Investigation of the molecular similarity in closely related protein systems: The PrP case study

Abstract

The amyloid conversion is a massive detrimental modification affecting several proteins upon specific physical or chemical stimuli characterizing a plethora of diseases. In many cases, the amyloidogenic stimuli induce specific structural features to the protein conferring the propensity to misfold and form amyloid deposits. The investigation of mutants, structurally similar to their native isoform but inherently prone to amyloid conversion, may be a viable strategy to elucidate the structural features connected with amyloidogenesis. In this article, we present a computational protocol based on the combination of molecular dynamics (MD) and grid-based approaches suited for the pairwise comparison of closely related protein structures. This method was applied on the cellular prion protein (PrP(C)) as a case study and, in particular, addressed to the quali/quantification of the structural features conferred by either E200K mutations and treatment with CaCl(2), both able to induce the scrapie conversion of PrP. Several schemes of comparison were developed and applied to this case study, and made up suitable of application to other protein systems. At this purpose an in-house python codes has been implemented that, together with the parallelization of the GRID force fields program, will spread the applicability of the proposed computational procedure.

The Effects of Ca2+ Concentration and E200K Mutation on the Aggregation Propensity of PrPC: A Computational Study

“…Several elements of novelty characterize the present investigation compared to the previously reported one [18]: i) two PrP segments, namely 125–228 and 120–231, were used to model 90–231 PrP C systems, their responsivity to the either E200K mutation of Ca 2+ treatment were tested; ii) The effect of Ca 2+ at different concentrations, i.e. 5, 10, and 20 mM, was monitored to model the progressive structural modifications, with the associated increase of aggregation propensity, induced by the Ca 2+ binding at PrP C ; iii) The computational tools for the analysis of molecular interaction properties were potentiated to identify regions of PrP surrounding space involved in the aggregation process; we showed how electrostatics and hydrophobic/hydrophilic character of the PrP C surface or outer space may be used to draw hypotheses on the protein self-assembly.…”

“…The computational workflow adopted in this work to investigate the molecular interaction properties of PrP systems is partially analogous to the one already reported in our previous work [18]. …”

“…After local minimization and alignment, the representative subsets are ready to be subjected to the analysis of molecular interaction properties that, as shown, follows two parallel branches of the workflow (Fig 1). By one side, the electrostatic properties affecting the considered PrP C systems are analyzed through the calculation of the molecular electrostatic potential (MEP) and compared in terms of MEP cross-similarity using the Carbò index (CI) [18, 19]. The MEP calculation and subsequent CI computation have been performed by using an in-house utility developed in Python [18, 20].…”

“…the well known pathogenic E200K mutation [13, 14] and the treatment of wild type PrP C with moderate Ca 2+ concentration [15–18]. By the use of a newly developed computational approach, we have eventually evidenced that both Ca 2+ concentration and E200K mutation induce a similar electrostatic asset and a similar increased aggregation propensity in the structure of PrP C [18], although several aspects are still to be elucidated: Which intermolecular forces do mainly determine the PrP C self-assembly? Which residues do play a major role in the self-assembly of PrP C , and are the same or different residues involved in either wild type, E200K mutant, or Ca 2+ -bound PrP C aggregation?…”

“…In this paper, we used a computational approach, mostly based on the already reported computational workflow [18], to elucidate in details the aggregation propensity of PrP protein systems including wild type, wild type treated at different [Ca 2+ ] or E200K mutant. Several elements of novelty characterize the present investigation compared to the previously reported one [18]: i) two PrP segments, namely 125–228 and 120–231, were used to model 90–231 PrP C systems, their responsivity to the either E200K mutation of Ca 2+ treatment were tested; ii) The effect of Ca 2+ at different concentrations, i.e.…”