Department of Chemistry and Biochemistry
Harper Cancer Research Institute
University of Notre Dame



Custodio JM, Ayres CM, Rosales TJ, Brambley CA, Arbuiso AG, Landau LM, Keller GLJ, Srivastava PK, and Baker BM. Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopesProceedings of the National Academy of Sciences, USA [link]

Khorki ME, Shi T, Cianciolo EE, Burg AR, Chukwuma PC, Picarsic JL, Ferguson A, Katz J, Baker BM, and Hildeman DA. Prior viral infection primes cross-reactive CD8+ T cells that respond to mouse heart allografts. Frontiers in Immunology [link]

Klebanoff CA, Chandran SS, Baker BM, Quezada SA, and Ribas A. T cell receptor therapeutics: immunological targeting of the intracellular cancer proteome. Nature Reviews Drug Discovery [link]

Gillig MA, Brennick CA, George MM, Balsbaugh JL, Shcheglova TV, Mandoiu II, Rosales T, Baker BM, Srivastava PK, and Karandikar SH. CD8+ T cell-dependent anti-tumor activity in vivo of a mass spectrometry-identified neoepitope despite undetectable CD8+ immunogenicity in vitro. Journal of Immunology [link]

Ayres CM, Corcelli SA, and Baker BM. The energetic landscape of catch bonds in T cell receptor interfaces. Journal of Immunology [link]

Shi T, Burg AR, Caldwell JT, Roskin KM, Castro-Rojas CM, Chukwuma PC, Gray GI, Foote SG, Alonso JA, Cuda CM, Allman DA, Rush JS, Regnier CH, Wieczorek G, Alloway RR, Shields AR, Baker BM, Woodle ES, and Hildeman DA. Single cell transcriptomic analysis of renal allograft rejection reveals insights into intragraft TCR clonality. Journal of Clinical Investigation [link]


Singh NK, Alonso JA, Devlin JR, Keller GLJ, Chiranjivi AK, Foote SG, Landau LM, Arbuiso AG, Weiss LI, Rosenberg AM, Hellman LM, Nishimura MI, and Baker BM. A class-mismatched TCR bypasses MHC restriction via an unorthodox but fully functional binding geometry. Nature Communications [link]

Chandran SS, Ma J, Klatt MG, Dundar F, Bandlamudi C, Razavi P, Wen HY, Weigelt B, Zumbo P, Fu SN, Banks LB, Bestman WD, Drilon A, Betel D, Scheinberg DA, Baker BM, and Klebanoff CA. Immunogenicity of a public neoantigen derived from mutated PIK3CA. Nature Medicine [link]

Liu C, Liu H, Dasgupta M, Hellman LM, Zhang X, Qu K, Xue H, Wang Y, Fan F, Chang Q, Yu D, Ge L, Zhang Y, Cui Z, Zhang P, Heller B, Zhang H, Shi B, Baker BM, and Liu L. Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinomaScientific Reports [link]

Ayres CM and Baker BM. Peptide-dependent tuning of major histocompatibility complex motional properties and the consequences for cellular immunityCurrent Opinion in Immunology [link]

Keller GLJ, Weiss LI, and Baker BM. Physicochemical heuristics for identifying high fidelity, near-native structural models of peptide/MHC complexes. Frontiers in Immunology [link]

Rosales TJ and Baker BM. Chaperoning the dance of antigen presentationNature Chemical Biology [link]

Rosenberg AM and Baker BM. Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting diseaseCurrent Opinion in Structural Biology [link]

Richards KA, Lavery C, Keller GLJ, Baker BM, and Sant AJ. A previously unappreciated polymorphism in the beta chain of I-As expressed in autoimmunity-prone SJL mice: Combined impact on antibody, CD4 T cell recognition and MHC class II dimer structural stability. Molecular Immunology [link]


Shi T, Roskin K, Baker BM, Woodle ES, and Hildeman H. Genomics-Based Approaches for Defining Allograft Rejection with Single Cell Resolution. Frontiers in Immunology [link]

Ebrahimi-Nik H, Moussa M, Englander RP, Singhaviranon S, Michaux J, Pak H, Miyadera M, Corwin WL, Keller GLJ, Hagymasi AT, Shcheglova TV, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, and Srivastava PK. Reversion analysis reveals the immunogenicity in vivo of a poorly MHC I binding cancer neoepitope. Nature Communications [link]

