Mode of interaction of calcium oxalate crystal with human phosphate cytidylyltransferase 1: a novel inhibitor purified from human renal stone matrix

Abstract

Nephrolithiasis is a common clinical disorder, and calcium oxalate (CaOx) is the principal crystalline component in approximately 75% of all renal stones. It is widely believed that proteins act as inhibitors of crystal growth and aggregation. Acidic amino acids present in these proteins play a significant role in the inhibition process. In this study, interaction of cal-cium oxalate with human phosphate cytidylyltrans-ferase 1(CCT), a novel calcium oxalate crystal growth inhibitor purified from human renal stone matrix has been elucidated in silico and involvement of acidic amino acids in the same. As only sequence of CCT is available, henceforth its 3-D structure was modeled via Homology modeling using Prime module of Schrodinger package. Molecular dynamic simulation of modeled protein with solvation was done by mac-romodel (Schrodinger). The quality of modeled pro-tein was validated by JCSG protein structure valida-tion (PROCHECK & ERRAT) server. To analyze the interaction of modeled protein CCT with calcium oxalate along with role played by acidic amino acids, ‘Docking simulation’ was done using MOE–Dock. Interaction between calcium oxalate and CCT was also studied by substituting acidic amino acid in the active sites of the protein with neutral and positively charged amino acids. The in silico analysis showed the bond formation between the acidic amino acids and calcium atom, which was further substantiated when substitution of these acidic amino acids with alanine, glycine, lysine, arginine and histidine com-pletely diminished the interaction with calcium ox-alate

Peeping into Human Renal Calcium Oxalate Stone Matrix: Characterization of Novel Proteins Involved in the Intricate Mechanism of Urolithiasis

“…Homology model building of the identified proteins: ethanolamine-phosphate cytidylyltransferase and macrophage-capping protein was done using molecular operating environment (MOE) [28], [29]. The template used for model building of ethanolamine-phosphate cytidylyltransferase was the crystal structure of human CTP: Phosphoethanolamine Cytidylyltransferase in complex with CMP [PDB ID: 3ELB_A] with a query coverage of 85% and sequence identity of 98%.…”

Surface-modified bacterial nanofibrillar PHB scaffolds for bladder tissue repair

“…Further, it has been reported that the molecular weight of polyethylene glycol is mainly decisive on the inhibition performance of the calcium oxalate crystals due to charge and hydrophilic effects and the smaller molecular weight of polyethylene glycol inhibit calcium oxalate crystals more stronger (Deng 2007). In addition to that, proteins are known to act as inhibitors of crystal growth and nucleation (Pathak et al 2011). Recent studies shown that the inhibition effect of amino acids on crystallization increased with increasing of basic -NH 2 groups or presence of -OH groups (Yehia et al 2012).…”