Structural selection of ionic-complementary peptides with electrostatic interactions

Can Simple Interaction Models Explain Sequence-Dependent Effects in Peptide Homodimerization?

The development of rapid methods to explain and predict peptide interactions, aggregation, and self-assembly has become important to understanding amyloid disease pathology, the shelf stability of peptide therapeutics, and the design of novel peptide materials. Although experimental aggregation databases have been used to develop correlative and statistical models, molecular simulations offer atomic-level details that potentially provide greater physical insight and allow one to single out the most explanatory simple models. Here, we outline one such approach using a case study that develops homodimerization models for serine-glycine peptides with various hydrophobic leucine mutations. Using detailed all-atom simulations, we calculate reference dimerization free energy profiles and binding constants for a small peptide library. We then use statistical methods to systematically assess whether simple interaction models, which do not require expensive simulations and free energy calculation, can capture them. Surprisingly, some combinations of a few simple scaling laws well recapitulate the detailed, all-atom results with high accuracy. Specifically, we find that a recently proposed phenomenological hydrophobic force law and coarse measures of entropic effects in binding offer particularly high explanatory power, underscoring the physical relevance to association that these driving forces can play.

Graphene oxide inhibits hIAPP amyloid fibrillation and toxicity in insulin-producing NIT-1 cells

Human islet amyloid polypeptide (hIAPP or amylin) aggregation is directly associated with pancreatic β-cell death and subsequent insulin deficiency in type 2 diabetes (T2D). Since no cure is currently available for T2D, it is of great benefit to devise new anti-aggregation molecules, which protect β-cells against hIAPP aggregation-induced toxicity. Engineered nanoparticles have been recently exploited as anti-aggregation nanomedicines. In this work, we studied graphene oxide (GO) nanosheets for their potential for hIAPP aggregation inhibition by combining computational modeling, biophysical characterization and cell toxicity measurements. Using discrete molecular dynamics (DMD) simulations and in vitro studies, we showed that GO exhibited an inhibitory effect on hIAPP aggregation. DMD simulations indicated that the strong binding of hIAPP to GO nanosheets was driven by hydrogen bonding and aromatic stacking and that the strong peptide-GO binding efficiently inhibited hIAPP self-association and aggregation on the nanosheet surface. Secondary structural changes of hIAPP upon GO binding derived from DMD simulations were consistent with circular dichroism (CD) spectroscopy measurements. Transmission electron microscopy (TEM) images confirmed the reduction of hIAPP aggregation in the presence of GO. Furthermore, we carried out a cell toxicity assay and found that these nanosheets protected insulin-secreting NIT-1 pancreatic β-cells against hIAPP-induced toxicity. Our multidisciplinary study suggests that GO nanosheets have the potential to be utilized as an anti-aggregation nanomedicine itself in addition to a biosensor or delivery vehicle for the mitigation of T2D progression.

pH-dependent self-assembly of EAK16 peptides in the presence of a hydrophobic surface: coarse-grained molecular dynamics simulation

Self-assembly behavior of the three types of ionic peptide, EAK16, is studied in the presence of a hydrophobic surface using coarse-grained molecular dynamics simulations at three pH ranges of the solution. It is found that the peptide chains of all the three types assemble on the hydrophobic surface. EAK16-I and EAK16-II peptides assemble into ribbon-like structures, regardless of the value of pH. EAK16-IV peptide chains, however, assemble into ribbon-like structures at low and high pH ranges and form disc-shaped assemblies on the hydrophobic surface at the isoelectric point, pH = 7. Strong intra-chain electrostatic interactions in the case of EAK16-IV peptide play the main role in dependence of its self-assembly behavior on pH and the different morphology of its assembly relative to those of the two other types. Kinetics of growth of the assemblies on the hydrophobic surface is also studied.