Conformational states of human rat sarcoma (Ras) protein complexed with its natural ligand GTP and their role for effector interaction and GTP hydrolysis.

PubWeight™: 1.12‹?› | Rank: Top 10%

🔗 View Article (PMC 3000958)

Published in J Biol Chem on October 11, 2010

Authors

Michael Spoerner1, Constantin Hozsa, Johann A Poetzl, Kerstin Reiss, Petra Ganser, Matthias Geyer, Hans Robert Kalbitzer

Author Affiliations

1: Universität Regensburg, Institut für Biophysik und Physikalische Biochemie, Universitätsstrasse 31, 93053 Regensburg, Germany.

Articles citing this

Structural Insights into the Dynamic Process of β2-Adrenergic Receptor Signaling. Cell (2015) 1.68

Pooled analysis of the prognostic and predictive effects of KRAS mutation status and KRAS mutation subtype in early-stage resected non-small-cell lung cancer in four trials of adjuvant chemotherapy. J Clin Oncol (2013) 1.66

Analysis of binding site hot spots on the surface of Ras GTPase. J Mol Biol (2011) 1.22

GTP-Dependent K-Ras Dimerization. Structure (2015) 1.07

Solution structure of the state 1 conformer of GTP-bound H-Ras protein and distinct dynamic properties between the state 1 and state 2 conformers. J Biol Chem (2011) 1.07

Parkinson disease-associated mutation R1441H in LRRK2 prolongs the "active state" of its GTPase domain. Proc Natl Acad Sci U S A (2014) 1.05

Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations. Proc Natl Acad Sci U S A (2012) 0.99

The role of conserved waters in conformational transitions of Q61H K-ras. PLoS Comput Biol (2012) 0.90

Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: simulations with the MARTINI force field. PLoS One (2013) 0.87

The role of magnesium for geometry and charge in GTP hydrolysis, revealed by quantum mechanics/molecular mechanics simulations. Biophys J (2012) 0.87

Differential reprogramming of isogenic colorectal cancer cells by distinct activating KRAS mutations. J Proteome Res (2015) 0.86

Specific Conformational States of Ras GTPase upon Effector Binding. J Chem Theory Comput (2012) 0.85

Binding hotspots on K-ras: consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis. Proteins (2015) 0.82

Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view. Chem Soc Rev (2016) 0.80

Probing the wild-type HRas activation mechanism using steered molecular dynamics, understanding the energy barrier and role of water in the activation. Eur Biophys J (2014) 0.78

Activated Ras as a Therapeutic Target: Constraints on Directly Targeting Ras Isoforms and Wild-Type versus Mutated Proteins. ISRN Oncol (2013) 0.78

Molecular Mechanism for Conformational Dynamics of Ras·GTP Elucidated from In-Situ Structural Transition in Crystal. Sci Rep (2016) 0.77

Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy. J Biol Chem (2015) 0.77

Monitoring Ras Interactions with the Nucleotide Exchange Factor Son of Sevenless (Sos) Using Site-specific NMR Reporter Signals and Intrinsic Fluorescence. J Biol Chem (2015) 0.77

Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions. Sci Rep (2016) 0.76

Plasma membrane regulates Ras signaling networks. Cell Logist (2016) 0.76

Distinct dynamics and interaction patterns in H- and K-Ras oncogenic P-loop mutants. Proteins (2017) 0.76

The small GTPases K-Ras, N-Ras, and H-Ras have distinct biochemical properties determined by allosteric effects. J Biol Chem (2017) 0.75

The RAS-Binding Domain of Human BRAF Protein Serine/Threonine Kinase Exhibits Allosteric Conformational Changes upon Binding HRAS. Structure (2015) 0.75

Inhibition of prenylated KRAS in a lipid environment. PLoS One (2017) 0.75

High pressure (31)P NMR spectroscopy on guanine nucleotides. J Biomol NMR (2016) 0.75

Articles cited by this

The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science (1997) 9.21

Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis. EMBO J (1990) 6.51

Multiple Ras functions can contribute to mammalian cell transformation. Cell (1995) 5.24

Expression of p21 proteins in Escherichia coli and stereochemistry of the nucleotide-binding site. EMBO J (1986) 2.85

Kinetics of interaction of nucleotides with nucleotide-free H-ras p21. Biochemistry (1990) 2.55

Ras/Rap effector specificity determined by charge reversal. Nat Struct Biol (1996) 2.52

