Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles

Abstract

MHC class I molecules load antigenic peptides in the endoplasmic reticulum and present them at the cell surface. Efficiency of peptide loading depends on the class I allele and can involve interaction with tapasin and other proteins of the loading complex. Allele HLA-B*4402 (Asp at position 116) depends on tapasin for efficient peptide loading, whereas HLA-B*4405 (identical to B*4402 except for Tyr116) can efficiently load peptides in the absence of tapasin. Both alleles adopt very similar structures in the presence of the same peptide. Comparative unrestrained molecular dynamics simulations on the alpha(1)/alpha(2) peptide binding domains performed in the presence of bound peptides resulted in structures in close agreement with experiments for both alleles. In the absence of peptides, allele-specific conformational changes occurred in the first segment of the alpha(2)-helix that flanks the peptide C-terminal binding region (F-pocket) and contacts residue 116. This segment is also close to the proposed tapasin contact region. For B*4402, a shift toward an altered F-pocket structure deviating significantly from the bound form was observed. Subsequent free energy simulations on induced F-pocket opening in B*4402 confirmed a conformation that deviated significantly from the bound structure. For B*4405, a free energy minimum close to the bound structure was found. The simulations suggest that B*4405 has a greater tendency to adopt a peptide receptive conformation in the absence of peptide, allowing tapasin-independent peptide loading. A possible role of tapasin could be the stabilization of a peptide-receptive class I conformation for HLA-B*4402 and other tapasin-dependent alleles.

Figure 1.

Top view of the α₁/α₂ peptide binding domain of MHC class I molecules HLA-B*4402 (PDB entry 1M6O) and HLA-B*4405 (PDB entry 1SYV). Both molecules are complexed with an antigenic peptide consisting of nine residues (peptide sequence: EEFGRAFSF). The two alleles differ only at residue 116, which is given in ball-and-stick representation (B*4402, aspartate; B*4405, tyrosine). The proposed tapasin contact region and the α-helical segments are indicated (for B*4402).

Figure 2.

RMSD time course (moving average) for backbone atoms of the α₁/α₂-domains of B*4402 and B*4405 with respect to the X-ray start structure. Time courses are shown over 21-nsec trajectories (two independent simulations) for the peptide-bound (black) and ligand-free forms (gray), respectively. (Thick lines) Average of two independent simulations.

Figure 3.

Superposition of average peptide-bound structures (approximately the same point of view) obtained during the MD simulations (gray) on the crystal start structure (black) of B*4402 and B*4405.

Figure 4.

Conformational flexibility of the α₁/α₂-domain of HLA-B*4402 and HLA-B*4405 in complex with an antigenic peptide (peptide bound) and in the absence of peptide (peptide free). Averages of mean square fluctuations per residue are shown for the two independent simulations at 300 K.

Figure 5.

Superposition of the average structure obtained from the simulation of HLA B*4402 in the absence of a peptide (gray) on the X-ray start structure (black). (Straight light-gray lines) Helical segments that flank the F-pocket (binding region for the peptide C-terminal anchor) and segments used to monitor the F-pocket opening and to drive F-pocket opening during free energy simulations (residues 74–85 and 138–149, respectively); (light-gray double arrows) increased distance between the two segments observed during the unrestrained simulations.

Figure 6.

Distribution of the center-of-mass distance between the two α-helical segments (residues 74–85 of the α₁-helix and residues 138–149 of the α_2–1-helix) that flank the class I F-pocket observed during unrestrained MD simulations. Two independent simulations (thin continuous and dashed lines) were performed (each 21 nsec) for peptide-bound (black) and peptide-free (gray) class I molecules. (Thick lines) Sum of the distance distributions from the two independent simulations.

Figure 7.

Free energy vs. distance between helical segments that flank the F-pocket HLA-B*4402 (black) and HLA-B*4405 (gray) obtained during umbrella sampling simulations in the absence of peptides. Free energy changes were extracted from simulations with different reference distances (ranging from 12–18 Å in steps of 0.5 Å: 13 reference distances). Data gathering at each reference distance was performed for 3 nsec. (Continuous, dashed, and dotted lines) Free energy results were extracted from different intervals of the data-gathering simulation time at each reference distance (see graph legend).