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Article: Using Global Analysis to Extend the Accuracy and Precision of Binding Measurements with T cell Receptors and Their Peptide/MHC Ligands.

Blevins, Sydney J / Baker, Brian M

2017 Volume 4, Page(s) 2

Abstract: In cellular immunity, clonally distributed T cell receptors (TCRs) engage complexes of peptides bound to major histocompatibility complex proteins (pMHCs). In the interactions of TCRs with pMHCs, regions of restricted and variable diversity align in a ... ...

Abstract	In cellular immunity, clonally distributed T cell receptors (TCRs) engage complexes of peptides bound to major histocompatibility complex proteins (pMHCs). In the interactions of TCRs with pMHCs, regions of restricted and variable diversity align in a structurally complex fashion. Many studies have used mutagenesis to attempt to understand the "roles" played by various interface components in determining TCR recognition properties such as specificity and cross-reactivity. However, these measurements are often complicated or even compromised by the weak affinities TCRs maintain toward pMHC. Here, we demonstrate how global analysis of multiple datasets can be used to significantly extend the accuracy and precision of such TCR binding experiments. Application of this approach should positively impact efforts to understand TCR recognition and facilitate the creation of mutational databases to help engineer TCRs with tuned molecular recognition properties. We also show how global analysis can be used to analyze double mutant cycles in TCR-pMHC interfaces, which can lead to new insights into immune recognition.
Language	English
Publishing date	2017-01-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2017.00002
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Article ; Online: Killer T cells with a beta-flavi(r) for dengue.

Blevins, Sydney / Huseby, Eric S

Nature immunology

2017 Volume 18, Issue 11, Page(s) 1186–1188

MeSH term(s)	Dengue ; Dengue Virus ; Germ Cells ; Humans ; Serogroup ; T-Lymphocytes, Cytotoxic
Language	English
Publishing date	2017-10-11
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	2016987-5
ISSN	1529-2916 ; 1529-2908
ISSN (online)	1529-2916
ISSN	1529-2908
DOI	10.1038/ni.3833
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Article ; Online: A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3

Stadinski, Brian D / Blevins, Sydney J / Spidale, Nicholas A / Duke, Brian R / Huseby, Priya G / Stern, Lawrence J / Huseby, Eric S

Nature immunology

2019 Volume 20, Issue 8, Page(s) 1046–1058

Abstract: The neonatal thymus generates ... ...

Abstract	The neonatal thymus generates Foxp3
MeSH term(s)	Animals ; Autoantigens/immunology ; Autoimmunity/immunology ; Cell Differentiation/immunology ; Cell Line ; Female ; Forkhead Transcription Factors/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Protein-Arginine Deiminases/metabolism ; Receptors, Antigen, T-Cell, alpha-beta/immunology ; Self Tolerance/immunology ; T-Lymphocytes, Regulatory/cytology ; T-Lymphocytes, Regulatory/immunology ; Thymus Gland/cytology
Chemical Substances	Autoantigens ; Forkhead Transcription Factors ; Foxp3 protein, mouse ; Receptors, Antigen, T-Cell, alpha-beta ; Padi4 protein, mouse (EC 3.5.3.15) ; Protein-Arginine Deiminases (EC 3.5.3.15)
Language	English
Publishing date	2019-06-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2016987-5
ISSN	1529-2916 ; 1529-2908
ISSN (online)	1529-2916
ISSN	1529-2908
DOI	10.1038/s41590-019-0414-1
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Article ; Online: The basis for limited specificity and MHC restriction in a T cell receptor interface.

Piepenbrink, Kurt H / Blevins, Sydney J / Scott, Daniel R / Baker, Brian M

Nature communications

2013 Volume 4, Page(s) 1948

Abstract: αβ T cell receptors (TCRs) recognize peptides presented by major histocompatibility complex (MHC) proteins using multiple complementarity-determining region (CDR) loops. TCRs display an array of poorly understood recognition properties, including ... ...

