ArticleProceedings of the National Academy of Sciences of the United States of America2004
Global analysis of predicted proteomes: functional adaptation of physical properties.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 75 citations in OpenAlex.
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- Protein pI and Intracellular Localization.Frontiers in molecular biosciences · 2021Review
- Localization-specific distributions of protein pI in human proteome are governed by local pH and membrane charge.BMC molecular and cell biology · 2019Article
- The molecular mass and isoelectric point of plant proteomes.BMC genomics · 2019Article
- Misprediction of Structural Disorder in Halophiles.Molecules (Basel, Switzerland) · 2019Article
- Marginal protein stability drives subcellular proteome isoelectric point.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Local and global anatomy of antibody-protein antigen recognition.Journal of molecular recognition : JMR · 2018Article
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- Improvement of Mitochondria Extract from Saccharomyces cerevisiae Characterization in Shotgun Proteomics Using Sheathless Capillary Electrophoresis Coupled to Tandem Mass Spectrometry.Journal of chromatographic science · 2016Article
- Limitation of tuning the antibody-antigen reaction by changing the value of pH and its consequence for hyperthermia.Journal of biochemistry · 2016Article
- Interactions of proteins with biogenic iron oxyhydroxides and a new culturing technique to increase biomass yields of neutrophilic, iron-oxidizing bacteria.Frontiers in microbiology · 2014Article
- Function-valued traits in evolution.Journal of the Royal Society, Interface · 2013Article
- Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome.Proteomics · 2013Article
- Systematic comparison of ultraviolet photodissociation and electron transfer dissociation for peptide anion characterization.Journal of the American Society for Mass Spectrometry · 2012Article
- A theoretical and experimental proteome map of Pseudomonas aeruginosa PAO1.MicrobiologyOpen · 2012Article
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4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The physical characteristics of proteins are fundamentally important in organismal function. We used the complete predicted proteomes of >100 organisms spanning the three domains of life to investigate the comparative biology and evolution of proteomes. Theoretical 2D gels were constructed with axes of protein mass and charge (pI) and converted to density estimates comparable across all types and sizes of proteome. We asked whether we could detect general patterns of proteome conservation and variation. The overall pattern of theoretical 2D gels was strongly conserved across all life forms. Nevertheless, coevolved replicons from the same organism (different chromosomes or plasmid and host chromosomes) encode proteomes more similar to each other than those from different organisms. Furthermore, there was disparity between the membrane and nonmembrane subproteomes within organisms (proteins of membrane proteomes are on the average more basic and heavier) and their variation across organisms, suggesting that membrane proteomes evolve most rapidly. Experimentally, a significant positive relationship independent of phylogeny was found between the predicted proteome and Biolog profile, a measure associated with the ecological niche. Finally, we show that, for the smallest and most alkaline proteomes, there is a negative relationship between proteome size and basicity. This relationship is not adequately explained by AT bias at the DNA sequence level. Together, these data provide evidence of functional adaptation in the properties of complete proteomes.
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