Computational design of new Peptide inhibitors for amyloid Beta (aβ) aggregation in Alzheimer's disease: application of a novel methodology.

Alzheimer's disease is the most common form of dementia. It is a neurodegenerative and incurable disease that is associated with the tight packing of amyloid fibrils. This packing is facilitated by the compatibility of the ridges and grooves on the amyloid surface. The GxMxG motif is the major factor creating the compatibility between two amyloid surfaces, making it an important target for the design of amyloid aggregation inhibitors. In this study, a peptide, experimentally proven to bind Aβ40 fibrils at the GxMxG motif, was mutated by a novel methodology that systematically replaces amino acids with residues that share similar chemical characteristics and subsequently assesses the energetic favorability of these mutations by docking. Successive mutations are combined and reassessed via docking to a desired level of refinement. This methodology is both fast and efficient in providing potential inhibitors. Its efficiency lies in the fact that it does not perform all possible combinations of mutations, therefore decreasing the computational time drastically. The binding free energies of the experimentally studied reference peptide and its three top scoring derivatives were evaluated as a final assessment/valuation. The potential of mean forces (PMFs) were calculated by applying the Jarzynski's equality to results of steered molecular dynamics simulations. For all of the top scoring derivatives, the PMFs showed higher binding free energies than the reference peptide substantiating the usage of the introduced methodology to drug design

Forces Applied to Unbind the Peptides.

<p>The red curve shows the average force applied along the reaction coordinate to unbind the top scoring inhibitor candidate whereas the black line shows the forces applied to unbind the reference peptide. Averages were taken over all SMD trajectories.</p

Structure of Protofilament Subunit of Aβ42.

<p>The Amyloid fibril (PDB ID: 2BEG) is shown in two separate representations; (i) Molecules are drawn as surfaces and (ii) molecules are drawn as secondary structure cartoons. Coloring is performed according to the residue type (non-polar residues (white), basic residues (blue), acidic residues (red) and polar residues (green)). Images were rendered using VMD.<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066178#pone.0066178-Humphrey1" target="_blank">[38]</a></p

Docking Scores of RGTFEGKF and its Derivatives.

<p>Mutated residues are underlined.</p

Potential of Mean Force for Unbinding.

<p>PMFs of the top scoring mutated peptides in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066178#pone-0066178-t002" target="_blank">Table 2</a> and the reference peptide with respect to the RC .</p

Flowchart of the Methodology.

<p>Flowchart of the Methodology.</p

Grouping System and Hydrophobicity Index[39] Used in This Study.

<p>Grouping System and Hydrophobicity Index<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066178#pone.0066178-Kyte1" target="_blank">[39]</a> Used in This Study.</p

Single Residue Mutations.

<p>Tested single residue mutations based on grouping system. Residues shown in red indicate mutations that resulted in higher docking scores.</p

Infrared spectroscopy of proteins in reverse micelles

AbstractReverse micelles are a versatile model system for the study of crowded microenvironments containing limited water, such as those found in various tissue spaces or endosomes. They also preclude protein aggregation. Reverse micelles are amenable to study by linear and nonlinear infrared spectroscopies, which have demonstrated that the encapsulation of polypeptides and enzymatically active proteins into reverse micelles leads to conformational changes not seen in bulk solution. The potential value of this model system for understanding the folding and kinetic behavior of polypeptides and proteins in biologically important circumstances warrants increased study of reverse micelle systems by infrared spectroscopy. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies