6FWW

GFP/KKK. A redesigned GFP with improved solubility


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.131 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein Solubility.

Gil-Garcia, M.Bano-Polo, M.Varejao, N.Jamroz, M.Kuriata, A.Diaz-Caballero, M.Lascorz, J.Morel, B.Navarro, S.Reverter, D.Kmiecik, S.Ventura, S.

(2018) Mol. Pharm. 15: 3846-3859

  • DOI: 10.1021/acs.molpharmaceut.8b00341

  • PubMed Abstract: 
  • The aggregation propensity of each particular protein seems to be shaped by evolution according to its natural abundance in the cell. The production and downstream processing of recombinant polypeptides implies attaining concentrations that are order ...

    The aggregation propensity of each particular protein seems to be shaped by evolution according to its natural abundance in the cell. The production and downstream processing of recombinant polypeptides implies attaining concentrations that are orders of magnitude above their natural levels, often resulting in their aggregation; a phenomenon that precludes the marketing of many globular proteins for biomedical or biotechnological applications. Therefore, there is a huge interest in methods aimed to increase the proteins solubility above their natural limits. Here, we demonstrate that an updated version of our AGGRESCAN 3D structural aggregation predictor, that now takes into account protein stability, allows for designing mutations at specific positions in the structure that improve the solubility of proteins without compromising their conformation. Using this approach, we have designed a highly soluble variant of the green fluorescent protein and a human single-domain VH antibody displaying significantly reduced aggregation propensity. Overall, our data indicate that the solubility of unrelated proteins can be easily tuned by in silico-designed nondestabilizing amino acid changes at their surfaces.


    Organizational Affiliation

    Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular , Universitat Autònoma de Barcelona , Bellaterra (Barcelona) 08193 , Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
266Aequorea victoriaMutation(s): 7 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
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: 1.131 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 31.814α = 90.00
b = 60.861β = 90.00
c = 106.401γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Database references