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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.

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Related in: MedlinePlus

Residue-residue plot of correlated motions.The extent of correlation for all residue pairs (of Cα atomic displacement) during selected portions of the wild-type GTP (upper triangle) and wild-type GDP (lower triangle) Ras aMD simulations. The color scale runs from pink (for values ranging between −1 to −0.75), through white (−0.25 to 0.25) to cyan (0.75 to 1). Negative values are indicative of displacements along opposite directions, namely anticorrelated motions, whereas positive values depict correlated motions occurring along the same direction. Major secondary structure elements are indicated schematically with helices in black and strands in gray.
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pcbi-1000325-g003: Residue-residue plot of correlated motions.The extent of correlation for all residue pairs (of Cα atomic displacement) during selected portions of the wild-type GTP (upper triangle) and wild-type GDP (lower triangle) Ras aMD simulations. The color scale runs from pink (for values ranging between −1 to −0.75), through white (−0.25 to 0.25) to cyan (0.75 to 1). Negative values are indicative of displacements along opposite directions, namely anticorrelated motions, whereas positive values depict correlated motions occurring along the same direction. Major secondary structure elements are indicated schematically with helices in black and strands in gray.

Mentions: To examine whether the motions of one residue are related to the motions of another (distant) residue, the correlation of the displacements of all residue pairs were determined (Figure 3). As expected, the strongest positive correlations exist between covalently bonded residues and those residing within secondary structure elements (see Figures S5 and S6 for reference contact maps). Moving up the diagonal, the first area of notable correlations corresponds to helix α1 (residues 16 to 25) with loop2 (residues 26 to 40). The next area of significant correlation corresponds to the β2-loop3-β3 region (residues 38 to 57). The consistent appearance of correlated motions for these regions in each simulation and the cross-correlation (off-diagonal peak) with β1 (residues 2 to 10) highlights the subdomain-like structure and dynamics of these three N-terminal strands. The remaining strands, β4 to β6, display consistent positive cross-correlations with each other but not with strands β1 to β3. Note the off-diagonal peaks for β4 (residues 77 to 83) with β5 (residues 111 to 115) and β5 with β6 (residues 141 to 144). Moving further up the diagonal the next major correlations correspond to the SII region, encompassing loop4 and helix α2 (residues 58 to 74).


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

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

Residue-residue plot of correlated motions.The extent of correlation for all residue pairs (of Cα atomic displacement) during selected portions of the wild-type GTP (upper triangle) and wild-type GDP (lower triangle) Ras aMD simulations. The color scale runs from pink (for values ranging between −1 to −0.75), through white (−0.25 to 0.25) to cyan (0.75 to 1). Negative values are indicative of displacements along opposite directions, namely anticorrelated motions, whereas positive values depict correlated motions occurring along the same direction. Major secondary structure elements are indicated schematically with helices in black and strands in gray.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1000325-g003: Residue-residue plot of correlated motions.The extent of correlation for all residue pairs (of Cα atomic displacement) during selected portions of the wild-type GTP (upper triangle) and wild-type GDP (lower triangle) Ras aMD simulations. The color scale runs from pink (for values ranging between −1 to −0.75), through white (−0.25 to 0.25) to cyan (0.75 to 1). Negative values are indicative of displacements along opposite directions, namely anticorrelated motions, whereas positive values depict correlated motions occurring along the same direction. Major secondary structure elements are indicated schematically with helices in black and strands in gray.
Mentions: To examine whether the motions of one residue are related to the motions of another (distant) residue, the correlation of the displacements of all residue pairs were determined (Figure 3). As expected, the strongest positive correlations exist between covalently bonded residues and those residing within secondary structure elements (see Figures S5 and S6 for reference contact maps). Moving up the diagonal, the first area of notable correlations corresponds to helix α1 (residues 16 to 25) with loop2 (residues 26 to 40). The next area of significant correlation corresponds to the β2-loop3-β3 region (residues 38 to 57). The consistent appearance of correlated motions for these regions in each simulation and the cross-correlation (off-diagonal peak) with β1 (residues 2 to 10) highlights the subdomain-like structure and dynamics of these three N-terminal strands. The remaining strands, β4 to β6, display consistent positive cross-correlations with each other but not with strands β1 to β3. Note the off-diagonal peaks for β4 (residues 77 to 83) with β5 (residues 111 to 115) and β5 with β6 (residues 141 to 144). Moving further up the diagonal the next major correlations correspond to the SII region, encompassing loop4 and helix α2 (residues 58 to 74).

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