Protein Primer

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

PXR: Pregnane Xenobiotic Receptor SR12813

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

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…

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 ATOM 2 O GLY ATOM 3 N GLY ATOM 4 CA GLY ATOM 5 N LEU ATOM 6 CA LEU ATOM 7 CB LEU ATOM 8 CG LEU ATOM 9 CD1 LEU ATOM 10 CD2 LEU ATOM 11 C LEU ATOM 12 O LEU ATOM 13 N THR ATOM 14 CA THR ATOM 2395 O HOH ATOM 2396 O HOH ATOM 2397 O HOH ATOM 2398 O HOH ATOM 2399 O HOH ATOM 2400 O HOH ATOM 2401 O HOH ATOM 2402 O HOH ATOM 2403 O HOH ATOM 2404 O HOH ATOM 2405 O HOH ATOM 2406 O HOH END 2380 lines later…

UNC Graphic Lab: An NIH center for molecular graphics

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

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”

Primary: amino acid sequence

Secondary structure:  -helices n Stability by hydrogen bonds

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

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

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

Quaternary: relation between molecules n Docking & interfaces

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…

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

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

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

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

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

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.

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