Comparing function and structure between entire proteomes

By Jinfeng Liu, Burkhard Rost. 2001

283 citations recorded by the source corpus.

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 ∼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 ∼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 ∼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.

Subfields: Molecular Biology

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Citations in the corpus

Analysis of molecular recognition features (MoRFs). (2006, background): “This increased prediction of disorder in eukaryotes compared with the prokaryotes or the archaea has been hypothesized to be a consequence of the increased need for cell signaling and regulation.(15,22,24,25) The functional importance of protein disorder is further emphasized by its role in various ”
Better prediction of sub‐cellular localization by combining evolutionary and structural information (2003, background): “For entire genomes, this number has previously been estimated to be at most half this size.(9,32)”
The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database (2022, unknown): “To uncover the connection between organism evolution and protein evolution (Liu and Rost 2001; Koonin et al. 2002; Pál et al. 2006; Zeldovich and Shakhnovich 2008; Sikosek and Chan 2014), combining the view of evolution from two perspectives may be necessary.”
Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling (2005, background): “kingdoms has been suggested to be a consequence of the increased need for cell signaling and regulation (Dunker et al., 2000, 2001; Liu and Rost, 2001; Iakoucheva et al., 2002; Vucetic et al., 2003).”
Flexible nets (2005, background): “To explain this and similar observations, it was hypothesized that the higher abundance of intrinsic disorder in eukaryotes could be a consequence of the increased need for cell signaling and regulation in higher organisms [34,35,58,60,63,64].”
Mimicking cellular sorting improves prediction of subcellular localization. (2005, background): “Overall, known and predicted sequence motifs enable annotating about 30% of the proteins in six entirely sequenced eukaryotic proteomes.(4,41,42) Other methods that can be reliably used to annotate localization but are not always applicable are annotation transfer from sequence homologues(43) and te”
Multipass membrane protein structure prediction using Rosetta (2005, unknown): “1 Helical TM proteins are predicted to encode 20–30% of all open reading frames of known genomes 2–4 ; however, currently, all types of membrane proteins represent only about 0.6% (168 5 of 28,000) of solved protein structures in the Protein Data Bank (PDB).”
From primordial clocks to circadian oscillators (2023, background): “Given that this simple heptad repeat sequence emerged multiple times and is found throughout all kingdoms of life 35 , it is an example of convergent evolution.”
Computational modeling of membrane proteins (2014, background): “109,110 Even though a variety of sequence-based techniques exists for this subclass of proteins, de novo structure prediction remains challenging, especially for large MPs.”