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Open AccessUncovering new families and folds in the natural protein universe
We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database1. These models cover nearly all ...
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GREENER principles for environmentally sustainable computational science
The carbon footprint of scientific computing is substantial, but environmentally sustainable computational science (ESCS) is a nascent field with many opportunities to thrive. To realize the immense green oppo...
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Open AccessA structural biology community assessment of AlphaFold2 applications
Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have ...
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Bacterial retrons encode phage-defending tripartite toxin–antitoxin systems
Retrons are prokaryotic genetic retroelements encoding a reverse transcriptase that produces multi-copy single-stranded DNA1 (msDNA). Despite decades of research on the biosynthesis of msDNA2, the function and ph...
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Using deep learning to annotate the protein universe
Understanding the relationship between amino acid sequence and protein function is a long-standing challenge with far-reaching scientific and translational implications. State-of-the-art alignment-based techni...
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Open AccessHighly accurate protein structure prediction for the human proteome
Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis. After decad...
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Open AccessDiscovery of fibrillar adhesins across bacterial species
Fibrillar adhesins are long multidomain proteins that form filamentous structures at the cell surface of bacteria. They are an important yet understudied class of proteins composed of adhesive and stalk domain...
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Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states
RNA polymerase III (Pol III) synthesizes transfer RNAs and other short, essential RNAs. Human Pol III misregulation is linked to tumor transformation, neurodegenerative and developmental disorders, and increas...
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Open AccessSolution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum
Human myeloid-derived growth factor (hMYDGF) is a 142-residue protein with a C-terminal endoplasmic reticulum (ER) retention sequence (ERS). Extracellular MYDGF mediates cardiac repair in mice after anoxic inj...
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Open AccessDomain atrophy creates rare cases of functional partial protein domains
Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising l...
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Open AccessStructure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis
CA_C2195 from Clostridium acetobutylicum is a protein of unknown function. Sequence analysis predicted that part of the protein contained a metallopeptidase-related domain. There are over 200 homologs of similar ...
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Open AccessLUD, a new protein domain associated with lactate utilization
A novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved LutABC operon, which has been implicated in lactat...
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Open AccessFilling out the structural map of the NTF2-like superfamily
The NTF2-like superfamily is a versatile group of protein domains sharing a common fold. The sequences of these domains are very diverse and they share no common sequence motif. These domains serve a range of ...
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Open AccessTwo Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila
Every genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying seque...
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Open AccessGenome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling
The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an an...
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Time to underpin Wikipedia wisdom
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Open AccessQuantifying the mechanisms of domain gain in animal proteins
Protein domains are protein regions that are shared among different proteins and are frequently functionally and structurally independent from the rest of the protein. Novel domain combinations have a major ro...
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SnoPatrol: how many snoRNA genes are there?
Small nucleolar RNAs (snoRNAs) are among the most evolutionarily ancient classes of small RNA. Two experimental screens published in BMC Genomics expand the eukaryotic snoRNA catalog, but many more snoRNAs remain...
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Open AccessThe structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes
Many Gram-positive lactic acid bacteria (LAB) produce anti-bacterial peptides and small proteins called bacteriocins, which enable them to compete against other bacteria in the environment. These peptides fall...
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Open AccessPepsin homologues in bacteria
Peptidase family A1, to which pepsin belongs, had been assumed to be restricted to eukaryotes. The tertiary structure of pepsin shows two lobes with similar folds and it has been suggested that the gene has ar...
