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C. O’Connor, E. Kovrigin (2012)
Assignments of backbone 1H, 13C and 15N resonances in H-Ras (1–166) complexed with GppNHp at physiological pHBiomolecular NMR Assignments, 6
Michiko Nishigaki, K. Aoyagi, I. Danjoh, Masahide Fukaya, K. Yanagihara, H. Sakamoto, Teruhiko Yoshida, H. Sasaki (2005)
Discovery of aberrant expression of R-RAS by cancer-linked DNA hypomethylation in gastric cancer using microarrays.Cancer research, 65 6
M. Spoerner, Constantin Hozsa, Johann Poetzl, K. Reiss, P. Ganser, M. Geyer, H. Kalbitzer (2010)
Conformational States of Human Rat Sarcoma (Ras) Protein Complexed with Its Natural Ligand GTP and Their Role for Effector Interaction and GTP Hydrolysis*The Journal of Biological Chemistry, 285
Izumi Oinuma, H. Katoh, A. Harada, M. Negishi (2003)
Direct Interaction of Rnd1 with Plexin-B1 Regulates PDZ-RhoGEF-mediated Rho Activation by Plexin-B1 and Induces Cell Contraction in COS-7 Cells*Journal of Biological Chemistry, 278
P. Aspenström, Å. Fransson, J. Saras (2004)
Rho GTPases have diverse effects on the organization of the actin filament system.The Biochemical journal, 377 Pt 2
Hui Wang, P. Hota, Y. Tong, Buren Li, Limin Shen, L. Nedyalkova, Susmita Borthakur, SoonJeung Kim, W. Tempel, M. Buck, Hee-won Park (2011)
Structural Basis of Rnd1 Binding to Plexin Rho GTPase Binding Domains (RBDs)*The Journal of Biological Chemistry, 286
D. Wishart, B. Sykes (1994)
The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift dataJournal of Biomolecular NMR, 4
S. Matthews (2004)
Perdeuteration/site-specific protonation approaches for high-molecular-weight proteins.Methods in molecular biology, 278
B. Vayssière, G. Zalcman, Y. Mahé, G. Mirey, T. Ligensa, K. Weidner, P. Chardin, J. Camonis (2000)
Interaction of the Grb7 adapter protein with Rnd1, a new member of the Rho familyFEBS Letters, 467
K. Wennerberg, M. Forget, S. Ellerbroek, W. Arthur, K. Burridge, J. Settleman, C. Der, S. Hansen (2003)
Rnd Proteins Function as RhoA Antagonists by Activating p190 RhoGAPCurrent Biology, 13
(2006)
1H, 15N, 13C assignments
I. Sethson, U. Edlund, T. Holak, A. Ross, B. Jonsson (1996)
Sequential assignment of 1H, 13C and 15N resonances of human carbonic anhydrase I by triple-resonance NMR techniques and extensive amino acid-specific 15N-labelingJournal of Biomolecular NMR, 8
(2000)
Rnd 1 , a novel Rho family GTPase , induces the formation of neuritic processes in PC 12 cells
(2000)
nucleotide-binding site. Biochemistry
G. Gasmi-Seabrook, C. Marshall, Melissa Cheung, Bryant Kim, Feng Wang, Y. Jang, T. Mak, V. Stambolic, M. Ikura (2009)
Real-time NMR Study of Guanine Nucleotide Exchange and Activation of RhoA by PDZ-RhoGEF*The Journal of Biological Chemistry, 285
David Jones (1999)
Protein secondary structure prediction based on position-specific scoring matrices.Journal of molecular biology, 292 2
A. Harada, H. Katoh, M. Negishi (2005)
Direct Interaction of Rnd1 with FRS2β Regulates Rnd1-induced Down-regulation of RhoA Activity and Is Involved in Fibroblast Growth Factor-induced Neurite Outgrowth in PC12 Cells*Journal of Biological Chemistry, 280
F. Momboisse, S. Houy, S. Ory, V. Calco, M. Bader, S. Gasman (2011)
How important are Rho GTPases in neurosecretion?Journal of Neurochemistry, 117
R. Foster, K. Hu, LU Yu, Katherine Nolan, J. Thissen, J. Settleman (1996)
Identification of a novel human Rho protein with unusual properties: GTPase deficiency and in vivo farnesylationMolecular and Cellular Biology, 16
Yang Shen, F. Delaglio, Gabriel Cornilescu, A. Bax (2009)
TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shiftsJournal of Biomolecular NMR, 44
K. Warton, Natasha Foster, W. Gold, K. Stanley (2004)
A novel gene family induced by acute inflammation in endothelial cells.Gene, 342 1
H. Katoh, A. Harada, K. Mori, M. Negishi (2002)
