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



Spear TT, Wang Y, Foley KC, Murray DC, Scurti GM, Simms PE, Garrett-Mayer E, Hellman LM, Baker BM, and Nishimura MI (2017). 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 (2017). 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, & Weng Z (2017) ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexesProteins Structure, Function, and Bioinformatics [link]

Blevins SJ & Baker BM (2017). 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 & Evavold BD (2017). 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, & Kranz DM (2016). Deep mutational scans as a guide to engineering high-affinity T cell receptor interactions with peptide-bound MHCJournal of Biological Chemistry [link]

Singh NK &Baker BM (2016) 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, & Baker BM (2016) 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, & Baker BM (2016) An engineered switch in T cell receptor specificity leads to an unusual but functional binding geometry. Structure [link]

Ayres CM, Scott DR, Corcelli SA, & Baker BM (2016). 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, & Baker BM (2016). Computational modeling of TCR-pMHC complexes. Methods in Molecular Biology [link]

Riley TP, Singh NK, Pierce BG, Baker BM, & Weng Z (2016). 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, & Nishimura M (2016). 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, & Baker BM (2016). 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, & Baker BM (2016). 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, & Garcia KC (2015). 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,  & Watkins SK (2015). FOXO3-NF-kB protein complexes reduce pro-inflammatory cell signaling and function. Journal of Immunology [link]

Belden O, Baker SC, & Baker BM (2015). Citizens unite for computational immunology! Trends in Immunology [link]


Smitth SN, Wang Y, Baylon JL, Singh NK, Baker BM, Tajkhorshid E, & Kranz DM (2014). 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 & Srivastava PK (2014). 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, & Baker BM (2014). 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, & Baker BM (2014). 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, & Kranz D. M. (2013). 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, & 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, & Li Y (2013). 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, & Baker BM (2013). 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, & Cole DK (2013). T-cell receptor specificity maintained by altered thermodynamics. Journal of Biological Chemistry [link]


Scott DR, Vardeman CF, Corcelli SA, & Baker BM (2012). 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, & Sewell AK (2012). 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, & Hawse WF (2012). 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, & Baker BM (2012). 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, & DM Kranz (2012). 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, & SM Mobashery (2012). 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, & Baker BM (2011). 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, & Baker BM (2011). 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, & Mobashery SM (2011). 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, & Baker BM (2011). 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, & Kranz DM (2011). 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, & Baker BM (2011). 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, & Quideau S (2010). 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, & Quideau S (2010). 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, & Baker BM (2010). 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, & Baker BM (2009). T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility. Immunity [link]

Piepenbrink KH, Gloor BE, Armstrong KM, & Baker BM (2009). Methods for Quantifying T cell Receptor Binding Affinities and Thermodynamics. Methods in Enzymology [link]

Insaidoo FK, Zajicek J, & Baker BM (2009). 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, & Baker BM (2009). 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, & Kranz DM (2009). 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, & Baker BM (2008). Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes. Biochemical Journal [link]

Armstrong KM, Insaidoo FK, & Baker BM (2008). Thermodynamics of T cell receptor – peptide/MHC interactions: progress and opportunities. Journal of Molecular Recognition [link]

Loaiza A, Armstrong KM, Baker BM, & Abu-Omar MM (2008). 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, & Baker BM (2007). 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 & Baker BM (2007). A comprehensive calorimetric investigation of an entropically driven T cell receptor – peptide/major histocompatibility complex interaction. Biophysical Journal [link]

Davis-Harrison RL, Insaidoo FK, & Baker BM (2007). 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, & Baker BM (2006). T cell receptor recognition via cooperative conformational plasticity. Journal of Molecular Biology [link]


Borbulevych O, Baxter TK, Yu Z, Restifo NP, & Baker BM (2005). 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, & Baker BM (2005). 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, & Baker BM (2005). Two different T cell receptors use different thermodynamic strategies to recognize the same ligand. Journal of Molecular Biology [link]

Folker ES, Baker BM, & Goodson HV (2005). 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, & Restifo NP (2004). 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, & Baker BM (2004). 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, & Wiley DC (2004). Full-length influenza hemagglutinin HA2 refolds into the trimeric low-pH-induced conformation. Biochemistry [link]


Binz AK, Rodriguez RC, Biddison WE, & Baker BM (2003). 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, & Biddison WE (2002). MHC allele-specific molecular features determine peptide/HLA-A2 conformations that are recognized by HLA-A2-restricted T cell receptors. Journal of Immunology [link]