Table 3.

Epitope prediction of HLA-II-restrict T cells using Rm39, Rm180, Rm239 and Rm76 protein sequences with TEPITOPE and NetMHCII software

TEPITOPE
Native antigen (full-length sequence)	No. of peptidesa	No. of allelesb	Scorec
Rm239 (500 amino acids)	2,023	54	31.22
Rm76 (152 amino acids)	867	54	30.85
Rm180 (186 amino acids)	105	53	43.27
Rm39 (105 amino acids)	38	34	4.05
Recombinant vaccine antigend (partial sequence)	Positionf	No. of allelesb	Scoreg
Rm180	25	53	24.9
Rm39	69	5	0.6
	30	9	2.3
Rm239	79	2	0.23
	59	27	3.06
	38	5	1.30
Rm76e	157	52	24.5
	137	52	9.7
	132	52	2.4
	129	53	6.2
	122	53	25.7
	121	53	17.8
	120	52	7.5
	117	54	5.7
	116	53	5.0
	66	52	15.0
	62	35	3.3
	56	53	22.1
	50	1	1.2
	46	53	11.9
	40	53	5.0
	39	53	15.7
	37	3	2.4
	36	53	12.0
NetMHCII
Recombinant vaccine antigene	No of peptidesh	No of Allelesi	Strong ligandsj
Rm180	52	10	33
Rm39	72	6	–
Rm239	130	14	75
Rm76 e1	138	14	166

^aTotal number of epitopes with positive score

^bA total of 54 HLA-DR alleles were used by TEPITOPE. The values refer to the number of HLA-DRB alleles that binds to predicted epitopes

^cThe score (ranging from negative to positive values) is a calculated value to define the binding affinity between peptide and HLA, therefore the higher the score, the higher the binding affinity. The values are expressed as the mean of scores from predicted bindings

^dData from sequences (partial) of recombinant proteins used in this study

^eRm76 was the only antigen cloned as full-length sequence

^fPosition of the first amino acid of the HLA class II binding peptide on the protein sequence

^gOnly the positive scores were considered, i.e. those with the most binding affinity properties

^hTotal number of possible peptides based on each protein size

ⁱA total of 14 HLA-DR alleles were used by NetMHCII v. 2.2. The values refer to the number of alleles that presents predicted ligands

^jThe binding affinity to HLA-DR is based on IC₅₀ values in nM. The threshold for strong ligands is IC₅₀ = 50. Only results for strong ligands are shown