Juan Carlos Aledo
Protein Evolution and Post-translational Modifications
Our research interest spans various aspects of computational evolutionary biology. Generally speaking, our work seeks to better understand how proteins evolve . In particular, we are interested in understanding the very diverse roles that methionine residues fulfil in proteins (reviewed in  and ), and how these functions have evolved in organisms. Along these lines, we have devoted great attention to methionine sulfoxidation as a bone-fide post-translational modification [3-7].
We tackle these problems by gathering and curating experimental data and developing computational tools to be applied on the gathered data. In this sense, we have developed and made available a software package, ptm, for the analysis of post-translational modifications , as well as a collection of data and references to methionines that may be involved in regulatory processes. Thus, MetOSite is a web-based searchable database that currently contains over 7500 methionine sulfoxide sites found in over 3700 different proteins from more than 30 species .
- Multisite phosphorylation provides a reliable mechanism for making decisions in noisy environments. FEBS J. 2018 Oct;285(20):3729-3737. doi: 10.1111/febs.14636. Epub 2018 Sep 4.
- Methionine in proteins: The Cinderella of the proteinogenic amino acids. Protein Sci. 2019 Oct;28(10):1785-1796. doi: 10.1002/pro.3698.
- The role of methionine residues in the regulation of liquid-liquid phase separation. Biomolecules. 2021 Aug 21;11(8):1248. doi: 10.3390/biom11081248.
- Susceptibility of protein methionine oxidation in response to hydrogen peroxide treatment –ex vivo versus in vitro-: a computational insight. Antioxidants (Basel). 2020 Oct 13;9(10):987. doi: 10.3390/antiox9100987.
- Inferring methionine sulfoxidation and serine phosphorylation crosstalk from phylogenetic analyses. BMC Evol Biol. 2017 Jul 27;17(1):171. doi: 10.1186/s12862-017-1017-9.
- Methionine residues around phosphorylation sites are preferentially oxidized in vivo under stress conditions. Sci Rep. 2017 Jan 12;7:40403. doi: 10.1038/srep40403.
- Sulfur atoms from methionines interacting with aromatic residues are less prone to oxidation. Sci Rep. 2015 Nov 24;5:16955. doi: 10.1038/srep16955.
- ptm: an R package for the study of methionine sulfoxidation and other post-translational modifications. Bioinformatics. 2021 May 8:btab348. doi: 10.1093/bioinformatics/btab348.
- MetOSite: an integrated resource for the study of methionine residue sulfoxidation. Bioinformatics. 2019 Nov 1;35(22):4849-4850. doi: 10.1093/bioinformatics/btz462