Proton Wire Dynamics in the Green Fluorescent Protein
1The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel.
Proton wires in green fluorescent protein (GFP) dynamically change, with water insertion and side chain rotations influencing proton pathways. New water wires facilitate proton exit or migration, reconciling experimental data.
Area of Science:
- Biophysics
- Computational Biology
- Protein Dynamics
Background:
- Protons move within proteins via proton wires (PWs).
- Green fluorescent protein (GFP) is a widely studied protein with known X-ray structures.
- Understanding proton transport mechanisms is crucial for various biological processes.
Purpose of the Study:
- To investigate the dynamic changes in proton wires (PWs) within wild-type green fluorescent protein (GFP) over time.
- To elucidate the role of specific amino acid residues (Thr203, Ser205, Glu222) in shaping PWs.
- To identify and characterize water wires (WWs) and their role in proton transport in GFP.
Main Methods:
- 306 ns molecular dynamics (MD) simulation of wild-type GFP.
- Analysis of proton wire pathways and water molecule dynamics.
- Investigation of amino acid side chain rotations and their impact on PWs.
Main Results:
- Observed rapid water molecule insertion into the chromophore-proximal PW (Ser205-Glu222).
- Identified alternative PWs and the significant influence of Thr203 and Ser205 side chain rotations.
- Discovered two novel water wires (WWs) connecting the chromophore to the bulk and a water pool (WP1).
- Proposed a temperature-dependent protonation/ion pairing mechanism involving Glu222 and WP1.
Conclusions:
- GFP's proton wire network is highly dynamic, influenced by water and amino acid side chain conformations.
- Newly identified water wires provide pathways for proton exit or internal migration.
- The proposed mechanism reconciles conflicting experimental and theoretical findings on proton motion in GFP.
More Related Videos
10:50Using In Vitro Fluorescence Resonance Energy Transfer to Study the Dynamics Of Protein Complexes at a Millisecond Time Scale
Published on: March 14, 2019
11:51Engineering 'Golden' Fluorescence by Selective Pressure Incorporation of Non-canonical Amino Acids and Protein Analysis by Mass Spectrometry and Fluorescence
Published on: April 27, 2018
Related Concept Videos
Protein Dynamics in Living Cells
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Reporter Genes
Protein Diffusion in the Membrane
