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

qq

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