Clarety K, Park R, Singh NK, Koundakjian D, Bashirova A, Garcia Beltran W, Overbeck C, Ma J, Senjobe F, Nathan A, Tano-Menka R, Khatri A, Piechocka-Trocha A, Waring M, Baker BM, Carrington M, Walker BD, and Gaiha GD. HLA class-I-peptide stability mediates CD8+ T cell immunodominance hierarchies and facilitates HLA-associated immune control of HIV. Cell Reports [link]

Alonso JA, Smith AR, and Baker BM. Tumor rejection properties of gp100209-specific T cells correlate with T cell receptor binding affinity towards the wild type rather than anchor-modified antigen. Molecular Immunology [link]

Ma J, Ayres CM, Hellman LM, Devlin JR, and Baker BM. Dynamic allostery controls the peptide sensitivity of the Ly49C natural killer receptor. Journal of Biological Chemistry [link]

Schmidt J, Smith AR, Magnin M, Racle J, Devlin JR, Bobisse S, Cesbron J, Bonnet V, Carmona SJ, Huber F, Ciriello G, Speiser DE, Bassani-Sternberg M, Coukos G, Baker BM, Harari A, and Gfeller D. Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and immunoediting in human cancer. Cell Reports Medicine [link]

Smith AR, Alonso JA, Ayres CM, Singh NK, Hellman LM, and Baker BM. Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor dependent manner. Proceedings of the National Academy of Sciences, USA [link]

Brennick CA, George MM, Moussa MR, Hagymasi AT, Al Seesi S, Shcheglova TV, Englander RP, Keller GLJ, Balsbaugh JL, Baker BM, Schietinger A, Mandoiu II, and Srivastava PK. An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejectionJournal of Clinical Investigation [link]


Borrman T, Pierce BG, Vreven T, Baker BM, and Weng Z. High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptidesBioinformatics [link]

Devlin JR, Alonso JA, Ayres CM, Keller GLJ, Bobisse S, Vander Kooi CW, Coukos G, Gfeller D, Harari A, and Baker BM. Structural dissimilarity from self drives neoepitope escape from immune tolerance. Nature Chemical Biology [link]

Singh NK, Alonso JA, Harris DT, Anderson SD, Ma J, Hellman LM, Rosenberg AM, Kolawole EM, Evavold BD, Kranz DM, and Baker BM. An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding ModesBiochemistry [link]

Tarbe M, Miles JJ, Edwards ESJ, Sewell, AK, Baker BM, and Quideau S. Synthesis and biological evaluation of hapten‐clicked analogues of the antigenic peptide Melan‐A/MART‐126(27L)‐35. ChemMedChem [link]


Singh NK, Abualrous ET, Ayres CM, Noé F, Gowthaman R, Pierce BG, and Baker BM. Geometrical characterization of T cell receptor binding modes reveals class‐specific binding to maximize access to antigenProteins [link]

Spear TT, Evavold BD, Baker BM, and Nishimura MI. Understanding TCR affinity, antigen specificity, and cross-reactivity to improve TCR gene-modified T cells for cancer immunotherapyCancer Immunology, Immunotherapy [link]

McGrath E, Waschbusch D, Baker BM, and Khan AR. LRRK2 is an effector of the Rab32 subfamily: Mapping of the interactions between the armadillo domain and the switch regions of Rab GTPases. Small GTPases [link]

Riley TP, Keller GLJ, Smith AR, Davancaze LM, Arbuiso AG, Devlin JR, and Baker BM. Structure-Based Prediction of Neoantigen ImmunogenicityFrontiers in Immunology [link]

Ebrahimi-Nik H, Michaux J, Corwin WL, Keller GLJ, Shcheglova T, Pak H, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, and Srivastava PK. Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejectionJournal of Clinical Investigation Insight [link]

Ayres CM, Abualrous ET, Bailey A, Abraham C, Hellman LM, Corcelli SA, Noé F, Elliott E, and Baker BM. Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility. Frontiers in Immunology [link]

Hellman LM, Foley KC, Singh NK, Alonso JA, Riley TP, Devlin JR, Ayres CM, Keller GLJ, Zhang Y, Vander Kooi CW, Nishimura MI, and Baker BM. Improving T Cell Receptor On-Target Specificity via Structure-Guided DesignMolecular Therapy [link]


Riley TP and Baker BM. The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeuticsSeminars in Cell & Developmental Biology [link]

