Structural Analysis of TCRpMHC Complexes Using Computational Tools. Feroze Mohideen Briarcliff High School

Transcription

1 Structural Analysis of TCRpMHC Complexes Using Computational Tools Feroze Mohideen Briarcliff High School

2 TCR-pMHC Complexes Peptide Structure of TCR-pMHC complex PDB AO7

3 Crossreactivity is the ability of a TCR to recognize more than one pmhc complex Immature T-cells that are too crossreactive may be the basis of autoimmune diseases (Stephens et al., ) Ding et al., 999 Studied crossreactivity of TCR A6 with four different peptides in complex with HLA- A*: Lysis assay IFN-γ assayin both cases, mutation at position 7 induces some crossreactivity, whereas other mutations induce negligible crossreactivity even at higher concentrations of peptide TCR Crossreactivity

4 Goals Perform structural analysis of TCR crossreactivity Four A6 TCR-pMHC complexes (Tax peptide) (Ding et al.,999) View TCR binding patterns with viral peptides and mutated versions of them Identify patterns found in TCR interactions with pmhc complexes Compare analysis with computational structures to results found in experimental procedures Begin investigation into importance of CDR loops in crossreactivity

5 Methodology Use the Protein Databank* (PDB), a source for computational structures of TCR-pMHC complexes derived from completed experiments Use Chimera and PyMOL for molecular visualization of structures Access the IMGT database, another tool for analysis of structures IMGT holds data on more than, D structures of antibodies, TCRs, MHCs and other proteins related to the immune response Includes contact analyses, individual chain details, residue details, etc. *The PDB holds, structures as of August,.

6 Analysis of TCR-pMHC Complexes Hydrogen Bonding Electromagnetic attractive interaction between polar molecules Hydrogen is bound to a highly electronegative atom, such as nitrogen, oxygen or fluorine Important in TCR interaction with peptide-mhc complexes Hydrophobic (non-polar) contacts van der Waals forces 6

7 Studied Structures PDB ID TCR-HLA complex Peptide Origin Amino-acid Sequence Mutation ao7 A6 TCR/HLA A*: Tax peptide - 9 LLFGYPVYV No Mutation qrn A6 TCR/HLA A*: Tax peptide - 9 LLFGYAVYV P6A qse A6 TCR/HLA A*: Tax peptide - 9 LLFGYPRYV V7R qsf A6 TCR/HLA A*: Tax peptide - 9 LLFGYPVAV Y8A Ding et al., 999

8 Structural Visualization Example Viral peptide V-alpha chain V-beta chain PDB: AO7

9 Beta Chain Alpha Chain Wild Type Tax Peptide-TCR Interaction Analysis

10 Beta Chain Alpha Chain P6A Tax Peptide-TCR Interaction Analysis 7 6 Wild Type 7 6 Mutant

11 Beta Chain Alpha Chain V7R Tax Peptide-TCR Interaction Analysis 7 6 Wild Type 7 6 Mutant

12 (LEU) (LEU) (PHE) (GLY) (TYR) 6 (PRO) 7 (VAL) 8 (ALA) 9 (VAL) Beta Chain (LEU) (LEU) (PHE) (GLY) (TYR) 6 (PRO) 7 (VAL) 8 (ALA) 9 (VAL) Alpha Chain Y8A Tax Peptide-TCR Interaction Analysis 7 6 Wild Type 7 6 Mutant

13 Summary and Conclusions TCR crossreactivity is important for understanding of autoimmune disorders and T- cell maturity Computational structural analysis conducted to understand TCR crossreactivity Studied four different Tax pmhcs in complex with the same TCR Hydrogen bonding and hydrophobic contacts In the complex with the WT peptide 6 th position hydrogen bonds, hydrophobic contacts 7 th position hydrogen bonds, hydrophobic contacts 8 th position hydrogen bonds, hydrophobic contacts After mutations 6 th position hydrogen bonds, hydrophobic contact 7 th position hydrogen bonds, 8 hydrophobic contacts 8 th position hydrogen bonds, hydrophobic contacts Sixth and eighth residue mutations to alanine formed fewer contacts with TCR than seventh residue mutation to arginine Explains the results from experimental data

