ArticlePloS one2012
Analysis of domain-swapped oligomers reveals local sequence preferences and structural imprints at the linker regions and swapped interfaces.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Comparative molecular dynamics simulations of pathogenic and non-pathogenic huntingtin protein monomers and dimers.Frontiers in molecular biosciences · 2023Article
- Human FoxP Transcription Factors as Tractable Models of the Evolution and Functional Outcomes of Three-Dimensional Domain Swapping.International journal of molecular sciences · 2021Review
- Monothiol and dithiol glutaredoxin-1 fromIUCrJ · 2020Article
- A five-residue motif for the design of domain swapping in proteins.Nature communications · 2019Article
- An acidic model pro-peptide affects the secondary structure, membrane interactions and antimicrobial activity of a crotalicidin fragment.Scientific reports · 2018Article
- Exploring the Roles of Proline in Three-Dimensional Domain Swapping from Structure Analysis and Molecular Dynamics Simulations.The protein journal · 2018Article
- Amino-acid composition after loop deletion drives domain swapping.Protein science : a publication of the Protein Society · 2017Article
- Understanding protein domain-swapping using structure-based models of protein folding.Progress in biophysics and molecular biology · 2017Review
- Article
- Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information.PloS one · 2016Article
- Energetic Calculations to Decipher pH-Dependent Oligomerization and Domain Swapping of Proteins.PloS one · 2015Article
- Essential role of the C-terminal helical domain in active site formation of selenoprotein MsrA from Clostridium oremlandii.PloS one · 2015Article
- Article
- Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization.Progress in molecular biology and translational science · 2013Review
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2 authors.
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Abstract
background3D domain swapping is an oligomerization process in which structural elements get exchanged between subunits. This mechanism grasped interest of many researchers due to its association with neurodegenerative diseases like Alzheimer's disease, spongiform encephalopathy etc. Despite the biomedical relevance, very little is known about understanding this mechanism. The quest for ruling principles behind this curious phenomenon that could enable early prediction provided an impetus for our bioinformatics studies. METHODOLOGY: A novel method, HIDE, has been developed to find non-domain-swapped homologues and to identify hinge from domain-swapped oligomers. Non-domain-swapped homologues were identified from the protein structural databank for majority of the domain-swapped entries and hinge boundaries could be recognised automatically by means of successive superposition techniques. Different sequence and structural features in domain-swapped proteins and related proteins have also been analysed.
conclusionsThe HIDE algorithm was able to identify hinge region in 83% cases. Sequence and structural analyses of hinge and interfaces reveal amino acid preferences and specific conformations of residues at hinge regions, while comparing the domain-swapped and non-domain-swapped states. Interactions differ significantly between regular dimeric interfaces and interface formed at the site of domain-swapped examples. Such preferences of residues, conformations and interactions could be of predictive value.
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