DEALING WITH SEQUENCE VARIABILITY DURING THE COMPARATIVE HYDROGEN EXCHANGE MASS SPECTROMETRY ANALYSIS OF MULTIPLE ALLELIC VARIANTS

摘要

Pep tide ma p s that were g enerated from online p ep sin di g estion were not identical. Two separate peptide regions showed a decrease in deuterium incorporation when in complex with HckSH3. The change in deuterium incorporation kinetics for SH3 bound Nef are different between both regions as well as across the four Nef proteins. There is also evidence for a decrease in deuterium incorporation for the modeled N-terminal α-helix for both ConsensusG2E and NL4-3 Nefs, which might have implications for Nef function. Using multiple methods of da ta visualization will be necessary to compare the HX-MS data obtained for Nef from all the major clades of HIV-1. Interpretation of HXMS data for multiple allelic variants is most valuable when the interpretation of exchange is based on the tertiary structure.