How old is your fold?

Winstanley, H.F.; Abeln, Sanne; Deane, Charlotte M.

doi:10.1093/bioinformatics/bti1008

Cited by 65 publications

(76 citation statements)

References 26 publications

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“…This is consistent with the random origin hypothesis of proteins (192). A similar conclusion was recently reached when tracing fold occurrence along branches of proteome trees (193). Remarkably, the most ancestral folds harbored interleaved beta-sheets and alpha-helices and barrel structures, many important structural designs were derived in the tree (including polyhedral folds in the all-alpha class and betasandwiches, beta-propellers and beta-prisms in the all-beta class), and protein transformation pathways describing likely scenarios of structural evolution (194,195) and other patterns could be traced in the trees (18).…”

Section: Evolution Of Domain Structure and Organizationsupporting

confidence: 90%

Origins and evolution of modern biochemistry: insights from genomes and molecular structure

et al. 2008

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Section: Evolution Of Domain Structure and Organizationsupporting

confidence: 90%

Origins and evolution of modern biochemistry: insights from genomes and molecular structure

et al. 2008

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“…This is particularly true for adenine-binding folds studied here. They are found throughout fold space and have been predicated among the most ancient folds by several studies (12,13,(65)(66)(67)(68). It is possible that a small molecule containing an adenine fragment was the first ligand recognized by a protein (69).…”

Section: Discussionmentioning

confidence: 99%

“…A central question is: What were the early protein folds and how did these folds change over long evolutionary time scales (4-7)? Comparative genomics studies and structural and phylogenetic analyses (8)(9)(10) have established that a subset of proteins, dominated by the structure classification of proteins (SCOP) (11) ␣/␤ class, were likely present in the last universal common ancestor (12,13). Concurrently, growing evidence suggests that recurring substructures, that is, 3D fragments of noncontiguous sequence shared between different folds, may be clues that protein fold space is more continuous than discreet (14,15).…”

mentioning

confidence: 99%

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile–profile alignments

Xie

Bourne²

2008

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

237

284

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Here, a scalable, accurate, reliable, and robust protein functional site comparison algorithm is presented. The key components of the algorithm consist of a reduced representation of the protein structure and a sequence order-independent profile-profile alignment (SOIPPA). We show that SOIPPA is able to detect distant evolutionary relationships in cases where both a global sequence and structure relationship remains obscure. Results suggest evolutionary relationships across several previously evolutionary distinct protein structure superfamilies. SOIPPA, along with an increased coverage of protein fold space afforded by the structural genomics initiative, can be used to further test the notion that fold space is continuous rather than discrete.functional site ͉ structure T he evolutionary relationship between protein sequences, protein structures, and their associated function(s) remains a central topic of molecular biology and one resulting in the development of many computational methods (1-3). A central question is: What were the early protein folds and how did these folds change over long evolutionary time scales (4-7)? Comparative genomics studies and structural and phylogenetic analyses (8-10) have established that a subset of proteins, dominated by the structure classification of proteins (SCOP) (11) ␣/␤ class, were likely present in the last universal common ancestor (12, 13). Concurrently, growing evidence suggests that recurring substructures, that is, 3D fragments of noncontiguous sequence shared between different folds, may be clues that protein fold space is more continuous than discreet (14, 15). The sequence/ structure similarity of such substructures correlates well with the similarity of function found between the different folds containing these substructures (16). The notion that protein fold space is a continuum is further supported by recent studies that show that protein domains can adopt different topologies through combination, swapping, deletion (4, 17, 18), and cyclic permutation (19, 20) of subdomains. Likewise, new folds can emerge from accretion (21) or embellishment (22) of substructures around a core of conserved secondary structures. Given these findings concerning the dynamic nature of protein structure and the possible continuous nature of protein fold space, it is important to distinguish proteins that share a common ancestor (divergent evolution) from those that have adopted common structural constraints (convergent evolution).Typically, evolutionary relationships between protein sequence, structure, and function are deduced from the respective comparisons among known genes and their products. These comparisons are made at various levels, from genome sequences to protein domains and motifs to biochemical pathways. Such comparisons may miss important relationships because sequence relationships may be too weak to detect, and/or fail to identify complex evolutionary events such as domain swapping and cyclic permutation. Likewise, differences in global protein structure may disgu...

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“…Some of our conclusion is consistent with others. For example, the ␣͞␤ class proteins as the most ancient proteins also have been suggested by parsimonious scenario of fold occurrence in genomes (20), and birth, death, and diversification of genes have been described in ref. 21.…”

Section: Discussionmentioning

confidence: 99%

Evolution of protein structural classes and protein sequence families

Choi

Kim

2006

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

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In protein structure space, protein structures cluster into four elongated regions when mapped based solely on similarity among the 3D structures. These four regions correspond to the four major classes of present-day proteins defined by the contents of secondary structure types and their topological arrangement. Evolution of and restriction to these four classes suggest that, in most cases, the evolution of genes may have been constrained or selected to those genetic changes that results in structurally stable proteins occupying one of the four ''allowed'' regions of the protein structure space, ''structural selection,'' an important component of natural selection in gene evolution. Our studies on tracing the ''common structural ancestor'' for each protein sequence family of known structure suggest that: (i) recently emerged proteins belong mostly to three classes; (ii) the proteins that emerged earlier evolved to gain a new class; and (iii) the proteins that emerged earliest evolved to become the present-day proteins in the four major classes, with the fourth-class proteins becoming the most dominant population. Furthermore, our studies also show that not all present-day proteins evolved from one single set of proteins in the last common ancestral organism, but new common ancestral proteins were ''born'' at different evolutionary times, not traceable to one or two ancestral proteins: ''the multiple birth model'' for the evolution of protein sequence families.protein fold classes ͉ common structural ancestor ͉ evolutionary age ͉ protein structure universe

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How old is your fold?

Abstract: http://www.stats.ox.ac.uk/~abeln/foldage.

Cited by 65 publications

References 26 publications

Origins and evolution of modern biochemistry: insights from genomes and molecular structure

Origins and evolution of modern biochemistry: insights from genomes and molecular structure

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile–profile alignments

Evolution of protein structural classes and protein sequence families

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