Assessing the role of phospholipid-protein interactions in calcium pump dynamics: insights from in silico studies

BARRERA GUISASOLA, EXEQUIEL E.; PANTANO, SERGIO

Congreso; Reunión conjunta de Sociedades de Biociencias; 2017

Sarcoplasmic reticulum Ca2+-ATPase (SERCA) is a P-type iontransporter from skeletal muscle whose function consists in pumpingCa2+ from the cytoplasm into the reticulum with the consequentmuscle relaxation. This active transport has been previously describedby means of X-ray experiments involving large-scale rearrangementsof both cytoplasmic and transmembrane domains.Here, with the object of studying the structural and dynamic behaviorof SERCA we performed molecular dynamics simulations at acoarse grained (CG) level. This kind of simplified representationsallow the study of large size simulation boxes reaching multimicrosecondtimescales. As a preliminary step, we developed a set of CGtopologies for phospholipids compatible with the SIRAH force field(http://www.sirahff.com). Simulations were performed using GROMACS4.6.7. Starting configurations were generated embedding theSERCA reaction state E1-Ca2+ (PDB:5XA7) in planar lipid bilayers ofdifferent composition and simulating them by triplicate through 3msat a temperature of 310K. Specific phospholipid-protein interactionsreported from crystallographic structures were monitored during thesimulations. Basic residues and lipid phosphate groups formed saltbridges showing two classes of interactions: i) side chains emergingfrom the hydrophobic region and fixing particular phospholipids (i.eLys262) and ii) side chains approaching the polar head groups fromthe cytoplasm and changing interacting partners (i.e. Arg110). Alongthe simulations the transmembrane domain tilted 35º, as observedin experimental data. This behavior was governed by a Trp beltdistributed in the membrane-water interface. Combined with experimentaldata, this in silico approach contributes to better understandthe dynamic behavior of SERCA being also a promising strategy tostudy other transmembrane proteins.