NMR paper Chemical shift assignments and folding topology of the Ras-binding domain of human Ra

		BioNMR > Educational resources > Journal club
[NMR paper] Chemical shift assignments and folding topology of the Ras-binding domain of human Ra

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

08-22-2010, 03:33 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Chemical shift assignments and folding topology of the Ras-binding domain of human Ra

Chemical shift assignments and folding topology of the Ras-binding domain of human Raf-1 as determined by heteronuclear three-dimensional NMR spectroscopy.

Related Articles Chemical shift assignments and folding topology of the Ras-binding domain of human Raf-1 as determined by heteronuclear three-dimensional NMR spectroscopy.

Biochemistry. 1994 Jun 28;33(25):7745-52

Authors: Emerson SD, Waugh DS, Scheffler JE, Tsao KL, Prinzo KM, Fry DC

Raf-1 is a 74-kDa serine-threonine kinase which serves as the immediate downstream target of Ras in the cell growth signal transduction pathway. Recent genetic and biochemical experiments have demonstrated that (1) Ras interacts directly with the amino-terminal domain of Raf and (2) residues 51-131 of the Raf sequence are sufficient to mediate this interaction [Vojtek, A. B., Hollenberg, S. M., & Cooper, J. A. (1993) Cell 74, 205-214]. We have expressed a corresponding segment of the human Raf sequence (Raf55-132) in Escherichia coli as a fusion with maltose binding protein. The fusion protein was purified by affinity chromatography and cleaved at a pre-engineered site with factor Xa protease to liberate the 78-residue fragment of Raf. Raf55-132 bound to Ras with high affinity in a competition assay with GAP. An unlabeled version of Raf55-132 was studied by 2D homonuclear NMR, and uniformly 15N- and 13C/15N-labeled versions of Raf55-132 were studied by 2D and 3D heteronuclear NMR. Nearly complete sequence-specific assignments were made for the backbone HN, H alpha, 15N, and 13C alpha resonances. NOEs were used to determine regions of secondary structure and the overall folding topology. Raf55-132 is an independently folded domain composed of a five-stranded beta-sheet, a three-turn alpha-helix, and possibly an additional one-turn helix. Its structure resembles that of ubiquitin, even though there is no more than 11% sequence homology between the two proteins.

PMID: 8011639 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Backbone and Ile-?1, Leu, Val Methyl (1)H, (13)C and (15)N NMR chemical shift assignments for human interferon-stimulated gene 15 protein. Backbone and Ile-?1, Leu, Val Methyl (1)H, (13)C and (15)N NMR chemical shift assignments for human interferon-stimulated gene 15 protein. Backbone and Ile-?1, Leu, Val Methyl (1)H, (13)C and (15)N NMR chemical shift assignments for human interferon-stimulated gene 15 protein. Biomol NMR Assign. 2011 May 5; Authors: Yin C, Aramini JM, Ma LC, Cort JR, Swapna GV, Krug RM, Montelione GT Human interferon-stimulated gene 15 protein (ISG15), also called ubiquitin cross-reactive protein (UCRP), is the first identified ubiquitin-like protein containing...	nmrlearner	Journal club	0	05-06-2011 12:02 PM
[NMR paper] Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis. Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis. Related Articles Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis. J Am Chem Soc. 2005 Sep 7;127(35):12291-305 Authors: Franks WT, Zhou DH, Wylie BJ, Money BG, Graesser DT, Frericks HL, Sahota G, Rienstra CM Magic-angle spinning...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies. Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies. Related Articles Over-expression and purification of isotopically labeled recombinant ligand-binding domain of orphan nuclear receptor human B1-binding factor/human liver receptor homologue 1 for NMR studies. Protein Expr Purif. 2006 Jan;45(1):99-106 Authors: Chen X, Tong X, Xie Y, Wang Y, Ma J, Gao D, Wu H, Chen H The human hepatitis B virus enhancer II...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] NMR chemical shift perturbation study of the N-terminal domain of Hsp90 upon binding NMR chemical shift perturbation study of the N-terminal domain of Hsp90 upon binding of ADP, AMP-PNP, geldanamycin, and radicicol. Related Articles NMR chemical shift perturbation study of the N-terminal domain of Hsp90 upon binding of ADP, AMP-PNP, geldanamycin, and radicicol. Chembiochem. 2003 Sep 5;4(9):870-7 Authors: Dehner A, Furrer J, Richter K, Schuster I, Buchner J, Kessler H Hsp90 is one of the most abundant chaperone proteins in the cytosol. In an ATP-dependent manner it plays an essential role in the folding and activation of a...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
[NMR paper] NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from t NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1. Protein Sci. 1997 Sep;6(9):1835-48 ...	nmrlearner	Journal club	0	08-22-2010 05:08 PM
[NMR paper] Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronu Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronuclear NMR spectroscopy. Related Articles Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronuclear NMR spectroscopy. J Biomol NMR. 1996 Mar;7(2):89-98 Authors: Wang YS, Frederick AF, Senior MM, Lyons BA, Black S, Kirschmeier P, Perkins LM, Wilson O The growth factor receptor-bound protein-2 (Grb-2) is an adaptor protein that mediates signal transduction pathways. Chemical shift assignments were obtained for the SH2 domain of...	nmrlearner	Journal club	0	08-22-2010 02:27 PM
[NMR paper] Chemical shift assignments and folding topology of the Ras-binding domain of human Ra Chemical shift assignments and folding topology of the Ras-binding domain of human Raf-1 as determined by heteronuclear three-dimensional NMR spectroscopy. Related Articles Chemical shift assignments and folding topology of the Ras-binding domain of human Raf-1 as determined by heteronuclear three-dimensional NMR spectroscopy. Biochemistry. 1994 Jun 28;33(25):7745-52 Authors: Emerson SD, Waugh DS, Scheffler JE, Tsao KL, Prinzo KM, Fry DC Raf-1 is a 74-kDa serine-threonine kinase which serves as the immediate downstream target of Ras in the...	nmrlearner	Journal club	0	08-22-2010 03:33 AM
[NMR paper] Sequence-specific 1H-NMR assignments and folding topology of human CD59. Sequence-specific 1H-NMR assignments and folding topology of human CD59. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Sequence-specific 1H-NMR assignments and folding topology of human CD59. Protein Sci. 1993 Dec;2(12):2015-27 Authors: Fletcher CM, Harrison RA, Lachmann PJ, Neuhaus D CD59 is a recently...	nmrlearner	Journal club	0	08-22-2010 03:01 AM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off