Identification of CD8+ cytotoxic T lymphocyte epitopes from porcine reproductive and respiratory syndrome virus matrix protein in BALB/c mice

Zhang, Weijun; Lin, Yan; Bai, Yu; Tong, Tiegang; Wang, Qun; Liu, Nihong; Liu, Guangliang; Xiao, Yihong; Yang, Tao; Bu, Zhigao; Tong, Guangzhi; Wu, Donglai

doi:10.1186/1743-422X-8-263

Virology Journal

Table 2 Predicted M protein peptides chemically synthesized and screened to identify CTL epitopes

From: Identification of CD8⁺ cytotoxic T lymphocyte epitopes from porcine reproductive and respiratory syndrome virus matrix protein in BALB/c mice

Bioinformatics Methods
	SYFPEITHI		BIMAS		PRED^BALB/c
	Peptides	Bingding score	Peptides	Bingding score	Peptides	Bingding score
H-2K^d	K₉₃FITSRCRL	BS = 23	K₉₃FITSRCRL	BS = 2304.000	K₉₃FITSRCRL	BS = 9.70
	T₂₅YTPVMIYA	BS = 24	T₂₅YTPVMIYA	BS = 72.000	T₂₅YTPVMIYA	BS = 5.3
	S₁₂TAPQKVLL	BS = 20	S₁₂TAPQKVLL	BS = 57.600	S₁₂TAPQKVLL	BS = 6.10
	S₁₄₀TTVNGTLV	BS = 19	S ₁₄₀TTVNGTLV	BS = 14.400	S ₁₄₀TTVNGTLV	BS = 6.10
	T₁₄₆LVPGLKGL	BS = 19	T₁₄₆LVPGLKGL	BS = 115.200	T₁₄₆LVPGLKGL	BS = 9.10
	A₂₁FSITYTPV	BS = 18	A₂₁FSITYTPV	BS = 345.600	A₂₁FSITYTPV	BS = 9.54
	R₄₀LLGLLHLL	BS = 18	R₄₀LLGLLHLL	BS = 96.00	R₄₀LLGLLHLL	BS = 7.80
	L₃₄KVSRGRLL	BS = 17	L₃₄KVSRGRLL	BS = 9.600	L₃₄KVSRGRLL	BS = 5.64
	H₆₄FQSTNRVA	BS = 17	H₆₄FQSTNRVA	BS = 28.800	H₆₄FQSTNRVA	BS = 5.64
	C₁₀₂LLGRKYIL	BS = 17	C₁₀₂LLGRKYIL	BS = 96.00	C₁₀₂LLGRKYIL	BS = 7.84
	Q₁₆KVLLAFSI	BS = 16	L₁₆₂KVSRGRLL	BS = 11.520	L₁₆₂KVSRGRLL	BS = 5.80
	L₁₆₂KVSRGRLL	BS = 16	L₁₆₂KVSRGRLL	BS = 0.012	L₁₆₂KVSRGRLL	BS = 6.10
	S₂₃ITYTPVMI	BS = 14	S₂₃ITYTPVMI	BS = 48.000	S₂₃ITYTPVMI	BS = 8.50
H-2D^d			Y₂₆TPVMIYAL	BS = 20.000	Y₂₆TPVMIYAL	BS = 9.82
			F₅₇GYMTFVHF	BS = 7.200	F₅₇GYMTFVHF	BS = 10.00
			T₁₃APQKVLLA	BS = 12.000	T₁₃APQKVLLA	BS = 8.58
			Q₁₆₄GVVNLVKY	BS = 2.000	Q₁₆₄GVVNLVKY	BS = 9.40
			F₁₂₂HPIAANDN	BS = 2.400	F₁₂₂HPIAANDN	BS = 9.20
			P₁₃₈GSTTVNGT	BS = 0.200	P₁₃₈GSTTVNGT	BS = 9.20
H-2L^d	A₁₄PQKVLLAF	BS = 24	A₁₄PQKVLLAF	BS = 450.000	A₁₄PQKVLLAF	BS = 9.38
	V₁₄₈PGLKGLVL	BS = 24	V₁₄₈PGLKGLVL	BS = 150.000	V₁₄₈PGLKGLVL	BS = 9.50
	D₁₁STAPQKVL	BS = 20	D₁₁STAPQKVL	BS = 25.000	D₁₁STAPQKVL	BS = 7.50
	Y₈₆SAIETWKF	BS = 20	Y₈₆SAIETWKF	BS = 50.000	Y₈₆SAIETWKF	BS = 7.50
	E₁₁₇SAAGFHPI	BS = 20	E₁₁₇SAAGFHPI	BS = 6.500	E₁₁₇SAAGFHPI	BS = 4.70
	T₉₆SRCRLCLL	BS = 19	T₉₆SRCRLCLL	BS = 7.500	T₉₆SRCRLCLL	BS = 7.60
	G₁₃₉STTVNGTL	BS = 18	G₁₃₉STTVNGTL	BS = 25.000	G₁₃₉STTVNGTL	BS = 7.40
	F₂₂SITYTPVM	BS = 15	F₂₂SITYTPVM	BS = 25.000	F₂₂SITYTPVM	BS = 7.00

Note: The 27 peptides with highest binding score (BS) as predicted by each algorithm are shown, starting with the peptide giving the highest score at the top for each protein. Sequences of 9 mers are given from BIMAS, SYFPEITHI and PRED^BALB/c predictions, respectively. The N-terminal amino acid position is indicated for epitopes predicted from the whole M protein.

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ISSN: 1743-422X

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