Substrate-assisted catalysis as a mechanism for GTP hydrolysis of p21ras and other GTP-binding proteins. Nat Struct Biol (1995) 2.32

Kinetic and structural analysis of the Mg(2+)-binding site of the guanine nucleotide-binding protein p21H-ras. J Biol Chem (1993) 2.23

Differential interaction of the ras family GTP-binding proteins H-Ras, Rap1A, and R-Ras with the putative effector molecules Raf kinase and Ral-guanine nucleotide exchange factor. J Biol Chem (1996) 2.14

Dynamic properties of the Ras switch I region and its importance for binding to effectors. Proc Natl Acad Sci U S A (2001) 1.99

Quantitative analysis of the complex between p21ras and the Ras-binding domain of the human Raf-1 protein kinase. J Biol Chem (1995) 1.94

The pre-hydrolysis state of p21(ras) in complex with GTP: new insights into the role of water molecules in the GTP hydrolysis reaction of ras-like proteins. Structure (1999) 1.80

Conformational transitions in p21ras and in its complexes with the effector protein Raf-RBD and the GTPase activating protein GAP. Biochemistry (1996) 1.69

Allosteric modulation of Ras positions Q61 for a direct role in catalysis. Proc Natl Acad Sci U S A (2010) 1.62

Thermodynamic and kinetic characterization of the interaction between the Ras binding domain of AF6 and members of the Ras subfamily. J Biol Chem (1999) 1.36

Transformation efficiency of RasQ61 mutants linked to structural features of the switch regions in the presence of Raf. Structure (2007) 1.26

Structural basis for conformational dynamics of GTP-bound Ras protein. J Biol Chem (2010) 1.26

Stabilizing a weak binding state for effectors in the human ras protein by cyclen complexes. Angew Chem Int Ed Engl (2010) 1.25

Structure of the G60A mutant of Ras: implications for the dominant negative effect. J Biol Chem (2005) 1.21

Crystal structure of M-Ras reveals a GTP-bound "off" state conformation of Ras family small GTPases. J Biol Chem (2005) 1.21

Solution structure and dynamics of the small GTPase RalB in its active conformation: significance for effector protein binding. Biochemistry (2009) 1.12

Structural and biochemical analysis of Ras-effector signaling via RalGDS. FEBS Lett (1999) 1.10

Perturbation of the conformational equilibria in Ras by selective mutations as studied by 31P NMR spectroscopy. FEBS Lett (2004) 1.08

Indirect Referencing of 31P and 19F NMR Spectra J Magn Reson B (1996) 1.07

Structure of the Ras-binding domain of RalGEF and implications for Ras binding and signalling. Nat Struct Biol (1997) 1.03

Effector proteins exert an important influence on the signaling-active state of the small GTPase Cdc42. J Biol Chem (2008) 1.02

Slow conformational dynamics of the guanine nucleotide-binding protein Ras complexed with the GTP analogue GTPgammaS. FEBS J (2007) 1.02

Surface change of Ras enabling effector binding monitored in real time at atomic resolution. Chembiochem (2007) 1.01

Linear free energy relationships in the intrinsic and GTPase activating protein-stimulated guanosine 5'-triphosphate hydrolysis of p21ras. Biochemistry (1996) 0.97

Conformational states of Ras complexed with the GTP analogue GppNHp or GppCH2p: implications for the interaction with effector proteins. Biochemistry (2005) 0.93

Fundamental link between folding states and functional states of proteins. J Am Chem Soc (2009) 0.91

Solution structure of the Ras binding domain of the protein kinase Byr2 from Schizosaccharomyces pombe. Structure (2001) 0.89

A novel mechanism for the modulation of the Ras-effector interaction by small molecules. Biochem Biophys Res Commun (2005) 0.85

Conformational states of the nuclear GTP-binding protein Ran and its complexes with the exchange factor RCC1 and the effector protein RanBP1. Biochemistry (1999) 0.84

Observation of slow dynamic exchange processes in Ras protein crystals by 31P solid state NMR spectroscopy. J Mol Biol (2002) 0.83

Kinetic determination of the GTPase activity of Ras proteins by means of a luminescent terbium complex. Anal Bioanal Chem (2008) 0.80

Solid-state 31P NMR spectroscopy of microcrystals of the Ras protein and its effector loop mutants: comparison between crystalline and solution state. J Mol Biol (2004) 0.78

