Network Re-Wiring During Allostery and Protein-Protein Interactions: A Graph Spectral Approach

GraSp-PSN: A web server for graph spectra based analysis of protein structure networks

The function of a protein is most of the time achieved due to minute conformational changes in its structure due to ligand binding or environmental changes or other interactions. Hence the analysis of structure of proteins should go beyond the analysis of mere atom contacts and should include the emergent global structure as a whole. This can be achieved by graph spectra based analysis of protein structure networks. GraSp-PSN is a web server that can assist in (1) acquiring weighted protein structure network (PSN) and network parameters ranging from atomic level to global connectivity from the three dimensional coordinates of a protein, (2) generating scores for comparison of a pair of protein structures with detailed information of local to global connectivity, and (3) assigning perturbation scores to the residues and their interactions, that can prioritise them in terms of residue clusters. The methods implemented in the server are generic in nature and can be used for comparing networks in any discipline by uploading adjacency matrices in the server. The webserver can be accessed using the following link: https://pople.mbu.iisc.ac.in/.

Revisiting structural organization of proteins at high temperature from a network perspective

Interactions between distantly placed amino acids in the primary chain (long-range) play a very crucial role in the formation and stabilization of the tertiary structure of a protein, while interactions between closely placed amino acids in the primary chain (short-range) mostly stabilize the secondary structures. Every protein needs to maintain marginal stability in order to perform its physiological functions in its native environment. The requirements for this stability in mesophilic and thermophilic proteins are different. Thermophilic proteins need to form more interactions as well as more stable interactions to survive in the extreme environment, they live in. Here, we aim to find out how the interacting amino acids in three-dimensional space are positioned in the primary chains in thermophilic and mesophilic. How does this arrangement help thermophiles to maintain their structural integrity at high temperatures? Working on a dataset of 1560 orthologous pairs we perceive that thermophiles are not only enriched with long-range interactions, they feature bigger connected clusters and higher network densities compared to their mesophilic orthologs, at higher interaction strengths between the amino acids. Moreover, we have observed the enrichment of different types of interactions at different secondary structural regions.

Allostery, engineering and inhibition of tryptophan synthase

The final two steps of tryptophan biosynthesis are catalyzed by the enzyme tryptophan synthase (TS), composed of alpha (αTS) and beta (βTS) subunits. Recently, experimental and computational methods have mapped "allosteric networks" that connect the αTS and βTS active sites. In αTS, allosteric networks change across the catalytic cycle, which might help drive the conformational changes associated with its function. Directed evolution studies to increase catalytic function and expand the substrate profile of stand-alone βTS have also revealed the importance of αTS in modulating the conformational changes in βTS. These studies also serve as a foundation for the development of TS inhibitors, which can find utility against Mycobacterium tuberculosis and other bacterial pathogens.

From Distinct to Differential Conformational Dynamics to Map Allosteric Communication Pathways in Proteins

Initiation of biological processes involving protein-ligand binding, transient protein-protein interactions, or amino acid modifications alters the conformational dynamics of proteins. Accompanying these biological processes are ensuing coupled atomic level conformational changes within the proteins. These conformational changes collectively connect multiple amino acid residues at distal allosteric, binding, and/or active sites. Local changes due to, for example, binding of a regulatory ligand at an allosteric site initiate the allosteric regulation. The allosteric signal propagates throughout the protein structure, causing changes at distal sites, activating, deactivating, or modifying the function of the protein. Hence, dynamical responses within protein structures to stimuli contain critical information on protein function. In this Perspective, we examine the description of allosteric regulation from protein dynamical responses and associated alternative and emerging computational approaches to map allosteric communication pathways between distal sites in proteins at the atomic level.

Networks of Networks: An Essay on Multi-Level Biological Organization

The multi-level organization of nature is self-evident: proteins do interact among them to give rise to an organized metabolism, while in the same time each protein (a single node of such interaction network) is itself a network of interacting amino-acid residues allowing coordinated motion of the macromolecule and systemic effect as allosteric behavior. Similar pictures can be drawn for structure and function of cells, organs, tissues, and ecological systems. The majority of biologists are used to think that causally relevant events originate from the lower level (the molecular one) in the form of perturbations, that “climb up” the hierarchy reaching the ultimate layer of macroscopic behavior (e.g., causing a specific disease). Such causative model, stemming from the usual genotype-phenotype distinction, is not the only one. As a matter of fact, one can observe top-down, bottom-up, as well as middle-out perturbation/control trajectories. The recent complex network studies allow to go further the pure qualitative observation of the existence of both non-linear and non-bottom-up processes and to uncover the deep nature of multi-level organization. Here, taking as paradigm protein structural and interaction networks, we review some of the most relevant results dealing with between networks communication shedding light on the basic principles of complex system control and dynamics and offering a more realistic frame of causation in biology.

Allosteric communication regulates ligand-specific GPCR activity

G protein-coupled receptors (GPCRs) are membrane-bound proteins that are ubiquitously expressed in many cell types and take part in mediating multiple signaling pathways. GPCRs are dynamic proteins and exist in an equilibrium between an ensemble of conformational states such as inactive and fully active states. This dynamic nature of GPCRs is one of the factors that confers their basal activity even in the absence of any ligand-mediated activation. Ligands selectively bind and stabilize a subset of the conformations from the ensemble leading to a shift in the equilibrium toward the inactive or the active state depending on the nature of the ligand. This ligand-selective effect is achieved through allosteric communication between the ligand binding site and G protein or β-arrestin coupling site. Similarly, the G protein coupling to the receptor exerts the allosteric effect on the ligand binding region leading to increased binding affinity for agonists and decreased affinity for antagonists or inverse agonists. In this review, we enumerate the current state of our understanding of the mechanism of allosteric communication in GPCRs with a specific focus on the critical role of computational methods in delineating the residues involved in allosteric communication. Analyzing allosteric communication mechanism using molecular dynamics simulations has revealed (a) a structurally conserved mechanism of allosteric communication that regulates the G protein coupling, (b) a rational structure-based approach to designing selective ligands, and (c) an approach to designing allosteric GPCR mutants that are either ligand and G protein or β-arrestin selective.