ArticleGenome biology and evolution2012
The plant proteome folding project: structure and positive selection in plant protein families.
Article in Genome biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed, 14 citations in OpenAlex.
- SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation.Communications biology · 2020Article
- Applying evolutionary genetics to developmental toxicology and risk assessment.Reproductive toxicology (Elmsford, N.Y.) · 2017Review
- Sucrose metabolism gene families and their biological functions.Scientific reports · 2015Article
- Rapid diversification of five Oryza AA genomes associated with rice adaptation.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Article
- Saffron'omics': The challenges of integrating omic technologies.Avicenna journal of phytomedicineReview
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite its importance, relatively little is known about the relationship between the structure, function, and evolution of proteins, particularly in land plant species. We have developed a database with predicted protein domains for five plant proteomes (http://pfp.bio.nyu.edu) and used both protein structural fold recognition and de novo Rosetta-based protein structure prediction to predict protein structure for Arabidopsis and rice proteins. Based on sequence similarity, we have identified ~15,000 orthologous/paralogous protein family clusters among these species and used codon-based models to predict positive selection in protein evolution within 175 of these sequence clusters. Our results show that codons that display positive selection appear to be less frequent in helical and strand regions and are overrepresented in amino acid residues that are associated with a change in protein secondary structure. Like in other organisms, disordered protein regions also appear to have more selected sites. Structural information provides new functional insights into specific plant proteins and allows us to map positively selected amino acid sites onto protein structures and view these sites in a structural and functional context.
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Registered trials
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