Riley TP, Hellman LM, Gee MH, Mendoza JL, Alonso JA, Foley KC, Nishimura MI, Vander CW Kooi, Garcia KC, and Baker BM. T cell receptor cross-reactivity expanded by dramatic peptide/MHC adaptability. Nature Chemical Biology [link]

Eby JM, Smith AR, Riley TP, Cosgrove C, Ankney CM, Henning SW, Paulos CM, Garrett-Mayer E, Luiten RM, Nishimura MI, Baker BM, and Le Poole IC. Molecular properties of gp100-reactive T cell receptors drive the cytokine profile and antitumor efficacy of transgenic host T cellsPigment Cell and Melanoma Research [link] 

Spear TT, Wang Y, Smith TW, Simms PE, Garrett-Mayer E, Hellman LM, Baker BM, and Nishimura MI. Altered peptide ligands impact the diversity of polyfunctional phenotypes in T cell receptor gene-modified T cellsMolecular Therapy [link]

Moore T, Wagner CR, Scurti GM, Hutchens KA, Godellas C, Clark AL, Kolawole EM, Hellman LM, Singh NK, Huyke FA, Wang S, Calabrese KM, Embree HD, Orentas R, Shirai K, Dellacecca E, Garrett‑Mayer E, Li M, Eby JM, Stiff PJ, Evavold BD, Baker BM, Le Poole IC, Dropulic B, Clark JI, and Nishimura MI. Clinical and immunologic evaluation of three metastatic melanoma patients treated with autologous melanoma‑reactive TCR‑transduced T cells. Cancer Immunology, Immunotherapy [link]


Singh NK, Riley TP, Baker SCB, Borrman T, Weng Z, and Baker BM. Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes. Journal of Immunology [link]

Ayres CM, Corcelli SA, and Baker BM. Peptide and Peptide-Dependent Motions in MHC Proteins: Immunological Implications and Biophysical Underpinnings. Frontiers in Immunology [link]

Ayres CM, Riley TP, Corcelli SA, and Baker BM. Modeling Sequence Dependent Peptide Fluctuations in Immunologic Recognition. Journal of Chemical Information and Modeling [link]

Spear TT, Wang Y, Foley KC, Murray DC, Scurti GM, Simms PE, Garrett-Mayer E, Hellman LM, Baker BM, and Nishimura MI. Critical biological parameters modulate affinity as a determinant of function in T-cell receptor gene-modified T-cells. Cancer Immunology, Immunotherapy [link]

Wang Y, Singh NK, Spear TT, Hellman LM, Piepenbrink KH, McMahan RH, Rosen HR, Vander Kooi CW, Nishimura MI, and Baker BM. How an alloreactive T cell receptor achieves peptide and MHC specificity. Proceedings of the National Academy of Sciences, USA [link]

Borrman TT, Cimons J, Cosiano M, Purcaro M, Pierce BG, Baker BM, and Weng Z. ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexesProteins Structure, Function, and Bioinformatics [link]

Blevins SJ and Baker BM. Using global analysis to extend the accuracy and precision of binding measurements with T cell receptors and their peptide/MHC ligandsFrontiers in Molecular Biosciences [link]

Baker BM and Evavold BD. MHC bias by T cell receptors:  Genetic evidence for MHC and TCR coevolutionTrends in Immunology [link]


Harris DT, Wang N, Riley TP, Anderson SD, Singh NK, Procko E, Baker BM, and Kranz DM. Deep mutational scans as a guide to engineering high-affinity T cell receptor interactions with peptide-bound MHCJournal of Biological Chemistry [link]

Singh NK and Baker BM. Ligand-Driven T Cell Receptor Selection in Celiac Disease. Structure [link]

Riley TP, Ayres CM, Hellman LM, Singh NK, Cosiano M, Cimons JM, Anderson MJ, Piepenbrink KH, Pierce BG, Weng Z, and Baker BM. A generalized framework for computational design and mutational scanning of T-cell receptor binding interfacesProtein Engineering, Design & Selection [link]

Harris DT, Singh NK, Cai Q, Smith SN, Vander Kooi C, Procko E, Kranz DM, and Baker BM. An engineered switch in T cell receptor specificity leads to an unusual but functional binding geometry. Structure [link]

Ayres CM, Scott DR, Corcelli SA, and Baker BM. Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity. Scientific Reports [link]

Riley TP, Singh NK, Pierce BG, Weng Z, and Baker BM. Computational modeling of TCR-pMHC complexes. Methods in Molecular Biology [link]

Riley TP, Singh NK, Pierce BG, Baker BM, and Weng Z. Computational reprogramming of T cell antigen receptor binding properties. Methods in Molecular Biology [link]

Spear TT, Riley TP, Lyons GE, Callendar GG, Roszkowski JJ, Wang Y, Simms PE, Scurti GM, Foley KC, Murray DC, Hellman LM, McMahan RH, Iwashima M, Garrett-Mayer E, Rosen HR, Baker BM, and Nishimura MI. Hepatitis C virus cross-reactive TCR gene modified T cells: a model for immunotherapy against diseases with genomic instabilityJournal of Leukocyte Biology [link]

Blevins SJ, Pierce BG, Singh NK, Riley TP, Wang Y, Spear TT, Nishimura MI, Weng Z, and Baker BM. How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoireProceedings of the National Academy of Sciences USA [link]

Hellman LM, Yin Liusong, Wang Y, Blevins SJ, Riley TP, Belden OS, Spear TT, Nishimura MI, Stern LJ, and Baker BM. Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide–MHC complexesJournal of Immunological Methods [link]


Adams JJ, Narayanan S, Birnbaum ME, Sidhu SS, Blevins SJ, Baker BM, Kranz DK, and Garcia KC. Structural interplay between adaptive and germline recognition determines the functional bandwidth of TCR/peptide-MHC cross-reactivityNature Immunology [link]

Thompson MG, Virdine A, Barrios K, Meyers K, Simms P, Hellman LM, Baker BM, and Watkins SK. FOXO3-NF-kB protein complexes reduce pro-inflammatory cell signaling and function. Journal of Immunology [link]

Belden O, Baker SC, and Baker BM. Citizens unite for computational immunology! Trends in Immunology [link]


Smith SN, Wang Y, Baylon JL, Singh NK, Baker BM, Tajkhorshid E, and Kranz DM. Changing the peptide specificity of a human T-cell receptor by directed evolutionNature Communications [link]

Duan F, Duitama J, Al Seesi S, Ayres CM, Corcelli SA, Pawashe AP, Blanchard T, McMahon D, Sidney J, Sette A, Baker BM, Mandoiu II and Srivastava PK. Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity. Journal of Experimental Medicine [link]

Pierce BG, Hellman LM, Hossain M, Singh NK, Vander Kooi CW, Weng Z, and Baker BM. Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor. PLOS Computational Biology [link]

Hawse WF, De S, Greenwood AI, Nicholson LK, Zajicek J, Kovrigin EL, Kranz DM, Garcia KC, and Baker BM. TCR Scanning of Peptide/MHC through Complementary Matching of Receptor and Ligand Molecular Flexibility. Journal of Immunology [link]


Smith SN, Sommermeyer D, Piepenbrink KH, Blevins SJ, Bernhard H, Uckert W, Baker BM, and Kranz DM. Plasticity in the Contribution of T Cell Receptor Variable Region Residues to Binding of Peptide–HLA-A2 Complexes. Journal of Molecular Biology [link]

Hawse WF, Gloor BE, Ayres CM, Kho K, Nuter E, and Baker BM (2013). Peptide modulation of class I major histocompatibility complex protein molecular flexibility and the implications for immune recognition. Journal of Biological Chemistry [link]

Cole DK, Sami M, Scott DR, Rizkallah PJ, Borbulevych OY, Todorov PT, Moysey RK, Jakobsen BK, Boulter JM, Baker BM, and Li Y. Increased peptide contacts govern high affinity binding of a modified TCR whilst maintaining a native pMHC docking mode. Frontiers in Immunology [link]

Piepenbrink KH, Blevins SJ, Scott DR, and Baker BM. The basis for limited specificity and MHC restriction in a T cell receptor interface. Nature Communications [link]

Madura F, Rizkallah PJ, Miles KM, Holland CJ, Bulek AM, Fuller A, Schauenburg AJ, Miles JJ, Liddy N, Sami M, Li Y, Hossain M, Baker BM, Jakobsen BK, Sewell AK, and Cole DK. T-cell receptor specificity maintained by altered thermodynamics. Journal of Biological Chemistry [link]


Scott DR, Vardeman CF, Corcelli SA, and Baker BM. Limitations of time-resolved fluorescence suggested by molecular simulations: assessing the dynamics of T cell receptor binding loops. Biophysical Journal [link]

