Rapid motif-based prediction of circular permutations in multi-domain proteins

Weiner, January; Thomas, Geraint; Bornberg‐Bauer, Erich

doi:10.1093/bioinformatics/bti085

Cited by 33 publications

(39 citation statements)

References 26 publications

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“…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.…”

mentioning

confidence: 59%

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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mentioning

confidence: 59%

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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“…Interesting developments have also been made in this direction. A few alignment-free techniques were developed for this purpose [72,73], while the majority of methods that employ sequence-order-independent comparisons are optimized for multi-domain proteins [74][75][76][77].…”

Section: Evolutionary Information: Profile -Profile Alignmentsmentioning

confidence: 99%

From local structure to a global framework: recognition of protein folds

Joseph

Brevern

2014

J. R. Soc. Interface.

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Protein folding has been a major area of research for many years. Nonetheless, the mechanisms leading to the formation of an active biological fold are still not fully apprehended. The huge amount of available sequence and structural information provides hints to identify the putative fold for a given sequence. Indeed, protein structures prefer a limited number of local backbone conformations, some being characterized by preferences for certain amino acids. These preferences largely depend on the local structural environment. The prediction of local backbone conformations has become an important factor to correctly identifying the global protein fold. Here, we review the developments in the field of local structure prediction and especially their implication in protein fold recognition.

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“…After duplication, a subdomain swap could create the compact domains, and deletion of the termini (the domain) would leave the domain, which would appear as a CP in the sequence. The extent of rotation through the sequence would depend on the relative sizes of A and B. Globular Proteins Using a sequence alignment algorithm designed to detect cyclic permutation, Weiner and colleagues (Weiner et al, 2005) describe some novel examples and make the distinction between proper CPs as described above and incomplete CPs, where the deletion has been made at only one of the termini. The permutations examined in this way all occur at the level of intact domains in multidomain proteins, and it is always possible that other mechanisms of gene rearrangement (such as exon shuffling) might produce the same change.…”

Section: Cyclic Permutationmentioning

confidence: 99%