Solution structure of lactam analogue DapD of HIV gp41 600-612 loop
Structural and immunological characterisation of heteroclitic peptide analogues corresponding to the 600-612 region of the HIV envelope gp41 glycoprotein.
1J8N contains the beta3-ser analogue peptide (HSER)
1J8Z contains the beta3-Cys analogue peptide (HCYS)
1J9V contains the lactam analogue peptide DabD
1JAR contains the lactam analogue peptidev DDab
1JC8 contains the lactam analogue peptide DDap
1JAA contains the lactam analogue peptide DapE
1JCP contains the lactam analogue peptide EDap
The parent peptide (IWGCSGKLICTTA) occurs naturally in HIV gp41
Classical 2D homonuclear NMR technques were used. Different NOESY with different mixing time (from 80ms to 800ms) were recorded in order to determine the best conditions without spin diffusion.
50 initial structures were generated using DYANA software, followed by 500 steps restrained minimization.Then using DISCOVER 3, 35 ps MD and 750 steps conjugate gradient EM.
torsion dynamics, molecular dynamics, energy minimization
Bartels C., Billeter M., Guentert P. and Wuethrich K. (1995) J.Biomol. NMR, 5, 1-10
Guentert P., Mumenthaler C. and Wuethrich K. (1997) J. Mol. Biol., 273,283-298
cyclic peptide, gp41, HIV, lactam bond, pseudopeptide, Viral protein