Research Interests

The Ytreberg group uses physics principles and computer simulations to understand protein structure, function and evolution. Examples of specific research projects are outlined below.

p53 protein bound to MDM2 protein Developing free energy methods. The free energy is a direct measure of how strongly proteins interact with ligands or with other proteins. Estimating free energies using computer simulation is useful for a wide variety of applications such as designing new drugs and predicting how amino acid changes modify protein interactions. Calculating free energy values for proteins is challenging and requires a lot of simulation time. The Ytreberg group is interested in developing methods that improve the speed and accuracy of free energy calculations for proteins.
phiX174 bacteriophage virus Determining the biophysical mechanisms for protein evolution. It is recognized that protein-protein interactions are a vital component of evolution since it is thought that well over half of proteins exist in complexes with other proteins. However, little is known about the biophysical connection between protein-protein interactions and protein evolution. The Ytreberg group is interested in determining this biophysical connection by studying the effects of amino acid changes on protein-protein interactions in biological systems such as viruses.
p53 protein structures Structure, function and evolution of intrinsically disordered proteins. Intrinsically disordered proteins are common in humans and their dysfunction is associated with many human diseases, including cancer and neurodegenerative disease. Most experimental and computational methods in structural biology are not suitable for disordered proteins because they are highly dynamic and do not form compact structures. The Ytreberg group is interested in determining structural ensembles for disordered proteins, in studying their evolution, and in designing drugs that bind to these proteins.