Comparative analysis of permanent and transient domain-domain
interactions in multi-domain proteins
Protein domains are structural, functional, and evolutionary units.
These domains bring out the diversity of functionality by means of
interactions with other co-existing domains and provide stability.
Hence, it is important to study intra-protein inter-domain interactions
from the perspective of types of interactions. Domains within a chain
could interact over short timeframes or permanently, rather like
protein-protein interactions (PPIs). However, no systematic study has
been carried out between two classes, namely permanent and transient
domain-domain interactions (DDIs). In this work, we studied 264
two-domain proteins, belonging to either of these classes and their
interfaces on the basis of several factors, such as interface area and
details of interactions (number, strengths, and types of interactions).
We also characterized them based on residue conservation at the
interface, correlation of residue motions across domains, its
involvement in repeat formation, and their involvement in particular
molecular processes. Finally, we could analyse the interactions arising
from domains in two-domain monomeric proteins, and we observed
significant differences between these two classes of domain interactions
and a few similarities. This study will help to obtain a better
understanding of structure-function and folding principles of