Socius Is a Novel Rnd GTPase-Interacting Protein Involved in Disassembly of Actin Stress FibersMolecular and Cellular Biology, 22
R. Brüschweiler (2003)
New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins.Current opinion in structural biology, 13 2
Izumi Oinuma, Yukio Ishikawa, H. Katoh, M. Negishi (2004)
The Semaphorin 4D Receptor Plexin-B1 Is a GTPase Activating Protein for R-RasScience, 305
C. Nobes, I. Lauritzen, M. Mattei, S. Paris, A. Hall, P. Chardin (1998)
A New Member of the Rho Family, Rnd1, Promotes Disassembly of Actin Filament Structures and Loss of Cell AdhesionThe Journal of Cell Biology, 141
Y. Tong, P. Hota, J. Penachioni, M. Hamaneh, SoonJeung Kim, R. Alviani, Limin Shen, Hao He, W. Tempel, L. Tamagnone, Hee-won Park, M. Buck (2009)
Structure and Function of the Intracellular Region of the Plexin-B1 Transmembrane Receptor*The Journal of Biological Chemistry, 284
K. Tong, Masayuki Yamamoto, Toshiyuki Tanaka (2008)
A simple method for amino acid selective isotope labeling of recombinant proteins in E. coliJournal of Biomolecular NMR, 42
L. Lian, I. Barsukov, A. Golovanov, D. Hawkins, R. Badii, K. Sze, N. Keep, G. Bokoch, G. Roberts (2000)
Mapping the binding site for the GTP-binding protein Rac-1 on its inhibitor RhoGDI-1.Structure, 8 1
S. Zanata, I. Hovatta, Beate Rohm, A. Püschel (2002)
Antagonistic Effects of Rnd1 and RhoD GTPases Regulate Receptor Activity in Semaphorin 3A-Induced Cytoskeletal CollapseThe Journal of Neuroscience, 22
Yukio Ishikawa, H. Katoh, M. Negishi (2003)
A Role of Rnd1 GTPase in Dendritic Spine Formation in Hippocampal NeuronsThe Journal of Neuroscience, 23
T. Cierpicki, J. Bielnicki, Meiying Zheng, J. Gruszczyk, M. Kasterka, M. Petoukhov, Aming Zhang, E. Fernandez, D. Svergun, U. Derewenda, J. Bushweller, Z. Derewenda (2009)
The solution structure and dynamics of the DH‐PH module of PDZRhoGEF in isolation and in complex with nucleotide‐free RhoAProtein Science, 18
(2012)
Strategies for optimization and stabilization of Rho GTPases for solution NMR studies : the case of Rnd 1
R. Modha, L. Campbell, D. Nietlispach, H. Buhecha, D. Owen, H. Mott (2008)
The Rac1 Polybasic Region Is Required for Interaction with Its Effector PRK1*♦Journal of Biological Chemistry, 283
(2006)
1 H , 15 N , 13 C assignments for the activated form of the small Rho - GTPase Rac 1
(2003)
Backbone 1H, 13C, and 15N resonance assignments for the 21 kDa GTPase Rac1 complexed to GDP and Mg
P. Adams, R. Oswald (2006)
Solution structure of an oncogenic mutant of Cdc42Hs.Biochemistry, 45 8
Sabine Bouguet-Bonnet, Matthias Buck (2008)
Compensatory and long-range changes in picosecond-nanosecond main-chain dynamics upon complex formation: 15N relaxation analysis of the free and bound states of the ubiquitin-like domain of human plexin-B1 and the small GTPase Rac1.Journal of molecular biology, 377 5
(2007)
NMR assignment of Cdc 42 ( T 35 A ) , an active switch I mutant of Cdc 42
M. Buck, Wei Xu, M. Rosen (2004)
A two-state allosteric model for autoinhibition rationalizes WASP signal integration and targeting.Journal of molecular biology, 338 2
P. Adams, A. Loh, R. Oswald (2004)
Backbone dynamics of an oncogenic mutant of Cdc42Hs shows increased flexibility at the nucleotide-binding site.Biochemistry, 43 31
J. Feltham, Volker Dötsch, Sami Raza, Danny Manor, R. Cerione, Michael Sutcliffe, Gerhard Wagner, Robert Oswald (1997)
Definition of the switch surface in the solution structure of Cdc42Hs.Biochemistry, 36 29
Y. Tong, Preeti Chugha, P. Hota, R. Alviani, Mei Li, W. Tempel, Limin Shen, Hee-won Park, M. Buck (2007)
Binding of Rac1, Rnd1, and RhoD to a Novel Rho GTPase Interaction Motif Destabilizes Dimerization of the Plexin-B1 Effector Domain*Journal of Biological Chemistry, 282
A. Loh, Wei Guo, Linda Nicholson, Robert Oswald (1999)
