Citations in PubMed

Primary Citation PubMed: 9631087 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 18

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Single fluorescent protein-based Ca2+ sensors with increased dynamic range.

(2007) BMC Biotechnol 7

PubMed: 17603870 | PubMedCentral: PMC1931437 | DOI: 10.1186/1472-6750-7-37

Therefore, it is likely that in Pericams and GCaMPs the amino acid residues 148 and 145 are in a close proximity to the chromophore, similarly to the native avGFP (PDB ID: 1GFL) [ 15 ].

Publication Year: 2007

Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design.

(2009) J Biol Chem 284

PubMed: 19098007 | PubMedCentral: PMC2649101 | DOI: 10.1074/jbc.M807657200

Structural superimposition of the cpEGFP domain of either monomeric or dimeric GCaMP2 with the native GFP structures (PDB codes 1GFL ( 30 ) or 1EMA ( 31 )) shows root mean square deviations of only &#... 0223c;0.4 Å when comparing all common 220 C α atoms (supplemental Fig.

Publication Year: 2009

Photophysics and dihedral freedom of the chromophore in yellow, blue, and green fluorescent protein.

(2009) J Phys Chem B 113

PubMed: 19067572 | PubMedCentral: PMC2671006 | DOI: 10.1021/jp806285s

Experimental Section The coordinates of three crystal structures (1GFL,( 57 ) 1MYW,( 58 ) 2EMD( 59 )) were obtained from the Protein Data Bank (PDB),( 56 ) and hydrogen atoms were added to protein and... solvent atoms as required.

Publication Year: 2009

RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites.

(2011) Nat Chem Biol 7

PubMed: 21926996 | PubMedCentral: PMC3201715 | DOI: 10.1038/nchembio.657

Figure 4 Ten UAG sites are simultaneously suppressed with natural or unnatural amino acids in JX33 ( a ) GFP structure (PDB 1GFL) illustrating the sites where 10 UAG codons were introduced.

Publication Year: 2011

Deciphering the preference and predicting the viability of circular permutations in proteins.

(2012) PLoS One 7

PubMed: 22359629 | PubMedCentral: PMC3281007 | DOI: 10.1371/journal.pone.0031791

They were DHFR (PDB entry: 1RX4), disulfide oxidoreductase DsbA (PDB entry: 1A2J), wild-type GFP (PDB entry: 1GFL), GFP superfolder (PDB entry: 2B3P), GFP folding reporter (PDB entry: 2B3Q), myoglobin... (PDB entry: 5MBN) and phosphoribosylanthranilate isomerase domain (ePRAI; PDB entry: 1PII, residue: 256–452).

Well-defined protein splitting sites for PCA (see [77] for a summary), protein trans-splicing [75] , [76] and domain insertion [28] include residue 35 of ubiquitin (PDB entry: 1UBQ), 197 and 198 of β-lactamase (PDB entry: 1TEM), 106 of DHFR, 102 and 123 and 131 of intein (PDB entry: 2KEQ), 438 of firefly luciferase (PDB entry: 1BA3), 158 of green fluorescent protein (GFP; PDB entry: 1GFL), and 145 of enhanced yellow fluorescent protein (PDB entry: 1YFP).

Publication Year: 2012

FRET-based localization of fluorescent protein insertions within the ryanodine receptor type 1.

(2012) PLoS One 7

PubMed: 22719904 | PubMedCentral: PMC3374828 | DOI: 10.1371/journal.pone.0038594

The chromophoric center of the crystal structure of GFP (PDB ID 1GFL) [26] was then placed at the intersection point of these spheres.

Publication Year: 2012

A study on the effect of surface lysine to arginine mutagenesis on protein stability and structure using green fluorescent protein.

(2012) PLoS One 7

PubMed: 22792305 | PubMedCentral: PMC3392243 | DOI: 10.1371/journal.pone.0040410

Graphical image was generated using Discovery Studio Visualizer from Accelrys Software Inc. Results Analysis of the Electrostatic Interactions in GFP The electrostatic interactions in GFP were analyze... using the wild type GFP crystal structure with PDB Id 1GFL [29] .

The GFP crystal structure with PDB Id 1GFL [29] was used as a template structure in the modeling, which allowed us to assume that the local energy minimum of the modeled GFP variant was its native state.

Modeling and Molecular Dynamics Simulation of the GFP Variants The three dimensional structure of GFP con and the variant were modeled using the GFP structure with PDB Id 1GFL as the template [29] .

Publication Year: 2012

Intracellular CXCR4? cell targeting with T22-empowered protein-only nanoparticles.

(2012) Int J Nanomedicine 7

PubMed: 22923991 | PubMedCentral: PMC3423154 | DOI: 10.2147/IJN.S34450

17 Also, different Haddock models were obtained, in which the binding residues were established using crystallographic data from multimeric forms of GFP (1GFL, 1JC0, 3GJ2, 2QLE, 1EMC) and the higher i... teraction energy solutions resulting from protein-protein docking calculation.

