Mapping allosteric pathway in NIa-Pro using computational approach

Abstract

Background: Computer simulation studies complement in vitro experiments and provide avenue to understand allosteric regulation in the absence of other molecular viewing techniques. Molecular dynamics captures internal motion within the protein and enables tracing the communication path between a catalytic site and a distal allosteric site. In this article, we have identified the communication pathway between the viral protein genome linked (VPg) binding region and catalytic active site in nuclear inclusion protein-a protease (NIa-Pro).

Methods: Molecular dynamics followed by in silico analyses have been used to map the allosteric pathway.

Results: This study delineates the residue interaction network involved in allosteric regulation of NIa-Pro activity by VPg. Simulation studies indicate that point mutations in the VPg interaction interface of NIa-Pro lead to disruption in these networks and change the orientation of catalytic residues. His142Ala and His167Ala mutations do not show a substantial change in the overall protease structure, but rather in the residue interaction network and catalytic site geometry.

Conclusion: Our mutagenic study delineates the allosteric pathway and facilitates the understanding of the modulation of NIa-Pro activity on a molecular level in the absence of the structure of its complex with the known regulator VPg. Additionally, our in silico analysis explains the molecular concepts and highlights the dynamics behind the previously reported wet lab study findings.

Author summary

Allosteric control of enzymes is a key regulatory process, ubiquitous in all kingdoms of life. It involves the binding of the specific regulatory molecule (either an activator or an inhibitor) to a location distal from the enzyme’s active site. Our research provides a simple in silico methodology for gaining insight into the allosteric pathways that regulate specific enzyme activity. In the presence of a 3D structure of the enzyme and the knowledge of specific interaction sites with its regulator, this methodology can be applied to understand enzyme regulation, even in the absence of the structure of the enzyme-regulator complex.

Graphical abstract

Keywords

NIa-Pro / VPg / simulation / residue interaction network / allostery

References

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SUPPLEMENTARY MATERIALS

The supplementary materials can be found online with this article at https://doi.org/10.15302/J-QB-022-0296.

ACKNOWLEDGMENTS

We thank Prof. H. S. Savithri from Indian Institute of Sciences for providing intellectual inputs on the project and funding Dr. Panigrahi for two months while she designed and performed this computational project using her personal resources.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Rashmi Panigrahi and Senthilkumar Kailasam declare that they have no conflict of interests.

All procedures performed in studies were in accordance with the ethical standards of the institution or practice at which the studies were conducted.

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