ArticleProtein science : a publication of the Protein Society2001
Comparing function and structure between entire proteomes.
Article in Protein science : a publication of the Protein Society, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
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Who cites it
105 citing papers in PubMed, 273 citations in OpenAlex.
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- Joubert syndrome causing mutation in C2 domain of CC2D2A affects structural integrity of cilia and cellular signaling molecules.Experimental brain research · 2024Article
- From primordial clocks to circadian oscillators.Nature · 2023Article
- The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database.Molecular biology and evolution · 2022Article
- Identification and characterization of coiled-coil motifs across Autographa californica multiple nucleopolyhedrovirus genome.Heliyon · 2022Article
- TMbed: transmembrane proteins predicted through language model embeddings.BMC bioinformatics · 2022Article
- Prerequisites for Stabilizing Long-Range Synergistic Interactions amongBiochemistry · 2022Article
- Production of an Active, Human Membrane Protein inInternational journal of molecular sciences · 2022Article
- Critical assessment of coiled-coil predictions based on protein structure data.Scientific reports · 2021Article
- A new type of flexible CP12 protein in the marine diatom Thalassiosira pseudonana.Cell communication and signaling : CCS · 2021Article
- Prediction of Protein-Protein Binding Interactions in Dimeric Coiled Coils by Information Contained in Folding Energy Landscapes.International journal of molecular sciences · 2021Article
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- Tunable Protein Hydrogels: Present State and Emerging Development.Advances in biochemical engineering/biotechnology · 2021Article
- Self-Assembly and Genetically Engineered Hydrogels.Advances in biochemical engineering/biotechnology · 2021Review
45 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
More than 30 organisms have been sequenced entirely. Here, we applied a variety of simple bioinformatics tools to analyze 29 proteomes for representatives from all three kingdoms: eukaryotes, prokaryotes, and archaebacteria. We confirmed that eukaryotes have relatively more long proteins than prokaryotes and archaes, and that the overall amino acid composition is similar among the three. We predicted that approximately 15%-30% of all proteins contained transmembrane helices. We could not find a correlation between the content of membrane proteins and the complexity of the organism. In particular, we did not find significantly higher percentages of helical membrane proteins in eukaryotes than in prokaryotes or archae. However, we found more proteins with seven transmembrane helices in eukaryotes and more with six and 12 transmembrane helices in prokaryotes. We found twice as many coiled-coil proteins in eukaryotes (10%) as in prokaryotes and archaes (4%-5%), and we predicted approximately 15%-25% of all proteins to be secreted by most eukaryotes and prokaryotes. Every tenth protein had no known homolog in current databases, and 30%-40% of the proteins fell into structural families with >100 members. A classification by cellular function verified that eukaryotes have a higher proportion of proteins for communication with the environment. Finally, we found at least one homolog of experimentally known structure for approximately 20%-45% of all proteins; the regions with structural homology covered 20%-30% of all residues. These numbers may or may not suggest that there are 1200-2600 folds in the universe of protein structures. All predictions are available at http://cubic.bioc.columbia.edu/genomes.
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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.