The long-term objective of this work is to contribute to the fundamental understanding and eventual control of the 3-dimensional structures of proteins and the folding process by which those structures are achieved.
The specific aims i nclude the de novo design, synthesis and study of small model proteins; finding patterns and generalizations in the data base of known structures; and further development of methods for the display, analysis, and modeling of molecular structures. Past work has demonstrated the production of approximately correct tertiary structure for de novo designs of a helix bundle (Felix), two beta sandwiches (Betabellin and Betadoublet) and a (betaalpha)8 barrel (Babarellin); however, none of them (nor designs by other groups) shows unique, ell-ordered interiors. Therefore, the main thrust of this project for the next 5 year period will be working to understand (for natural proteins) and to produce (for designed proteins) the determination of unique conformations as opposed to molten-globule-like states. The primary tool for analyzing known structures and designing new ones will be interactive computer graphics; we are developing those methods both at the high end with a """"""""protein sculpting"""""""" tool that allows interactive modeling while doing energy minimization in real time, and at the low end with """"""""kinemages: that enable both communication and useful research with protein graphics on a Mac or PC. De novo design of new model proteins will attempt to integrate all that is known about the target structure type. Some of those designed proteins will be made by peptide synthesis, while most will be made by nucleic acid synthesis, cloning, and expression. After purification, initial characterization will be done primarily by circular dichroism (including cooperativity of unfolding); fluorescence, both of tryptophan and of bound ANS dye; and by nuclear magnetic resonance (NMR). When possible, full 3-D structures will be done wither by x-ray crystallography or by multi-dimensional NMR. These designed model proteins and variants of them will be used to test hypotheses about protein structure and folding, which should led to improvement of prediction methods and to improved control of biological, industrial, and clinical processes that depend on the folding, structure, and interaction of particular proteins. Eventually, such designed proteins should be capable of serving as controllable templates onto which desired new binding and catalytic functions will be built.
| Richardson, Jane S; Richardson, David C (2014) Biophysical highlights from 54 years of macromolecular crystallography. Biophys J 106:510-25 |
| Richardson, Jane S; Richardson, David C (2013) Studying and polishing the PDB's macromolecules. Biopolymers 99:170-82 |
| Richardson, Jane S; Richardson, David C (2013) Doing molecular biophysics: finding, naming, and picturing signal within complexity. Annu Rev Biophys 42:1-28 |
| Wales, Thomas E; Richardson, Jane S; Fitzgerald, Michael C (2004) Facile chemical synthesis and equilibrium unfolding properties of CopG. Protein Sci 13:1918-26 |
