Proteins are nanoscale molecules that perform functions essential for biological life. Membranes surrounding cells, for example, contain receptor proteins that mediate communication between the cell and the external milieu, membrane transporters that transport ions and larger compounds across the membranes, and enzymes that catalyze chemical reactions. Likewise, soluble proteins found in interior of the cell include motor proteins that move other proteins around, enzymes that bind to and repair breaks in the DNA, and proteins that help control the cellular clock. Mutations in genes that encode proteins can cause disease, as is the case of cystic fibrosis, a disease that associates with mutation of a chloride channel called the cystic fibrosis transmembrane conductance regulator.1 The essential functions they perform in the cell makes proteins essential drug targets for modern bio-medical applications. An important example here is the programmed death ligand-1 (PD-L1), which is a valuable target for modern immunotherapy.2-4 Predicting how a protein responds to a drug molecule, or using the protein as inspiration for biotechnological applications, require knowledge of how that protein works. As proteins are dynamic entities and protein dynamics are essential for function,5-8 describing the mechanism of action of a protein requires knowledge about the protein motions in fluid environments. Theoretical biophysics provides valuable tools to characterize protein reaction mechanisms and protein motions at the atomic level of detail.
This Habilitation Thesis presents research on using theoretical biophysics approaches to decipher how proteins work. The focus of the research is on membrane proteins and reactions that occur at lipid membrane interfaces. The central question I address is the role of dynamic hydrogen (H) bonds in protein function and membrane interactions. The methods used include quantum mechanical (QM) computations of small molecules, combined quantum mechanics/molecular mechanics (QM/MM) of chemical reactions in protein environments, classical mechanical computations of large protein and membrane systems, and bridging numerical simulations to bioinformatics. In my research group we developed algorithms to identify H-bond networks in proteins and membrane environments, and to characterize the dynamics of these networks. To extend the applicability of numerical computations to bio-systems that bind drug-like compounds, we derive parameters for a potential energy function widely used in the field. The main research topics and specific questions addressed are summarized below together with a discussion of the computational approaches used.