31P-NMR spectra of the Ha-ras p21.nucleotide complexes. Biochem Biophys Res Commun (1986) 0.78

Articles by these authors

FMNL2 drives actin-based protrusion and migration downstream of Cdc42. Curr Biol (2012) 2.18

The control of HIV transcription: keeping RNA polymerase II on track. Cell Host Microbe (2011) 2.05

Tat competes with HEXIM1 to increase the active pool of P-TEFb for HIV-1 transcription. Nucleic Acids Res (2007) 2.02

Structures of the dual bromodomains of the P-TEFb-activating protein Brd4 at atomic resolution. J Biol Chem (2009) 1.96

The human formin FHOD1 contains a bipartite structure of FH3 and GTPase-binding domains required for activation. Structure (2008) 1.85

The RNA polymerase II carboxy-terminal domain (CTD) code. Chem Rev (2013) 1.82

Identification of a cyclin T-binding domain in Hexim1 and biochemical analysis of its binding competition with HIV-1 Tat. J Biol Chem (2005) 1.71

Fifteen formins for an actin filament: a molecular view on the regulation of human formins. Biochim Biophys Acta (2010) 1.56

Serine-7 but not serine-5 phosphorylation primes RNA polymerase II CTD for P-TEFb recognition. Nat Commun (2012) 1.49

Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions. J Biomol NMR (2007) 1.44

Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell (2013) 1.40

Structural insights into the cyclin T1-Tat-TAR RNA transcription activation complex from EIAV. Nat Struct Mol Biol (2008) 1.36

Circulating Nef induces dyslipidemia in simian immunodeficiency virus-infected macaques by suppressing cholesterol efflux. J Infect Dis (2010) 1.34

Biochemical characterization of the diaphanous autoregulatory interaction in the formin homology protein FHOD1. J Biol Chem (2005) 1.30

Mechanistic investigation of poly(ethylene imine)-based siRNA delivery: disulfide bonds boost intracellular release of the cargo. J Control Release (2008) 1.29

HIV-1 Nef membrane association depends on charge, curvature, composition and sequence. Nat Chem Biol (2009) 1.29

Stabilizing a weak binding state for effectors in the human ras protein by cyclen complexes. Angew Chem Int Ed Engl (2010) 1.25

Biochemical indication for myristoylation-dependent conformational changes in HIV-1 Nef. Biochemistry (2006) 1.24

Specific and distinct determinants mediate membrane binding and lipid raft incorporation of HIV-1(SF2) Nef. Virology (2006) 1.21

The Diaphanous-related Formin FHOD1 associates with ROCK1 and promotes Src-dependent plasma membrane blebbing. J Biol Chem (2008) 1.20

Role of entropy in protein thermostability: folding kinetics of a hyperthermophilic cold shock protein at high temperatures using 19F NMR. Biochemistry (2002) 1.11

Delivery of nucleic acids via disulfide-based carrier systems. Adv Mater (2009) 1.10

Structure of the Cyclin T binding domain of Hexim1 and molecular basis for its recognition of P-TEFb. Proc Natl Acad Sci U S A (2007) 1.09

Human immunodeficiency virus type 1 Nef protein modulates the lipid composition of virions and host cell membrane microdomains. Retrovirology (2007) 1.08

Perturbation of the conformational equilibria in Ras by selective mutations as studied by 31P NMR spectroscopy. FEBS Lett (2004) 1.08

In vitro treatment of human monocytes/macrophages with myristoylated recombinant Nef of human immunodeficiency virus type 1 leads to the activation of mitogen-activated protein kinases, IkappaB kinases, and interferon regulatory factor 3 and to the release of beta interferon. J Virol (2006) 1.07

Biophysical analysis of the interaction of Rab6a GTPase with its effector domains. J Biol Chem (2008) 1.05

Large-scale candidate gene analysis of HDL particle features. PLoS One (2011) 1.04

Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). J Biomol NMR (2002) 1.04

Conformation of the dileucine-based sorting motif in HIV-1 Nef revealed by intermolecular domain assembly. Traffic (2011) 1.02

Slow conformational dynamics of the guanine nucleotide-binding protein Ras complexed with the GTP analogue GTPgammaS. FEBS J (2007) 1.02

When the lymphocyte loses its clothes. Immunity (2003) 0.99

NMR-spectroscopic mapping of an engineered cavity in the I14A mutant of HPr from Staphylococcus carnosus using xenon. J Am Chem Soc (2003) 0.97

