scholarly journals The First Mutant of the Aequorea victoria Green Fluorescent Protein That Forms a Red Chromophore†

Biochemistry ◽  
2008 ◽  
Vol 47 (16) ◽  
pp. 4666-4673 ◽  
Author(s):  
Alexander S. Mishin ◽  
Fedor V. Subach ◽  
Ilia V. Yampolsky ◽  
William King ◽  
Konstantin A. Lukyanov ◽  
...  
Keyword(s):  
Green Fluorescent Protein ◽  
Fluorescent Protein ◽  
Aequorea Victoria ◽  
Green Fluorescent

scholarly journals Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein

1997 ◽  
Vol 94 (6) ◽  
pp. 2306-2311 ◽  
Author(s):  
K. Brejc ◽  
T. K. Sixma ◽  
P. A. Kitts ◽  
S. R. Kain ◽  
R. Y. Tsien ◽  
...  
Keyword(s):  
Green Fluorescent Protein ◽  
Fluorescent Protein ◽  
Structural Basis ◽  
Aequorea Victoria ◽  
Green Fluorescent

scholarly journals Photoacid behaviour in a fluorinated green fluorescent protein chromophore: ultrafast formation of anion and zwitterion states

2016 ◽  
Vol 7 (9) ◽  
pp. 5747-5752 ◽  
Author(s):  
S. P. Laptenok ◽  
J. Conyard ◽  
P. C. Bulman Page ◽  
Y. Chan ◽  
M. You ◽  
...  
Keyword(s):  
Excited State ◽  
Green Fluorescent Protein ◽  
Proton Transfer ◽  
Transfer Reaction ◽  
Fluorescent Protein ◽  
Proton Transfer Reaction ◽  
Aequorea Victoria ◽  
Excited State Proton Transfer ◽  
Green Fluorescent

The photophysics of the chromophore of the green fluorescent protein in Aequorea victoria (avGFP) are dominated by an excited state proton transfer reaction.

Crystal Structure of the Aequorea victoria Green Fluorescent Protein

Science ◽  
1996 ◽  
Vol 273 (5280) ◽  
pp. 1392-1395 ◽  
Author(s):  
M. Orm  ◽  
A. B. Cubitt ◽  
K. Kallio ◽  
L. A. Gross ◽  
R. Y. Tsien ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Green Fluorescent Protein ◽  
Fluorescent Protein ◽  
Aequorea Victoria ◽  
Green Fluorescent

Accurate and efficient structure-based computational mutagenesis for modeling fluorescence levels of Aequorea victoria green fluorescent protein mutants

2020 ◽  
Vol 33 ◽  
Author(s):  
Majid Masso
Keyword(s):  
Green Fluorescent Protein ◽  
Fluorescent Protein ◽  
Classification Performance ◽  
Machine Learning Algorithms ◽  
Sequence Structure ◽  
Aequorea Victoria ◽  
Function Relationship ◽  
Green Fluorescent ◽  
The Impact ◽  
Computational Mutagenesis

Abstract A computational mutagenesis technique was used to characterize the structural effects associated with over 46 000 single and multiple amino acid variants of Aequorea victoria green fluorescent protein (GFP), whose functional effects (fluorescence levels) were recently measured by experimental researchers. For each GFP mutant, the approach generated a single score reflecting the overall change in sequence-structure compatibility relative to native GFP, as well as a vector of environmental perturbation (EP) scores characterizing the impact at all GFP residue positions. A significant GFP structure–function relationship (P < 0.0001) was elucidated by comparing the sequence-structure compatibility scores with the functional data. Next, the computed vectors for GFP mutants were used to train predictive models of fluorescence by implementing random forest (RF) classification and tree regression machine learning algorithms. Classification performance reached 0.93 for sensitivity, 0.91 for precision and 0.90 for balanced accuracy, and regression models led to Pearson’s correlation as high as r = 0.83 between experimental and predicted GFP mutant fluorescence. An RF model trained on a subset of over 1000 experimental single residue GFP mutants with measured fluorescence was used for predicting the 3300 remaining unstudied single residue mutants, with results complementing known GFP biochemical and biophysical properties. In addition, models trained on the subset of experimental GFP mutants harboring multiple residue replacements successfully predicted fluorescence of the single residue GFP mutants. The models developed for this study were accurate and efficient, and their predictions outperformed those of several related state-of-the-art methods.

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