Study of Functional and Allosteric Sites in Protein Superfamilies

Abstract

The interaction of proteins (enzymes) with a variety of low-molecular-weight compounds, as well as protein-protein interactions, is the most important factor in the regulation of their functional properties. To date, research effort has routinely focused on studying ligand binding to the functional sites of proteins (active sites of enzymes), whereas the molecular mechanisms of allosteric regulation, as well as binding to other pockets and cavities in protein structures, remained poorly understood. Recent studies have shown that allostery may be an intrinsic property of virtually all proteins. Novel approaches are needed to systematically analyze the architecture and role of various binding sites and establish the relationship between structure, function, and regulation. Computational biology, bioinformatics, and molecular modeling can be used to search for new regulatory centers, characterize their structural peculiarities, as well as compare different pockets in homologous proteins, study the molecular mechanisms of allostery, and understand the communication between topologically independent binding sites in protein structures. The establishment of an evolutionary relationship between different binding centers within protein superfamilies and the discovery of new functional and allosteric (regulatory) sites using computational approaches can improve our understanding of the structure-function relationship in proteins and provide new opportunities for drug design and enzyme engineering.

Chemical space of Escherichia coli dihydrofolate reductase inhibitors: New approaches for discovering novel drugs for old bugs

“…In other words, there is more selective pressure on the active site and hence more severe penalties in terms of fitness lost due to mutations on the active site. However, allosteric sites are organism specific and, to the best of our knowledge, are almost unknown in EcDHFR indicating that they may be either dispensable or are under less evolutionary pressure and hence, likely to be more mutable.…”

Probing the Structural Dynamics of the Plasmodium falciparum Tunneling-Fold Enzyme 6-Pyruvoyl Tetrahydropterin Synthase to Reveal Allosteric Drug Targeting Sites

“…However, discovering allosteric sites that have a dominant effect on protein conformation and respective compounds that modulate these sites is far more challenging than orthosteric drug discovery ( Lu et al, 2019 ; Amamuddy et al, 2020 ). As in many cases, the location of allosteric sites is often unknown and their effects on the intrinsic motion of the protein are difficult to determine experimentally ( Suplatov and Švedas, 2015 ). Our recent review article proposes a number of integrated computational approaches to identify allosteric sites ( Amamuddy et al, 2020 ).…”

CASBench: A Benchmarking Set of Proteins with Annotated Catalytic and Allosteric Sites in Their Structures

“…It has become clear that allostery is not an exclusive property of sophisticated multi-subunit complexes, but rather a widespread phenomenon that plays a key role in the regulation of many biological processes [4-8]. Computational biology methods were applied to study allostery in an attempt to understand the relationship between function and regulation [6, 9]. Bioinformatic analysis showed that the amino acid sequence of regulatory sites is less conserved and more variable compared to that in catalytic sites [10].…”

“…Analysis of correlated substitutions in the amino acid sequences of topologically independent but functionally coupled sites on the surface of evolutionary related proteins is increasingly being used to study the molecular mechanisms of allostery [9, 14]. It was shown that such correlating/co-evolving positions can form a network of interacting residues located between the catalytic and regulatory sites in a protein structure, which provides communication between them due to the sequential conformational changes initiated by the binding of a regulatory agent [15, 16].…”

“…The anticipation of the discovery of a new regulatory mechanism in proteins currently considered as non-allosteric has generated intense attention to the field, driven by a fundamental interest in establishing new ways of regulating proteins/ enzymes, and the prospects for creating novel allosteric drugs having a lower toxicity due to higher binding selectivity [4, 23-26]. In recent years, a number of computational methods have been developed to search for new regulatory sites in protein structures, as well as complementary selective ligands that can influence the functional activity upon binding to the biopolymer [9]: using geometric [27-30], energy-based [31, 32] or bioinformatic criteria [13, 33, 34, 35], training sets of experimentally annotated sites [36, 37], and high-throughput virtual screening procedures [38, 39]. The currently available computer programs usually predict multiple sites in the structure of a selected protein (tens or even hundreds, depending on the globule size and the selected parameters).…”