ArticleProceedings of the National Academy of Sciences of the United States of America1997
A structural census of the current population of protein sequences.
Article in Proceedings of the National Academy of Sciences of the United States of America, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 105 citations in OpenAlex.
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- The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis.Journal of molecular evolution · 2012Article
- Emerging area: biomaterials that mimic and exploit protein motion.Soft matter · 2011Article
- Lineage-specific differences in the amino acid substitution process.Journal of molecular biology · 2010Article
- Engineering of functional replication protein a homologs based on insights into the evolution of oligonucleotide/oligosaccharide-binding folds.Journal of bacteriology · 2008Article
- Protein abundance profiling of the Escherichia coli cytosol.BMC genomics · 2008Article
- Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins.Biochemistry · 2007Article
- Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales.BMC evolutionary biology · 2005Article
- A glimpse at the organization of the protein universe.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Universal sharing patterns in proteomes and evolution of protein fold architecture and life.Journal of molecular evolution · 2005Article
- Molecular models of protein targets from Mycobacterium tuberculosis.Journal of molecular modeling · 2005Article
- Structural characterization of genomes by large scale sequence-structure threading.BMC bioinformatics · 2004Article
- Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.Nucleic acids research · 2002Article
- Comparing function and structure between entire proteomes.Protein science : a publication of the Protein Society · 2001Article
- PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.Nucleic acids research · 2001Article
- Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome.Nucleic acids research · 2001Article
- Global perspectives on proteins: comparing genomes in terms of folds, pathways and beyond.The pharmacogenomics journal · 2001Review
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We examine the occurrence of the approximately 300 known protein folds in different groups of organisms. To do this, we characterize a large fraction of the currently known protein sequences ( approximately 140,000) in structural terms, by matching them to known structures via sequence comparison (or by secondary-structure class prediction for those without structural homologues). Overall, we find that an appreciable fraction of the known folds are present in each of the major groups of organisms (e.g., bacteria and eukaryotes share 156 of 275 folds), and most of the common folds are associated with many families of nonhomologous sequences (i.e., >10 sequence families for each common fold). However, different groups of organisms have characteristically distinct distributions of folds. So, for instance, some of the most common folds in vertebrates, such as globins or zinc fingers, are rare or absent in bacteria. Many of these differences in fold usage are biologically reasonable, such as the folds of metabolic enzymes being common in bacteria and those associated with extracellular transport and communication being common in animals. They also have important implications for database-based methods for fold recognition, suggesting that an unknown sequence from a plant is more likely to have a certain fold (e.g., a TIM barrel) than an unknown sequence from an animal.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.