Ekeruche-Makinde J, Clement M, Cole DK, Edwards ES, Ladell K, Miles JJ, Matthews KK, Fuller A, Lloyd KA, Madura F,Dolton GM, Pentier J, Lissina A, Gostick E, Baxter TK, Baker BM, Rizkallah PJ, Price DA, Wooldridge L, and Sewell AK. T cell receptor optimized peptide skewing of the T-cell repertoire can enhance antigen targeting. Journal of Biological Chemistry [link]

Baker BM, Scott DR, Blevins SJ, and Hawse WF. Structural and dynamic control of T-cell receptor specificity, cross-reactivity, and binding mechanism. Immunological Reviews [link]

Hawse WF, Champion MM, Joyce MV, Hellman LM, Hossain M, Ryan V, Pierce BG, Weng Z, and Baker BM. Cutting Edge: Evidence for a dynamically driven T cell signaling mechanism. Journal of Immunology [link]

DH Aggen, AS Chervin, TM Schmitt, B Engels, JD Stone, SA Richman, KH Piepenbrink, BM Baker, PD Greenberg, H Schreiber, and DM Kranz. Single-chain VαVβ T-cell receptors function without mispairing with endogenous TCR chains. Gene Therapy [link]

M Kumarasiri, LI Llarrull, O Borbulevych, J Fishovitz, E Lastochkin, BM Baker BM, and SM Mobashery. An amino acid position at crossroads of evolution of protein function: antibiotic sensor domain of BlaR1 protein from Staphylococcus aureus versus class D β-lactamases. Journal of Biological Chemistry [link]


Scott DR, Borbulevych OY, Piepenbrink KH, Corcelli SA, and Baker BM. Disparate degrees of hypervariable loop flexibility control T-cell receptor cross-reactivity, specificity, and binding mechanism. Journal of Molecular Biology [link] (cover article)

Insaidoo FK, Borbulevych OY, Hossain M, Santhanagopolan SM, Baxter TK, and Baker BM. Loss of T cell antigen recognition arising from changes in peptide and major histocompatibility complex protein flexibility: implications for vaccine design. Journal of Biological Chemistry [link]

Borbulevych O, Kumarasiri M, Wilson B, Llarrull LI, Lee M, Hesek D, Shi Q, Peng P, Baker BM, and Mobashery SM. Lysine NZ-decarboxylation switch and activation of the b-lactam sensor domain of BlaR1 protein of methicillin-resistant Staphylococcus aureus. Journal of Biological Chemistry [link]

Borbulevych OY, Santhanagopolan SM, Hossain M, and Baker BM. TCRs used in cancer gene therapy cross-react with MART-1/Melan-A tumor antigens via distinct mechanisms. Journal of Immunology [link]

Aggen DH, Chervin AS, Insaidoo FK, Piepenbrink KH, Baker BM, and Kranz DM. Identification and engineering of human variable regions that allow expression of stable single-chain T cell receptors. Protein Engineering, Design and Selection [link]

Borbulevych OY, Piepenbrink K, and Baker BM. Conformational melding permits a conserved binding geometry in TCR recognition of foreign and self molecular mimics. Journal of Immunology [link]


Tarbe M, Itxaso A, Balentov E, Miles JJ, Edwards EE, Miles KM, Do P, Baker BM, Sewell AK, Aizpurua JM, Douat-Casassus C, and Quideau S. Design, synthesis and evaluation of b-lactam antigenic peptide hybrids; unusual opening of the b-lactam ring in acidic media. Organic & Biomolecular Chemistry [link]

Douat-Casassus, C, Borbulevych OY, Tarbe M, Gervois N, Jotereau F, Baker BM, and Quideau S. Crystal structures of HLA-A*0201 complexed with Melan-A/MART-1 26(27L)-35 peptidomimetics reveal conformational heterogeneity and highlight the degeneracy of T cell recognition. Journal of Medicinal Chemistry [link]

Borbulevych OY, Do P, and Baker BM. Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A*0201: implications for WT1-based cancer therapeutics. Molecular Immunology [link]


Borbulevych OY, Piepenbrink KH, Gloor BE, Scott DR, Sommese RF, Cole DK, Sewell AK, and Baker BM. T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility. Immunity [link]

Piepenbrink KH, Gloor BE, Armstrong KM, and Baker BM. Methods for Quantifying T cell Receptor Binding Affinities and Thermodynamics. Methods in Enzymology [link]

