Unraveling the structural landscape of intra-chain domain interfaces: Implication in the evolution of domain-domain interactions

PloS One
Rivi Verma, Shashi Bhushan Pandit

Abstract

Intra-chain domain interactions are known to play a significant role in the function and stability of multidomain proteins. These interactions are mediated through a physical interaction at domain-domain interfaces (DDIs). With a motivation to understand evolution of interfaces, we have investigated similarities among DDIs. Even though interfaces of protein-protein interactions (PPIs) have been previously studied by structurally aligning interfaces, similar analyses have not yet been performed on DDIs of either multidomain proteins or PPIs. For studying the structural landscape of DDIs, we have used iAlign to structurally align intra-chain domain interfaces of domains. The interface alignment of spatially constrained domains (due to inter-domain linkers) showed that ~88% of these could identify a structural matching interface having similar C-alpha geometry and contact pattern despite that aligned domain pairs are not structurally related. Moreover, the mean interface similarity score (IS-score) is 0.307, which is higher compared to the average random IS-score (0.207) suggesting domain interfaces are not random. The structural space of DDIs is highly connected as ~84% of all possible directed edges among interfaces are found to...Continue Reading

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Citations

Nov 10, 2020·Protein Science : a Publication of the Protein Society·Anna HadarovichIlya A Vakser

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Software Mentioned

BLAST
i Align
SURFNET
iAlign
PSI
digrah
SMART
align
TM

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