Computational Modelling Group

MHC Class I docking with Tapasin:

Tapasin is depicted in green and MHC Class I allele HLA-B*0801 is depicted with the heavy chain in blue and red and the B2m sub-unit in grey:

(A) The docking of Tapasin and MHC is driven by biochemical interaction information. The TN6 region of Tapasin identified by Dong et al. is docked using HADDOCK with residue T134 of MHC. T134 has been identified as key to Tapasin-MHC interaction. An open structure of MHC Class I allele HLA-B0801 (pdb ID: 1agb) is generated by molecular dynamic simulation. The human Tapasin structure is completed from the crystal structure (pdb ID: 38fu) using homology modelling.

(B) Tapasin residue R187 of the TN6 region nds a favourable interaction with T134. The side chain of T134 of the peptide-bound crystal Structure of HLA-B*0801 is depicted in gold and the docked structures side chains are shown in red, white and blue. Movement of the alpha2-1 helix (red) widens the F-pocket at the peptide C-terminus by about 3 Angstroms as previously observed by Sieker et al. This movement of the alpha2-1 helix corresponds with a movement of T134 by about 2 Angstroms from the closed structure to nd its interaction with R187 on Tapasin in this simulation. E185 on Tapasin appears to form a structural interaction with R187.

(C) Colours as panels B. The simulation independently identifies a favourable C-terminus interaction between Tapasin residue R333 and E222 on MHC. An E222K mutation of murine MHC allele H2-Dd has been shown to prevent binding to Tapasin.

A putative model of the Peptide Loading Complex:

A simulated peptide free MHC Class I-2m dimer HLA-B*0801 (yellow) is docked to Tapasin (green) using HADDOCK.

ERp57 (purple) forms a conjugate with Tapasin.

A model structure of Calreticulin (orange) is positioned approximately with the glycan binding sites close to that of MHC I and the proline domain tip close to the domain residues of ERp57 with which it is believed to interact.

TAP is not shown as no structure is available.

MHC CLass I Structure:

(a) A Van der Waals surface representation of lumenal domains of HLA-B*0801 heterodimer.

(b) A ribbon representation indicating Ig-type 3 domain, 1 and 2 helices and  sheets create the peptide binding groove. The alpha-2 helix is thought to be where Tapasin interacts. Ig-type protein B2m is noncovalently bound, but provides rigidity to the protein.

(c) Plan view of the peptide binding groove with a bound peptide coloured orange. It is the most polymorphic part of MHC Class I proteins, where 8-10 residue peptides bind forming complexes for presentation to CD8+ T-Cells. Pockets identified as anchors for the peptide are annotated B in yellow, C in dark blue, D in pink and F in red.

(d) A cartoon representation of MHC Class I structure indicating the transmembrane nature of the protein with the C-terminus tail that extends across membranes which is not seen in the lumenal domains comprising the crystal structures shown in (a) or (b).

A kinetic model of peptide editing:

In this graphical representation the yellow shapes represent MHC I-B2m dimers, the red shapes are peptides and the green shapes represent Tapasin.

Each box represents a reaction. A reversible reaction box contains two rates with the forward reaction rate on top and the backward reaction rate below.

Irreversible reactions contains only one reaction rate.

Incoming arrows represent reactants and outgoing arrows represent products.

Crossed circles represent generation or degradation of a protein species.

A cartoon representation of the MHC Class I antigen processing pathway

HLA-B*0801 molecular dynamics simulation using Gromacs

Click on the image to start the animation.

Project Map showing all the people, techniques and alleles involved