Global Conformational Dynamics in Ras

O’Connor, Casey M.; Kovrigin, Evgenii L.

doi:10.1021/bi801076c

Cited by 70 publications

(86 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The ␣3-helix and P-loop were thought to be rather immobile from crystallographic studies. However, the backbone amide 15 N spin relaxation rcCPMG measurements by O'Connor et al (32) suggested that they exhibit a significant mobility upon state transition, which is further supported by our latest study 4 of 15 N relaxation times and heteronuclear nuclear Overhauser effects of H-RasT35S-GppNHp. As already proposed (21), the various events relevant to the state transition could be targeted for development of Ras inhibitors, i.e.…”

Section: Conservation Of the Roles Of The Novel Intramolecular Interasupporting

confidence: 73%

Critical Roles of Interactions among Switch I-preceding Residues and between Switch II and Its Neighboring α-Helix in Conformational Dynamics of the GTP-bound Ras Family Small GTPases

Matsumoto

Shima

Muraoka

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

Section: Conservation Of the Roles Of The Novel Intramolecular Interasupporting

confidence: 73%

Critical Roles of Interactions among Switch I-preceding Residues and between Switch II and Its Neighboring α-Helix in Conformational Dynamics of the GTP-bound Ras Family Small GTPases

Matsumoto

Shima

Muraoka

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…A coordinated analysis of X-ray and NMR data uncovered a correspondence between the regions of the protein that are sensitive to cooling and those that are mobile in solution. To test the generality of this idea, we analyzed the small GTPase H-Ras bound to the GTP-analog, GMPPNP, by comparing high-resolution room-temperature (1.31 Å) and cryogenic (1.26 Å) X-ray data (25) to NMR relaxation dispersion experiments (26).…”

Section: Resultsmentioning

confidence: 99%

Accessing protein conformational ensembles using room-temperature X-ray crystallography

Fraser

Bedem

Samelson

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

556

471

View full text Add to dashboard Cite

Modern protein crystal structures are based nearly exclusively on X-ray data collected at cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little bias in the functional interpretation of structural results, because cryogenic temperatures minimally perturb the overall protein backbone fold. In contrast, here we show that flash cooling biases previously hidden structural ensembles in protein crystals. By analyzing available data for 30 different proteins using new computational tools for electron-density sampling, model refinement, and molecular packing analysis, we found that crystal cryocooling remodels the conformational distributions of more than 35% of side chains and eliminates packing defects necessary for functional motions. In the signaling switch protein, H-Ras, an allosteric network consistent with fluctuations detected in solution by NMR was uncovered in the room-temperature, but not the cryogenic, electron-density maps. These results expose a bias in structural databases toward smaller, overpacked, and unrealistically unique models. Monitoring room-temperature conformational ensembles by X-ray crystallography can reveal motions crucial for catalysis, ligand binding, and allosteric regulation.protein conformational dynamics | energy landscape | Ringer | qFit M acromolecular X-ray crystallographic diffraction experiments provide powerful insights into the relationship between structure and biological function. Although macromolecules populate vast ensembles of alternative conformational substates (1), crystallographic models depicting the major average conformation have provided foundational ideas about the mechanisms of biochemical reactions. By slowing radiation damage to the sample, crystal cooling has catalyzed a revolution in structural biology, enabling structure determinations from tiny crystals using bright synchrotron X-ray sources (2-4). It is estimated that more than 95% of the >65;000 crystal structures deposited in the Protein Data Bank (PDB) are based on cryogenic data (5).Crystal cooling is generally thought to introduce little bias in the functional interpretation of structural results. Some investigators have suggested that the standard practice of plunging crystals into liquid nitrogen and collecting X-ray diffraction data at 100 K traps a representative set of conformations populated at room temperature (6, 7). In contrast, early structural comparisons by Petsko, Frauenfelder, and colleagues indicated that cooling myoglobin crystals causes a small reduction in the protein volume due to anisotropic displacements of atomic positions and subtle changes of contacts between α-helices (8). A landmark study of crystalline ribonuclease A (RNaseA) by Tilton, Petsko, and coworkers revealed diverse temperature-dependent changes in the average structure, ranging from shrinkage at low temperatures to increased loop disorder at 47°C (9). A recent analysis comparing 15 room-temperature and cryogenic crystal structures documented that cryocooling generally increas...

show abstract

“…A challenging aspect of directly targeting RAS in its GTPbound form is the fact that switch I and switch II are disordered in solution (11,58,61), as is also the case in RAS-GDP (62), making it difficult for small molecules to bind. When bound to RAF-RBD, switch I is in state 2 and Y32 interacts with the g-phosphate of GTP via a bridging water molecule (Fig.…”

Section: Intramolecular Communication In the Structure Of Wild-type Imentioning

confidence: 99%

“…Furthermore, Q61L is also unique in that it has a strong tendency to stabilize the T state in the anticatalytic conformation when bound to RAF, abolishing even the slow hydrolysis rate observed in the uncomplexed protein (14,15,73). In the absence of binding partners, both switch I and switch II are disordered in solution (11,61), and they become stabilized by interactions with other proteins (15,30,76,77). In the crystal structures we have discussed, switch I is stabilized in state 2 by crystal contacts in the conformation found in the RAS/RAF-RBD complex (15) or in the RAS/NORE1A complex (78) and switch II is less constrained by crystal contacts.…”

Section: Effects Of Oncogenic Mutations On Intramolecular Communicatimentioning

confidence: 99%

Direct Attack on RAS: Intramolecular Communication and Mutation-Specific Effects

Marcus

Mattos

2015

Clinical Cancer Research

View full text Add to dashboard Cite

The crystal structure of RAS was first solved 25 years ago. In spite of tremendous and sustained efforts, there are still no drugs in the clinic that directly target this major driver of human cancers. Recent success in the discovery of compounds that bind RAS and inhibit signaling has fueled renewed enthusiasm, and in-depth understanding of the structure and function of RAS has opened new avenues for direct targeting. To succeed, we must focus on the molecular details of the RAS structure and understand at a high-resolution level how the oncogenic mutants impair function. Structural networks of intramolecular communication between the RAS active site and membraneinteracting regions on the G-domain are disrupted in oncogenic mutants. Although conserved across the isoforms, these networks are near hot spots of protein-ligand interactions with amino acid composition that varies among RAS proteins. These differences could have an effect on stabilization of conformational states of interest in attenuating signaling through RAS. The development of strategies to target these novel sites will add a fresh direction in the quest to conquer RAS-driven cancers.

show abstract

Global Conformational Dynamics in Ras

Cited by 70 publications

References 24 publications

Critical Roles of Interactions among Switch I-preceding Residues and between Switch II and Its Neighboring α-Helix in Conformational Dynamics of the GTP-bound Ras Family Small GTPases

Critical Roles of Interactions among Switch I-preceding Residues and between Switch II and Its Neighboring α-Helix in Conformational Dynamics of the GTP-bound Ras Family Small GTPases

Accessing protein conformational ensembles using room-temperature X-ray crystallography

Direct Attack on RAS: Intramolecular Communication and Mutation-Specific Effects

Contact Info

Product

Resources

About