Functional conservation of HIV-1 Gag: implications for rational drug design

Retrovirology

Table 1 Natural polymorphism proportions in gag domains and drug binding positions across 8 HIV-1 subtypes and CRFs (%)

	B	A1	C	D	F1	G	01_AE	02_AG	Mean
Matrix[132/13]	57.6/38.5	62.1/46.2	59.1/46.2	64.4/53.8	52.3/46.2	66.7/61.5	61.4/46.2	56.1/30.8	59.9/46.2
Capsid[231/98]	27.3/30.6	34.2/33.7	29.4/29.6	27.7/27.6	31.2/37.8	30.3/28.6	28.1/28.6	27.3/27.6	29.4/30.5
p2[14/8]	71.4/62.5	64.3/62.5	64.3/62.5	64.3/62.5	57.1/62.5	71.4/62.5	64.3/62.5	50.0/50.0	63.4/60.9
NC[55/17]	56.4/58.8	41.8/35.3	38.2/41.2	36.4/29.4	34.5/23.5	54.5/58.8	43.6/35.3	34.5/41.2	42.5/40.4
p1[16/0]	37.5/-	25.0/-	31.2/-	43.8/-	25.0/-	31.2/-	31.2/-	12.5/-	29.7/-
p6[52/0]	76.9/-	69.2/-	69.2/-	55.8/-	65.4/-	61.5/-	69.2/-	57.7/-	65.6/-
Mean	45.2/36.8	46.6/36.8	43.4/34.6	42.8/32.4	41.2/38.2	47.0/37.5	44.0/33.1	39.0/30.9	43.6/35.0

Each gag protein is demonstrated with its total AA and drug binding positions (e.g. Matrix [132/13]: 132 AA positions/13 drug binding positions). Natural polymorphism proportion (%) is indicated for each protein and subtype with respect to the total number of AAs and to the number of drug binding positions (e.g. 57.6/38.5 shows that for subtype B matrix, 57.6% of all 132 positions and 38.5% of 13 drug binding positions are polymorphic). Mean values across gag domains and across HIV-1 subtypes are indicated in the last row and column respectively.

ISSN: 1742-4690