Experimental and Computational Studies of Pulmonary Surfactant Protein SP-B Interacting with Lipid Bilayers

Abstract

Pulmonary lung surfactant protein B (SP-B) is a 79 residue hydrophobic protein, from the Saposin superfamily. Saposin super family proteins share common features including 3 intra-chain disulfide bonds and 4-5 helical regions. SP-B appears to carry out its essential functions in respiration by binding to and modifying the structures of phospholipid bilayers and monolayers at the air-water interface. Due to difficulties arising from SP-B's extreme hydrophobicity, the 3D structure of full SP-B is not yet known. Thus we are using computational methods in combination with solid-state NMR to investigate the structure of SP-B. Our approach is to generate candidate structures via computational methods, predict the 15N spectra for the computed configurations and then compare them to the experimental NMR spectra.For the computational studies, we employ Mini-b, a construct of SP-B with known structure, and add the rest of residues to make a full length SP-B. We use several positions of SP-B in a POPC bilayer as initial structures. Calculations are carried out using GROMACS, with OPLS-aa, an all-atom force field, as well as with PACE, a hybrid model force field. Simulation methods include Molecular Dynamics (MD) and Replica Exchange Molecular Dynamics (REMD). For the experimental part, we use recombinantly expressed 15N labeled SP-B in mechanically oriented POPC bilayers to collect 1D 15N solid-state NMR spectra.