Abstract	αβ T cell receptors (TCRs) recognize peptides presented by major histocompatibility complex (MHC) proteins using multiple complementarity-determining region (CDR) loops. TCRs display an array of poorly understood recognition properties, including specificity, crossreactivity and MHC restriction. Here we report a comprehensive thermodynamic deconstruction of the interaction between the A6 TCR and the Tax peptide presented by the class I MHC HLA-A*0201, uncovering the physical basis for the receptor's recognition properties. Broadly, our findings are in conflict with widely held generalities regarding TCR recognition, such as the relative contributions of central and peripheral peptide residues and the roles of the hypervariable and germline CDR loops in engaging peptide and MHC. Instead, we find that the recognition properties of the receptor emerge from the need to engage the composite peptide/MHC surface, with the receptor utilizing its CDR loops in a cooperative fashion such that specificity, crossreactivity and MHC restriction are inextricably linked.
MeSH term(s)	Complementarity Determining Regions/immunology ; Complementarity Determining Regions/metabolism ; Conserved Sequence ; Gene Products, tax/chemistry ; Gene Products, tax/immunology ; Gene Products, tax/metabolism ; HLA-A2 Antigen/chemistry ; HLA-A2 Antigen/genetics ; HLA-A2 Antigen/immunology ; HLA-A2 Antigen/metabolism ; Humans ; Major Histocompatibility Complex/immunology ; Models, Molecular ; Mutant Proteins/chemistry ; Mutant Proteins/metabolism ; Mutation/genetics ; Peptides/chemistry ; Peptides/immunology ; Peptides/metabolism ; Protein Binding ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell/chemistry ; Receptors, Antigen, T-Cell/immunology ; Receptors, Antigen, T-Cell/metabolism
Chemical Substances	Complementarity Determining Regions ; Gene Products, tax ; HLA-A2 Antigen ; Mutant Proteins ; Peptides ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2013-06-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/ncomms2948
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Article ; Online: Structural and dynamic control of T-cell receptor specificity, cross-reactivity, and binding mechanism.

Baker, Brian M / Scott, Daniel R / Blevins, Sydney J / Hawse, William F

Immunological reviews

2012 Volume 250, Issue 1, Page(s) 10–31

Abstract: Over the past two decades, structural biology has shown how T-cell receptors engage peptide/major histocompatibility complex (MHC) complexes and provided insight into the mechanisms underlying antigen specificity and cross-reactivity. Here we review and ... ...

Abstract	Over the past two decades, structural biology has shown how T-cell receptors engage peptide/major histocompatibility complex (MHC) complexes and provided insight into the mechanisms underlying antigen specificity and cross-reactivity. Here we review and contextualize our contributions, which have emphasized the influence of structural changes and molecular flexibility. A repeated observation is the presence of conformational melding, in which the T-cell receptor (TCR), peptide, and in some cases, MHC protein cooperatively adjust in order for recognition to proceed. The structural changes reflect the intrinsic dynamics of the unligated proteins. Characterization of the dynamics of unligated TCR shows how binding loop motion can influence TCR cross-reactivity as well as specificity towards peptide and MHC. Examination of peptide dynamics indicates not only peptide-specific variation but also a peptide dependence to MHC flexibility. This latter point emphasizes that the TCR engages a composite peptide/MHC surface and that physically the receptor makes little distinction between the peptide and MHC. Much additional evidence for this can be found within the database of available structures, including our observations of a peptide dependence to the TCR binding mode and structural compensations for altered interatomic interactions, in which lost TCR-peptide interactions are replaced with TCR-MHC interactions. The lack of a hard-coded physical distinction between peptide and MHC has implications not only for specificity and cross-reactivity but also the mechanisms underlying MHC restriction as well as attempts to modulate and control TCR recognition.
MeSH term(s)	Animals ; Antigens/chemistry ; Antigens/immunology ; Antigens/metabolism ; Binding Sites ; Cross Reactions ; Humans ; Lymphocyte Activation ; Major Histocompatibility Complex/immunology ; Mice ; Models, Molecular ; Peptides/chemistry ; Peptides/immunology ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Receptors, Antigen, T-Cell/chemistry ; Receptors, Antigen, T-Cell/immunology ; Receptors, Antigen, T-Cell/metabolism ; T-Cell Antigen Receptor Specificity ; T-Lymphocytes/cytology ; T-Lymphocytes/immunology ; T-Lymphocytes/metabolism
Chemical Substances	Antigens ; Peptides ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2012-10-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	391796-4
ISSN	1600-065X ; 0105-2896
ISSN (online)	1600-065X
ISSN	0105-2896
DOI	10.1111/j.1600-065X.2012.01165.x
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Article ; Online: Plasticity in the contribution of T cell receptor variable region residues to binding of peptide-HLA-A2 complexes.

