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RMSF versus MD simulation time for the HLA-Cw4-β2m-KIR2DL1 protein backbone.

RMSF versus MD simulation time for the HLA-Cw4-β2m-KIR2DL1 protein backbone.

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Fig. 1. MHC class I molecules.
Fig. 2. RMSD versus MD simulation time for the HLA-Cw4-β2m-KIR2DL1...
Fig. 3. RMSF versus MD simulation time for the HLA-Cw4-β2m-KIR2DL1...
Fig. 4. Ramachandran Plot for the final frame of the 100 ns MD simulation.
+5 Fig. 5. Hydrogen Bonding at the HLA-Cw4 and the KIR2DL1 interface.
Molecular Dynamics Simulations of HLA-CW4-Β2M-KIR2DL1 Protein and Homology Modeling of a Complex Associated with Psoriasis Disease (HLA-CW6-Β 2M-KIR2DS1)
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  • Dec 2021
Molecular dynamics (MD) simulation was used to study the interactions of two immune proteins of HLA-Cw4-β2m-KIR2DL1 complex with small peptide QYDDAVYKL (nine amino acids) in an aqueous solution. This study aims to gain a detailed information about the conformational changes and the dynamics of the complex. The right parameters and force field for...
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... copyright holder for this preprint this version posted December 20, 2021. ; https://doi.org/10. 1101/2021 The RMSF values that represent the average over time of the RMSD over protein backbone atoms. The average value of the RMSF for the protein backbone was 0.484 Å, as shown in Fig. 3. Ramachandran plot analysis indicates whether the backbone torsion angles (/) of our structure are within the allowed region. Most of the peptide residues have (/) angles typical for an extended β strand and α helix. On the other hands, some residues adopt (/) angles that are found in a left-handed helix, and they are usually ...