A structural study for the optimisation of functional motifs encoded in protein sequences-4

<p><b>Copyright information:</b></p><p>Taken from "A structural study for the optimisation of functional motifs encoded in protein sequences"</p><p>BMC Bioinformatics 2004;5():50-50.</p><p>Published online 30 Apr 2004</p><p>PMCID:PMC420233.</p><p>Copyright © 2004 Via and Helmer-Citterich; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</p>re clearly not correctly structurally aligned, though they fall in the same cell of the HET. The 3D multiple alignment grid is represented in green as a 2D grid. Structure segments of protein A and B are reported in red and black, respectively. This pair of residues is discarded after visual analysis. b. Two different residues (ARG and ASP) belonging to two aligned proteins (protein A and B), which clearly correspond though they do not fall in the same cell of the HET. This pair of residues is included in the R-HET after visual inspection

Superimposed ligands and matching pseudoatoms.

<p>The ligands of serine racemase from <i>Schizosaccharomyces pombe</i> (2zpu) and Argininosuccinate synthetase from <i>Thermus thermophilus</i> (1kor) superimposed according to the binding site similarity identified by superpose3D. This residue description uses pseudoatoms representing specific side-chain groups. The matching pseudoatoms are shown as spheres. 2zpu is shown with darker colors.</p

Two enzymes with similar substrate binding sites.

<p>The figure depicts the active sites of the teichoic acid phosphorylcholine esterase Pce from <i>Streptococcus pneumoniae</i> (2bib, left) and a methionine aminopeptidase from <i>Escherichia coli</i> (2gg8, right). These unrelated enzymes use similar mechanisms and have analogous binding modes for the substrate (left) and an inhibitor (right).</p

Alternative residue representations.

<p>Three alternative ways to represent histidine, along with the corresponding syntax used by superpose3D. The atoms are named according to the PDB standard. The “avg(ND1,ND2):bar” statement (middle) defines a pseudoatom named “bar” whose coordinates correspond to the geometric centroid of the ND1 and NE2 atoms. The “\N;\O” statement (right) specifies that all the atoms that contain an “N” or “O” in their names should be included in the representation.</p

Comparison of two metal coordination sites.

<p>The proeins involved are Lysyl oxidase from <i>Pichia pastoris</i> (1w7c, left) and rabbit glycogenin-1 (1ll2, right).</p

Comparison of two anion binding loops.

<p>The loop on the left binds phosphate while the right one binds the O2 and O3′ of the riboflavine moiety of FAD. Left: dethiobiotin synthetase from <i>Escherichia coli</i> (1dak); right: D-amino acid oxidase from the yeast <i>Rhodotorula gracilis</i> (1c0i). In this figure and in the following ones protein residues are represented as sticks and ligands as ball and sticks. Moreover ligand names are written in bold.</p

Comparison of two FAD binding sites including side chain information.

<p>The same binding pockets depicted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011988#pone-0011988-g003" target="_blank">Figure 3</a> were compared using a description that includes side-chain information. The residues comprising the β-sheets were not used in the comparison. See text for details.</p

Comparison of two FAD binding sites.

<p>The two binding pockets belong to proteins of different Rossmann-like folds. Left: human monoamine oxidase B (2v61); right: Electron transfer flavoprotein from <i>Methylophilus methylotrophus</i> (3clt). The central β-sheets that characterize these structures are shown in the picture but only the binding site residues were used in the comparison.</p

Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites-0

<p><b>Copyright information:</b></p><p>Taken from "Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S24</p><p>BMC Bioinformatics 2007;8(Suppl 1):S24-S24.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885854.</p><p></p> number and type of aligned amino acids. The arrows describe permutations and inversions in protein sequences; the N to C-term direction is colour-coded (blue is associated to N-term and red to C-term). a) The residues involved in the match bind S-adenosyl-homocysteine (1boo) and S-adenosyl-methionine (1vidA), and share a high structural similarity. b) Matching residues bind ADP, Mg and PHY in the 1iow structure; and ADP, Mg and GSH in the 2hgs structure c) The 1dljA residues involved in the match bind a 1,4-dihydronicotinamide adenine dinucleotide; 1say is 92% identical to 1pjc, which binds nicotinamide-adenine-dinucleotide with the residues involved in the 3D match. d) In 1b0uA, the matching residues bind an ATP molecule; 1kklA is 100% identical to 1jb1A, which binds PO4 with the residues involved in the 3D match (see Results)

Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites-2

<p><b>Copyright information:</b></p><p>Taken from "Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S24</p><p>BMC Bioinformatics 2007;8(Suppl 1):S24-S24.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885854.</p><p></p>and the HPr K/P protein chains are shown as blue and red ribbons. The local match of 1b0uA and 1kklA residues is highlighted in cyan and yellow, respectively