Mechanical stability and thermal conductivity of β-barrel in green fluorescent protein by steered molecular dynamics

RSC Advances ◽  
2014 ◽  
Vol 4 (13) ◽  
pp. 6513 ◽  
Author(s):  
Chang-Li Cheng ◽  
Ming-Zhen Zhang ◽  
Guang-Jiu Zhao
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Green Fluorescent Protein ◽  
Fluorescent Protein ◽  
Mechanical Stability ◽  
Steered Molecular Dynamics ◽  
Green Fluorescent

scholarly journals Single-Molecule Imaging and Computational Microscopy Approaches Clarify the Mechanism of the Dimerization and Membrane Interactions of Green Fluorescent Protein

2019 ◽  
Vol 20 (6) ◽  
pp. 1410 ◽  
Author(s):  
Xiaohua Wang ◽  
Kai Song ◽  
Yang Li ◽  
Ling Tang ◽  
Xin Deng
Keyword(s):  
Molecular Dynamics ◽  
Green Fluorescent Protein ◽  
Single Molecule ◽  
Fluorescent Protein ◽  
Hydrophobic Interactions ◽  
Site Directed Mutagenesis ◽  
Single Amino Acid ◽  
Single Mutation ◽  
Functional Protein ◽  
Green Fluorescent

Green fluorescent protein (GFP) is widely used as a biomarker in living systems; however, GFP and its variants are prone to forming low-affinity dimers under physiological conditions. This undesirable tendency is exacerbated when fluorescent proteins (FP) are confined to membranes, fused to naturally-oligomeric proteins, or expressed at high levels in cells. Oligomerization of FPs introduces artifacts into the measurement of subunit stoichiometry, as well as interactions between proteins fused to FPs. Introduction of a single mutation, A206K, has been shown to disrupt hydrophobic interactions in the region responsible for GFP dimerization, thereby contributing to its monomerization. Nevertheless, a detailed understanding of how this single amino acid-dependent inhibition of dimerization in GFP occurs at the atomic level is still lacking. Single-molecule experiments combined with computational microscopy (atomistic molecular dynamics) revealed that the amino group of A206 contributes to GFP dimer formation via a multivalent electrostatic interaction. We further showed that myristoyl modification is an efficient mechanism to promote membrane attachment of GFP. Molecular dynamics-based site-directed mutagenesis has been used to identify the key functional residues in FPs. The data presented here have been utilized as a monomeric control in downstream single-molecule studies, facilitating more accurate stoichiometry quantification of functional protein complexes in living cells.

scholarly journals A molecular dynamics model for glycosylphosphatidyl-inositol anchors: “flop down” or “lollipop”?

2018 ◽  
Vol 20 (46) ◽  
pp. 29314-29324
Author(s):  
Pallavi Banerjee ◽  
Marko Wehle ◽  
Reinhard Lipowsky ◽  
Mark Santer
Keyword(s):  
Molecular Dynamics ◽  
Green Fluorescent Protein ◽  
Computational Model ◽  
Fluorescent Protein ◽  
Dynamics Model ◽  
Green Fluorescent ◽  
Glycosylphosphatidyl Inositol

Computational model for GPI anchors tested in DMPC and POPC bilayers. The free anchor rarely occurs as an erected “lollipop-like” conformation, it rather “flops down” onto the bilayer surface. Yet an attached protein (here green fluorescent protein) exhibits extensive orientational flexibility due to the phospho-ethanolamine linker.

Analysis of the Unfolding Process of Green Fluorescent Protein by Molecular Dynamics Simulation

2008 ◽  
Vol 112 (29) ◽  
pp. 8672-8680 ◽  
Author(s):  
Yoshihiro Hisatomi ◽  
Daisuke Katagiri ◽  
Saburo Neya ◽  
Masahiko Hara ◽  
Tyuji Hoshino
Keyword(s):  
Molecular Dynamics ◽  
Green Fluorescent Protein ◽  
Molecular Dynamics Simulation ◽  
Fluorescent Protein ◽  
Dynamics Simulation ◽  
Green Fluorescent
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