David Richardson, Biochemistry

The theme of our laboratory is the analysis and design of proteins, from X-ray crystal structure determination, to analyzing patterns within all the known structures, to designing new proteins from scratch and synthesizing and characterizing them.

Good visualization of the features under study has always been an important aspect of our work, aided by our new methods for the representation and modeling of macromolecules: e.g.,

• ribbon drawings to show overall folds,
• kinemages and the associated Mage program to discover and communicate 3D ideas as open-ended graphics on low-end (or high-end) computers,
• Sculpt for interactive modeling where real-time energy minimization keeps the model physically realistic while you tug on it, and
• our two new programs, Probe and Reduce, for improving detailed structural accuracy.

Our study of the known protein structures has shown such features as Greek key beta barrels, right handed crossover connections, beta bulges, and helix N- and C-caps. Now our contact-dot methodology is revealing very specific packing of the hydrogen atoms. Protein design is a good way for all of us, including our students and trainees, to ask fundamental questions about why certain sequences form the specific structures they do, because starting over from scratch makes you stumble over any wrong assumptions. Our lab has designed and made examples of many structure types: e.g., helical Felix, beta-sheet Betabellin, and small SS-rich SScorin.

The most interesting discovery so far is that protein design (and probably folding and prediction as well) actually happens in two stages and the first stage is the easier one. That easier first step, which we and others have often done successfully now, is achieving the approximately correct tertiary structure. The second, much harder step is achieving a unique, non-molten, native-like structure with a well-ordered interior. For both stages, negative design (actively avoiding other alternatives) is at least as important as positive design, and we believe that understanding the details of internal packing will be crucial to the second stage. Laboratory methodology now uses the contact-dot surfaces (displayed in kinemages) to study packing in very high-resolution protein structures and to learn how to achieve such good fit in designed models.

Our current research focus is on the adaptive connection of sequence choice and local backbone conformation - i.e. the actual point of evolutionary change and adaption of protein structure, and on the actual nature of the protein surface sidechains with their alternate conformations that are the interface of recognition and control between proteins themselves and proteins and their effectors.