Protein Primer
Protein Primer
Outline Protein representations Structure of Proteins
– Primary: amino acid sequence– Secondary: -helices & -sheets– Tertiary: folding of a single molecule– Quaternary: relation between molecules
Computations on Proteins– Structure determination by X-ray crystallography– Electrostatic potential: docking studies– Molecular dynamics: folding and other interactions– Protein design
PXR: Pregnane Xenobiotic
ReceptorOH
P
P
O
O
O
O
O O
SR12813
Diagramatic representations
PXR with bound ligandBall & stick /
van der Waals spheres
Model diagram
Solvent accessible surface
Geometry on computers
Where we can see structure, shape, connections, regions,
The computer sees only coordinates
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 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…
UNC Graphic Lab: An NIH center for molecular graphics
Outline Protein representations Structure of Proteins
– Primary: amino acid sequence– Secondary: -helices & -sheets– Tertiary: folding of a single molecule– Quaternary: relation between molecules
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
20 amino acids Backbone: linked
peptide units Side chains differ Geometry: ,
angles at bonds with “-carbon”
Primary: amino acid sequence
Secondary structure: -helices
Stability by hydrogen bonds
Secondary structure: -sheets Parallel and
Anti-parallel
Also stabilized by H-bonds
Tertiary: folding e.g. myoglobin
Critically important: Structure Function
Several representations:– Spheres– Ribbons– Ball-stick, worms, …
Folds
Examples of patterns that occur often.
Biochemists like to classify…
Quaternary: relation between molecules
Docking & interfaces
X-ray crystallography
Atomic coordinates from X-ray experiments
Obtain magnitudes of coefficients of Fourier transform
Invert to find map of electron density
This is an under-constrained problem…
From crystal to structure
Data from X-ray diffractionElectron 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
Collect the forces on a molecule and integrate
Simulation steps in femto-seconds; activity in nano- to micro-seconds.
Some examples from Klaus Schulten’s group at UIUC
Simplifications, calibrated with experimental data
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
bonds
eqr rrK 2)(
angles
eqK 2)(
dihedrals
nVn
)cos(12
ji ij
ji
ij
ij
ij
ij
DR
R
B
R
A612
Electrostatic potential
Interaction between charged parts of molecule and charged atoms, such as H2O or ligands.
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 H2O (randomly oriented dipoles): 1/(Dr6).
Early use of Argonne arm: docking with force-feedback
Surface interaction energiesProteins interact with water and other molecules in their environment.
Depicted is a representation by Edelsbrunner et al. that has exact shape complementarity.
Protein design Dezymer software
– H. Hellinga, L. Looger– Input: fixed backbone
and ligand– Output: top-ranked
receptor designs
Example: RBP (Ribose Binding Protein) – Redesigned receptor site to bind TNT– Generated different receptor designs with modified
backbone