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1.  Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis 
The yellow fluorescent protein phiYFPv with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium.
The yellow fluorescent protein phiYFPv (λem max ≃ 537 nm) with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The latter fluorescent protein is one of only two known cases of naturally occurring proteins that exhibit emission spectra in the yellow–orange range (535–555 nm). Here, the crystal structure of phiYFPv has been determined at 2.05 Å resolution. The ‘yellow’ chromophore formed from the sequence triad Thr65-Tyr66-Gly67 adopts the bicyclic structure typical of fluorophores emitting in the green spectral range. It was demonstrated that perfect antiparallel π-stacking of chromophore Tyr66 and the proximal Tyr203, as well as Val205, facing the chromophore phenolic ring are chiefly responsible for the observed yellow emission of phiYFPv at 537 nm. Structure-based site-directed mutagenesis has been used to identify the key functional residues in the chromophore environment. The obtained results have been utilized to improve the properties of phiYFPv and its homologous monomeric biomarker tagYFP.
doi:10.1107/S0907444913004034
PMCID: PMC3663121  PMID: 23695245
yellow fluorescent protein; Phialidium; structure–function relationship; chromophores; oligomeric structure; intersubunit surface
2.  Structural basis for bathochromic shift of fluorescence in far-red fluorescent proteins eqFP650 and eqFP670 
The crystal structures of the far-red fluorescent proteins eqFP650 and eqFP670 have been solved at 1.8 and 1.6 Å resolution, respectively. This permitted identification of the structural elements responsible for the bathochromic shift in both considered far-red fluorescent proteins.
The crystal structures of the far-red fluorescent proteins (FPs) eqFP650 (λex max/λem max 592/650 nm) and eqFP670 (λex max/λem max 605/670 nm), the successors of the far-red FP Katushka (λex max/λem max 588/635 nm), have been determined at 1.8 and 1.6 Å resolution, respectively. An examination of the structures demonstrated that there are two groups of changes responsible for the bathochromic shift of excitation/emission bands of these proteins relative to their predecessor. The first group of changes resulted in an increase of hydrophilicity at the acylimine site of the chromophore due to the presence of one and three water molecules in eqFP650 and eqFP670, respectively. These water molecules provide connection of the chromophore with the protein scaffold via hydrogen bonds causing an ∼15 nm bathochromic shift of the eqFP650 and eqFP670 emission bands. The second group of changes observed in eqFP670 arises from substitution of both Ser143 and Ser158 by asparagines. Asn143 and Asn158 of eqFP670 are hydrogen bonded with each other, as well as with the protein scaffold and with the p-hydroxyphenyl group of the chromophore, resulting in an additional ∼20 nm bathochromic shift of the eqFP670 emission band as compared to eqFP650. The role of the observed structural changes was verified by mutagenesis.
doi:10.1107/S0907444912020598
PMCID: PMC3489099  PMID: 22948909
far-red fluorescent proteins; cell imaging; tissue visualization; Katushka
3.  Structure of the N-terminal fragment of Escherichia coli Lon protease 
The medium-resolution structure of the N-terminal fragment of E. coli Lon protease shows that this part of the enzyme consists of two compact domains and a very long α-helix.
The structure of a recombinant construct consisting of residues 1–245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2.6 Å resolution utilizing trigonal crystals that contained one molecule in the asymmetric unit. The molecule consists of two compact subdomains and a very long C-terminal α-helix. The structure of the first subdomain (residues 1–117), which consists mostly of β-strands, is similar to that of the shorter fragment previously expressed and crystallized, whereas the second subdomain is almost entirely helical. The fold and spatial relationship of the two subdomains, with the exception of the C-terminal helix, closely resemble the structure of BPP1347, a 203-amino-acid protein of unknown function from Bordetella parapertussis, and more distantly several other proteins. It was not possible to refine the structure to satisfactory convergence; however, since almost all of the Se atoms could be located on the basis of their anomalous scattering the correctness of the overall structure is not in question. The structure reported here was also compared with the structures of the putative substrate-binding domains of several proteins, showing topological similarities that should help in defining the binding sites used by Lon substrates.
doi:10.1107/S0907444910019554
PMCID: PMC2917273  PMID: 20693685
anomalous diffraction; ATP-dependent proteases; protein domains; structure quality; Lon protease
4.  Structure of the unbound form of HIV-1 subtype A protease: comparison with unbound forms of proteases from other HIV subtypes 
The crystal structure of the unbound form of HIV-1 subtype A protease has been determined to 1.7 Å resolution. A detailed structural analysis and comparison of the unbound subtype A, B and C protease structures is presented. The results showed that although no inhibitor is present in the active site, the subtype A protease has flaps in the closed position.
The crystal structure of the unbound form of HIV-1 subtype A protease (PR) has been determined to 1.7 Å resolution and refined as a homodimer in the hexagonal space group P61 to an R cryst of 20.5%. The structure is similar in overall shape and fold to the previously determined subtype B, C and F PRs. The major differences lie in the conformation of the flap region. The flaps in the crystal structures of the unbound subtype B and C PRs, which were crystallized in tetragonal space groups, are either semi-open or wide open. In the present structure of subtype A PR the flaps are found in the closed position, a conformation that would be more anticipated in the structure of HIV protease complexed with an inhibitor. The amino-acid differences between the subtypes and their respective crystal space groups are discussed in terms of the differences in the flap conformations.
doi:10.1107/S0907444909054298
PMCID: PMC2827345  PMID: 20179334
HIV-1 proteases; HIV-1 protease subtype A; unbound; crystal packing
5.  Structure of the Taz2 domain of p300: insights into ligand binding 
The crystal structure of the Taz2 zinc-finger domain of the human p300 transcriptional coactivator was determined using the anomalous diffraction signal of the bound Zn ions. Crystal contacts suggested a possible novel mode of Taz2–peptide ligand interactions.
CBP and its paralog p300 are histone acetyl transferases that regulate gene expression by interacting with multiple transcription factors via specialized domains. The structure of a segment of human p300 protein (residues 1723–1836) corresponding to the extended zinc-binding Taz2 domain has been investigated. The crystal structure was solved by the SAD approach utilizing the anomalous diffraction signal of the bound Zn ions. The structure comprises an atypical helical bundle stabilized by three Zn ions and closely resembles the solution structures determined previously for shorter peptides. Residues 1813–1834 from the current construct form a helical extension of the C-terminal helix and make extensive crystal-contact interactions with the peptide-binding site of Taz2, providing additional insights into the mechanism of the recognition of diverse transactivation domains (TADs) by Taz2. On the basis of these results and molecular modeling, a hypothetical model of the binding of phosphorylated p53 TAD1 to Taz2 has been proposed.
doi:10.1107/S0907444909040153
PMCID: PMC2789004  PMID: 19966416
zinc-finger proteins; anomalous diffraction; protein recognition; transcription regulation
6.  Is too ‘creative’ language acceptable in crystallography? 
A brief comment is made on the need to use carefully selected, novel terms in crystallographic publications, especially publications addressing non-specialists.
While figures of speech are often useful and even educational, flashy titles combined with hyperbolae and imprecise language can mislead or deceive non-specialist readers and should therefore be avoided. The possibility of such confusion exists when poorly defined terms like ‘structure quality’ or ‘super-resolution’ are used to describe a protein structure.
doi:10.1107/S090744491002799X
PMCID: PMC2935284  PMID: 20823556
letters to the editor; crystallographic terminology

Results 1-6 (6)