2O29

Spectroscopic and Structural Study of the Heterotropic Linkage between Halide and Proton Ion Binding to Gfp Proteins: E2(GFP)-BR Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Spectroscopic and Structural Study of Proton and Halide Ion Cooperative Binding to GFP.

Arosio, D.Garau, G.Ricci, F.Marchetti, L.Bizzarri, R.Beltram, F.

(2007) Biophys.J. 93: 232-244

  • DOI: 10.1529/biophysj.106.102319
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • This study reports the influence of halogens on fluorescence properties of the Aequorea victoria Green Fluorescent Protein variant S65T/T203Y (E(2)GFP). Halide binding forms a specific nonfluorescent complex generating a substantial drop of the fluor ...

    This study reports the influence of halogens on fluorescence properties of the Aequorea victoria Green Fluorescent Protein variant S65T/T203Y (E(2)GFP). Halide binding forms a specific nonfluorescent complex generating a substantial drop of the fluorescence via static quenching. Spectroscopic analysis under different solution conditions reveals high halogen affinity, which is strongly dependent on the pH. This evidences the presence in E(2)GFP of interacting binding sites for halide ions and for protons. Thermodynamic link and cooperative interaction are assessed demonstrating that binding of one halide ion is associated with the binding of one proton in a cooperative fashion with the formation, in the pH range 4.5-10, of a single fully protonated E(2)GFP.halogen complex. To resolve the structural determinants of E(2)GFP sensitivity to halogens, high-resolution crystallographic structures were obtained for the halide-free and I(-), Br(-), and Cl(-) bound E(2)GFP. Remarkably the first high-resolution (1.4 A) crystallographic structure of a chloride-bound GFP is reported. The chloride ion occupies a specific and unique binding pocket in direct contact (3.4 A) with the chromophore imidazolidinone aromatic ring. Unanticipated flexibility, strongly modulated by halide ion interactions, is observed in the region surrounding the chromophore. Furthermore molecular dynamics simulations identified E222 residue (along with the chromophore Y66 residue) being in the protonated state when E(2)GFP.halogen complex is formed. The impact of these results on high-sensitivity biosensor design will be discussed.


    Organizational Affiliation

    Scuola Normale Superiore, National Enterprise for nanoScience and nanoTechnology-Consiglio Nazionale delle Ricerche-Instituto Nazionale di Fisica della Materia, Pisa, Italy. d.arosio@sns.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
244Aequorea victoriaMutation(s): 3 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download SDF File 
Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRO
Query on CRO
A
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.144α = 90.00
b = 62.852β = 90.00
c = 69.172γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-11-29 
  • Released Date: 2007-05-15 
  • Deposition Author(s): Garau, G.

Revision History 

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance