Simulations of Potentials of Mean Force for Separating a Leucine Zipper Dimer and the Basic Region of a Basic Region Leucine Zipper Dimer

Self-assembling study of sarcolipin and its mutants in multiple molecular dynamic simulations

The Sarcolipin (SLN) is a single trans-membrane protein that can self-assembly to dimer and oligomer for playing importantphysiological function. In this work, we addressed the dimerization of wild type SLN (wSLN) and its mutants (mSLNs) - I17A and I20A, using both coarse-grained (CG) and atomistic (AT) molecular dynamics (MD) simulations. Our results demonstrated that wSLN homodimer assembled as a left-handed helical complex, while mSLNs heterodimers assembled as right-handed complexes. Analysis of residue-residue contacts map indicated that isoleucine (Ile)-leucione (Leu) zipper domain played an important role in dimerization. The potential of mean force (PMF) demonstrated that wSLN homodimer was more stable than mSLNs heterodimers. Meanwhile, the mSLNs heterodimers preferred right-handed rather than left-handed helix. AT-MD simulations for wSLN and mSLNs were also in line with CG-MD simulations. These results provided the insights for understanding the mechanisms of SLNs self-assembling. Proteins 2017; 85:1065-1077. © 2017 Wiley Periodicals, Inc.