Molecular dynamics study of tropical calcific pancreatitis (TCP) associated calcium-sensing receptor single nucleotide variation

Ashish Shrivastava; Kartavya Mathur; Rohit Kumar Verma; Sri Krishna Jayadev Magani; Deepak Krishna Vyas; Ashutosh Singh

doi:10.3389/fmolb.2022.982831

Molecular dynamics study of tropical calcific pancreatitis (TCP) associated calcium-sensing receptor single nucleotide variation

Front Mol Biosci. 2022 Oct 4:9:982831. doi: 10.3389/fmolb.2022.982831. eCollection 2022.

Authors

Ashish Shrivastava¹, Kartavya Mathur¹, Rohit Kumar Verma¹, Sri Krishna Jayadev Magani², Deepak Krishna Vyas³, Ashutosh Singh¹

Affiliations

¹ Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India.
² Cancer Biology Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India.
³ Department of Biotechnology, Lachoo Memorial College of Science and Technology, Jodhpur, RJ, India.

Abstract

Tropical Calcific Pancreatitis (TCP) is a chronic non-alcoholic pancreatitis characterised by extensive calcification. The disease usually appears at a younger age and is more common in tropical regions. This disease's progression can lead to pancreatic diabetes, which can subsequently lead to pancreatic cancer. The CASR gene encodes a calcium-sensing receptor (CaSR), which is a GPCR protein of class C. It is expressed in the islets of Langerhans, the parathyroid gland, and other tissues. It primarily detects small gradients in circulating calcium concentrations and couples this information to intracellular signalling, which helps to regulate PTH (parathyroid hormone) secretion and mineral ion homeostasis. From co-leading insulin release, CaSR modulates ductal HCO_3- secretion, Ca²⁺ concentration, cell-cell communication, β-cell proliferation, and intracellular Ca²⁺ release. In pancreatic cancer, the CaSR limits cell proliferation. TCP-related four novel missense mutations P163R, I427S, D433H and V477A, found in CaSR extracellular domain (ECD) protein, which were reported in the mutTCPdb Database (https://lms.snu.edu.in/mutTCPDB/index.php). P163R mutation occurs in ligand-binding domain 1 (LBD-1) of the CaSR ECD. To investigate the influence of these variations on protein function and structural activity multiple in-silico prediction techniques such as SIFT, PolyPhen, CADD scores, and other methods have been utilized. A 500 ns molecular dynamic simulation was performed on the CaSR ECD crystal structure and the corresponding mutated models. Furthermore, Principal Component Analysis (PCA) and Essential Dynamics analysis were used to forecast collective motions, thermodynamic stabilities, and the critical subspace crucial to CaSR functions. The results of molecular dynamic simulations showed that the mutations P163R, I427S, D433H, and V477A caused conformational changes and decreased the stability of protein structures. This study also demonstrates the significance of TCP associated mutations. As a result of our findings, we hypothesised that the investigated mutations may have an effect on the protein's structure and ability to interact with other molecules, which may be related to the protein's functional impairment.

Keywords: CaSR; calcium sensing receptor; molecular dynamics simulation; mutTCPdb; pancreatitis; single nucleotide variants; tropical calcific pancreatitis.