Correlation between N-terminus anchoring and threonin-rich motif elongation at H2 domain.

<p>Anchoring of the N-terminus expressed as the average distance between residues 122–123 and 184–189 and elongation of threonin-rich motif expressed as the average distance between residues 190 and 194. Standard deviation bars and the regression coefficient (R) between the two data sets were also reported.</p

Hypothesized structures of E200K-PrP^C aggregates.

<p>(A) Representation of the E200K-PrP^C with its clusters of DRY (yellow) and HOH (red) minima. (B) Two E200K mutants chained through region 1-region 3 interactions. (C) Interaction of two E200K tetramers by the approach of hydrophobic clusters on region 2.</p

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

<div><p>The propensity of cellular prion protein to aggregation is reputed essential for the initiation of the amyloid cascade that ultimately lead to the accumulation of neurotoxic aggregates. In this paper, we extended and applied an already reported computational workflow [Proteins 2015; 83: 1751–1765] to elucidate in details the aggregation propensity of PrP protein systems including wild type, wild type treated at different [Ca²⁺] and E200K mutant. The application of the computational procedure to two segments of PrP^C, i.e. 125–228 and 120–231, allowed to emphasize how the inclusion of complete C-terminus and last portion (120–126) of the neurotoxic segment 106–126 may be crucial to unveil significant and unexpected interaction properties. Indeed, the anchoring of N-terminus on H2 domain detected in the wild type resulted to be disrupted upon either E200K mutation or Ca²⁺ binding, and to unbury hydrophobic spots on the PrP^C surface. A peculiar dinuclear Ca²⁺ binding motif formed by the C-terminus and the S2-H2 loop was detected for [Ca²⁺] > 5 mM and showed similarities with binding motifs retraced in other protein systems, thus suggesting a possible functional meaning for its formation. Therefore, we potentiated the computational procedure by including a tool that clusterize the minima of molecular interaction fields of a proteinand delimit the regions of space with higher hydrophobic or higher hydrophilic character, hence, more likely involved in the self-assembly process. Plausible models for the self-assembly of either the E200K mutated or Ca²⁺-bound PrP^C were sketched and discussed. The present investigation provides for structure-based information and new prompts that may represent a starting point for future experimental or computational works on the PrP^C aggregation.</p></div

Structural Reshaping of the Zinc-Finger Domain of the SARS-CoV‑2 nsp13 Protein Using Bismuth(III) Ions: A Multilevel Computational Study

The identification of novel therapeutics against the pandemic SARS-CoV-2 infection is an indispensable new address of current scientific research. In the search for anti-SARS-CoV-2 agents as alternatives to the vaccine or immune therapeutics whose efficacy naturally degrades with the occurrence of new variants, the salts of Bi3+ have been found to decrease the activity of the Zn2+-dependent non-structural protein 13 (nsp13) helicase, a key component of the SARS-CoV-2 molecular tool kit. Here, we present a multilevel computational investigation based on the articulation of DFT calculations, classical MD simulations, and MIF analyses, focused on the examination of the effects of Bi3+/Zn2+ exchange on the structure and molecular interaction features of the nsp13 protein. Our calculations confirmed that Bi3+ ions can replace Zn2+ in the zinc-finger metal centers and cause slight but appreciable structural modifications in the zinc-binding domain of nsp13. Nevertheless, by employing an in-house-developed ATOMIF tool, we evidenced that such a Bi3+/Zn2+ exchange may decrease the extension of a specific hydrophobic portion of nsp13, responsible for the interaction with the nsp12 protein. The present study provides for a detailed, atomistic insight into the potential anti-SARS-CoV-2 activity of Bi3+ and, more generally, evidences the hampering of the nsp13–nsp12 interaction as a plausible therapeutic strategy

Averaged MEP isosurfaces.

<p>Reported PrP were Ib (left), IIb (middle), and Vb (right) subsets. Positive and negative isosurfaces are depicted as blue and red meshes, respectively. Qualitative insight of the charge amount per region is also reported.</p

Simplified scheme of the formation of PrP aggregates.

<p>Simplified scheme of the formation of PrP aggregates.</p

Comparison of PrP primary structures.

<p>Segment a (125–228,top), segment b (120–231, middle), and whole 90–231 segment(down) of the human prion protein. * indicates amide capping by acetyl or N-methyl amide of N or C terminal, respectively. The neurotoxic peptide segment 106–126 is underlined.</p

Atomic fluctuations of PrP backbone.

<p>Root mean squared fluctuations per residue (rmsf) for I (circle), II (square), and V (triangle) systems and II-I (bold, square) and V-I (bold, triangle) rmsf difference per residue (Δrmsf); a and b systems reported on top and bottom, respectively. Boxes highlight the residues with Δrmsf values outside the range of −0.05–0.05 nm (dashed lines).</p

Summary of the investigated PrP systems and their labels.

<p>Summary of the investigated PrP systems and their labels.</p

The Ca²⁺-coordinating sites on the PrP structure.

<p>(A) Distribution of Ca²⁺ coordination sites by the superposition of all III-V systems. Details of the dinuclear coordination motif detected in region 1 obtained by (B) molecular dynamics simulation and (C) quantum mechanical optimization of a reduced model retrieved from system Vb.</p