title: Calcium binding to the transmembrane domain of the sarcoplasmic reticulum Ca2+-ATPase: insights from molecular modeling.
abstract: Sarcoplasmic reticulum Ca(2+)- ATPase pumps Ca(2+) ions from muscle cells to the sarcoplasmic reticulum. Here we use molecular dynamics and electrostatic modeling to investigate structural and dynamical features of key intermediates in the Ca(2+) binding process of the protein. Structural models of the protein (containing either two, one, or no calcium ions in the transmembrane domain) are constructed based on the X-ray structure by Toyoshima et al. (Nature 2000;405:647-655). The protein is embedded in a water/octane bilayer, which mimics the water/membrane environment. Our calculations provide information on the hydration of the two Ca(2+) ions, not emerging from the X-ray structure. Furthermore, they indicate that uptake of the metal ions causes large structural rearrangements of the metal binding sites. In addition, they suggest that the two ions reach their binding sites via two specific pathways. Finally, they allow identification of residues in the outer mouth of the protein that might interact with the Ca(2+) ions during the binding process.
authors.affiliation: International School for Advanced Studies (ISAS-SISSA) and INFM-DEMOCRITOS National Simulation Center, Trieste, Italy.
authors.forename: Valeria
authors.initials: V
authors.lastname: Costa
authors.forename: Paolo
authors.initials: P
authors.lastname: Carloni
mesh_terms: D001665:Binding Sites; D002118:Calcium / Q000737:chemistry / Q000378:metabolism*; D000252:Calcium-Transporting ATPases / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D015394:Molecular Structure; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011522:Protons; D053498:Sarcoplasmic Reticulum Calcium-Transporting ATPases; D055672:Static Electricity; D014867:Water / Q000737:chemistry
chemical_list: D011522:Protons; D014867:Water; D053498:Sarcoplasmic Reticulum Calcium-Transporting ATPases; D000252:Calcium-Transporting ATPases; D002118:Calcium