dorsal/arxiv
View SchemaScenarios for protein aggregation: Molecular Dynamics simulations and Bioinformatic Analysis
| Authors | Ruxandra I. Dima, Bogdan Tarus, John E. Straub, D. Thirumalai |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0608041 |
| URL | https://arxiv.org/abs/q-bio/0608041 |
Abstract
The need to understand the assembly kinetics of fibril formation has become urgent because of the realization that soluble oligomers of amyloidogenic peptides may be even more neurotoxic than the end product, namely, the amyloid fibrils. In order to fully understand the routes to fibril formation one has to characterize the major species in the assembly pathways. The characterization of the energetics and dynamics of oligomers (dimers, trimers etc) is difficult using experiments alone because they undergo large conformational fluctuations. In this context, carefully planned molecular dynamics simulation studies, computations using coarse-grained models, and bioinformatic analysis have given considerable insights into the early events in the route to fibril formation. Here, we describe progress along this direction using examples taken largely from our own work. In this chapter, we focus on aspects of protein aggregation using Abeta-peptides and prion proteins as examples.
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"abstract": "The need to understand the assembly kinetics of fibril formation has become\nurgent because of the realization that soluble oligomers of amyloidogenic\npeptides may be even more neurotoxic than the end product, namely, the amyloid\nfibrils. In order to fully understand the routes to fibril formation one has to\ncharacterize the major species in the assembly pathways. The characterization\nof the energetics and dynamics of oligomers (dimers, trimers etc) is difficult\nusing experiments alone because they undergo large conformational fluctuations.\nIn this context, carefully planned molecular dynamics simulation studies,\ncomputations using coarse-grained models, and bioinformatic analysis have given\nconsiderable insights into the early events in the route to fibril formation.\nHere, we describe progress along this direction using examples taken largely\nfrom our own work. In this chapter, we focus on aspects of protein aggregation\nusing Abeta-peptides and prion proteins as examples.",
"arxiv_id": "q-bio/0608041",
"authors": [
"Ruxandra I. Dima",
"Bogdan Tarus",
"John E. Straub",
"D. Thirumalai"
],
"categories": [
"q-bio.BM"
],
"title": "Scenarios for protein aggregation: Molecular Dynamics simulations and Bioinformatic Analysis",
"url": "https://arxiv.org/abs/q-bio/0608041"
},
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