ChemInform Abstract: Green Fluorescent Protein: Structure, Folding and Chromophore Maturation

ChemInform ◽  
2010 ◽  
Vol 41 (3) ◽  
Author(s):  
Timothy D. Craggs
Keyword(s):  
Green Fluorescent Protein ◽  
Protein Structure ◽  
Fluorescent Protein ◽  
Green Fluorescent

scholarly journals Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein

2016 ◽  
Author(s):  
Eleisha L. Jackson ◽  
Stephanie J. Spielman ◽  
Claus O. Wilke
Keyword(s):  
Green Fluorescent Protein ◽  
Protein Structure ◽  
Amino Acid ◽  
Protein Design ◽  
Fluorescent Protein ◽  
Computational Prediction ◽  
Single Amino Acid ◽  
Dimensional Structure ◽  
Amino Acid Deletion ◽  
Green Fluorescent

AbstractProteins evolve through two primary mechanisms: substitution, where mutations alter a protein’s amino-acid sequence, and insertions and deletions (indels), where amino acids are either added to or removed from the sequence. Protein structure has been shown to influence the rate at which substitutions accumulate across sites in proteins, but whether structure similarly constrains the occurrence of indels has not been rigorously studied. Here, we investigate the extent to which structural properties known to covary with protein evolutionary rates might also predict protein tolerance to indels. Specifically, we analyze a publicly available dataset of single–amino-acid deletion mutations in enhanced green fluorescent protein (eGFP) to assess how well the functional effect of deletions can be predicted from protein structure. We find that weighted contact number (WCN), which measures how densely packed a residue is within the protein’s three-dimensional structure, provides the best single predictor for whether eGFP will tolerate a given deletion. We additionally find that using protein design to explicitly model deletions results in improved predictions of functional status when combined with other structural predictors. Our work suggests that structure plays fundamental role in constraining deletions at sites in proteins, and further that similar biophysical constraints influence both substitutions and deletions. This study therefore provides a solid foundation for future work to examine how protein structure influences tolerance of more complex indel events, such as insertions or large deletions.

scholarly journals Crystal structures of green fluorescent protein with the unnatural amino acid 4-nitro-L-phenylalanine

2018 ◽  
Vol 74 (10) ◽  
pp. 650-655
Author(s):  
Nicole Maurici ◽  
Nicole Savidge ◽  
Byung Uk Lee ◽  
Scott H. Brewer ◽  
Christine M. Phillips-Piro
Keyword(s):  
Green Fluorescent Protein ◽  
Protein Structure ◽  
Amino Acid ◽  
Crystal Structures ◽  
Fluorescent Protein ◽  
Unnatural Amino Acid ◽  
Asymmetric Unit ◽  
Space Group ◽  
Green Fluorescent ◽  
Amber Codon Suppression

The X-ray crystal structures of two superfolder green fluorescent protein (sfGFP) constructs containing a genetically incorporated spectroscopic reporter unnatural amino acid, 4-nitro-L-phenylalanine (pNO2F), at two unique sites in the protein have been determined. Amber codon-suppression methodology was used to site-specifically incorporate pNO2F at a solvent-accessible (Asp133) and a partially buried (Asn149) site in sfGFP. The Asp133pNO2F sfGFP construct crystallized with two molecules per asymmetric unit in space group P3221 and the crystal structure was refined to 2.05 Å resolution. Crystals of Asn149pNO2F sfGFP contained one molecule of sfGFP per asymmetric unit in space group P4122 and the structure was refined to 1.60 Å resolution. The alignment of Asp133pNO2F or Asn149pNO2F sfGFP with wild-type sfGFP resulted in small root-mean-square deviations, illustrating that these residues do not significantly alter the protein structure and supporting the use of pNO2F as an effective spectroscopic reporter of local protein structure and dynamics.

Visualizing Proton Antenna in a High-Resolution Green Fluorescent Protein Structure

2010 ◽  
Vol 132 (32) ◽  
pp. 11093-11102 ◽  
Author(s):  
Ai Shinobu ◽  
Gottfried J. Palm ◽  
Abraham J. Schierbeek ◽  
Noam Agmon
Keyword(s):  
Green Fluorescent Protein ◽  
Protein Structure ◽  
High Resolution ◽  
Fluorescent Protein ◽  
Green Fluorescent
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