title: Self-assembling study of sarcolipin and its mutants in multiple molecular dynamic simulations.
abstract: 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.
authors.affiliation: School of Physics, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China.
authors.forename: Yipeng
authors.identifier: 0000-0003-4149-2403
authors.initials: Y
authors.lastname: Cao
authors.affiliation: School of Physics, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China.
authors.forename: Xue
authors.initials: X
authors.lastname: Wu
authors.affiliation: School of Medicine, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China.
authors.forename: Rui
authors.initials: R
authors.lastname: Yang
authors.affiliation: School of Physics, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China.
authors.forename: Xinyu
authors.initials: X
authors.lastname: Wang
authors.affiliation: School of Physics, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China.
authors.forename: Haiying
authors.initials: H
authors.lastname: Sun
authors.affiliation: School of Physics, Nankai University, 94 Weijin Road, Tianjin, 300071, P.R.China.
authors.forename: Imshik
authors.initials: I
authors.lastname: Lee
mesh_terms: D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry*; D000409:Alanine / Q000737:chemistry*; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D002135:Calcium-Binding Proteins / Q000737:chemistry; D006801:Humans; D007532:Isoleucine / Q000737:chemistry*; D008051:Lipid Bilayers / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009124:Muscle Proteins / Q000737:chemistry*; D009154:Mutation; D000072756:Protein Conformation, alpha-Helical; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D011510:Proteolipids / Q000737:chemistry*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013816:Thermodynamics; D000099211:Phospholamban
chemical_list: D015060:1,2-Dipalmitoylphosphatidylcholine; D000409:Alanine; D002135:Calcium-Binding Proteins; D007532:Isoleucine; D008051:Lipid Bilayers; D009124:Muscle Proteins; D011510:Proteolipids; D000099211:Phospholamban; C077258:sarcolipin
keywords: CG-MD simulation; membrane protein; sarcolipin; self-assembly