Interaction of propionylated and butyrylated histone H3 lysine marks with Brd4 bromodomains. Angew Chem Int Ed Engl (2010) 0.96

FHOD1 is a combined actin filament capping and bundling factor that selectively associates with actin arcs and stress fibers. J Cell Sci (2013) 0.96

Genetic associations with lipoprotein subfractions provide information on their biological nature. Hum Mol Genet (2011) 0.95

Observation of intermediate states of the human prion protein by high pressure NMR spectroscopy. BMC Struct Biol (2006) 0.95

DLC1 activation requires lipid interaction through a polybasic region preceding the RhoGAP domain. Mol Biol Cell (2009) 0.94

Molecular design, functional characterization and structural basis of a protein inhibitor against the HIV-1 pathogenicity factor Nef. PLoS One (2011) 0.94

Ca2+-dependent conformational changes in a C-terminal cytosolic domain of polycystin-2. J Biol Chem (2009) 0.94

High-resolution structure of the histidine-containing phosphocarrier protein (HPr) from Staphylococcus aureus and characterization of its interaction with the bifunctional HPr kinase/phosphorylase. J Bacteriol (2004) 0.94

Conformational states of Ras complexed with the GTP analogue GppNHp or GppCH2p: implications for the interaction with effector proteins. Biochemistry (2005) 0.93

Cyclin box structure of the P-TEFb subunit cyclin T1 derived from a fusion complex with EIAV tat. J Mol Biol (2007) 0.93

The lipoprotein subfraction profile: heritability and identification of quantitative trait loci. J Lipid Res (2007) 0.92

Reacquisition of Nef-mediated tetherin antagonism in a single in vivo passage of HIV-1 through its original chimpanzee host. Cell Host Microbe (2012) 0.92

Complex formation and light activation in membrane-embedded sensory rhodopsin II as seen by solid-state NMR spectroscopy. Structure (2010) 0.92

Fundamental link between folding states and functional states of proteins. J Am Chem Soc (2009) 0.91

Structure determination and ligand interactions of the PDZ2b domain of PTP-Bas (hPTP1E): splicing-induced modulation of ligand specificity. J Mol Biol (2003) 0.91

Farnesylation of the SNARE protein Ykt6 increases its stability and helical folding. J Mol Biol (2008) 0.91

Metal-bis(2-picolyl)amine complexes as state 1(T) inhibitors of activated Ras protein. Angew Chem Int Ed Engl (2012) 0.90

NMR spectroscopic investigation of early events in IAPP amyloid fibril formation. Chembiochem (2009) 0.90

Oligomerization of the diaphanous-related formin FHOD1 requires a coiled-coil motif critical for its cytoskeletal and transcriptional activities. FEBS Lett (2005) 0.89

Improved simulation of NOESY spectra by RELAX-JT2 including effects of J-coupling, transverse relaxation and chemical shift anisotrophy. J Biomol NMR (2004) 0.89

Optimized chimeras between kinase-inactive mutant Cdk9 and truncated cyclin T1 proteins efficiently inhibit Tat transactivation and human immunodeficiency virus gene expression. J Virol (2002) 0.88

Extracellular HIV-1 Nef increases migration of monocytes. Exp Cell Res (2006) 0.88

Efficient Nef-mediated downmodulation of TCR-CD3 and CD28 is associated with high CD4+ T cell counts in viremic HIV-2 infection. J Virol (2012) 0.88

Infrequent cavity-forming fluctuations in HPr from Staphylococcus carnosus revealed by pressure- and temperature-dependent tyrosine ring flips. Protein Sci (2004) 0.88

Specificity of Hexim1 and Hexim2 complex formation with cyclin T1/T2, importin alpha and 7SK snRNA. J Mol Biol (2009) 0.88

HIV-1 Nef induces proinflammatory state in macrophages through its acidic cluster domain: involvement of TNF alpha receptor associated factor 2. PLoS One (2011) 0.87

Separate domains of fission yeast Cdk9 (P-TEFb) are required for capping enzyme recruitment and primed (Ser7-phosphorylated) Rpb1 carboxyl-terminal domain substrate recognition. Mol Cell Biol (2012) 0.87

A minimal chimera of human cyclin T1 and tat binds TAR and activates human immunodeficiency virus transcription in murine cells. J Virol (2002) 0.87

Identification of a highly conserved valine-glycine-phenylalanine amino acid triplet required for HIV-1 Nef function. Retrovirology (2012) 0.87

