Protein G selects two binding sites for carbon nanotube with dissimilar behavior; a molecular dynamics study

Ebrahim Habibi, M. B ; Sharif University of Technology | 2019

790 Viewed
  1. Type of Document: Article
  2. DOI: 10.1016/j.jmgm.2018.12.007
  3. Publisher: Elsevier Inc , 2019
  4. Abstract:
  5. Background: Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure. Methods: Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized. Results: Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the first (PGB-CNT1) and the aromatic residues in the second (PGB-CNT2) surface patch. Displacement of amino acids in the PGB-CNT2 complex occurred during the simulation and it caused an increase in its stability at the end of simulation. The amino acids’ displacements diminished the PGB α-helix structure by breakage of hydrogen bonds and generated more transient structures. Principal component analysis determined that the interaction of the CNT with the second surface patch of the PGB raised the extent and modes of the PGB motions. In contrast, insignificant structural changes induced in the PGB while the CNT bonded through the first surface patch. Conclusion: Even though neither of the PGB-CNT complexes could prevent structural changes in the PGB, development of the PGB-CNT1 complex induce slight structural changes in its fragment of crystallizable receptor (FCR). Dissimilar structural changes induced in the PGB-CNT complexes are possibly related to various characteristics of the PGB binding sites
  6. Keywords:
  7. Carbon nanotube ; Molecular dynamics ; Principle component analysis ; Protein G ; Structural changes ; Binding sites ; Hydrogen bonds ; Principal component analysis ; Proteins ; Yarn ; Carbon Nanostructures ; Molecular dynamics simulations ; Protein interaction ; Protein structures ; Transient structure ; Carbon nanotubes ; Amino acid ; Bacterial protein ; IgG Fc-binding protein, Streptococcus ; Adsorption ; Alpha helix ; Binding site ; Conformational transition ; Controlled study ; Enzyme linked immunosorbent assay ; Hydrogen bond ; Molecular docking ; Priority journal ; Protein conformation ; Reduction (chemistry) ; Simulation ; Surface property ; Chemistry ; Conformation ; Amino Acids ; Bacterial Proteins ; Molecular Conformation ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Nanotubes, Carbon ; Protein Binding
  8. Source: Journal of Molecular Graphics and Modelling ; Volume 87 , 2019 , Pages 257-267 ; 10933263 (ISSN)
  9. URL: https://www.sciencedirect.com/science/article/pii/S1093326318306624