Li J, Li Y, Li Y, Liu X, Lo M, Lopez K, Melo A, Moss F, Nguyen P, Paulino J, Pawar K, Peters J, Pospiech T, Safari M, Sangwan S, Schaefer K, Thomas P, Thwin A, Trenker R, Tse E, Tsui T, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Trinidad D, Agard D, Cheng Y, Fraser J, Frost A, Jura N, Kortemme T, Manglik A, Southworth D, Stroud R, Rosenberg O, Verba K, Damas J, Hughes G, Keough K, Painter C, Persky N, Corbo M, Kirilenko B, Hiller M, Koepfli K, Kaplow I, Wirthlin M, Pfenning A, Zhao H, Genereux D, Swofford R, Lind A, Pollard K, Ryderq O, Nweeia M, Meadows J, Dong M, Wallerman O, Marinescu V, Lindblad-Toh K, Ray D, Power S, Teeling E, Chauhan G, Li S, Karlsson E, Lewin H. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science 2020, 370: eabe9403. PMID: 33060197, PMCID: PMC7808408, DOI: 10.1126/science.abe9403.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsConserved SequenceCoronavirus Nucleocapsid ProteinsCOVID-19Cryoelectron MicroscopyHost Microbial InteractionsHumansMitochondrial Membrane Transport ProteinsMitochondrial Precursor Protein Import Complex ProteinsPhosphoproteinsProtein ConformationProtein Interaction MapsSARS-CoV-2Severe Acute Respiratory SyndromeSevere acute respiratory syndrome-related coronavirusConceptsSARS-CoV-1SARS-CoV-2 ORF9bProtein localization analysisProtein interaction networkMitochondrial chaperone proteinProtein-protein interactionsFunctional genetic screensHost factorsPatient genetic dataCryo-electron microscopyGenetic dataGenetic screeningInteraction networkChaperone proteinsSARS-CoV-2Molecular mechanismsMiddle East respiratory syndrome coronavirusPotential drug treatmentsDisease mechanismsRespiratory syndrome coronavirusMERS-CoVLocal analysisSyndrome coronavirusCoronavirus proliferationHostStaphylococcus aureus cell growth and division are regulated by an amidase that trims peptides from uncrosslinked peptidoglycan
Do T, Schaefer K, Santiago A, Coe K, Fernandes P, Kahne D, Pinho M, Walker S. Staphylococcus aureus cell growth and division are regulated by an amidase that trims peptides from uncrosslinked peptidoglycan. Nature Microbiology 2020, 5: 291-303. PMID: 31932712, PMCID: PMC7046134, DOI: 10.1038/s41564-019-0632-1.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsPeptidoglycan synthesisCell divisionCell growthUncrosslinked peptidoglycanStem peptidesCell cycleDefects due to lossMembrane protein complexesTransposon screenPeptidoglycan synthasesDivision sitePartner proteinsAssembled enzymeSubcellular locationCell peripheryPolymerase activityProtein complexesDaughter cellsPeptidoglycanAssembly sitesStaphylococcus aureusAmidaseCell expansionSynthase activityPeptide
2019
Direction of Chain Growth and Substrate Preferences of Shape, Elongation, Division, and Sporulation-Family Peptidoglycan Glycosyltransferases
Welsh M, Schaefer K, Taguchi A, Kahne D, Walker S. Direction of Chain Growth and Substrate Preferences of Shape, Elongation, Division, and Sporulation-Family Peptidoglycan Glycosyltransferases. Journal Of The American Chemical Society 2019, 141: 12994-12997. PMID: 31386359, PMCID: PMC6738341, DOI: 10.1021/jacs.9b06358.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsPeptidoglycan glycosyltransferasesSubstrate preferenceLipid IICell wallMature cell wallsBacterial cell wallGlycan strandsSEDS proteinsGlycan chainsDecades bacteriaPeptidoglycan polymerasesPeptidoglycanGlycopeptide precursorsLipid requirementsFtsWII monomerGlycosyltransferasesPolymeraseGlycansStructural studiesBacteriaRodAEnzymeLipidAntibiotics
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Microbial Pathogenesis
295 Congress Ave, BCMM 345/443
New Haven, CT 06519
United States
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295 Congress Avenue, Rm 454A
New Haven, CT 06510
Boyer Center for Molecular Medicine
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295 Congress Avenue, Rm 443
New Haven, CT 06510
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