Project Summary The advance in understanding of the molecular basis of human health in the past few decades has been tremendous. However, we are far behind in terms of the conversion of the information about structures and sequence of proteins into the corresponding functions. The progress on this front can be greatly advanced by multiscale computer simulations that can treat different systems with increased level of complexity. At this stage we are ready to apply such methods to systems whose understanding are relevant to important medical problems, including studies of enzyme design, drug resistance and transport mechanism of protons and ions, thereby elucidating the basis of catalytic control, bioenergetics and energy transduction in living systems. Our proposed concerted directions are listed below. A.1 Control of Biochemical Processes by Enzymes: Many diseases can be controlled by developing drugs that block the action of enzymes in crucial biological pathways. The great advances in structural and biochemical studies have not yet led to a quantitative understanding of the energetics of enzymatic reactions. Further quantitative progress requires reliable tools for the structure-function correlation of enzymes. Our advances in this direction have led to the development of effective multiscale methods for simulating enzyme catalysis. At this stage it is important to exploit our advances and to progress simultaneously in the following directions: (a) Quantifying computer-aided enzyme design by: (i) reproducing the observed catalytic effects of key designer enzymes by the EVB and other multiscale approaches. (ii) Using our multiscale approaches in enzyme design projects, including changing the action of promiscuous enzymes, improving available designer enzymes and helping in the design of new enzymes. After exploring the predictive power of our approaches, we will use them in collaboration with research groups that are involved in enzyme design experiments. (b) Continuing to advance quantitative computational methods, including: (i) using our PD QM(ai)/MM in evaluating the ab initio free energy surfaces of enzymatic reactions; (ii) using the PD approach to automatically refine EVB surfaces for exploring long distance mutational effects and catalytic landscapes; and (iii) Quantifying the relationship between folding and stability. (c) Exploring the catalytic effect of directed evolution and determining its relationship to natural evolution. (d) Conducting studies of important classes of enzymatic reactions. (e) The relations of our finding to medical problems (including drug resistance) will be explored. A.2 Multiscale Modeling of the energetics and functions of complex biological systems: Proteins that guide the transport of electrons, protons and ions underpin basic functions of living cells. For example, proton pumps regulate the electrochemical gradient that drives the transport of molecules across membranes. Similarly, ion channels play a vit...