PROTEIN AGGREGATION DISORDERS

Motivation: Misfolding, aggregation, and accumulation of diverse proteins in various organs lead to protein aggregation disorders. Type 2 diabetes (T2D) and cataract are two highly prevalent illnesses that we plan to investigate. Protein aggregation in cataract is a collaboration project with the Computational Soft Matter Group at the Chemical Engineering Department, Yale University.

Figure 3: A) Diabetes – a 21st century challenge, B) (PDB) human Islet amyloid polypeptide, C) Cataract, and D) (PDB) γD-crystallin

Type 2 diabetes – Intrinsically Disordered Proteins

In the traditional paradigm of structural biology, the functionality of biomolecules is thought to rely on their folding into welldefined three-dimensional structures. However, in the last decade, it has become increasingly clear that many intrinsically disordered proteins (IDPs) perform biological functions despite existing in largely unstructured states under physiological conditions, and their aggregation can lead to disorders. Islet amyloid polypeptide (IAPP) is an IDP found in pancreatic Beta-cells and its aggregation, which is inhibited by insulin oligomers in healthy cells, is associated with Type II Diabetes (T2D) (Fig. 3A-B). Although IAPPs have been the focus of many biochemical, pathological and pharmaceutical studies, major gaps remain in understanding IAPP binding and aggregation mechanisms and kinetics, and whether IAPP aggregation is the cause or the consequence of T2D. Previous studies have identified several gene variations associated with T2D, but their relation to IAPP aggregation is not addressed except for a gene that regulates Zn +2 ion concentration. It is speculated that Zn+2 affects aggregation indirectly through modulating insulin concentration, but due to the delicate balance between these perturbations and seemingly paradoxical experimental results, its role in aggregation remains elusive. A systematic computational investigation of IAPP aggregation can assist experimental efforts by allowing to probe various factors and the interplay between them in a controlled way.

In the initial stage of the project, our goal is to investigate the binding mechanisms of the intrinsically disordered IAPP to target molecules, using molecular dynamics combined with advanced sampling (i.e. replica exchange molecular dynamics, metadynamics) and free energy calculation techniques, and dimensionality reduction methods. Particularly, we plan to study IAPP dimerization and oligomerization in the presence of insulin and Zn+2. We will address the following questions:

1. What is the detailed mechanism insulin oligomerization in the presence of Zn+2?

2. How is the mechanism of IAPP aggregation affected by the competition/interaction between Zn+2 and insulin molecules?

3. How do the direct interactions between Zn+2 and IAPP affect IAPP aggregation?

In the long-run, our goal is to address questions like the effect of other environmental perturbations, posttranslational modifications and mutations on IAPP structure, function, and binding/folding mechanisms and dynamics. We are also interested in studying other IDPs associated with diseases (α-synuclein, tau protein, p53, and BRCA1). Coarse-graining efforts to reduce the computational cost of such simulations will assist in realizing this goal.

Cataract

Human lens at its core is comprised of an ordered arrangement of elongated fiber cells (Fig. 3C). Each fiber cell has a transparent cytosol highly concentrated with a family of water-soluble proteins known as crystallins (Fig. 3D). Misfolding of these crystallins can lead to the formation of protein aggregates in the lens, leading to a significant reduction in vision. It is recently discovered that lanosterol can potentially inhibit crystallin aggregation. Lanosterol’s active role in aggregation inhibition is proposed to stem from its amphiphilic nature that leads to strong specific interactions with the hydrophobic residues that are exposed to solvent. Nevertheless, the underlying mechanism still remains elusive as similar amphiphilic molecules, such as cholesterol, do not inhibit aggregation. Molecular dynamics simulations can complement the experimental endeavors in understanding crytallin aggregation by elucidating molecular characteristics on time and length scales that are not accessible to current experimental methods.

Initially, our goal is to investigate the early crystallin aggregation mechanism that leads to cataract, using atomistic molecular simulations and free energy calculations. We plan to probe the aggregation events both in pure water and aqueous mixtures containing amphiphilic molecules (i.e. lanosterol). In the medium-run, we plan to study the advanced stages of aggregation, as well as aggregation dynamics, which require coarse-graining efforts due to the high computational cost associated with atomistic models. Our long-term goal is to extend this project to protein aggregation disorders that are triggered by protein misfolding.

Electrical Double Layer Capacitors: From Fundamental Understanding to Design

Overview

The fast energy storage capability, durability and safety of EDLCs make them attractive candidates for use in high power applications such as pitch-control systems and back-up power for windmills, regenerative braking technologies and battery-assist devices for electric/hybrid cars, and replacements for truck, bus, crane and lifting vehicle engine starts. Despite these advantages, the widespread adoption of EDLC technology has been restricted due to EDLC’s limited energy storage capability. The main goal of the proposed work is to rationally design and manufacture electrical double layer capacitors with superior energy density that will maintain high power density, cycle life and safety while simultaneously lowering production costs. In this endeavor, we plan to combine functionalized two-dimensional carbon/boron composite sheets with room temperature ionic liquids enriched with carbon nanodots by molecularly self-assembling them into lamellar electrode-electrolyte nanocomposites. The high intrinsic capacitance and specific surface area of carbon-boron nanocomposites, combined with the high electrochemical stability of room temperature ionic liquids, and enhanced electronic conductivity in the presence of carbon nanodots will significantly improve device performance.

Intellectual Merit

The project will use a combined molecular simulation/machine learning and experimental approach to

1. Elucidate charge/discharge mechanisms to rationally tailor electrolyte/ electrode materials and seek out combinations with improved capacitive and electronic performance (i.e., intrinsic capacitance, electrochemical stability, conductivity),

2. Understand the mode and kinetics of charge transport in electrical double layer capacitors,

3. Apply this fundamental knowledge to develop process-ing strategies for optimized architecture,

4. Deliver electrical double layer capacitors with energy densi-ties (∼80-120 Wh/kg) with the intrinsic advantages of high power density (>104 W/kg), rapid charging (on the order of seconds), and long life (∼106 charge/discharge cycles).

The cost-effective scale-up potential of our device consolidation process will provide competitive performance to cost ratios compared to conventional commercially available electrical double layer capacitors. The innovation potential of the present proposal in relation to sectors which underpin the competitiveness and economic development of Turkey is substantial. To focus on a marketable product throughout the program, our team will initiate discussions that engage potential integrators to discuss specific product needs, which in turn will allow for rapid transition to practical applications in various areas ranging from electric vehicles, trains to wind turbine systems. If successful, incorporation of electrical double layer capacitors into these sectors will both help satisfy the growing need to be environmentally conscious by reducing greenhouse gas emissions and hazardous waste disposal, and decrease Turkey’s energy imports. It will also expand the high-end applications of boron-containing materials.