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

CONTENTS OF THIS DATASET1) 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.本数据集包含以下文件： 1) ADK_characteristics.csv：收录本研究涉及的70种腺苷酸激酶（adenylate kinases, ADK）的核心特征数据集，字段涵盖登录号、超界、物种、单体型vs三聚体型、短LIDvs长LID及天然温度分组。 2) ADK_gene_tree.nwk：70种ADK的最大似然基因树。 3) alignment_of_all_ADKs.fasta：70种ADK的多序列比对（multiple sequence alignment）文件。 4) alignment_of_monomeric_ADKs.fasta：58种单体型ADK的多序列比对文件。 5) alignment_of_trimeric_ADKs.fasta：12种三聚体型ADK的多序列比对文件。 6) amino_acid_contacts.zip：压缩目录包，内含70种ADK分子动力学模拟（molecular dynamics simulation）过程中观测到的氨基酸残基对接触信息的相关目录。 7) amino_acid_contacts_dataset.csv：各ADK分子动力学模拟中观测到的4类氨基酸接触的计数数据集。 8) kinetic_dataset.csv：Muir等人2024年发表于bioRxiv的193物种ADK动力学参数测量数据集的子集，仅包含本研究与Muir等人研究共有的17种ADK的测量数据。 9) phylogenetic_random_effect_ln_neg_pol.csv：针对ln(neg-pol)截距项的系统发育随机效应估计值数据集。 10) phylogenetic_random_effect_ln_pol_pol.csv：针对ln(pol-pol)截距项的系统发育随机效应估计值数据集。 11) phylogenetic_random_effect_rgyr.csv：针对回转半径（radius of gyration, rgyr）截距项的系统发育随机效应估计值数据集。 12) phylogenetic_random_effect_RMSF.csv：针对均方根波动（root mean square fluctuation, RMSF）截距项的系统发育随机效应估计值数据集。 13) phylogenetic_random_effect_SASA.csv：针对溶剂可及表面积（solvent-accessible surface area, SASA）截距项的系统发育随机效应估计值数据集。 14) RMSF_SASA_rgyr_dataset.csv：各ADK的均方根波动、溶剂可及表面积及回转半径的均值与标准误。若模拟在“非天然”温度下进行，则相关信息将在“Offset_from_native_temperature（与天然温度的偏移量）”列中注明。 15) species_tree_with_node_IDs.pdf：经时间校准的物种树可视化图，每个节点均标注有编号ID。 16) time_calibrated_species_tree.nwk：本研究分析所用的经时间校准的物种树文件。 有关本数据集各文件的详细信息可参见本研究原文。