Smith, Sheena N / Sommermeyer, Daniel / Piepenbrink, Kurt H / Blevins, Sydney J / Bernhard, Helga / Uckert, Wolfgang / Baker, Brian M / Kranz, David M

Journal of molecular biology

2013 Volume 425, Issue 22, Page(s) 4496–4507

Abstract: One hypothesis accounting for major histocompatibility complex (MHC) restriction by T cell receptors (TCRs) holds that there are several evolutionary conserved residues in TCR variable regions that contact MHC. While this "germline codon" hypothesis is ... ...

Abstract	One hypothesis accounting for major histocompatibility complex (MHC) restriction by T cell receptors (TCRs) holds that there are several evolutionary conserved residues in TCR variable regions that contact MHC. While this "germline codon" hypothesis is supported by various lines of evidence, it has been difficult to test. The difficulty stems in part from the fact that TCRs exhibit low affinities for pep/MHC, thus limiting the range of binding energies that can be assigned to these key interactions using mutational analyses. To measure the magnitude of binding energies involved, here we used high-affinity TCRs engineered by mutagenesis of CDR3. The TCRs included a high-affinity, MART-1/HLA-A2-specific single-chain TCR and two other high-affinity TCRs that all contain the same Vα region and recognize the same MHC allele (HLA-A2), with different peptides and Vβ regions. Mutational analysis of residues in CDR1 and CDR2 of the three Vα2 regions showed the importance of the key germline codon residue Y51. However, two other proposed key residues showed significant differences among the TCRs in their relative contributions to binding. With the use of single-position, yeast-display libraries in two of the key residues, MART-1/HLA-A2 selections also revealed strong preferences for wild-type germline codon residues, but several alternative residues could also accommodate binding and, hence, MHC restriction. Thus, although a single residue (Y51) could account for a proportion of the energy associated with positive selection (i.e., MHC restriction), there is significant plasticity in requirements for particular side chains in CDR1 and CDR2 and in their relative binding contributions among different TCRs.
MeSH term(s)	Amino Acid Sequence ; Cell Surface Display Techniques ; Complementarity Determining Regions/chemistry ; Complementarity Determining Regions/metabolism ; Gene Expression ; HLA-A2 Antigen/chemistry ; HLA-A2 Antigen/genetics ; HLA-A2 Antigen/immunology ; HLA-A2 Antigen/metabolism ; Humans ; MART-1 Antigen/immunology ; Models, Molecular ; Mutagenesis, Site-Directed ; Peptides/chemistry ; Peptides/metabolism ; Protein Binding ; Protein Conformation ; Receptors, Antigen, T-Cell, alpha-beta/chemistry ; Receptors, Antigen, T-Cell, alpha-beta/genetics ; Receptors, Antigen, T-Cell, alpha-beta/immunology ; Receptors, Antigen, T-Cell, alpha-beta/metabolism ; Single-Chain Antibodies/chemistry ; Single-Chain Antibodies/genetics ; Single-Chain Antibodies/immunology ; Single-Chain Antibodies/metabolism ; Solubility
Chemical Substances	Complementarity Determining Regions ; HLA-A2 Antigen ; MART-1 Antigen ; Peptides ; Receptors, Antigen, T-Cell, alpha-beta ; Single-Chain Antibodies
Language	English
Publishing date	2013-08-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2013.08.007
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Article ; Online: How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire.

Blevins, Sydney J / Pierce, Brian G / Singh, Nishant K / Riley, Timothy P / Wang, Yuan / Spear, Timothy T / Nishimura, Michael I / Weng, Zhiping / Baker, Brian M

Proceedings of the National Academy of Sciences of the United States of America

2016 Volume 113, Issue 9, Page(s) E1276–85

Abstract: How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and ... ...

Abstract	How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged "hot-spot" region that is almost exclusive to the α1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Vα and Vβ genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs.
MeSH term(s)	HLA-A2 Antigen/chemistry ; Humans ; Protein Conformation ; Receptors, Antigen, T-Cell, alpha-beta/chemistry ; Static Electricity
Chemical Substances	HLA-A2 Antigen ; Receptors, Antigen, T-Cell, alpha-beta
Language	English
Publishing date	2016-02-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1522069113
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Article ; Online: Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide-MHC complexes.

