title: Position of Proline Mediates the Reactivity of S-Palmitoylation.
abstract: Palmitoylation, a post-translational modification in which a saturated 16-carbon chain is added predominantly to a cysteine residue, participates in various biological functions. The position of proline relative to other residues being post-translationally modified has been previously reported as being important. We determined that proline is statistically enriched around cysteines known to be S-palmitoylated. The goal of this work was to determine how the position of proline influences the palmitoylation of the cysteine residue. We established a mass spectrometry-based approach to investigate time- and temperature-dependent kinetics of autopalmitoylation in vitro and to derive the thermodynamic parameters of the transition state associated with palmitoylation; to the best of our knowledge, our work is the first to study the kinetics and activation properties of the palmitoylation process. We then used these thermochemical parameters to determine if the position of proline relative to the modified cysteine is important for palmitoylation. Our results show that peptides with proline at the -1 position of cysteine in their sequence (PC) have lower enthalpic barriers and higher entropic barriers in comparison to the same peptides with proline at the +1 position of cysteine (CP); interestingly, the free-energy barriers for both pairs are almost identical. Molecular dynamics studies demonstrate that the flexibility of the cysteine backbone in the PC-containing peptide when compared to the CP-containing peptide explains the increased entropic barrier and decreased enthalpic barrier observed experimentally.
authors.affiliation: Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University , Bloomington, Indiana 47405, United States.
authors.forename: Neelam
authors.initials: N
authors.lastname: Khanal
authors.affiliation: Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University , Bloomington, Indiana 47405, United States.
authors.forename: Vikas
authors.initials: V
authors.lastname: Pejaver
authors.affiliation: Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University , Bloomington, Indiana 47405, United States.
authors.forename: Zhiyu
authors.initials: Z
authors.lastname: Li
authors.affiliation: Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University , Bloomington, Indiana 47405, United States.
authors.forename: Predrag
authors.initials: P
authors.lastname: Radivojac
authors.affiliation: Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University , Bloomington, Indiana 47405, United States.
authors.forename: David E
authors.initials: DE
authors.lastname: Clemmer
authors.affiliation: Departments of †Chemistry, ‡Computer Science and Informatics, and §Biology, Indiana University , Bloomington, Indiana 47405, United States.
authors.forename: Suchetana
authors.initials: S
authors.lastname: Mukhopadhyay
mesh_terms: D003545:Cysteine / Q000737:chemistry*; D054878:Lipoylation; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D019308:Palmitic Acid / Q000737:chemistry / Q000378:metabolism*; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011392:Proline / Q000737:chemistry*; D011499:Protein Processing, Post-Translational
chemical_list: D010455:Peptides; D019308:Palmitic Acid; D011392:Proline; D003545:Cysteine