Abstract
Recently it has been proposed a model for fibrils of human insulin in which the fibril growth proceeds via stacking LVEALYL (fragment 11–17 from chain B of insulin) into pairs of tightly interdigitated -sheets. The experiments have also shown that LVEALYL has high propensity to self-assembly and binding to insulin. This necessitates study of oligomerization of LVEALYL and its binding affinity to full-length insulin. Using the all-atom simulations with Gromos96 43a1 force field and explicit water it is shown that LVEALYL can aggregate. Theoretical estimation of the binding free energy of LVEALYL to insulin by the molecular mechanic Poisson-Boltzmann surface area method reveals its strong binding affinity to chain B, implying that, in agreement with the experiments, LVEALYL can affect insulin aggregation via binding mechanism. We predict that, similar to LVEALYL, peptide RGFFYT (fragment B22-27) can self-assemble and bind to insulin modulating its fibril growth process. The binding affinity of RGFFYT is shown to be comparable with that of LVEALYL.
Highlights
Study of protein aggregation is of paramount importance as it is associated with a number of diseases such as Alzheimer’s disease, Hungtinton disease, spinocerebellar ataxia, type II diabetes [1,2,3,4,5] etc
Using all-atom simulations with the Gromos 43a1 force field and the simple point charge (SPC) water model, we show that LVEALYL forms antiparallel fibril
To probe the propensity of LVEALYL to fibrillation we have carried 8 Molecular dynamics (MD) runs starting from random conformations
Summary
Study of protein aggregation is of paramount importance as it is associated with a number of diseases such as Alzheimer’s disease, Hungtinton disease, spinocerebellar ataxia, type II diabetes [1,2,3,4,5] etc. Motivated by experimental results of Ivanova et al [18], in this paper we study self-assembly of peptide LVEALYL and its binding affinity to full-length insulin. LVEALYL peptide forms three hydrogen bonds with residues ILE-A2, GLN-A5, and THR-B27 of insulin molecule (Fig. 4).
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