1. How do proteins fold? Gary Benz and Claudia Winkler

2. What is a protein? Polymer (“necklace”) of amino acids 20 types of amino acids

3. What do proteins do? How is this possible? –By “folding” into a particular shape –Folding is fast (milliseconds) and reliable Carry out molecular function –Antibodies, enzymes, signals, etc –Proteins = Nature’s “nanomachines”

4. From necklace to protein: Hydrogen bonds are the glue Two key models of hydrogen bonding: alpha helix and beta sheets (A) is example of an alpha helix. The hydrogen bonds (dotted lines) are between oxygen atoms (red) and hydrogen atoms (white) (shown in this case as occurring every fourth pair of amino acids along the protein). (B) shows examples of beta-sheets held together by hydrogen bonds. When the protein folds onto itself completely it is said to make a “hairpin”

5. Protein folding mechanisms The next few slides show four different protein folding mechanisms currently being studied. These mechanisms describe different possible sequences and paths, shown with arrows, that the chains of amino acids can follow to go from the unfolded state to the final protein form, called the native state.

6. Diffusion/Collision First form secondary structure by diffusion/collision) –Hierarchical: form helices & hairpins, decrease entropy unfolded state formation of microdomains diffusion and collision of microdomains native state

7. Nucleation –Form nucleus of structure, then grow (ala 1 st order phase trans) unfolded state formation of a nucleus native state

8. Collapse Collapse first –Hydrophobically driven: remove water to form hydrogen bonds unfolded state collapse native state

9. Topomer search Form rough native shape first (topomer search) –Find the right “topology” first, then pack side chains unfolded state "topomer" native state

10. Evolution will use any mechanism that works! No single mechanism is observed, different examples appear in nature –Form secondary structure first (BBA5) Hierarchical: form alpha-helices & beta- sheets –Collapse first (protein G Hairpin) Hydrophobically driven: remove water to form hydrogen bonds first –Form rough native shape first (Villin)

11. A folding simulation

12. Unfolding simulation