Solution structure of human proinsulin C-peptide. FEBS J (2005) 0.87

1H-NMR parameters of common amino acid residues measured in aqueous solutions of the linear tetrapeptides Gly-Gly-X-Ala at pressures between 0.1 and 200 MPa. Biophys Chem (2002) 0.87

Structure of the leech protein saratin and characterization of its binding to collagen. J Mol Biol (2008) 0.86

Species-specific differences in the intermediate states of human and Syrian hamster prion protein detected by high pressure NMR spectroscopy. J Biol Chem (2007) 0.86

Glucosylation of Ras by Clostridium sordellii lethal toxin: consequences for effector loop conformations observed by NMR spectroscopy. Biochemistry (2003) 0.86

Comparison of design strategies for promotion of beta-peptide 14-helix stability in water. Chembiochem (2008) 0.85

Migratory potential of rheumatoid arthritis synovial fibroblasts: additional perspectives. Cell Cycle (2010) 0.85

A novel mechanism for the modulation of the Ras-effector interaction by small molecules. Biochem Biophys Res Commun (2005) 0.85

Reversible monomer-oligomer transition in human prion protein. Prion (2008) 0.85

The archaeal exosome: identification and quantification of site-specific motions that correlate with cap and RNA binding. Angew Chem Int Ed Engl (2013) 0.85

Relationship between nonlinear pressure-induced chemical shift changes and thermodynamic parameters. J Phys Chem B (2014) 0.84

Solution structures of the inactive and BeF3-activated response regulator CheY2. J Mol Biol (2004) 0.84

Dominant negative mutant cyclin T1 proteins inhibit HIV transcription by specifically degrading Tat. Retrovirology (2008) 0.84

Conformational states of the small G protein Arf-1 in complex with the guanine nucleotide exchange factor ARNO-Sec7. J Biol Chem (2004) 0.84

Solution structure of the matrix attachment region-binding domain of chicken MeCP2. Eur J Biochem (2003) 0.83

Structure-function analysis of Arabidopsis thaliana histidine kinase AHK5 bound to its cognate phosphotransfer protein AHP1. Mol Plant (2012) 0.83

Conformational states of human H-Ras detected by high-field EPR, ENDOR, and 31P NMR spectroscopy. Magn Reson Chem (2005) 0.83

Improved binding of raf to Ras.GDP is correlated with biological activity. J Biol Chem (2009) 0.83

Observation of slow dynamic exchange processes in Ras protein crystals by 31P solid state NMR spectroscopy. J Mol Biol (2002) 0.83

Pulsed pressure perturbations, an extra dimension in NMR spectroscopy of proteins. J Am Chem Soc (2011) 0.83

High-affinity target binding engineered via fusion of a single-domain antibody fragment with a ligand-tailored SH3 domain. PLoS One (2012) 0.82

Nef surfaces: where to interfere with function. Curr HIV Res (2011) 0.82

Stem cell metabolic and spectroscopic profiling. Trends Biotechnol (2013) 0.82

1H-nuclear magnetic resonance spectroscopy of glioblastoma cancer stem cells. Stem Cells Dev (2011) 0.82

NMR assignments of oxidised thioredoxin from Plasmodium falciparum. Biomol NMR Assign (2009) 0.81

Chemical shift optimization in multidimensional NMR spectra by AUREMOL-SHIFTOPT. J Biomol NMR (2009) 0.81

Human cytomegalovirus major immediate early 1 protein targets host chromosomes by docking to the acidic pocket on the nucleosome surface. J Virol (2013) 0.81

FHOD1 regulates stress fiber organization by controlling the dynamics of transverse arcs and dorsal fibers. J Cell Sci (2014) 0.81

A flexible bipartite coiled coil structure is required for the interaction of Hexim1 with the P-TEFB subunit cyclin T1. Biochemistry (2010) 0.81

Structure, dynamics, lipid binding, and physiological relevance of the putative GTPase-binding domain of Dictyostelium formin C. J Biol Chem (2011) 0.81

A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles. BMC Bioinformatics (2005) 0.81

Reduced cisplatin sensitivity of head and neck squamous cell carcinoma cell lines correlates with mutations affecting the COOH-terminal nuclear localization signal of p53. Clin Cancer Res (2005) 0.81

Mutation in a winged-helix DNA-binding motif causes atypical bare lymphocyte syndrome. Nat Immunol (2002) 0.81