The HLA-DP2 binding pocket in complex with the crystallized natural peptide of 15 residues.

<p>The 10 residues of the peptide used as a cutting template are shown in red with important residues having extended structure. The removed residues are in yellow. Key residues in HLA-DP2 are shown in green; the aspartic acid is labeled as <i>ASP</i> and the three glutamic acid residues are labeled as <i>GLU Pocket</i>.</p

Cartoon representation of HLA-DP2 protein (PDB ID 3LQZ).

<p>Peptide binding pocket is shown in light and dark purple. Residues taken into account for distance calculations are in red. Change in RMSD due to peptide/Be binding was analyzed for residues in dark purple. Illustration was made with Chimera software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111604#pone.0111604-Pettersen1" target="_blank">[33]</a>.</p

Graphical depiction of our investigation of the effects of the Be ion on the complex made up of a HLA-DP2 protein, the Be ion, and a small peptide.

<p>We investigated four types of small peptides (“Natural”, “Strong”, “Weak”, and “DR”) and two binding scenarios: (1) the ion bound to a small peptide and (2) the ion bound to the HLA-DP2 protein. Effect predictions include binding affinity, conformation changes of the peptide binding pocket, pKa shifts of titratable groups of the protein upon peptide and/or the Be ion binding.</p

Average distances between the CA atoms of residues forming peptide-binding pocket.

<p>Error bar illustrated as ± two values of standard deviation.</p

Illustration of the two investigated binding scenarios.

<p>In the top panel (A) the Be ion is in complex with the protein and then the peptides were added, peptide→(Be+protein) scenario; and in the bottom panel (B) the Be ion is in complex with the peptides and then the protein is added, (Be+peptide)→protein scenario.</p

The pKa shift of two ionizable residues βGlu26 and βGlu69 on (A) HLA-DP2 binds to peptides (Four types as “natural”, “strong”, “weak” and “DR”, the same to the followings) (B) peptides bind to the complex (Be+protein) (C) (Be+peptides) complex binds to HLA-DP2 protein from pKa of native unbond protein.

<p>The pKa value was calculated as the average of 10 structures for each type of peptides.</p

Selected distances between residues forming peptide-binding pocket of HLA-DP2.

<p>Selected distances between residues forming peptide-binding pocket of HLA-DP2.</p

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joskin... a stupid personPRINTED ITEM G. M. Story MAY 1970 JH MAY 1970Not UsedNot UsedWithdrawnChecked by Jordyn Hughes on Wed 07 Oct 201