ArticlePloS one2009
Length variations amongst protein domain superfamilies and consequences on structure and function.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
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- Learning the protein language of proteome-wide protein-protein binding sites via explainable ensemble deep learning.Communications biology · 2023Article
- Protposer: The web server that readily proposes protein stabilizing mutations with high PPV.Computational and structural biotechnology journal · 2022Article
- Identification and characterization of MADS box gene family in pigeonpea for their role during floral transition.3 Biotech · 2021Article
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- A tyrosinase, mTyr-CNK, that is functionally available as a monophenol monooxygenase.Scientific reports · 2017Article
- Measuring Accelerated Rates of Insertions and Deletions Independent of Rates of Nucleotide Substitution.Journal of molecular evolution · 2016Article
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- Diversity in protein domain superfamilies.Current opinion in genetics & development · 2015Review
- The Recent De Novo Origin of Protein C-Termini.Genome biology and evolution · 2015Article
- Domain atrophy creates rare cases of functional partial protein domains.Genome biology · 2015Article
- ProteinVolume: calculating molecular van der Waals and void volumes in proteins.BMC bioinformatics · 2015Article
- Use of a structural alphabet to find compatible folds for amino acid sequences.Protein science : a publication of the Protein Society · 2015Article
- Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
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7 authors.
Funding
Abstract
backgroundRelated protein domains of a superfamily can be specified by proteins of diverse lengths. The structural and functional implications of indels in a domain scaffold have been examined. METHODOLOGY: In this study, domain superfamilies with large length variations (more than 30% difference from average domain size, referred as 'length-deviant' superfamilies and 'length-rigid' domain superfamilies (<10% length difference from average domain size) were analyzed for the functional impact of such structural differences. Our delineated dataset, derived from an objective algorithm, enables us to address indel roles in the presence of peculiar structural repeats, functional variation, protein-protein interactions and to examine 'domain contexts' of proteins tolerant to large length variations. Amongst the top-10 length-deviant superfamilies analyzed, we found that 80% of length-deviant superfamilies possess distant internal structural repeats and nearly half of them acquired diverse biological functions. In general, length-deviant superfamilies have higher chance, than length-rigid superfamilies, to be engaged in internal structural repeats. We also found that approximately 40% of length-deviant domains exist as multi-domain proteins involving interactions with domains from the same or other superfamilies. Indels, in diverse domain superfamilies, were found to participate in the accretion of structural and functional features amongst related domains. With specific examples, we discuss how indels are involved directly or indirectly in the generation of oligomerization interfaces, introduction of substrate specificity, regulation of protein function and stability.
conclusionsOur data suggests a multitude of roles for indels that are specialized for domain members of different domain superfamilies. These specialist roles that we observe and trends in the extent of length variation could influence decision making in modeling of new superfamily members. Likewise, the observed limits of length variation, specific for each domain superfamily would be particularly relevant in the choice of alignment length search filters commonly applied in protein sequence analysis.
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