Motive for Designing Protein Binding Site - Management Assignment Help

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Motive for designing protein binding site
Protein often does not work alone, rather it interacts with other molecules to complete its role. These other molecules that bind to a specific protein are called ligands, which are typically made of a small number of atoms such as organic molecules, metal ions or DNA/RNA. The range of functional diversity exerted by proteins include, but not limited to, cell signalling, cell survival, energy metabolism etc. Many cellular functions within an organism are orchestrated by means of specific protein-ligand interaction. Among the multiple tasks, one of the essential roles of protein is to act as enzyme catalysing metabolic reactions within a cell. Since a large number of proteins serve as enzymes, the exact function of these entities are greatly influenced by the availability of ligand and the residue interacting with the ligand. Also From an equilibrium stand point, enzyme catalysis is much needed, as they greatly accelerate the rate of a chemical reaction.
Despite their role as enzymes, Many proteins are known to possess other sites where ligand recognition takes place. These other sites are termed as allosteric sites and ligands that sit in the allosteric sites are called allosteric ligands. Molecular recognition in the allosteric region directly regulates the function of protein by changing the conformation of binding site [2].In all these cases, one commonality that remains constant is the binding sites [add ref]. The need for studying binding sites greatly amplifies if the ligand in study is a drug. Physicochemical and molecular properties such as shape, volume, residue composition and geometry of site dictate the type of ligands to bind. Other factors such as free energy and binding affinity have to be taken into account as not all protein-ligand interactions are favourable.

Numerous papers have been published till date examining interplay between ligands and the protein binding sites towards the functional characterization of a protein. For example, many cases of convergent evolution are reported among proteins that are able to recognise ATP ligands. As such, these convergent evolutions enable proteins of different sequences and folds to bind to a common ligands. Bhagavat et al, analysed the structure of all NTP binding proteins from PDB and concluded that the binding sites share a common similarity even when there is no similarity detected at level of structural folds [3]. Using site comparison tools, they have derived 27 site-types motifs that are able to reflect the binding site space of all known NTP binding proteins in PDB.
Another interesting article was from the Nir Bie-Tal group published in 2020, where the author explored the evolution of protein-adenine fragments and derived a theme (specific amino acid segments) that is observed in different adenine proteins [4]. Adenine is a planar, triangle-like molecule found as a functional moiety in most of the ubiquitous ligands like ATP, SAM, FAD, CoA and NAD. Here, the author superimposed the binding site of 5 adenine containing ligands among themselves using adenine atom as a superposable fragment. Following that, the sites are examined for any motifs and found three known variants namely, reverse motif, direct motif and asp-motif whose prevalence vary, but exist, across all adenine binding folds. Both direct and reverse motifs represent a adenine binding loop differing in its backbone chain direction. a 3 residue loop whose position is consistent across all adenine binding proteins, that differs in its backbone chain direction. Few key findings are, In FAD-binding complexes, more than 60% of protein has a reverse motif while direct motis is completely absent. Also the interaction site for adenine was similar even for the cases where two proteins share different binding site topologies hinting importance of residue position towards function of a protein.

 

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