14 Future Goals Use the computational workflow to analyze more structures to further understand TCR cross-reactivity Further investigate the role of CDR in TCR specificity

15 References Structure of the complex between human T-cell receptor, viral peptide and HLA-A Garboczi et al., 996 Four A6-TCR/Peptide/HLA-A Structures that Generate Very Different T Cell Signals Are Nearly Identical Ding et al., 999 T Cell Receptor Recognition via Cooperative Conformational Plasticity Gagnon et al., 6 Fluorine substitutions in an antigenic peptide selectively modulate T cell receptor binding in a minimally perturbing manner Piepenbrink et al., Disparate Degrees of Hypervariable Loop Flexibility Control T-Cell Receptor Cross- Reactivity, Specificity, and Binding Mechanism Scott et al., T Cell Receptor Cross-reactivity Directed by Antigen-Dependent Tuning of Peptide-MHC Molecular Flexibility Borbulevych et al., 9 Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics Borbulevych et al.,

16 Beta Chain Alpha Chain Wild Type HIV Peptide-TCR Interaction Analysis Again, mainly first half of peptide interacts with V- alpha chain, second half interacts with V-beta chain Residues, and do not bond or form contacts at all with TCR Mainly residues -7 are responsible for TCRpeptide interaction

17 Beta Chain Alpha Chain F6L HIV Peptide-TCR Interaction Analysis Wild Type Mutant Mutation from phenylalanine to leucine created fewer contacts with beta chain Eight hydrophobic contacts became six to beta chain, same number of contacts in alpha chain

18 Beta Chain Alpha Chain Wild Type EBV Peptide-TCR Interaction Analysis Looking at B*8- HPVG(wt) vs B*8- HPVG-D(mut) in assay Residues -8 most responsible for interactions

19 (HIS) (PRO) (VAL) (GLY) (GLU) 6 (ALA) 7 (ASP) 8 (TYR) 9 (PHE) (GLU) (TYR) Beta Chain (HIS) (PRO) (VAL) (GLY) (GLU) 6 (ALA) 7 (ASP) 8 (TYR) 9 (PHE) (GLU) (TYR) Alpha Chain ED EBV Peptide-TCR Interaction Analysis 8 Wild Type 8 Mutant Mutant released more interferon gamma than wt Same number of contacts and bonds as wt as well

20 Summary and Conclusion

21 Acknowledgments Ankur Dhanik Susan Croll, Rachel Houghton and Anisha Murarka, and Catherine Morrison Molecular Profiling Mrs. Carnahan

22 Backup Slides

23 CDR Loops Read several articles about how TCR crossreactivity is mediated by CDR loops on V-alpha and V-beta chains (Reiser et al., ) Decided to look back on old data to analyze importance of CDR loops in peptide-tcr contacts Revisited the contact maps In V-alpha chain, CDR loop is residues 9- In V-beta, CDR loop is residues 9-7

24 h9s dv d9 gj6 qfj pwp qsf qse ftv qrn ao7

25 qsf h9s qse dv d9 ftv qrn qfj ao7 gj6 pwp

26 Work Done Last Year Focused on interactions between peptides and MHC class I molecules Confirmed basic patterns of interactions in pmhc complexes found in previous studies Learned how to use tools that apply to TCRpMHC complexes Goal this year was to analyze TCR and pmhc interactions, and understand TCR crossreactivity

27 TCR RESIDUE BURIAL Tax P6>A V7>R Y8>A

28 CONTACT MAPS Tax P6>A V7>R Y8>A

29 # of Hydrogen Bonds Peptide Residue Hydrogen Bonds to TCR in Tax and Mutated Tax Peptides... Tax peptide P6>A V7>R Y8>A Residue #

30

31 # of interactions van der Waals Interactions between TCR Chains and Mutated Tax Peptides 8 6 Tax peptide P6>A V7>R Y8>A V-alpha domain hydrogen bonds w/ligand V-alpha polar contacts w/ligand V-alpha nonpolar contacts w/ligand V-beta domain hydrogen bonds w/ligand V-beta polar contacts w/ligand V-beta nonpolar contacts w/ligand

