Refinement of homology-based protein structures by molecular dynamics simulation techniques

Abstract

The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to assess the efficiency of the ROSETTA method for ab initio protein structure prediction. For each protein, four models generated using the ROSETTA procedure were simulated for periods of between 5 and 400 nsec in explicit solvent, under identical conditions. In addition, the experimentally determined structure and the experimentally derived structure in which the side chains of all residues had been deleted and then regenerated using the WHATIF program were simulated and used as controls. A significant improvement in the deviation of the model structures from the experimentally determined structures was observed in several cases. In addition, it was found that in certain cases in which the experimental structure deviated rapidly from the initial structure in the simulations, indicating internal strain, the structures were more stable after regenerating the side-chain positions. Overall, the results indicate that molecular dynamics simulations on a tens to hundreds of nanoseconds time scale are useful for the refinement of homology or ab initio models of small to medium-size proteins.

Figure 1.

The time evolution of the backbone positional root mean square deviation (RMSD) of the ROSETTA model 1 for the protein 1afi after a least-squares best fit on all backbone atoms of experimental structure.

Figure 2.

(From left to right) ROSETTA model 1 of the protein 1afi, the final structure after 100 nsec of molecular dynamics (MD) simulation, and the structure of 1afi as determined experimentally using NMR. Below the first and second structures are given the backbone RMSDs (in nanometers) referring to the NMR structure.

Figure 3.

The time evolution of the backbone RMSD of the ROSETTA model 1 for 1afi (black line) and the ROSETTA model 2 for 1sro (gray line) with respect to the corresponding experimental structures.

Figure 4.

(From left to right) ROSETTA model 2 of 1afi, the final structure after 400 nsec of simulation, and the NMR structure of 1afi. The backbone RMSDs (in nanometers) are shown for each nonnative structure compared with the NMR structure.

Figure 5.

(From left to right) ROSETTA model 2 of 1sro, the final structure after 400 nsec of simulation, and the NMR structure of 1sro. The backbone RMSDs (in nanometers) are shown for each nonnative structure compared with the NMR structure.

Figure 6.

Refinement at different temperatures for model 1 of 1sap. (From left to right) The initial ROSETTA model, the models after 10 nsec of MD simulation at 300 K (top) and at 325 K (bottom), and the NMR structure of 1sap. The backbone RMSDs (in nanometers) are shown for the initial model and two models after simulation with respect to the NMR structure.

Figure 7.

Refinement at different temperatures for model 1 of 1lea. (From left to right) The initial ROSETTA model, the model after 10 nsec of MD simulation at 300 K (top) and at 325 K (bottom), and the NMR structure of 1lea. The backbone RMSDs (in nanometers) are shown for each nonnative structure as in Figure 6 ▶.