Data from: Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases

Name: Data from: Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases
Creator: Barraclough, Timothy G.; Patmanidis, Ilias; Kontopoulos, Dimitrios - Georgios; Pawar, Samraat
Published: 2025-08-21 00:00:00
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Figshare2025-08-21 更新2026-04-08 收录

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CONTENTS OF THIS DATASET 1) ADK_characteristics.csv: a dataset with the main characteristics (accession, superkingdom, species, monomeric vs trimeric, short vs long LID, native temperature group) of the 70 adenylate kinases (ADKs) included in our study. 2) ADK_gene_tree.nwk: maximum-likelihood tree of the 70 ADKs. 3) alignment_of_all_ADKs.fasta: multiple sequence alignment of all 70 ADKs. 4) alignment_of_monomeric_ADKs.fasta: multiple sequence alignment of the 58 monomeric ADKs. 5) alignment_of_trimeric_ADKs.fasta: multiple sequence alignment of the 12 trimeric ADKs. 6) amino_acid_contacts.zip: a compressed directory of directories with information regarding contacts between amino acid pairs, observed during molecular dynamics simulations of the 70 ADKs. 7) amino_acid_contacts_dataset.csv: a dataset of counts of the four types of amino acid contacts observed during molecular dynamics simulations of each ADK. 8) kinetic_dataset.csv: a subset of the 193-species Muir et al., bioRxiv, 2024 dataset of kinetic parameter measurements of ADKs. This file includes measurements for only the 17 ADKs that are shared between the Muir et al. dataset and our study. 9) phylogenetic_random_effect_ln_neg_pol.csv: the estimated values of the phylogenetic random effect on the intercept for ln(neg-pol). 10) phylogenetic_random_effect_ln_pol_pol.csv: the estimated values of the phylogenetic random effect on the intercept for ln(pol-pol). 11) phylogenetic_random_effect_rgyr.csv: the estimated values of the phylogenetic random effect on the intercept for the radius of gyration (rgyr). 12) phylogenetic_random_effect_RMSF.csv: the estimated values of the phylogenetic random effect on the intercept for the root mean square fluctuation (RMSF). 13) phylogenetic_random_effect_SASA.csv: the estimated values of the phylogenetic random effect on the intercept for the solvent-accessible surface area (SASA). 14) RMSF_SASA_rgyr_dataset.csv: mean and standard error of RMSF, SASA, and rgyr for each ADK. For simulations that were performed at a 'non-native' temperature, this is reported in the "Offset_from_native_temperature" column. 15) species_tree_with_node_IDs.pdf: visualization of the time-calibrated species tree, with each node being annotated with an ID number. 16) time_calibrated_species_tree.nwk: the time-calibrated species tree used for the analyses of the present study. Further information about the contents of these files can be found in our study.

提供机构：

Barraclough, Timothy G.; Patmanidis, Ilias; Kontopoulos, Dimitrios - Georgios; Pawar, Samraat

创建时间：

2025-02-19