Mimicking the action of GroEL in molecular dynamics simulations: application to the refinement of protein structures

Abstract

Bacterial chaperonin, GroEL, together with its co-chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release. Misfolded proteins first bind to an exposed hydrophobic surface on GroEL. GroES then encapsulates the substrate and triggers its release into the central cavity of the GroEL/ES complex for folding. In this work, we investigate the possibility to facilitate protein folding in molecular dynamics simulations by mimicking the effects of GroEL/ES namely, repeated binding and release, together with spatial confinement. During the binding stage, the (metastable) partially folded proteins are allowed to attach spontaneously to a hydrophobic surface within the simulation box. This destabilizes the structures, which are then transferred into a spatially confined cavity for folding. The approach has been tested by attempting to refine protein structural models generated using the ROSETTA procedure for ab initio structure prediction. Dramatic improvements in regard to the deviation of protein models from the corresponding experimental structures were observed. The results suggest that the primary effects of the GroEL/ES system can be mimicked in a simple coarse-grained manner and be used to facilitate protein folding in molecular dynamics simulations. Furthermore, the results support the assumption that the spatial confinement in GroEL/ES assists the folding of encapsulated proteins.

Figure 1.

(Top row) The time evolution of the backbone positional root mean square deviation (RMSD) of the elements of secondary structure for the NMR structure, 1afi, when subjected to each of the three refinement protocols: refolding in a hydrophilic cage (a); refolding in a repulsive cage (b); refolding in bulk water (c). (Middle row) The time evolution of the minimum distance between the protein substrate and the internal surface of the cage: refolding in a hydrophilic cage (d); refolding in a repulsive cage (e). (Bottom row) The time evolution of the internal potential energy of the protein: refolding in a hydrophilic cage (f); refolding in a repulsive cage (g); refolding in bulk water (h).

Figure 2.

(Upper graphs) The time evolution of the RMSD of the elements of secondary structure of the three ROSETTA models for the proteins 1vcc (a), 1sro (b), and 1afi (c) when refolding in a repulsive cage, and for 1vcc (d), 1sro (e), and 1afi (f) refolded in bulk water. (Lower graphs) The time evolution of the internal potential energy of the three protein models 1vcc (g), 1sro (h), and 1afi (i) refolding in a repulsive cage, and for 1vcc (j), 1sro (k), and 1afi (l) refolding in bulk water.

Figure 3.

(From left to right) The ROSETTA model of the protein 1vcc, the final structure after 150 nsec of refinement using 10 cycles of protocol II (repulsive cage), the structure of 1vcc determined experimentally (X-ray). The number below each figure corresponds to the backbone RMSD of the elements of secondary structure (nm) with respect to the experimental structure.

Figure 4.

(From left to right) The ROSETTA model of the protein 1sro, the final structure after 150 nsec of refinement using 10 cycles of protocol II (repulsive cage), the structure of 1sro determined experimentally (NMR). The number below each figure corresponds to the backbone RMSD of the elements of secondary structure (nm) with respect to the experimental structure.

Figure 5.

(From left to right) The ROSETTA model of the protein 1afi, the final structure after 150 nsec simulation using 10 cycles of protocol II (repulsive cage), the structure of 1afi determined experimentally (NMR). The number below each figure corresponds to the backbone RMSD of the elements of secondary structure (nm) with respect to the experimental structure.

Figure 6.

(From left to right) The relatively hydrophobic cage formed by a monolayer of densely packed CH2 particles incorporating only a small number of polar amide groups, the relatively hydrophilic cage consisting of a loosely packed hydrophobic surface and incorporating more amide groups, the repulsive cage formed from loosely packed repulsive particles.