Highlights In-depth sequence analysis reveals that the protein fold universe is more evolutionarily connected than previously assumed. Short ancestral fragments are observed to have propagated to many modern proteins and hint at possible evolutionary pathways. Experimental reconstruction of such events by chimeragenesis and directed evolution allows to test evolutionary relationships. Detailed knowledge of folding landscapes helps to understand evolutionary history and improve protein engineering. The ubiquitous and versatile TIM-barrel fold is a model system to explore evolution, folding, and design.

Background While childhood asthma prevalence is rising in Westernized countries, farm children are protected. The mitogen‐activated protein kinase (MAPK) pathway with its negative regulator dual‐specificity phosphatase‐1 (DUSP1) is presumably associated with asthma development. Objectives We aimed to investigate the role of MAPK signaling in childhood asthma and its environment‐mediated protection, including a representative selection of 232 out of 1062 children from two cross‐sectional cohorts and one birth cohort study. Methods Peripheral blood mononuclear cells (PBMC) from asthmatic and healthy children were cultured upon stimulation with farm‐dust extracts or lipopolysaccharide. In subgroups, gene expression was analyzed by qPCR (PBMCs, cord blood) and NanoString technology (dendritic cells). Protein expression of phosphorylated MAPKs was measured by mass cytometry. Histone acetylation was investigated by chromatin immunoprecipitation. Results Asthmatic children expressed significantly less DUSP1 (p = .006) with reduced acetylation at histone H4 (p = .012) compared with healthy controls. Farm‐dust stimulation upregulated DUSP1 expression reaching healthy levels and downregulated inflammatory MAPKs on gene and protein levels (PBMCs; p ≤ .01). Single‐cell protein analysis revealed downregulated pMAPKs upon farm‐dust stimulation in B cells, NK cells, monocytes, and T‐cell subpopulations. Conclusion Lower DUSP1 baseline levels in asthmatic children and anti‐inflammatory regulation of MAPK in several immune cell types by farm‐dust stimulation indicate a regulatory function for DUSP1 for future therapy contributing to anti‐inflammatory characteristics of farming environments.

Modern proteins have been shown to share evolutionary relationships via subdomain-sized fragments. The assembly of such fragments through duplication and recombination events led to the complex structures and functions we observe today. We previously implemented a pipeline that identified more than 1,000 of these fragments that are shared by different protein folds and developed a web interface to analyze and search for them. This resource named Fuzzle helps structural and evolutionary biologists to identify and analyze conserved parts of a protein but it also provides protein engineers with building blocks for example to design proteins by fragment combination. Here, we describe a new version of this web resource that was extended to include ligand information. This addition is a significant asset to the database since now protein fragments that bind specific ligands can be identified and analyzed. Often the mode of ligand binding is conserved in proteins thereby supporting a common evolutionary origin. The same can now be explored for subdomain-sized fragments within this database. This ligand binding information can also be used in protein engineering to graft binding pockets into other protein scaffolds or to transfer functional sites via recombination of a specific fragment. Fuzzle 2.0 is freely available at https://fuzzle.uni-bayreuth.de/2.0.

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Periplasmic binding proteins (PBPs) are a class of proteins that participate in the cellular transport of various ligands. They have been used as model systems to study mechanisms in protein evolution, such as duplication, recombination and domain swapping. It has been suggested that PBPs evolved from precursors half their size. Here, the crystal structures of two permuted halves of a modern ribose-binding protein (RBP) from Thermotoga maritima are reported. The overexpressed proteins are well folded and show a monomer–dimer equilibrium in solution. Their crystal structures show partially noncanonical PBP-like fold type I conformations with structural deviations from modern RBPs. One of the half variants forms a dimer via segment swapping, suggesting a high degree of malleability. The structural findings on these permuted halves support the evolutionary hypothesis that PBPs arose via a duplication event of a flavodoxin-like protein and further support a domain-swapping step that might have occurred during the evolution of the PBP-like fold, a process that is necessary to generate the characteristic motion of PBPs essential to perform their functions.