A coarse-grained model for disordered and multi-domain proteins

Many proteins contain more than one folded domain, and such modular multi-domain proteins help expand the functional repertoire of proteins. Because of their larger size and often substantial dynamics, it may be difficult to characterize the conformational ensembles of multi-domain proteins by simulations. Here, we present a coarse-grained model for multi-domain proteins that is both fast and provides an accurate description of the global conformational properties in solution. We show that the accuracy of a one-bead-per-residue coarse-grained model depends on how the interaction sites in the folded domains are represented. Specifically, we find excessive domain-domain interactions if the interaction sites are located at the position of the Cα atoms. We also show that if the interaction sites are located at the center of mass of the residue, we obtain good agreement between simulations and experiments across a wide range of proteins. We then optimize our previously described CALVADOS model using this center-of-mass representation, and validate the resulting model using independent data. Finally, we use our revised model to simulate phase separation of both disordered and multi-domain proteins, and to examine how the stability of folded domains may differ between the dilute and dense phases. Our results provide a starting point for understanding interactions between folded and disordered regions in proteins, and how these regions affect the propensity of proteins to self-associate and undergo phase separation.

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. In this work, we studied 263 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, strength, 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 analyze 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 multi-domain proteins.