Beta-Strand Interfaces of Non-Dimeric Protein Oligomers Are Characterized by Scattered Charged Residue Patterns

Protein oligomers are formed either permanently, transiently or even by default. The protein chains are associated through intermolecular interactions constituting the protein interface. The protein interfaces of 40 soluble protein oligomers of stœchiometries above two are investigated using a quantitative and qualitative methodology, which analyzes the x-ray structures of the protein oligomers and considers their interfaces as interaction networks. The protein oligomers of the dataset share the same geometry of interface, made by the association of two individual β-strands (β-interfaces), but are otherwise unrelated. The results show that the β-interfaces are made of two interdigitated interaction networks. One of them involves interactions between main chain atoms (backbone network) while the other involves interactions between side chain and backbone atoms or between only side chain atoms (side chain network). Each one has its own characteristics which can be associated to a distinct role. The secondary structure of the β-interfaces is implemented through the backbone networks which are enriched with the hydrophobic amino acids favored in intramolecular β-sheets (MCWIV). The intermolecular specificity is provided by the side chain networks via positioning different types of charged residues at the extremities (arginine) and in the middle (glutamic acid and histidine) of the interface. Such charge distribution helps discriminating between sequences of intermolecular β-strands, of intramolecular β-strands and of β-strands forming β-amyloid fibers. This might open new venues for drug designs and predictive tool developments. Moreover, the β-strands of the cholera toxin B subunit interface, when produced individually as synthetic peptides, are capable of inhibiting the assembly of the toxin into pentamers. Thus, their sequences contain the features necessary for a β-interface formation. Such β-strands could be considered as ‘assemblons’, independent associating units, by homology to the foldons (independent folding unit). Such property would be extremely valuable in term of assembly inhibitory drug development

Cholera Toxin B Subunits Assemble into Pentamers - Proposition of a Fly-Casting Mechanism

The cholera toxin B pentamer (CtxB5), which belongs to the AB5 toxin family, is used as a model study for protein assembly. The effect of the pH on the reassembly of the toxin was investigated using immunochemical, electrophoretic and spectroscopic methods. Three pH-dependent steps were identified during the toxin reassembly: (i) acquisition of a fully assembly-competent fold by the CtxB monomer, (ii) association of CtxB monomer into oligomers, (iii) acquisition of the native fold by the CtxB pentamer. The results show that CtxB5 and the related heat labile enterotoxin LTB5 have distinct mechanisms of assembly despite sharing high sequence identity (84%) and almost identical atomic structures. The difference can be pinpointed to four histidines which are spread along the protein sequence and may act together. Thus, most of the toxin B amino acids appear negligible for the assembly, raising the possibility that assembly is driven by a small network of amino acids instead of involving all of them

beta-Strand Interfaces of Non-Dimeric Protein Oligomers are Characterized by Scattered Charge Residues Pattern

International audienceProtein oligomers are formed either permanently, transiently or even by default. The protein chains are associated through intermolecular interactions constituting the protein interface. The protein interfaces of 40 soluble protein oligomers of stœchiometries above two are investigated using a quantitative and qualitative methodology, which analyzes the x-ray structures of the protein oligomers and considers their interfaces as interaction networks. The protein oligomers of the dataset share the same geometry of interface, made by the association of two individual β-strands (β-interfaces), but are otherwise unrelated. The results show that the β-interfaces are made of two interdigitated interaction networks. One of them involves interactions between main chain atoms (backbone network) while the other involves interactions between side chain and backbone atoms or between only side chain atoms (side chain network). Each interaction network has its own characteristics which can be associated to a distinct role. The secondary structure of the β-interfaces is implemented through the backbone networks which are enriched with the hydrophobic amino acids favored in intramolecular β-sheets (MCWIV). The intermolecular specificity is provided by the side chain networks via positioning different types of charge residues at the extremities (arginine) and in the middle (glutamic acid and histidine) of the interface. Such charge distribution helps discriminating between sequences of intermolecular β-strands, of intramolecular β- strands and of β-strands forming β-amyloid fibers. This might open new venues for drug designs and predictive tool developments. Moreover, the β-strands of the cholera toxin B subunit interface, when produced individually as synthetic peptides, are capable of inhibiting the assembly of the toxin into pentamers. Thus, their sequences contain the features necessary for a β-interface formation. Such β-strands could be considered as 'assemblons', independent associating units, by homology to the foldons (independent folding unit). Such property would be extremely valuable in term of assembly inhibitory drug development

Local propensity of the central hydrophobic residue of the BB sub-networks affecting the 2D-structure prediction.

<p>Local propensity of the central hydrophobic residue of the BB sub-networks affecting the 2D-structure prediction.</p

Anti-parallel BB sub-network and intramolecular hydrogen bond network.

<p><b>A.</b> Gemini graph of an anti-parallel intermolecular β-interface <b>B.</b> Schematics of the hydrogen bond network of anti-parallel intramolecular β-sheet. <b>C.</b> Ladder pattern observed in BB sub-network and also visible in anti-parallel intramolecular β-sheet.</p

x-ray structures of the protein oligomers of the dataset.

<p>The respective PDB codes are indicated above the structures. The figure was made using RasMol. Each chain is shown in a different color.</p

Protein oligomers containing a β-interface.

<p><b>A.</b> The 1Q3S octameric bacterial chaperone <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032558#pone.0032558-Shomura1" target="_blank">[67]</a> and <b>B.</b> The 1PVN tetrameric protozoa oxidoreductase <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032558#pone.0032558-Gan1" target="_blank">[68]</a>. Both structures are represented using RasMol. The chains are colored in light grey and the secondary-structures are represented by helices and strands. The β-strands of the interfaces are colored in black and dark grey in ribbons.</p

Schematic of the charge distribution in β-interactions.

<p>The amino acids are indicated using the single letter code.</p

Histogram of the whole chain lengths.

<p>The length of the whole chain (range) is indicated on the x axis as the total number of amino acids.</p

Global propensity of the charged residue in the SC sub-networks.

<p>Global propensity of the charged residue in the SC sub-networks.</p