Hellman, Lance M / Yin, Liusong / Wang, Yuan / Blevins, Sydney J / Riley, Timothy P / Belden, Orrin S / Spear, Timothy T / Nishimura, Michael I / Stern, Lawrence J / Baker, Brian M

Journal of immunological methods

2016 Volume 432, Page(s) 95–101

Abstract: Measurements of thermal stability by circular dichroism (CD) spectroscopy have been widely used to assess the binding of peptides to MHC proteins, particularly within the structural immunology community. Although thermal stability assays offer advantages ...

Abstract	Measurements of thermal stability by circular dichroism (CD) spectroscopy have been widely used to assess the binding of peptides to MHC proteins, particularly within the structural immunology community. Although thermal stability assays offer advantages over other approaches such as IC50 measurements, CD-based stability measurements are hindered by large sample requirements and low throughput. Here we demonstrate that an alternative approach based on differential scanning fluorimetry (DSF) yields results comparable to those based on CD for both class I and class II complexes. As they require much less sample, DSF-based measurements reduce demands on protein production strategies and are amenable for high throughput studies. DSF can thus not only replace CD as a means to assess peptide/MHC thermal stability, but can complement other peptide-MHC binding assays used in screening, epitope discovery, and vaccine design. Due to the physical process probed, DSF can also uncover complexities not observed with other techniques. Lastly, we show that DSF can also be used to assess peptide/MHC kinetic stability, allowing for a single experimental setup to probe both binding equilibria and kinetics.
MeSH term(s)	Circular Dichroism ; Fluorometry/methods ; HLA-A2 Antigen/chemistry ; HLA-A2 Antigen/metabolism ; HLA-DR1 Antigen/chemistry ; HLA-DR1 Antigen/metabolism ; Hot Temperature ; Humans ; Kinetics ; Peptides/chemistry ; Peptides/metabolism ; Protein Binding ; Protein Denaturation ; Protein Stability
Chemical Substances	HLA-A*02:01 antigen ; HLA-A2 Antigen ; HLA-DR1 Antigen ; Peptides
Language	English
Publishing date	2016-02-18
Publishing country	Netherlands
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	120142-6
ISSN	1872-7905 ; 0022-1759
ISSN (online)	1872-7905
ISSN	0022-1759
DOI	10.1016/j.jim.2016.02.016
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Article ; Online: Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.

Adams, Jarrett J / Narayanan, Samanthi / Birnbaum, Michael E / Sidhu, Sachdev S / Blevins, Sydney J / Gee, Marvin H / Sibener, Leah V / Baker, Brian M / Kranz, David M / Garcia, K Christopher

Nature immunology

2015 Volume 17, Issue 1, Page(s) 87–94

Abstract: The T cell antigen receptor (TCR)-peptide-major histocompatibility complex (MHC) interface is composed of conserved and diverse regions, yet the relative contribution of each in shaping recognition by T cells remains unclear. Here we isolated cross- ... ...

Abstract	The T cell antigen receptor (TCR)-peptide-major histocompatibility complex (MHC) interface is composed of conserved and diverse regions, yet the relative contribution of each in shaping recognition by T cells remains unclear. Here we isolated cross-reactive peptides with limited homology, which allowed us to compare the structural properties of nine peptides for a single TCR-MHC pair. The TCR's cross-reactivity was rooted in highly similar recognition of an apical 'hot-spot' position in the peptide with tolerance of sequence variation at ancillary positions. Furthermore, we found a striking structural convergence onto a germline-mediated interaction between the TCR CDR1α region and the MHC α2 helix in twelve TCR-peptide-MHC complexes. Our studies suggest that TCR-MHC germline-mediated constraints, together with a focus on a small peptide hot spot, might place limits on peptide antigen cross-reactivity.
MeSH term(s)	Amino Acid Sequence ; Animals ; Antigens/chemistry ; Antigens/immunology ; Cross Reactions/immunology ; Crystallography, X-Ray ; Humans ; Lymphocyte Activation/immunology ; Major Histocompatibility Complex/immunology ; Models, Molecular ; Molecular Sequence Data ; Peptides/immunology ; Protein Binding/immunology ; Protein Conformation ; Receptors, Antigen, T-Cell, alpha-beta/chemistry ; Receptors, Antigen, T-Cell, alpha-beta/immunology
Chemical Substances	Antigens ; Peptides ; Receptors, Antigen, T-Cell, alpha-beta
Language	English
Publishing date	2015-11-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2016987-5
ISSN	1529-2916 ; 1529-2908
ISSN (online)	1529-2916
ISSN	1529-2908
DOI	10.1038/ni.3310
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