A vocabulary of ancient peptides at the origin of folded proteins

Alva, Vikram; Söding, Johannes; Lupas, Andrei N.

doi:10.7554/elife.09410

Cited by 230 publications

(294 citation statements)

References 94 publications

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“…the mineralocorticoid receptor (9)). It is widely accepted that structural and functional complexity in domains evolved through fusion, recombination, accretion and repetition of a very small set of elementary functions (10,11). Therefore, units in tandem repeat proteins represent a fundamental source of information to explain contemporary structural diversity and the physico-chemical properties of highly designable folds (12).…”

Section: Introductionmentioning

confidence: 99%

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures

Paladin¹,

Hirsh²,

Piovesan³

et al. 2016

Nucleic Acids Res

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RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by an extensive manual validation for >60% of the entries. The updated web interface includes a new search engine for complex queries and a fully re-designed entry page for a better overview of structural data. It is now possible to compare unit positions, together with secondary structure, fold information and Pfam domains. Moreover, a new classification level has been introduced on top of the existing scheme as an independent layer for sequence similarity relationships at 40%, 60% and 90% identity.

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Section: Introductionmentioning

confidence: 99%

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures

Paladin¹,

Hirsh²,

Piovesan³

et al. 2016

Nucleic Acids Res

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show abstract

“…It is likely that extant protein structures evolved from the repetition of simpler domains that were assembled gradually through mechanisms of genetic recombination [21,22]. …”

Section: Evolutionary Strategies To Expand the Functional Boundarimentioning

confidence: 99%

What Froze the Genetic Code?

Pouplana

Torres

Rafels-Ybern

2017

Life

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The frozen accident theory of the Genetic Code was a proposal by Francis Crick that attempted to explain the universal nature of the Genetic Code and the fact that it only contains information for twenty amino acids. Fifty years later, it is clear that variations to the universal Genetic Code exist in nature and that translation is not limited to twenty amino acids. However, given the astonishing diversity of life on earth, and the extended evolutionary time that has taken place since the emergence of the extant Genetic Code, the idea that the translation apparatus is for the most part immobile remains true. Here, we will offer a potential explanation to the reason why the code has remained mostly stable for over three billion years, and discuss some of the mechanisms that allow species to overcome the intrinsic functional limitations of the protein synthesis machinery.

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“…For example, Kolodny and co-workers modeled domain space as a network, where domains were connected by sub-regions of similar structure and sequence, showing that this space is modular with regions of both low and high connectivity [8]. In another recent analysis of sub-domain modularity, Lupas and colleagues discovered a set of 40 super-secondary motifs representing possible remnants of a primordial RNA-peptide world by looking for similar sequence-structure patterns across unrelated proteins [9]. …”

Section: Introductionmentioning

confidence: 99%

Protein structural motifs in prediction and design

Mackenzie

Grigoryan

2017

Current Opinion in Structural Biology

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The Protein Data Bank (PDB) has been an integral resource for shaping our fundamental understanding of protein structure and for the advancement of such applications as protein design and structure prediction. Over the years, information from the PDB has been used to generate models ranging from specific structural mechanisms to general statistical potentials. With accumulating structural data, it has become possible to mine for more complete and complex structural observations, deducing more accurate generalizations. Motif libraries, which capture recurring structural features along with their sequence preferences, have exposed modularity in the structural universe and found successful application in various problems of structural biology. Here we summarize recent achievements in this arena, focusing on sub-domain level structural patterns and their applications to protein design and structure prediction, and suggest promising future directions as the structural database continues to grow.

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A vocabulary of ancient peptides at the origin of folded proteins

Cited by 230 publications

References 94 publications

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures

What Froze the Genetic Code?

Protein structural motifs in prediction and design

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