How to find simple and accurate rules for viral protease cleavage specificities

BMC Bioinformatics

Table 8 The HCV NS3 rules applied to the NS3 protease sequence.

P1	Decamer	Rule match	Mass (kDa)	Mass (kDa)
C16	RGLLGCIITS	HCVA	1.7	65.6
C47	TFLATCINGV	HCVA	5.0	62.3
C52	CINGVCWTVY	HCVA, HCVC	5.5	61.8
Q73	KGPVIQMYTN	HCVC	7.7	59.6
M74	GPVIQMYTNV	HCVC	7.8	59.4
V78	QMYTNVDQDL	HCVC	8.3	59.0
C97	RSLTPCTCGS	HCVA	10.3	56.9
C99	LTPCTCGSSD	HCVA	10.5	56.7
S102	CTCGSSDLYL	HCVB	10.7	56.5
T108	DLYLVTRHAD	HCVB	11.4	55.8
G120	PVRRRGDSRG	HCVB	12.8	54.4
S122	RRRGDSRGSL	HCVC	13.0	54.2
I132	LSPRPISYLK	HCVC	14.1	53.1
G137	ISYLKGSSGG	HCVB	14.7	52.6
C159	FRAAVCTRGV	HCVA	16.7	50.5
V163	VCTRGVAKAV	HCVC	17.1	50.1
K165	TRGVAKAVDF	HCVC	17.3	49.9
Q195	PPAVPQSFQV	HCVC	20.6	46.6
A240	TLGFGAYMSK	HCVC	25.1	42.2
C279	LADGGCSGGA	HCVA	29.2	38.1
C289	YDIIICDECH	HCVA, HCVC	30.2	37.1
C292	IICDECHSTD	HCVA	30.5	36.7
G314	QAETAGARLV	HCVC	32.6	34.6
V339	PNIEEVALST	HCVB	35.2	32.0
L341	IEEVALSTTG	HCVB	35.4	31.9
C368	RHLIFCHSKK	HCVA, HCVC	38.3	28.9
N387	VALGINAVAY	HCVC	40.3	26.9
L395	AYYRGLDVSV	HCVB, HCVC	41.2	26.0
T402	VSVIPTSGDV	HCVC	41.9	25.3
C428	DSVIDCNTCV	HCVA, HCVC	44.5	22.7
C431	IDCNTCVTQT	HCVA	44.9	22.4
S488	SGMFDSSVLC	HCVC	51.2	16.1
C492	DSSVLCECYD	HCVA	51.6	15.7
C494	SVLCECYDAG	HCVA	51.8	15.4
A497	CECYDAGCAW	HCVD	52.1	15.1
C499	CYDAGCAWYE	HCVA	52.3	14.9
V511	PAETTVRLRA	HCVB	53.6	13.6
L513	ETTVRLRAYM	HCVB, HCVC	53.9	13.3
C525	PGLPVCQDHL	HCVA	55.2	12.0
V535	EFWEGVFTGL	HCVC	56.5	10.8
I542	TGLTHIDAHF	HCVC	57.2	10.0
Q552	LSQTKQSGEN	HCVC	58.4	8.8
A562	FPYLVAYQAT	HCVB	59.5	7.8
C568	YQATVCARAQ	HCVA, HCVC	60.1	7.1
C584	DQMWKCLIRL	HCVA	62.0	5.2
C622	KYIMTCMSAD	HCVA	66.3	1.0

The table shows the result of applying the HCV NS3 cleavage rules to the NS3 protease amino acid sequence. Only decamers that are predicted to be cleaved are listed. The first column mentions the amino acid and the position in the NS3 sequence that occupies the P1 position in the decamer. The second column lists the decamer. The third column shows which HCV NS3 rules that the decamer matches to. The fourth and fifth column show the molecular masses of the cleavage products if NS3 is cleaved in that position.

ISSN: 1471-2105