Docking and molecular dynamics simulations of the Fyn-SH3 domain with free and phospholipid bilayer-associated 18.5-kDa myelin basic protein (MBP) – Insights into a non-canonical and fuzzy interaction
For the final version of the article please refer to Bessonov, Kyrylo, Kenrick A. Vassall, and George Harauz. "Docking and molecular dynamics simulations of the Fyn‐SH3 domain with free and phospholipid bilayer‐associated 18.5‐kDa myelin basic protein (MBP)–Insights into a non‐canonical and fuzzy interaction." Proteins: Structure, Function, and Bioinformatics (2017).
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[en] The molecular details of the association between the human Fyn-SH3 domain, and the fragment of 18.5-kDa myelin basic protein (MBP) spanning residues S38–S107 (denoted as xα2-peptide, murine sequence numbering), were studied in silico via docking and molecular dynamics over 50-ns trajectories. The results show that interaction between the two proteins is energetically favorable and heavily-dependent on the MBP proline-rich region (P93-P98) in both aqueous and membrane environments. In aqueous conditions, the xα2-peptide/Fyn-SH3 complex adopts a “sandwich”-like structure. In the membrane context, the xα2-peptide interacts with the Fyn-SH3 domain via the proline-rich region and the β-sheets of Fyn-SH3, with the latter wrapping around the proline-rich region in a form of a clip. Moreover, the simulations corroborate prior experimental evidence of the importance of upstream segments beyond the canonical SH3-ligand. This study thus provides a more-detailed glimpse into the context-dependent interaction dynamics and importance of the β-sheets in Fyn-SH3 and proline-rich region of MBP.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Bessonov, Kyrylo ; Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Bioinformatique
Harauz, George; Universtiy of Guelph (Canada) > Department of Cellular and Molecular Biology,Biophysics Interdepartmental Group, and Collaborative Program in Neuroscience
Vassall, Kenrick; Universtiy of Guelph (Canada) > Department of Cellular and Molecular Biology,Biophysics Interdepartmental Group, and Collaborative Program in Neuroscience
Language :
English
Title :
Docking and molecular dynamics simulations of the Fyn-SH3 domain with free and phospholipid bilayer-associated 18.5-kDa myelin basic protein (MBP) – Insights into a non-canonical and fuzzy interaction
Publication date :
12 April 2017
Journal title :
Proteins
ISSN :
0887-3585
eISSN :
1097-0134
Publisher :
Wiley Liss, Inc., New York, United States - New York
NSERC - Natural Sciences and Engineering Research Council
Commentary :
This is the submitted non-reviewed version of the article, for the final version please refer to Bessonov, Kyrylo, Kenrick A. Vassall, and George Harauz. "Docking and molecular dynamics simulations of the Fyn‐SH3 domain with free and phospholipid bilayer‐associated 18.5‐kDa myelin basic protein (MBP)–Insights into a non‐canonical and fuzzy interaction." Proteins: Structure, Function, and Bioinformatics (2017).
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