The structure of the protein universe and genome evolution

By Eugene V. Koonin, Yuri I. Wolf, G. Karev. Nature, 2002

585 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/a3f94235a6cf8a5954cc63d3b29ad4fdcd9faeb6

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In Molecular Biology

Citations in the corpus

Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655 (2003, background): “It is widely recognized that the thousands of components of a living cell are dynamically interconnected, so that cellular functional properties are a result of the complex intracellular web of molecular interactions within the cell (14, 22, 23).”
The Phyre2 web portal for protein modelling, prediction and analysis (2015, background): “The key principles on which such techniques work are: (i) that protein structure is more conserved in evolution than protein sequence, and (ii) that there is evidence of a finite and relatively small (1,000–10,000) number of unique protein folds in nature 2 .”
Network-based prediction of protein interactions (2018, background): “S8) and the Preferential Attachment principle (PA) [18, 19], a link prediction method that mimics unspecific binding between ”sticky” proteins by placing a link between two nodes with a score given by the”
Grammar of protein domain architectures (2019, background): “Protein domains are structural, functional, and evolutionary units of proteins (9, 10) and are thus analogous to words.”
The properties of protein family space depend on experimental design (2005, background): “Distribution of protein family sizes in protein families databases The size distributions of protein families, superfamilies and folds was shown to follow a power law in many individual genomes (13-15) and globally for all genomes in an analysis of the protein families in the TRIBES database (7).”
Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics (2014, background): “Second, some folds are highly represented while others are rare, giving rise to a distribution of usage of protein folds in a genome that is skewed and uneven [53].”
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. (2004, background): “The systematic comparative genome analysis (i) allows us to get insight into the evolutionary principles of gene duplication and gene loss (35) and (ii) permits to formulate hypotheses and subsequently to perform instructive experiments to unravel novel insights into the lifestyle of organisms.”
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.”
Scaling Laws in the Functional Content of Genomes (2003, background): “Power-law distributions are also found in the structure of the ‘protein universe’ [12]; the number of protein families per fold is power-law distributed, and so is the number of different assigned biological functions per fold [13].”
Green function of correlated genes in a minimal mechanical model of protein evolution (2018, methodology): “The epistasis Eij and the gene correlation Qij show similar patterns.”