32 REVIEW OF LIT CDR loops positioned over diverse peptides while less diverse CDR and CDR loops bind with less diverse MHC molecules (Garbozci et al., 996) The TCR fits diagonally across the MHC peptide-binding site Studies have found that peptide and MHC conformational changes can trigger alternate TCR loop conformations, while also altering the stability of the complex (Borbulevych et al., ) While these studies are generating results experimentally, I analyze these results to find explanations of these results

33 INITIAL PROCEDURES Used Chimera, loading files from PDB and manually searching through each residue of peptide and counting Hydrogen Bonds

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35

36 IMGT DATABASE Later realized that IMGT has almost all the data that I need, switched to gathering the data found on the website

37 Chain details for PDB ao7

38 Cards

39 General Contact Analysis

40 Phi, Psi Bond Angles and ASA

41 Contact Maps I noticed that one of the studies I read about included contact maps of the interactions between residues of the TCR and the peptide I tried to create contact maps of my own by installing VMD and CCP at home These programs were too complicated for me to learn about quickly, so I looked for better options Eventually found a website from SPACE - Tools for protein Structure Prediction and Analysis based on Complementarity and Environment

42 CMA: Contact Map Analysis

43 Displays residue-residue contacts

44 Generated Contact Maps

45 h9s dv d9 gj6 qfj pwp qsf qse ftv qrn ao7

46 qsf h9s ftv qse qrn dv d9 qfj ao7 gj6 pwp

47 Residue Hbonds to TR Residue Hbonds to TR Residue Hbonds to TR Residue Hbonds to TR Residue 7 Hbonds to TR Residue 8 Hbonds to TR Residue Hbonds to TR Residue 6 Hbonds to TR Residue 9 Hbonds to TR

48 Residue SAS Residue SAS Residue 7 SAS Residue SAS Residue SAS Residue 8 SAS Residue SAS Residue 6 SAS Residue 9 SAS

49 Assays

50 REFERENCES Structure of the complex between human T-cell receptor, viral peptide and HLA-A Garboczi et al., 996 Four A6-TCR/Peptide/HLA-A Structures that Generate Very Different T Cell Signals Are Nearly Identical Ding et al., 999 T Cell Receptor Recognition via Cooperative Conformational Plasticity Gagnon et al., 6 Fluorine substitutions in an antigenic peptide selectively modulate T cell receptor binding in a minimally perturbing manner Piepenbrink et al., Disparate Degrees of Hypervariable Loop Flexibility Control T-Cell Receptor Cross-Reactivity, Specificity, and Binding Mechanism Scott et al., T Cell Receptor Cross-reactivity Directed by Antigen-Dependent Tuning of Peptide-MHC Molecular Flexibility Borbulevych et al., 9 Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics Borbulevych et al.,

51 Experimental Results Study conducted in 999 by Ding et al. Analyzed three singly modified tax peptides and how they generate different T-Cell responses, even though they have similar structures Used T-cell assays, kinetic and thermodynamic measurements, and X-ray crystallography to conclude that P6A and Y8A mutations were more inhibitory to the strength of TCR-pMHC complex than V7R

52 Experimental Results % Specific Lysis assay: a measure of how the TCR is able to destroy an antigenpresenting cell after forming complex with pmhc IFN-γ assay: stable TCR-pMHC complexes will express IFN-γ as part of signaling process In both cases, mutation at position 7 induces some crossreactivity, whereas other mutations induce negligible crossreactivity even at higher concentrations of peptide

53 BURIED RESIDUES WITHOUT TCR Peptide Wild Type Exposed Exposed Exposed Exposed Exposed Exposed Exposed Exposed Exposed P6A Exposed Exposed Exposed Exposed Exposed Exposed Exposed Exposed Exposed V7R Exposed Exposed Exposed Exposed Exposed Exposed Exposed Exposed Buried Y8A Exposed Exposed Exposed Exposed Exposed Exposed Exposed Exposed Exposed

54 TCR BURIED RESIDUES Peptide Wild Type Exposed Exposed Exposed Buried Exposed Exposed Exposed Exposed Exposed P6A Exposed Buried Buried Buried Exposed Buried Exposed Exposed Exposed V7R Exposed Buried Exposed Buried Exposed Exposed Exposed Exposed Buried Y8A Exposed Buried Exposed Buried Exposed Exposed Exposed Exposed Exposed