Self-assembling peptides are a class of supramolecular biofunctional materials held together by noncovalent interactions. They serve for different biomedical purposes, such as scaffolds for regenerative medicine and cell cultures, carriers for drug and gene delivery. Researchers have observed the formation of fibrils, but the crystallographic structure is not always available. Molecular Dynamics simulations can be used to assess the precise architecture and chemical bonds involved in the formation of self-assembling peptides. Different amyloid-like structures may be possible for a given peptide under different experimental conditions, allowing its folding. The aim of this work is to evaluate the stability of different possible configurations for seven peptide sequences. The end goal is to identify the most probable structures of the fibrils observed experimentally, through a stability analysis of the hypothesized configurations. Furthermore, the investigation includes a comparison of different peptides, considering the influence of an amino acid substitution on self-assembly.
I peptidi autoassemblanti sono una classe di materiali sopramolecolari biofunzionali, tenuti insieme da interazioni non covalenti. Hanno diverse applicazioni biomediche, come scaffold in ingegneria dei tessuti e carriers per drug delivery e gene delivery. Sperimentalmente è stata osservata la formazione di fibrille, ma la struttura cristallografica non è sempre ottenibile. Le simulazioni di dinamica molecolare possono essere sfruttate per valutare la precisa architettura molecolare ed i legami chimici coinvolti nel processo di assembly spontaneo. L’obiettivo del lavoro consiste nella caratterizzazione strutturale di sette sequenze peptidiche, considerando diverse possibili configurazioni simil-amiloidi per ciascun peptide. Lo scopo finale è la valutazione della stabilità delle configurazioni, al fine di avanzare ipotesi sulla struttura delle fibrille osservate sperimentalmente. Lo studio include diverse sequenze peptidiche, per valutare l’effetto di sostituzioni amminoacidiche sul processo di self-assembly.
Structural characterization of self-assembling peptides via molecular dynamics simulations
Polenghi, Marianna
2019/2020
Abstract
Self-assembling peptides are a class of supramolecular biofunctional materials held together by noncovalent interactions. They serve for different biomedical purposes, such as scaffolds for regenerative medicine and cell cultures, carriers for drug and gene delivery. Researchers have observed the formation of fibrils, but the crystallographic structure is not always available. Molecular Dynamics simulations can be used to assess the precise architecture and chemical bonds involved in the formation of self-assembling peptides. Different amyloid-like structures may be possible for a given peptide under different experimental conditions, allowing its folding. The aim of this work is to evaluate the stability of different possible configurations for seven peptide sequences. The end goal is to identify the most probable structures of the fibrils observed experimentally, through a stability analysis of the hypothesized configurations. Furthermore, the investigation includes a comparison of different peptides, considering the influence of an amino acid substitution on self-assembly.File | Dimensione | Formato | |
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https://hdl.handle.net/10589/170306