The crowded and compartmentized environments inside cells are very different from the typical dilute conditions of in vitro and in silico biophysical studies of biomacromolecules. The long-term objectives of this project are to address the fundamental questions of how and how much macromolecular crowding and confinement affect thermodynamic and kinetic properties of biomolecules and to quantitatively reconstruct the influences of in vivo environments on these properties. The project has three integral components.
Aim 1 is to develop realistic theoretical models for crowding, which provide physical insight and yet allow for incorporation of molecular details.
Aim 2 is to carry out simulations and calculations for the interactions of proteins with atomistically detailed crowders, thereby direct quantitative comparison with in vitro experiments can be made.
Aim 3 is to validate theoretical predictions by in vitro experiments. Test problems encompass effects of crowding on the thermodynamics and kinetics of protein folding and protein binding. This project will overcome some of the major limitations of current approaches and make significant advances toward quantitatively reconstructing the influences of in vivo environments.
The proposed research will lead to a deeper understanding of biological processes inside cells and of pathological conditions such as Parkinson's disease in particular. This understanding may form the foundation for more accurate prognoses of and better therapies against such diseases.
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