1. Protein Primer

2. Outline n Protein representations n Structure of Proteins Structure of Proteins –Primary: amino acid sequence –Secondary:  -helices &  -sheets –Tertiary: folding of a single molecule –Quaternary: relation between molecules n Computations on Proteins –Structure determination by X-ray crystallography –Electrostatic potential: docking studies –Molecular dynamics: folding and other interactions –Protein design

3. PXR: Pregnane Xenobiotic Receptor SR12813

4. Diagramatic representations n PXR with bound ligand  Ball & stick / van der Waals spheres  Model diagram  Solvent accessible surface

5. Geometry on computers n Where we can see structure, shape, connections, regions, n The computer sees only coordinates n For example, this PXR protein & ligand is in the Protein Data Bank as…

6. HEADER GENE REGULATION 08-MAY-01 1ILG TITLE CRYSTAL STRUCTURE OF APO HUMAN PREGNANE X RECEPTOR LIGAND. AUTHOR R.E.WATKINS,M.R.REDINBO. ATOM 1 C GLY 142 -5.808 44.753 13.561 1.00 58.97 6 ATOM 2 O GLY 142 -5.723 45.523 14.515 1.00 59.54 8 ATOM 3 N GLY 142 -4.377 43.177 14.842 1.00 59.37 7 ATOM 4 CA GLY 142 -5.307 43.330 13.685 1.00 59.68 6 ATOM 5 N LEU 143 -6.324 45.108 12.387 1.00 58.87 7 ATOM 6 CA LEU 143 -6.839 46.455 12.152 1.00 58.50 6 ATOM 7 CB LEU 143 -6.483 46.907 10.736 1.00 57.90 6 ATOM 8 CG LEU 143 -5.849 48.290 10.555 1.00 57.77 6 ATOM 9 CD1 LEU 143 -4.599 48.411 11.407 1.00 56.51 6 ATOM 10 CD2 LEU 143 -5.505 48.492 9.090 1.00 56.92 6 ATOM 11 C LEU 143 -8.352 46.446 12.333 1.00 58.92 6 ATOM 12 O LEU 143 -9.046 45.640 11.714 1.00 59.85 8 ATOM 13 N THR 144 -8.862 47.341 13.174 1.00 58.88 7 ATOM 14 CA THR 144 -10.299 47.407 13.444 1.00 59.76 6 ATOM 2395 O HOH 1600 29.442 64.461 -1.726 1.00 66.79 8 ATOM 2396 O HOH 1601 19.427 85.921 -22.662 1.00 60.16 8 ATOM 2397 O HOH 1602 5.344 90.815 7.154 1.00 54.96 8 ATOM 2398 O HOH 1603 -14.216 50.571 5.561 1.00 54.96 8 ATOM 2399 O HOH 1604 5.533 45.964 0.404 1.00 62.55 8 ATOM 2400 O HOH 1605 -1.394 63.145 20.705 1.00 40.08 8 ATOM 2401 O HOH 1606 -2.578 54.566 22.874 1.00 57.40 8 ATOM 2402 O HOH 1607 3.600 69.196 22.807 1.00 54.51 8 ATOM 2403 O HOH 1608 6.139 65.007 -18.611 1.00 54.86 8 ATOM 2404 O HOH 1609 4.202 75.224 -27.568 1.00 58.04 8 ATOM 2405 O HOH 1610 -5.421 61.703 24.061 1.00 57.88 8 ATOM 2406 O HOH 1611 -11.943 45.372 11.041 1.00 62.72 8 END 2380 lines later…

7. UNC Graphic Lab: An NIH center for molecular graphics

8. Outline n Protein representations n Structure of Proteins Structure of Proteins –Primary: amino acid sequence –Secondary:  -helices &  -sheets –Tertiary: folding of a single molecule –Quaternary: relation between molecules n Computations on Proteins –Structure determination by X-ray crystallography –Electrostatic potential: docking studies –Molecular dynamics: folding and other interactions –Protein design

9. Primary: amino acid sequence n 20 amino acids 20 amino acids n Backbone: linked peptide units n Side chains differ Geometry: ,  angles at bonds with “  -carbon”

10. Primary: amino acid sequence

11. Secondary structure:  -helices n Stability by hydrogen bonds

12. Secondary structure:  -sheets n Parallel and Anti-parallel n Also stabilized by H-bonds

13. Tertiary: folding e.g. myoglobin n Critically important: Structure  Function Critically important n Several representations: –Spheres –Ribbons –Ball-stick, worms, …

14. Folds n Examples of patterns that occur often. n Biochemists like to classify…

15. Quaternary: relation between molecules n Docking & interfaces

16. X-ray crystallography n Atomic coordinates from X-ray experiments n Obtain magnitudes of coefficients of Fourier transform n Invert to find map of electron density n This is an under- constrained problem…

17. From crystal to structure Data from X-ray diffraction  Electron density maps  Threaded backbone ...

18. Crystallographic refinement clashes with hydrogen atoms (not seen by x- rays) better choice of side chain &modified backbone resolves clashes fit structure to electron density from x-ray diffraction

19. Molecular dynamics n Collect the forces on a molecule and integrate n Simulation steps in femto- seconds; activity in nano- to micro-seconds. n Some examples from Klaus Schulten’s group at UIUCKlaus Schulten’s group at UIUC

20. n Simplifications, calibrated with experimental data n A minimal set of forces: –Bond lengths: stretch from equilibrium –Bond angles: bending from equilibrium –Bond twist angles: rotation from equilibrium –van der Waals contact & electrostatic forces Forces on a molecule

21. Electrostatic potential n Interaction between charged parts of molecule and charged atoms, such as H 2 O or ligands. n Strength depends on distance r –Long range attraction: 1/(Dr). The dielectric const, D, is 80 in water, 2-4 in protein. –Short range attraction through H 2 O (randomly oriented dipoles): 1/(Dr 6 ). n Early use of Argonne arm: docking with force-feedback

22. Surface interaction energies Proteins interact with water and other molecules in their environment. Depicted is a representation by Edelsbrunner et al. that has exact shape complementarity.

23. Protein design n Dezymer software –H. Hellinga, L. Looger –Input: fixed backbone and ligand –Output: top-ranked receptor designs n Example: RBP (Ribose Binding Protein) –Redesigned receptor site to bind TNT –Generated different receptor designs with modified backbone