de Pablo Group: Protein Folding and Aggregation

Human Amylin

Islet amyloid polypeptide (IAPP), also known as amylin, is believed to be responsible for pancreatic amyloid fibrils prevalent in Type II Diabetes patients. The fibrils, as well as intermediates in their assembly, are cytotoxic to pancreatic ß-cells and are believed to contribute to the loss of ß-cell mass associated with Type II Diabetes. The factors that trigger islet amyloid deposition in vivo are not well understood, but peptide membrane interactions have been postulated to play an important role in islet amyloid formation. In order to better understand the mechanism and causes of aggregation, we use molecular simulations with a variety of novel, enhanced sampling and free-energy calculation techniques, including Metadynamics, replica exchange and bias-exchange. These are used to compare monomer structure and the early aggregation mechanisms in different environments, including water, 35% (wt) aqueous trehalose, and charged membranes.


Alzheimer’s Disease (AD) affects an estimated 5.4 million Americans and is the 6th leading cause of death in the US. Characteristic symptoms include profound episodic memory loss as well as cognitive decline. Beta-amyloid (Aβ) is responsible for amyloid plaques found in the neuronal tissue of AD patients. Aβ is produced from the cleavage of the transmembrane glycoprotein amyloid precursor protein by β- and γ-secretase and can range from 39-43 amino acids in length. The most predominant forms found are Aβ40 and Aβ42; furthermore there is a correlation between a higher ratio of Aβ42 to Aβ40 with AD. Similar to amylin, the protein deposits as well as the smaller oligomers are cytotoxic to neuronal cells. Currently, it is thought that the smaller oligomers are the more cytotoxic species. These small oligomers of Aβ may interfere with the permeability of the cellular membrane, which can lead to cellular death. Using molecular simulations and enhanced sampling techniques, we can learn more about this protein and its interactions at an atomistic level. With advance sampling methods such as metadynamics we can discern the prominent conformations of the protein and the influence of different environments on the free energy surface associated with the protein’s conformation and interactions. A better understanding of the mechanism of nucleation and aggregation at a molecular level as well as the effects induced by different environments may guide development of new drug therapies and further our understanding of Aβ‘s role in AD.


The aim of this project is to study, at a molecular detail, the folding and aggregation of long polyglutamine (PolyQ) chains. Under some circumstances, these peptides fold onto themselves adopting a metastable conformation that is believed to be the nucleus for subsequent polymerization of additional chains. Our work is motivated by a desire to understand the molecular mechanisms behind such a nucleated growth polymerization process, and by the fact that polyglutamine is of central importance in a number of neurodegenerative disorders, most notably Huntington’s Disease; literature studies concur in that a better understanding of the thermodynamics and kinetics of PolyQ folding and aggregation will accelerate the development of therapeutic treatments for Huntington’s and other expanded PolyQ diseases.

With this goal in mind, the project has been divided into several sub-projects involving:

  • The development of new simulation techniques that will enable efficient study of the PolyQ folding and aggregation processes, including a detailed analysis of the relevant transition states
  • The study of the folding process of individual PolyQ chains into plausible, metastable candidate folded structures
  • The study of the polymerization or aggregation process of multiple chains into stable oligomeric aggregates
  • The study of the effects of additives (solutes) and site mutations on the folding of individual chains and the aggregation of multiple chains

A detailed, atomic-level understanding of the pathways through which polyglutamine folds and polymerizes will emerge out of these studies, as well as methodological and fundamental advances that will have a positive, wide-ranging impact on the scientific community’s ability to understand protein misfolding and aggregation. Finally, the insights into PolyQ structure and dynamics under a variety of conditions will be of considerable use for development of therapeutic strategies.

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