Computational protocol: Solution structure of the Equine Infectious Anemia Virus p9 protein: a rationalization of its different ALIX binding requirements compared to the analogous HIV-p6 protein

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Protocol publication

[…] The structure of sp922-51 was determined from quantitative NOE data as described in detail elsewhere []. Structures were calculated on a Silicon Graphics Octane work station using the program CNS 1.0 with standard CNS parameters for protein data sets []. A total of 346 distance restraints were used to generate 100 conformations of which 20 conformations, exhibiting no restraint violations greater than 0.2 Å and having the lowest energy values, were used for the final fitting analysis.The heterogeneity within the final set of 20 structures was visualized using the consecutive segment approach which allows fitting regions for alignments to be defined (19). The central structure showing the lowest root mean square deviation (rmsd) of its fitting region to those of the other structures was then determined using the programs LSQMAN and MOLEMAN2 (Uppsala Software Factory) []. Finally, alignments were performed by superimposing the fitting regions of all other structures to that of the central structure and these were visualized with the PYMOL program http://www.pymol.org. The final structure of sp922-51 has been deposited in the Protein Data Bank under code PDBID 2K84.In this study the probability for helical or extended conformation of dipeptidic segments in the full length sp9 molecule was analyzed using the distances between 1H nuclei of adjacent residues, namely HN and Hα of residue i and HN of residue i+1 (dNN(i, i+1), dαN(i, i+1)) (22). The distances d which strictly correlate with signal intensities I (I ~1/d6) were obtained by transferring the intensities of the respective NOE signals into interproton distances using the Bruker program AURELIA. Only unambiguous signals were used for this analysis. For a few signals that were weakened by the pre-saturation of the water resonance a correction was applied (-1.5 Å when within 0.005 ppm of the water signal, -1 Å when within 0.025 ppm, and -0.5 Å when within 0.05 ppm), and a similar correction was made in cases where two or more signals could not be resolved individually due to close signal overlap. An equation given by Bradley et al. [] was then used to calculate probabilities for helical or extended conformations. […]

Pipeline specifications

Software tools CNS, PyMOL
Application Protein structure analysis
Organisms Human immunodeficiency virus 1, Equus caballus, Equine infectious anemia virus, Human immunodeficiency virus 2
Diseases Anemia, Equine Infectious Anemia, Neoplasms