Design of New Protein Catalysts using Rosetta .pptVIP

Enzyme design using Rosetta Alexandre Zanghellini, Baker lab Angles of attack for computational enzyme design Fundamental assumptions behind enzyme design Example of specificity identification: galactosidase Automated detection of homologs Screening of pocket complementarity using RosettaDesign Angles of attack for computational enzyme design Example of de-novo design : design of a Diels-Alderase Theozyme model : optimal catalytic side-chain placement Matching theozyme in scaffold: linking QM to protein science A native enzyme benchmark for RosettaMatch RosettaMatch is a robust method to identify active sites Design using RosettaDesign w/ small molecule “Dock perturbations” Adding internal ligand internal degrees of freedom during refinement The RosettaMatch Algorithm Fundamental assumption: catalytic side-chain can be treated separately Matching algorithm uses spatial hashing to identify transition state locations where all catalytic constraints can be satisfied by sidechain rotamers extending from the protein backbone Cite prebiotic hypothesis Say which part I have particularly developed. Cite prebiotic hypothesis * Specificity identification De novo design of activity In existing scaffold (fixed bb) Design of de novo scaffold with new activity/functions S TS P ?G Kcal/mol Simplified example of carbamate hydrolysis through nucleophilic attack Catalysis can be obtained by lowering the free energy of activation along the reaction pathway The physical forces that are involved in lowering the free energy of activation in enzyme active sites are the same that are involved in stabilizing proteins - H-bonding energy- electrostatic interaction - VdW interactions (dipole induced atom/atom interactions)- solvation As a first approximation, it is possible to focus on the highest energy barrier (i.e. deacylation) or only limited number of states Question: can we find an existing galactosidase that is specific for galactosylceramide but n