TCR-pMHC scanning.

<p>The crystal structure of (A) complex A and (B) complex B is in grey for reference and the maximum movement of the TCR during the respective simulations is superposed in light blue or dark blue. Orthogonal orientations are shown in the right hand panels. The arrow highlights the direction of TCR movement during the respective simulations.</p

The flexibility of the LPEP peptide within HLA-B*3508 while complexed to the SB27 TCR.

<p>(A) RMSFs as calculated from MD simulations for MHC and peptide residues. Only positions 1 to 180 of the MHC molecules are displayed with the MHC helices underlined. HLA-B*3508-LPEP simulations 1 and 2 are in red and orange respectively and HLA-B*3508-LPEP SB27 TCR simulations 1 and 2 are in dark purple and pink respectively. The boxed insert highlights the RMSFs of the peptide at positions 1 to 13; (B) Cartoon representation of the crystal structure of HLA-B*3508-LPEP SB27 TCR complex (PDB ID 2AK4) with helices coloured grey, peptide in yellow and polymorphic residue in green. For clarity the SB27 TCR has been removed. MD snapshots of the peptide taken every 10 ns are colour coded as per A.</p

Hydrogen bonds between the pMHC and the TCR observed over the course of the simulations.

<p>(-) indicates no interaction observed in simulation.</p

Overall cartoon of TCR-pMHC complex SB27-HLA-B*3508-LPEP (PDB ID 2AK4).

<p>(A) HLA-B*3508 shown in grey with polymorphic residue (R156) in green, LPEP peptide shown in red, SB27 TCR shown in yellow and cyan for α- and β- chains respectively; (B) Superposition of the two distinct TCR-pMHC complexes within the crystal structure, SB27 α- and β-chains of complex A coloured orange and dark blue respectively and complex B coloured as per (A); (C) aerial view of antigen binding cleft of HLA-B*3508-LPEP with colours as per (A) and the SB27 TCR removed with the exception of the CDR loops.</p

MHC and peptide conformational flexibility in MD simulations.

<p>(A) RMSFs as calculated from MD simulations for MHC and peptide residues (inset). Only positions 1 to 180 of the MHC molecules are displayed with the MHC helices underlined. HLA-B*3508 simulations 1 and 2 are in red and orange respectively and HLA-B*3501 simulations 1 and 2 are in dark and light blue respectively. The boxed inset highlights the RMSFs of the peptide at positions 1 to 13; (B) Cartoon representation of the crystal structure of HLA-B*3508-LPEP (PDB ID 1ZHL) with helices coloured grey, peptide in yellow and polymorphic residue in green. MD snapshots of the peptide taken every 10 ns and colour coded in red for simulation 1 and orange for simulation 2; (C) Cartoon representation of the crystal structure of HLA-B*3501-LPEP (PDB ID 1ZHK) with helices shown in grey, peptide in yellow and polymorphic residue in green. MD snapshots taken each 10 ns are colour coded dark blue for simulation 1 and light blue for simulation 2.</p

The SB27 TCR footprint on HLA-B*3508-LPEP following MD simulation.

<p>(A) A comparison of contacts observed in both the crystal structure and dynamics. MHC or peptide contacts observed in both the crystal structure and dynamics coloured red and orange respectively. Residues coloured in light or dark blue represent novel short-lived (&lt;50%) or long-lived (&gt;50%) interactions respectively that were observed only during the simulation. The footprint represents both complex A and complex B as all contacts were conserved between the two simulations with the exception of Arg157 which was a short-lived contact only observed in the simulation of complex A and Arg151 and Arg162 which were long-lived contacts only observed in the simulation of complex A; (B) The HLA-B*3508 and LPEP residues contacted by the TCR are coloured according to the CDR loop from which they are derived. The uncontacted regions of LPEP are in red, residues contacted by CDR2α in yellow, CDR3α in cyan, CDR1β in green and CDR2β in purple.</p

Instrument Integration: the key to accessing Science Gateways

Abstract for a demonstration at the International Workshop on Science Gateways at eResearch Australasia 2016 on the topic 'Instrument Integration: the key to accessing Science Gateways