A Practical Example: QUASI Analysis on the GP120 of HIV-1
- Gp120 is a surface protein of HIV-1. It mediates the entry of HIV-1 into host cells such as DCs, Lymphs, .....
HIV particle HIV Entry into Host Cell
Hiv particle derived from http://www.stanford.edu/group/virus/retro/2005gongishmail/HIV.html
Hiv entry into host cell: http://www.hivmedicine.com/textbook/haart/horizon.htm
2. Structure of HIV-1 gp 120 (Dr. Peter D.Kwong, etc. 1998. Nature. VoL 393:648-659)
- inner (more
conserved )and outer
domain (variable, contact with CD4,
CCR5/CXCR4 coreceptors)
- Contact sites (gp120 and CD4, coreceptor): LV1,LD, a3,ß15, ß20,ß21,ß23,ß24.
3. QUASI analysis on gp120
- 6151 gp120 analyzed
- Most of CD4/CD4i binding
sites are conserved, except 423 (CD4i)
and 474 (CD4)
- GPGRAF motif (red underline) is not conserved contrary to the previous study
- inner domain is not
conserved: lots of positively selected sites in this regions,
suggesting that other cell immune responses involved!
