Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy

BMC Bioinformatics

Table 3 Conserved and experimentally verified B cell epitopes from HCMV envelope proteins

Epitope	Antigen gene	^a Accession number	^b PDB	^c Flexibility	^d Accessibility (%)
VSIDDDTPML	UL75	Q6SW67	5VOB: A [238–247]	0.131	25.37
TNQYLIKGISYPVST	UL75	Q6SW67	5VOB: A [592–606]	0.09	32.63
AFHLLLNTYGR	UL75	Q6SW67	5VOB: A [37–47]	1.618	55.08
IFTEHVLGFELVPPS	UL115	F5HCH8	5VOB: B [173–187]	−0.275	11.71
TANQNPSPPWSKLTYSKPH	UL130	F5HCP3	5VOB: D [32–50]	0.104	39.64
WSTLTANQNPSPPWSKLTY	UL130	F5HCP3	5VOB: D [28–46]	0.138	33.37
FTYDTLRGYINRALA	UL55	F5HB53	5C6T: A [486–500]	− 0.644	64.02
LRGYINRALAQIAEA	UL55	F5HB53	5C6T: A [491–505]	−0.645	68.14
NRALAQIAEAWCVDQ	UL55	F5HB53	5C6T: A [496–510]	−0.724	63.41
QIAEAWCVDQRRTLE	UL55	F5HB53	5C6T: A [501–515]	−0.904	56.29
SAILSAIYNKPIAAR	UL55	F5HB53	5C6T: A [526–540]	−1.187	40.75
SKINPSAILSAIYNK	UL55	F5HB53	5C6T: A [521–535]	−1.241	46.13
VFKELSKINPSAILS	UL55	F5HB53	5C6T: A [516–530]	−1.322	38.57
YAQLQFTYDTLRGYI	UL55	F5HB53	5C6T: A [481–495]	−0.734	53.73
NVTFRGLQNKTEDFL	UL4	Q6SWC6	–	0.442	19.39

^a Accession number from UniProtKB database. ^b Tertiary structure of the antigen (PDB code) with epitope location in square brackets. ^c Average flexibility (F_b, Eq. 3) of epitope in arbitrary units. ^d Average relative solvent-exposed accessibility of epitope in percentage (A_b, Eq. 4). The epitopes AFHLLLNTYGR and WSTLTANQNPSPPWSKLTY, were part of the epitopes AASEALDPHAFHLLLNTYGR and SWSTLTANQNPSPPWSKLTY, respectively. Accessibility and flexibility of NVTFRGLQNKTEDFL was predicted upon the antigen amino acid sequence as it did not map onto any 3D-structure (details in Methods)

ISSN: 1471-2105