Parallel molecular mechanisms for enzyme temperature adaptation
Pinney, Margaux M. et al. (2020), Parallel molecular mechanisms for enzyme temperature adaptation, Dryad, Dataset, https://doi.org/10.5061/dryad.3ffbg79h2
and we establish the underlying physical mechanismsThis residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature in 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation. We assess the properties of these residues, molecular interactions and interaction networks that appear to underly temperature adaptation.
This Dryad data repository contains the starting datasets, analysis code and results (p-values and phylogenetic signals) for logistic regression models applied to 17,060,900 residue-positions in 2194 enzymes: Pinney, M.M, Mokhtari, D.A, Akiva, E., Yabukarski, F., Sanchez, D.M., Liang, R., Doukov, T., Martinez, T.J., Babbitt, P.C., Herschlag, D., Parallel Molecular Mechanisms for Enzyme Temperature Adaptation.
See Pinney, et. al., for detailed Materials and Methods on how this dataset was collected and analyzed and for all associated references.
This dataset contains two sets of files: (1) folders "Analysis", "Notebooks" and "References", which contain the datasets and step-by-step code used in the identification of temperature-associated residues and their phyogenetic signals, and (2) "SummaryCSVs", which containes summary csv files of the temperature-associated residues identified from this analysis and susbets of this dataset (see README files for all for more details).
Detailed explanations for how this data was collected and processed can be found in Pinney, et. al., Materials and Methods.
National Science Foundation, Award: MCB-1714723
National Institutes of Health, Award: R01 GM60595
Joint Genome Institute, Award: 503369