From protein sequence space to elementary protein modules

Frenkel, Zakharia M.; Trifonov, Edward N.

doi:10.1016/j.gene.2007.10.024

Cited by 12 publications

(6 citation statements)

References 30 publications

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“…Such similarities have also been described as protein motifs ( 16 , 49 – 52 ). To better understand the evolution of proteins, Lupas and coworkers ( 1 , 3 ) documented shared segments, referred to as “antecedent domain segments.” Following a similar reasoning, Frenkel and coworker ( 53 , 54 ) described the reuse of (very) short protein segments, referred to as “modalities,” and Goncearenco and Berezovsky ( 55 , 56 ) examined reuse of closed rings referred to as “elementary functional loops.”…”

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confidence: 99%

Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

Nepomnyachiy

Ben‐Tal

Kolodny

2017

Proc. Natl. Acad. Sci. U.S.A.

105

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SignificanceWe question a central paradigm: namely, that the protein domain is the “atomic unit” of evolution. In conflict with the current textbook view, our results unequivocally show that duplication of protein segments happens both above and below the domain level among amino acid segments of diverse lengths. Indeed, we show that significant evolutionary information is lost when the protein is approached as a string of domains. Our finer-grained approach reveals a far more complicated picture, where reused segments often intertwine and overlap with each other. Our results are consistent with a recursive model of evolution, in which segments of various lengths, typically smaller than domains, “hop” between environments. The fit segments remain, leaving traces that can still be detected.

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confidence: 99%

Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

Nepomnyachiy

Ben‐Tal

Kolodny

2017

Proc. Natl. Acad. Sci. U.S.A.

105

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“…The protein modules that are the most conserved since the last universal common ancestor (LUCA) correspond to closed loops [51]. Recently all prokaryotic proteins were decomposed into 20 residue fragments (possible closed loops) and clustered based on an identity threshold [52]. The authors found that fragments that corresponded to closed loops were more likely to form large clusters.…”

Section: Is the Domain The Correct Unit Of Classification?mentioning

confidence: 99%

Nothing about protein structure classification makes sense except in the light of evolution

Valas

Yang

Bourne

2009

Current Opinion in Structural Biology

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In this the 200th anniversary of Charles Darwin’s birth and the 150th anniversary of the publication of the Origin of Species it is fitting to revisit the classification of protein structures from an evolutionary perspective. Existing classifications use homologous sequence relationships, but knowing that structure is much more conserved that sequence creates an iterative loop from which structures can be further classified beyond that of the domain, thereby teasing out distant evolutionary relationships. The desired classification scheme is then one in which a fold is merely semantics and structure can be classified as either ancestral or derived.

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“…This exercise can be performed because translational machinery is conserved across all modern cellular life forms 55 and because the protein code 56 is something that is absolute in essence. 57,58 The protein code is partially due to the periodicity of secondary structures, but it is also due to the periodicity of hydrophobic amino acids in proteins. 59 P. falciparum (GC-poor) and C. reinhardtii (GC-rich) have genomes that exist at both extremities of GC variation among eukaryotes, while the H. sapiens genome occurs between these extremes.…”

Section: Discussionmentioning

confidence: 99%

An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences

Carels

León

2015

Bioinform Biol Insights

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Purine bias, which is usually referred to as an “ancestral codon”, is known to result in short-range correlations between nucleotides in coding sequences, and it is common in all species. We demonstrate that RWY is a more appropriate pattern than the classical RNY, and purine bias (Rrr) is the product of a network of nucleotide compensations induced by functional constraints on the physicochemical properties of proteins. Through deductions from universal correlation properties, we also demonstrate that amino acids from Miller’s spark discharge experiment are compatible with functional primeval proteins at the dawn of living cell radiation on earth. These amino acids match the hydropathy and secondary structures of modern proteins.

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From protein sequence space to elementary protein modules

Cited by 12 publications

References 30 publications

Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

Nothing about protein structure classification makes sense except in the light of evolution

An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences

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