Modeling the bound conformation of Pemphigus Vulgaris-associated peptides to MHC Class II DR and DQ Alleles

Immunome Research

Table 3 Comparison of core peptides (numbering according to Table 2) from structural docking in the different binding pockets with the sequence-based binding motifs. '+' indicates compliance of amino acid residues within the core (bold underlined) with the respective binding motifs defined by the groups of ^a Veldman [28] and ^bSinha [2, unpublished results].

No.	Residues	Peptide Sequence and positions in the bound conformation for DRB1*0402			Core peptide residue positions as defined by binding motifs
					p1		p4		p6		p9
			1 2 3 4 5 6 7 8 9		V ^a	S ^b	V	S	V	S	V	S
II	191–205	NSKIA	F K I V S Q E P A	G	+			+		+		+
III	206–220	TPM	F L L S R N T G E	VRT	+				+	+		+
IV	252–266	ECNI	K V K D V N D N F	PM					+	+
V	342–356	SVKL	S I A V K N K A E	FH				+	+	+		+
VI	380–394	GIA	F R P A S K T F T	VQK	+			+		+		+
VII	763–777	SGT	M R T R H S T G G	TNK	+	+	+	+	+	+		+
VIII	810–824	ND	C L L I Y D N E G	ADAT				+		+		+
IX	963–977	ERVICP	I S S V P G N L A		+	+		+				+