An improved understanding of TNFL/TNFR interactions using structure-based classifications

Tumor Necrosis Factor Ligand (TNFL)–Tumor Necrosis Factor Receptor (TNFR) interactions control key cellular processes; however, the molecular basis of the specificity of these interactions remains poorly understood. Using the T-RMSD (tree based on root mean square deviation), a newly developed struc...

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Bibliographic Details
Published in:Trends in biochemical sciences (Amsterdam. Regular ed.) 2012-09, Vol.37 (9), p.353-363
Main Authors: Magis, Cedrik, van der Sloot, Almer M., Serrano, Luis, Notredame, Cedric
Format: Article
Language:English
Subjects:
Animals
coevolution
cysteine
evolution
Humans
Ligands
MSA
Phylogeny
Protein Interaction Domains and Motifs
Receptors, Tumor Necrosis Factor - chemistry
Receptors, Tumor Necrosis Factor - genetics
Receptors, Tumor Necrosis Factor - metabolism
structure-activity relationships
structure-based classification
TNFL
TNFR
tumor necrosis factors
Tumor Necrosis Factors - chemistry
Tumor Necrosis Factors - metabolism
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Summary:Tumor Necrosis Factor Ligand (TNFL)–Tumor Necrosis Factor Receptor (TNFR) interactions control key cellular processes; however, the molecular basis of the specificity of these interactions remains poorly understood. Using the T-RMSD (tree based on root mean square deviation), a newly developed structure-based sequence clustering method, we have re-analyzed the available structural data to re-interpret the interactions between TNFLs and TNFRs. This improves the classification of both TNFLs and TNFRs, such that the new groups defined here are in much stronger agreement with structural and functional features than existing schemes. Our clustering approach also identifies traces of a convergent evolutionary process for TNFLs and TNFRs, leading us to propose the co-evolution of TNFLs and the third cysteine rich domain (CRD) of large TNFRs.
ISSN:0968-0004
1362-4326
DOI:10.1016/j.tibs.2012.06.002