Protein Structure Prediction and

Refinement

If the models are good enough to predict peptide structure.

Protein Structure Refinement

Why Refinement of Protein Structural Models.

• Homology models contain little additional information compared to the template structures (unless they can be refined).

Bi-annual CASP competitionCASP: Critical Assessment of techniques for protein Structure Prediction

• An inability to determine the relative merit of ab-initio models.

Aim: To refine models from ROSETTA1 (currently the best semi ab inito structure prediction algorithm.)

1. Baker et al. J. Mol. Biol. (2001) 306, 1191-1199.

Test-set: 20 proteins used by Baker et al. to test ROSETTA (J. Mol. Biol. (2001) 306, 1191-1199).

For each protein 4 ROSETTA models released from ROSETTA

1. The best (closest to experimental structure)2. The worst (furthest from experimental structure)3. Random example4. Random example

Proceedure:1. Build side-chains2. Simulate in explicit solvent3. Compare to the experimental structure (do we do better or worse).

Controls:1. Simulate experimental structure (NMR or x-ray).2. Simulate experimental structure with side-chains deleted and rebuilt.

Refinement of Protein Structural Models

MD refinement of the best Rosetta model for 1AIF(mercury detoxification protein)

NMR structure ROSETTA model

0.26 nm RMSD

RefinementMD 100 ns

0.16 nm RMSD

Fan Hao

MD Refinement of Rosetta models for 1AIF

Refinement is systematicgiven an ability to simulate

on a relevant time scale.

Fan Hao

NMR structure

ROSETTA models

2

3

4

0.90 nm RMSD

1.03 nm RMSD

0.91 nm RMSD

0.63 nm RMSD

0.92 nm RMSD

0.90 nm RMSD

after 5ns MD

1AIF

Some improvement in 3 of 4 cases

Fan Hao

ROSETTA model RefinementMD 5 ns

RefinementMD 400 ns

NMR structure

MD refinement of an alternate ROSETTA model for 1afi

0.87 nm RMSD 0.76 nm RMSD 0.70 nm RMSD

Refinement of an alternate model for 1afi

RMSD 0.87 nm

RMSD 0.76 nm

RMSD 0.70 nm

Refinement of 1sro(PNPase)

ROSETTA modelNMR structure

0.87 nm RMSD

Fan Hao

RMSD 0.88 nm

RMSD 0.67 nm RMSD 0.70 nm

NMRRefinement of 1sro

(PNPase)