Assessment of immunologically relevant dynamic tertiary structural features of the HIV-1 V3 loop crown R2 sequence by ab initio folding

Journal of Visualized Experiments

Volumn , Issue 43, 2010, Pages

  Almond, David ^a   Cardozo, Timothy ^a  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Ab initio simulations; Antibody mediated neutralization; HIV 1; Infection; Issue 43; Structure activity relationships; Vaccine design

Indexed keywords

EID: 80355141991     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/2118     Document Type: Article

References (5)

1. Almond, D., Kimura, T., Kong, X., Zolla-Pazner, S. & Cardozo, T. Dynamic characterization of the V3 loop crown. Antiviral Therapy 12, 13-31 (2007).
2. Almond, D., Kimura, T., Kong, X., Swetnam, J., Zolla-Pazner, S., Cardozo, T. Structural conservation predominates over sequence variability in the crown of HIV type 1's V3 loop. AIDS Res Hum Retroviruses. 26 (6), 717-23 (2010).
3. Abagyan, R., Totrov, M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 235, 983-1002 (1994).
4. Quinnan, G.V., Jr., Zhang, P.F., Fu, D.W., Dong, M. & Alter, H.J. Expression and characterization of HIV type 1 envelope protein associated with a broadly reactive neutralizing antibody response. AIDS Res Hum Retroviruses 15, 561-70 (1999).
5. Zhang, P.F., Bouma, P., Park, E.J., et al. A variable region 3 (V3) mutation determines a global neutralization phenotype and CD4-independent infectivity of a human immunodeficiency virus type 1 envelope associated with a broadly cross-reactive, primary virus-neutralizing antibody response. J Virol 76, 644-55 (2002).