Hydrogen Exchange Mass Spectrometry of Related Proteins with Divergent Sequences: A Comparative Study of HIV-1 Nef Allelic Variants

摘要: Hydrogen exchange mass spectrometry can be used to compare the conformation and dynamics of proteins that are similar in tertiary structure. If relative deuterium levels measured, differences sequence, forward- back-exchange, peptide retention time, protease digestion patterns all complicate data analysis. We illustrate what learned from such sets by analyzing five variants (Consensus G2E, SF2, NL4-3, ELI, LTNP4) HIV-1 Nef protein, both alone when bound human Hck SH3 domain. Regions with sequence could compared between variants. Although much hydrogen features were preserved across proteins, kinetics binding not same. These observations may related biological function, particularly for ELI where we also observed an impaired ability downregulate CD4 surface presentation. The some caveats must considered comparison experiments provide a framework investigations other protein relatives, families, superfamilies HX MS.