We propose to develop next generation of theory of protein folding that will be quantitative up to single residue resolution level. The theory will provide kinetic and thermodynamic """"""""fingerprints"""""""" of major protein folds outlining which residues are most important for thermodynamic stabilization and which ones are kinetic """"""""accelerator pedals"""""""". This will help to rationalize the emerging evolutionary data from multiple sequence alignments of natural proteins. In pursuing this goal we will develop a series of important techniques and theoretical approaches such as efficient Monte-Carlo protein design, analytical theory of sequence selection in proteins and fold designability, an evolutionary algorithm for selection of most kinetically competent sequences of real protein folds. Further, we will develop analytical theory and simulations to provide full rationale to the nucleation mechanism of folding, including the most important issue of what are the determinants of protein folding nucleus. As a corollary to this effort we will carry out experimental studies of protein """"""""surgery"""""""" and """"""""orthodontics"""""""" whereby we will transplant folding nucleus of a fast-folding protein ADA2h into its slow-folding structural homolog AcP in order to dramatically raise the folding rate of the latter. Furthermore we will test the theory of nucleation by experimental studies of villin where we will rationally redesign folding nucleus into aromatic core and will study functional, kinetic and thermodynamic consequences of nucleus shifts.