Backbone dynamics of inactive, active, and effector-bound Cdc42Hs from measurements of (15)N relaxation parameters at multiple field strengths.Biochemistry, 38 39
R. Chandrashekar, O. Salem, H. Křížová, R. McFeeters, P. Adams (2011)
A switch I mutant of Cdc42 exhibits less conformational freedom.Biochemistry, 50 28
M. Mazhab-Jafari, C. Marshall, Matthew Smith, G. Gasmi-Seabrook, V. Stambolic, R. Rottapel, B. Neel, M. Ikura (2009)
Real-time NMR Study of Three Small GTPases Reveals That Fluorescent 2′(3′)-O-(N-Methylanthraniloyl)-tagged Nucleotides Alter Hydrolysis and Exchange Kinetics*The Journal of Biological Chemistry, 285
Karen Lee, E. Androphy, J. Baleja (1995)
A novel method for selective isotope labeling of bacterially expressed proteinsJournal of Biomolecular NMR, 5
P. Hota, M. Buck (2009)
Thermodynamic characterization of two homologous protein complexes: Associations of the semaphorin receptor plexin‐B1 RhoGTPase binding domain with Rnd1 and active Rac1Protein Science, 18
O. Pertz (2010)
Spatio-temporal Rho GTPase signaling – where are we now?Journal of Cell Science, 123
D. Muchmore, Lawrence McIntosh, Russell Cb, Anderson De, Frederick Dahlquist (1989)
Expression and nitrogen-15 labeling of proteins for proton and nitrogen-15 nuclear magnetic resonance.Methods in enzymology, 177
K. Bryson, L. McGuffin, Russell Marsden, J. Ward, J. Sodhi, David Jones (2005)
Protein structure prediction servers at University College LondonNucleic Acids Research, 33
Rho GTPases have attracted considerable interest as signaling molecules due to their variety of functional roles in cells. Rnd1 is a relatively recently discovered Rho GTPase with no enzymatic activity against its bound GTP nucleotide, setting it apart from other family members. Research has revealed a critical role for Rnd1 not only in neurite outgrowth, dendrite development, axon guidance, but also in gastric cancer and in endothelial cells during inflammation. Structural information is crucial for understanding the mechanism that forms the basis for protein–protein interactions and functions, but until recently there were no reports of NMR studies directly on the Rnd1 protein. In this paper we report assignments for the majority of Rnd1 NMR resonances based on 2D and 3D NMR spectra. Rnd1 assignment was a challenging task, however, despite optimization strategies that have facilitated NMR studies of the protein (Cao and Buck in Small GTPase 2:295–304, 2012). Besides common triple-resonance experiments, 3D HNCA, 3D HN(CO)CA, 3D HNCO which are usually employed for sequence assignment, 3D NOESY experiments and specific labeling of 13 kinds of amino acids were also utilized to gain as many 1H(N), 13C, and 15N resonances assignments as possible. For 170 cross peaks observed out of 183 possible mainchain N–H correlations in the 1H–15N TROSY spectrum, backbone assignment was finally completed for 127 resonances. The secondary structure was then defined by chemical shifts and TALOS+ based on the assignments. The overall structure in solution compares well with that of Rnd1 in a crystal, except for two short segments, residues 77–83 and residues 127–131. Given that some features are shared among Rho GTPases, Rnd1 assignments are also compared with two other family members, Cdc42 and Rac1. The overall level of Rnd1 assignment is lower than for Cdc42 and Rac1, consistent with its lower stability and possibly increased internal dynamics. However, while the Rnd1 switch II region remained un-assigned, the switch I region could be more fully assigned compared to Cdc42 and Rac1. The NMR assignment and structure analysis reported here provides a robust basis for future study of the binding between Rnd1 and other proteins, as well as for further studies of the molecular function of this unusual GTPase.
Biomolecular NMR Assignments – Springer Journals
Published: May 22, 2012
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