Limits...
Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.

Grant BJ, Gorfe AA, McCammon JA - PLoS Comput. Biol. (2009)

Bottom Line: The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function.In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras.Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD) simulations, is a low-frequency motion intrinsic to the structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California, United States of America. bgrant@mccammon.ucsd.edu

ABSTRACT
Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states. Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling. We characterize nucleotide-dependent conformational transition using multiple-barrier-crossing accelerated molecular dynamics (aMD) simulations. These transitions, achieved for the first time for wild-type Ras, are impossible to observe with classical molecular dynamics (cMD) simulations due to the large energetic barrier between end states. Mapping the reaction path onto a conformer plot describing the distribution of the crystallographic structures enabled identification of highly populated intermediate structures. These structures have unique switch orientations (residues 25-40 and 57-75) intermediate between GTP and GDP states, or distinct loop3 (46-49), loop7 (105-110), and alpha5 C-terminus (159-166) conformations distal from the nucleotide-binding site. In addition, these barrier-crossing trajectories predict novel nucleotide-dependent correlated motions, including correlations of alpha2 (residues 66-74) with alpha3-loop7 (93-110), loop2 (26-37) with loop10 (145-151), and loop3 (46-49) with alpha5 (152-167). The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function. In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras. Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD) simulations, is a low-frequency motion intrinsic to the structure.

Show MeSH

Related in: MedlinePlus

Conformational sampling in cMD and aMD simulations: projection of transient conformers onto the principal components obtained from analysis of Ras's crystallographic structures.Crystallographic GTP conformers are colored red whilst GDP conformers are colored green. The distribution of MD conformers is depicted with density-shaded blue points. Each row corresponds to a single initial conformation, namely: (A–D) wtGTP, (E–H) wtGDP and (I–L) mutantGDP. cMD simulations are depicted in the two left panels (A, B, E, F, I, J) whilst aMD simulations are depicted in the two right panels (C, D G, H, K, L). Simulations were performed with bound GTP (A, C, E, G, I, K) and GDP (B, D, F, H, J, L). Inserts show distances between instantaneous trajectory conformations and the centroids of the main GTP and GDP crystal structure clusters in red and green respectively (see Methods for further details).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2651530&req=5

pcbi-1000325-g001: Conformational sampling in cMD and aMD simulations: projection of transient conformers onto the principal components obtained from analysis of Ras's crystallographic structures.Crystallographic GTP conformers are colored red whilst GDP conformers are colored green. The distribution of MD conformers is depicted with density-shaded blue points. Each row corresponds to a single initial conformation, namely: (A–D) wtGTP, (E–H) wtGDP and (I–L) mutantGDP. cMD simulations are depicted in the two left panels (A, B, E, F, I, J) whilst aMD simulations are depicted in the two right panels (C, D G, H, K, L). Simulations were performed with bound GTP (A, C, E, G, I, K) and GDP (B, D, F, H, J, L). Inserts show distances between instantaneous trajectory conformations and the centroids of the main GTP and GDP crystal structure clusters in red and green respectively (see Methods for further details).

Mentions: Figure 1 shows the conformational space sampled by simulations projected onto the lowest PCs determined from the distribution of X-ray structures. These projections illustrate the correspondence of the crystal structure distribution and those adopted during simulations. Also shown, in terms of collective coordinates, is the time evolution of the distances between GDP and GTP conformation cluster centroids for each trajectory. All aMD simulations were found to have significantly larger fluctuations in the plane defined by the lowest PCs, indicating that the main collective displacements in the crystal structure cluster are accessible during aMD simulations (Figure 1C, 1D, 1G, 1H, 1K, and 1L and Table S2). In contrast, cMD simulations display a more limited sampling (Figure 1A, 1B, 1E, 1F, and 1J). A notable exception is the cMD simulation of the oncogenic G12V variant (Figure 1I), where the introduction of GTP into an initially GDP-bound structure induced evolution towards the cluster populated by the experimental GTP-like conformers. Additional cMD simulations of this varient with different starting conditions consistently sampled two distinct regions: one near the cluster containing the inactive form of the G12V variant, and another close to the cluster of the active structures, suggesting a spontaneous inactive to active transition.


Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.

Grant BJ, Gorfe AA, McCammon JA - PLoS Comput. Biol. (2009)

Conformational sampling in cMD and aMD simulations: projection of transient conformers onto the principal components obtained from analysis of Ras's crystallographic structures.Crystallographic GTP conformers are colored red whilst GDP conformers are colored green. The distribution of MD conformers is depicted with density-shaded blue points. Each row corresponds to a single initial conformation, namely: (A–D) wtGTP, (E–H) wtGDP and (I–L) mutantGDP. cMD simulations are depicted in the two left panels (A, B, E, F, I, J) whilst aMD simulations are depicted in the two right panels (C, D G, H, K, L). Simulations were performed with bound GTP (A, C, E, G, I, K) and GDP (B, D, F, H, J, L). Inserts show distances between instantaneous trajectory conformations and the centroids of the main GTP and GDP crystal structure clusters in red and green respectively (see Methods for further details).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651530&req=5

pcbi-1000325-g001: Conformational sampling in cMD and aMD simulations: projection of transient conformers onto the principal components obtained from analysis of Ras's crystallographic structures.Crystallographic GTP conformers are colored red whilst GDP conformers are colored green. The distribution of MD conformers is depicted with density-shaded blue points. Each row corresponds to a single initial conformation, namely: (A–D) wtGTP, (E–H) wtGDP and (I–L) mutantGDP. cMD simulations are depicted in the two left panels (A, B, E, F, I, J) whilst aMD simulations are depicted in the two right panels (C, D G, H, K, L). Simulations were performed with bound GTP (A, C, E, G, I, K) and GDP (B, D, F, H, J, L). Inserts show distances between instantaneous trajectory conformations and the centroids of the main GTP and GDP crystal structure clusters in red and green respectively (see Methods for further details).
Mentions: Figure 1 shows the conformational space sampled by simulations projected onto the lowest PCs determined from the distribution of X-ray structures. These projections illustrate the correspondence of the crystal structure distribution and those adopted during simulations. Also shown, in terms of collective coordinates, is the time evolution of the distances between GDP and GTP conformation cluster centroids for each trajectory. All aMD simulations were found to have significantly larger fluctuations in the plane defined by the lowest PCs, indicating that the main collective displacements in the crystal structure cluster are accessible during aMD simulations (Figure 1C, 1D, 1G, 1H, 1K, and 1L and Table S2). In contrast, cMD simulations display a more limited sampling (Figure 1A, 1B, 1E, 1F, and 1J). A notable exception is the cMD simulation of the oncogenic G12V variant (Figure 1I), where the introduction of GTP into an initially GDP-bound structure induced evolution towards the cluster populated by the experimental GTP-like conformers. Additional cMD simulations of this varient with different starting conditions consistently sampled two distinct regions: one near the cluster containing the inactive form of the G12V variant, and another close to the cluster of the active structures, suggesting a spontaneous inactive to active transition.

Bottom Line: The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function.In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras.Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD) simulations, is a low-frequency motion intrinsic to the structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California, United States of America. bgrant@mccammon.ucsd.edu

ABSTRACT
Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states. Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling. We characterize nucleotide-dependent conformational transition using multiple-barrier-crossing accelerated molecular dynamics (aMD) simulations. These transitions, achieved for the first time for wild-type Ras, are impossible to observe with classical molecular dynamics (cMD) simulations due to the large energetic barrier between end states. Mapping the reaction path onto a conformer plot describing the distribution of the crystallographic structures enabled identification of highly populated intermediate structures. These structures have unique switch orientations (residues 25-40 and 57-75) intermediate between GTP and GDP states, or distinct loop3 (46-49), loop7 (105-110), and alpha5 C-terminus (159-166) conformations distal from the nucleotide-binding site. In addition, these barrier-crossing trajectories predict novel nucleotide-dependent correlated motions, including correlations of alpha2 (residues 66-74) with alpha3-loop7 (93-110), loop2 (26-37) with loop10 (145-151), and loop3 (46-49) with alpha5 (152-167). The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function. In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras. Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD) simulations, is a low-frequency motion intrinsic to the structure.

Show MeSH
Related in: MedlinePlus