Protein structural robustness to mutations: an in silico investigation.

Proteins possess qualities of robustness and adaptability to perturbations such as mutations, but occasionally fail to withstand them, resulting in loss of function. Herein, the structural impact of mutations is investigated independently of the functional impact. Primarily, we aim at understanding the mechanisms of structural robustness pre-requisite for functional integrity. The structural changes due to mutations propagate from the site of mutation to residues much more distant than typical scales of chemical interactions, following a cascade mechanism. This can trigger dramatic changes or subtle ones, consistent with a loss of function and disease or the emergence of new functions. Robustness is enhanced by changes producing alternative structures, in good agreement with the view that proteins are dynamic objects fulfilling their functions from a set of conformations. This result, robust alternative structures, is also coherent with epistasis or rescue mutations, or more generally, with non-additive mutational effects and compensatory mutations. To achieve this study, we developed the first algorithm, referred to as Amino Acid Rank (AAR), which follows the structural changes associated with mutations from the site of the mutation to the entire protein structure and quantifies the changes so that mutations can be ranked accordingly. Assessing the paths of changes opens the possibility of assuming secondary mutations for compensatory mechanisms.

Intermolecular ß-strand networks avoid hub residues and favor low interconnectedness: a potential protection mechanism against chain dissociation upon mutation.

Altogether few protein oligomers undergo a conformational transition to a state that impairs their function and leads to diseases. But when it happens, the consequences are not harmless and the so-called conformational diseases pose serious public health problems. Notorious examples are the Alzheimer's disease and some cancers associated with a conformational change of the amyloid precursor protein (APP) and of the p53 tumor suppressor, respectively. The transition is linked with the propensity of ß-strands to aggregate into amyloid fibers. Nevertheless, a huge number of protein oligomers associate chains via ß-strand interactions (intermolecular ß-strand interface) without ever evolving into fibers. We analyzed the layout of 1048 intermolecular ß-strand interfaces looking for features that could provide the ß-strands resistance to conformational transitions. The interfaces were reconstructed as networks with the residues as the nodes and the interactions between residues as the links. The networks followed an exponential decay degree distribution, implying an absence of hubs and nodes with few links. Such layout provides robustness to changes. Few links per nodes do not restrict the choices of amino acids capable of making an interface and maintain high sequence plasticity. Few links reduce the "bonding" cost of making an interface. Finally, few links moderate the vulnerability to amino acid mutation because it entails limited communication between the nodes. This confines the effects of a mutation to few residues instead of propagating them to many residues via hubs. We propose that intermolecular ß-strand interfaces are organized in networks that tolerate amino acid mutation to avoid chain dissociation, the first step towards fiber formation. This is tested by looking at the intermolecular ß-strand network of the p53 tetramer.

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 ß-strands (ß-interfaces), but are otherwise unrelated. The results show that the ß-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 ß-interfaces is implemented through the backbone networks which are enriched with the hydrophobic amino acids favored in intramolecular ß-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 ß-strands, of intramolecular ß-strands and of ß-strands forming ß-amyloid fibers. This might open new venues for drug designs and predictive tool developments. Moreover, the ß-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 ß-interface formation. Such ß-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.