Abstract
Proteins such as enzymes perform their function by predominant non-covalent bond interactions between transiently interacting units. There is an impact on the overall structural topology of the protein, albeit transient nature of such interactions, that enable proteins to deactivate or activate. This aspect of the alteration of the structural topology is studied by employing protein structural networks, which are node-edge representative models of protein structure, reported as a robust tool for capturing interactions between residues. Several methods have been optimised to collect meaningful, functionally relevant information by studying alteration of structural networks. In this article, different methods of comparing protein structural networks are employed, along with spectral decomposition of graphs to study the subtle impact of protein-protein interactions. A detailed analysis of the structural network of interacting partners is performed across a dataset of around 900 pairs of bound complexes and corresponding unbound protein structures. The variation in network parameters at, around and far away from the interface are analysed. Finally, we present interesting case studies, where an allosteric mechanism of structural impact is understood from communication-path detection methods. The results of this analysis are beneficial in understanding protein stability, for future engineering and docking studies.
Keywords: Protein structural networks, graph spectral analysis, protein-protein interaction, transient association, allostery, network alterations1. Introduction
The importance of molecular flexibility for a protein to function is well documented. The analysis of different structural states helps in analysing its function. Several proteins are very rigid and exist in fewer distinct conformations. However, most proteins exist predominantly in an inactive state and seldom in an active state. The difference between the structural states arises from subtle changes in local conformations at specific sites or from large structural excursions with altered topology. Some proteins also populate an intermediate state which may be stabilised in a dynamic equilibrium due to strong interactions. The stabilisation of such a transient state is generally brought about by external perturbations like post translational modifications, mutations, or various binding partners. One such scenario is the perturbation of the protein structure due to binding with another protein. The changes brought about at the site of their interface is generally allosterically transmitted across the structure of the protein to impact or present its active site. Although this is intuitive to understand, the mechanism of this signalling has not been thoroughly analysed across all proteins.
The analysis of allosteric signalling can often be approached using protein structural networks (PSN). It is a simplistic mathematical model of the residue interactions that exist in a well-ordered globular protein structure, where the residues are considered as nodes and any interaction between them is considered by drawing an edge between them. The edge signifies a relationship between the interacting residues, generally pertaining to features such as non-covalent bonding, proximity between atoms in space and sometimes also based on energy parameters that can be defined for interactions.
A further advancement on the use of these structure networks is the application of a graph-spectral method for the global comparison of proteins. This method is robust and sensitive to even minute structural perturbations that can be observed between any pair of networks that are given as input. The method described by Vasundhara and co-workers is an advanced comparison metric that has been applied in the validation of protein structure models and in understanding the amount of structural variability in an ensemble of structures of a given protein. The method has been employed in the current work for the global comparison of PSNs.
We have compared the bound and the unbound forms of the same protein, that has been crystallised when bound to interacting partners as well as independently. The ProPairs database is a large consortium of available bound and unbound proteins structures and provides this information. Any changes in network parameters, both local and global, are discussed along with interesting clinically relevant scenarios where the network may have changed considerably without affecting its overall structure topology. The rearrangement, gain and loss of network connectivity are discussed further, illustrated using case studies.