Assembly of proteins and peptides plays an essential role in the structure and inner-workings of the cell. On the other hand, uncontrolled aggregation of peptides is seen as the source of Neurodegenerative diseases such as Alzheimer's. In this project our aim is to understand the aggregation mechanism of proteins and peptides and to develop new techniques for controlling and guiding this assembly process. In particular we are interested in the role of macroscopic and molecular hydrophobic/hydrophilic interfaces. To this end we use atomistic and coarse-grained computer models to study the aggregation of these molecules. Within this project we are also collaborating with Prof. Christine Peter from University of Konstanz.
Engin, O. & Sayar, M. Adsorption, Folding and Packing of an Amphiphilic Peptide at
the Air/Water Interface. J. Phys. Chem. B 116 (7), 2198–2207 (2012).
Development of Transferable Coarse Grained Models for Proteins/Peptides
One common approach to bridge the time and length scale gap between MD simulations and biologically relevant events is to employ coarse-grained models of Proteins/Peptides. Most of the state of the art CG models are parameterized to represent a single state point, and their validity upon changing the state point (different temperature, concentration, conformational change, or aggregation) is questionable and has to be carefully analyzed before utilizing. In this project, we are developing a transferable coarse-grained model for proteins and peptides that can reproduce folding, aggregation and partitioning behaviour observed at hydrophobic/hydrophilic interfaces.
Conformation, Packing, and Aggregation of DNA
Understanding the supercoil and bubble formation energetics/dynamics in the DNA molecule is important for resolving the structure-function relationship, the melting behavior, twist-writhe interplay, etc. In recent years, several experimental and theoretical studies have focused on the DNA supercoils and bubbles. Theoretical models, such as the Peyrard-Bishop model or the Poland-Scheraga model, are typically over-simplified. Full atomistic computational models are feasible for short chains (10-15 bps) only. In this project, a coarse-grained model is developed. Our coarse-grained model successfully reproduces the local geometry of the DNA molecule, such as the 3'-5' directionality, major-minor groove structure, and the helical pitch. We compare the persistence length and melting behavior of the coarse-grained model with the experimental and theoretical results. This project is done in collaboration with Alkan Kabakcioglu. Snapshots of model DNA minicircles at three different lengths and three different excess linking numbers densities can be found here .