Insaidoo FK, Zajicek J, and Baker BM. A general and efficient approach for NMR studies of peptide dynamics in class I MHC peptide binding grooves. Biochemistry [link]

Piepenbrink KH, Borbulevych OY, Sommese RF, Clemens J, Armstrong KM, Desmond C, and Baker BM. Fluorine substitutions in an antigenic peptide selectively modulate T-cell receptor binding in a minimally perturbing manner. Biochemical Journal [link]

Bowerman NA, Crofts TS, Chlewicki L, Do, P, Baker BM, Garcia KC, and Kranz DM. Engineering the binding properties of the T cell receptor:peptide:MHC ternary complex that governs T cell activity. Molecular Immunology [link]


Armstrong KM, Piepenbrink KH, and Baker BM. Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes. Biochemical Journal [link]

Armstrong KM, Insaidoo FK, and Baker BM. Thermodynamics of T cell receptor – peptide/MHC interactions: progress and opportunities. Journal of Molecular Recognition [link]

Loaiza A, Armstrong KM, Baker BM, and Abu-Omar MM. Kinetics of thermal unfolding of phenylalanine hydroxylase variants containing different metal cofactors (FeII, CoII, and ZnII) and their isokinetic relationship. Inorganic Chemistry [link]


Borbulevych OY, Insaidoo FK, Baxter TK, Powell DJ Jr, Johnson LA, Restifo NP, and Baker BM. Structures of MART-126/27-35 Peptide/HLA-A2 complexes reveal a remarkable disconnect between antigen structural homology and T cell recognition. Journal of Molecular Biology [link]

Armstrong KM and Baker BM. A comprehensive calorimetric investigation of an entropically driven T cell receptor – peptide/major histocompatibility complex interaction. Biophysical Journal [link]

Davis-Harrison RL, Insaidoo FK, and Baker BM. T cell receptor binding transition states and recognition of peptide/MHC. Biochemistry [link]


Gagnon SJ, Borbulevych OY, Davis-Harrison RL, Baxter TK, Turner RV, Damirjian M, Wojnarowicz A, Biddison WE, and Baker BM. T cell receptor recognition via cooperative conformational plasticity. Journal of Molecular Biology [link]


Borbulevych O, Baxter TK, Yu Z, Restifo NP, and Baker BM. Increased immunogenicity of an anchor-modified tumor associated antigen is due to the enhanced stability of the peptide/MHC complex: implications for vaccine design. Journal of Immunology [link]

Gagnon SJ, Borbulevych OY, Davis-Harrison RL, Baxter TK, Clemens JR, Armstrong KM, Turner RV, Damirjian M, Biddison WE, and Baker BM. Unraveling a hotspot for TCR recognition on HLA-A2: Evidence against the existence of peptide-independent TCR binding determinants. Journal of Molecular Biology [link]

Davis-Harrison RL, Armstrong KM, and Baker BM. Two different T cell receptors use different thermodynamic strategies to recognize the same ligand. Journal of Molecular Biology [link]

Folker ES, Baker BM, and Goodson HV. Interactions between CLIP-170, tubulin, and microtubules: Implications for the mechanism of CLIP-170 plus-end tracking behavior. Molecular Biology of the Cell [link]


Yu Z, Theoret MR, Touloukian CE, Surman DR, Garman G, Baxter TK, Baker BM, and Restifo NP. Poor immunogenicity of a self/tumor antigen derives from peptide/MHC-I instability and is independent of tolerance. Journal of Clinical Investigation [link]

Baxter TK, Gagnon SJ, Davis-Harrison RL, Turner RV, Biddison WE, and Baker BM. Strategic mutations in the class I MHC HLA-A2 independently affect both peptide binding and T cell receptor recognition. Journal of Biological Chemistry [link]

Swalley SE, Baker BM, Calder LJ, Harrison SC, Skehel JJ, and Wiley DC. Full-length influenza hemagglutinin HA2 refolds into the trimeric low-pH-induced conformation. Biochemistry [link]


Binz AK, Rodriguez RC, Biddison WE, and Baker BM. Thermodynamic and kinetic analysis of a peptide-class I MHC interaction highlights the noncovalent nature and conformational dynamics of the class I heterotrimer. Biochemistry [link]


Wang Z, Turner RV, Baker BM, and Biddison WE. MHC allele-specific molecular features determine peptide/HLA-A2 conformations that are recognized by HLA-A2-restricted T cell receptors. Journal of Immunology [link]