Identification of Calcium binding sites on calsequestrin 1 and its implications to polymerization

• Published in: Molecular bioSystems 2013-04, Vol.9 (7), p.1949-1957
• Main Authors: Kumar, Amit, Chakravarty, Harapriya, Bal, Naresh C., Balaraju, Tuniki, Jena, Nivedita, Misra, Gauri, Bal, Chandralata, Pieroni, Enrico, Periasamy, Muthu, Sharon, Ashoke
• Format: Article
• Language: English
• ISSN: 1742-206X; 1742-2051
• DOI: 10.1039/c3mb25588c

Biophysical studies have shown that each molecule of calsequestrin 1 (CASQ1) can bind about 70–80 Ca 2+ ions. However, the nature of Ca 2+ -binding sites has not yet been fully characterized. In this study, we employed in-silico approaches to identify the Ca 2+ binding sites and to understand the molecular basis of CASQ1-Ca 2+ recognition. We built the protein model by extracting the atomic coordinates for the back-to-back dimeric unit from the recently solved hexameric CASQ1 structure (PDB id: 3UOM) and adding the missing C-terminal residues (aa350–364). Using this model we performed extensive 30 ns molecular dynamics simulations exposed to wide range of Ca 2+ concentrations ([Ca 2+ ]). Our results show that the Ca 2+ -binding sites on CASQ1 differ both in affinity and geometry. The high affinity Ca 2+ -binding sites share a similar geometry and interestingly, majority of them were found to be induced by increased [Ca 2+ ]. We also found that the system undergoes maximal Ca 2+ -binding to the CAS (consecutive aspartate stretch at the C-terminus) before the rest of the CASQ1 surface becomes saturated. Simulated data shows that the CASQ1 back-to-back stacking is progressively stabilized by emergence of an increasing number of hydrophobic interactions with increasing [Ca 2+ ]. Further, this study shows that the CAS domain assumes a compact structure with increase in Ca 2+ binding, which suggests that the CAS domain might function as a Ca 2+ -sensor that may be a novel structural motif to sense metal. We propose the term “D n -motif” for the CAS domain.