Publication Year: 2012

Crystal structure of enhanced green fluorescent protein to 1.35 resolution reveals alternative conformations for Glu222.

(2012) PLoS One 7

PubMed: 23077555 | PubMedCentral: PMC3473056 | DOI: 10.1371/journal.pone.0047132

Comparison of EGFP structures with wild-type GFP and S65T GFP structures Superpositioning of the structure obtained for EGFP with that of wt GFP (PDB entry 1GFL [7] ) and a S65T GFP mutant (PDB entry ... EMA [8] ) shows that the overall structures are very similar ( Figure 3A ); the RMSD over the backbone and all atoms of EGFP and wt GFP is 0.40 Å and 1.03 Å respectively, whilst the RMSD over backbone and all atoms of EGFP and S65T GFP are 0.29 Å and 0.85 Å, respectively.

Whilst all of these waters superimpose with waters from the lower resolution EGFP structure 2Y0G, two of the waters (W 5 and W 6 ) are absent in both structures for wt GFP (1GFL) and for S65T GFP (1EMA).

(B) Superposition of E222 sidechain conformer A (E222a; green) and B (E222b; yellow) with the E222 side chain from wt GFP (1GFL; grey) and S65T GFP (1EMA; cyan).

Publication Year: 2012

GFP's mechanical intermediate states.

(2012) PLoS One 7

PubMed: 23118864 | PubMedCentral: PMC3485268 | DOI: 10.1371/journal.pone.0046962

Materials and Methods Computational Methods Computer simulations of GFP were based on an experimentally solved X-ray structure for the wild type GFP deposited in the Protein Data Bank (PDB) as 1GFL [4... ] .

Publication Year: 2012

Deletional protein engineering based on stable fold.

(2012) PLoS One 7

PubMed: 23240034 | PubMedCentral: PMC3519881 | DOI: 10.1371/journal.pone.0051510

Molecular Dynamic Simulation of s-GFP and s-DL4 The three dimensional structure of s-GFP and s-DL4 were modeled with template crystal structure of GFP (PDB ID 1GFL) [32] which does not contain the chr... mophore using the same procedure mentioned above for modeling the s-GFP with chromophore.

Publication Year: 2012

PeptideBuilder: A simple Python library to generate model peptides.

(2013) PeerJ 1

PubMed: 23717802 | PubMedCentral: PMC3661355 | DOI: 10.7717/peerj.80

The gray backbone corresponds to chain A of crystal structure 1gfl (green fluorescent protein), and the rainbow-colored backbone corresponds to the reconstructed version thereof.

Publication Year: 2013

Detecting repetitions and periodicities in proteins by tiling the structural space.

(2013) J Phys Chem B 117

PubMed: 23758291 | PubMedCentral: PMC3807821 | DOI: 10.1021/jp402105j

The length ( L i ) and center ( Z i ) of the selected tile are (a) βγ-crystallin (pdb: 1h4a, X) L i = 43, Z i = 149.5; (b) myoglobin (pdb: 1mbd, A) L i = 18, Z i = 29; (c) green fluore... cent protein (pdb: 1gfl, A) L i = 15, Z i = 182.5; and (d) β-lactamase (pdb: 4blm, A) L i = 15, Z i = 185.5.

Publication Year: 2013

Patch cloning method for multiple site-directed and saturation mutagenesis.

(2013) BMC Biotechnol 13

PubMed: 24164925 | PubMedCentral: PMC3829206 | DOI: 10.1186/1472-6750-13-91

(a)  Three-dimensional structure of GFP (PDB ID: 1GFL) depicted using the ribbon model.

Publication Year: 2013

Delivery of chemical cargo to endogenous proteins on live cells.

(2014) Front Chem 2

PubMed: 24790980 | PubMedCentral: PMC3982513 | DOI: 10.3389/fchem.2014.00011

The size scale of the glutamate receptor GluA2 structure [PDB: 3KG2 (Sobolevsky et al., 2009 )], IgG (Clark, 1997 ), GFP [PDB: 1GFL (Yang et al., 1996 )], and Cy3 are identical.

Publication Year: 2014

Superresolution imaging reveals structural features of EB1 in microtubule plus-end tracking.

(2014) Mol Biol Cell 25

PubMed: 25355949 | PubMedCentral: PMC4263457 | DOI: 10.1091/mbc.E14-06-1133

Protein structure modeling GFP structure (PDB entry 1GFL; Yang et al. , 1996 ), EB1 CH domain (PDB entry 1PA7; Hayashi and Ikura, 2003 ), and EB domain (PDB entry 3GJO; Honnappa et al.... , 2009 ) were used in structure modeling as previously described ( Xia et al. , 2012 ).

Publication Year: 2014

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4329989

The wt-GFP (PDB ID: 1GFL) and circular permutated EGFP (PDB ID: 3EVP) show the conformation of T203 as the “in” state.

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4543927

The crystal structure of GFP was derived from Yang et al. (1996) (1GFL.

The crystal structure of GFP was derived from Yang et al. (1996) (1GFL.

Publication Year: 2015