Evolution of function in protein superfamilies, from a structural perspective.

By Annabel E. Todd, Christine A. Orengo, Janet M. Thornton. Journal of Molecular Biology, 2001

727 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/86d1a7b2d77fc52e7485392af85ec54ce04019dc

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In Materials Chemistry

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Citations in the corpus

Searching ECOD for homologous domains by sequence and structure (2018, background): “Domains within an H-group may perform similar reactions on differing substrates (Todd et al., 2001).”
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies (2009, background): “Previously, others have shown that annotation transfer at low levels of similarity greatly increase the likelihood of incorrect function annotation [53–55].”
Identification and distribution of protein families in 120 completed genomes using Gene3D (2005, background): “As discussed above, changes in the domain architectures of these proteins often modulate the functions of the domains 31 and this is clearly an important mechanism for expanding the functional repertoire of an organism.”
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data (2004, background): “Previous analysis (11) has shown that catalytic residues can be conserved in structure but not in sequence.”
Recognizing protein substructure similarity using segmental threading. (2010, background): “Moreover, since the gregarious proteins have usually different global folds, the conserved substructure motifs may reflect ancient evolutionary relationships and therefore are associated with special functional consequences (Harrison et al., 2002; Todd et al., 2001).”
A census of human transcription factors: function, expression and evolution (2009, background): “Previous studies of enzymes have shown that pairs of proteins with sequence similarities above 40% tend to share the same catalytic activit”
Analysis of protein sequence/structure similarity relationships. (2002, background): “(high sequence but low structural similarity) is well-represented by proteins that can accommodate large structural changes.”
mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements (2021, methodology): “The 40% identity cut-off is used by the enzyme commission to determine whether a protein fold retains the same function as a reference fold (52).”
Predicting protein function from sequence and structure (2007, background): “What level of sequence similarity within a protein family provides a safe threshold for inheriting functional annotation? In an early study of CATH enzyme superfamilie”
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007, background): “Despite many efforts to classify and organize proteins [1–6] from both structural and functional perspectives, we are far from a clear understanding of the size and diversity of the protein universe [7–9].”
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction (2006, background): “Homology-based methods for structure prediction rely on the observation that proteins that share a common ancestor will usually have similar sequences, and that, in turn, similar protein sequences produce proteins with similar fold and (often) similar functions [8].”
Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain (2010, background): “Large-scale database analysis has revealed that down to 30% sequence identity active site chemistry in protein superfamilies is maintained (5).”
UniqueProt: creating representative protein sequence sets (2003, background): “In fact, while such inferences are accurate for high levels of pairwise sequence similarity, they become accurate rather rapidly with the level of divergence between the two proteins (1,2).”