NMR paper Conformation of the TAR RNA-arginine complex by NMR spectroscopy.

		BioNMR > Educational resources > Journal club
[NMR paper] Conformation of the TAR RNA-arginine complex by NMR spectroscopy.

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

08-21-2010, 11:45 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,734

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

Conformation of the TAR RNA-arginine complex by NMR spectroscopy.

Conformation of the TAR RNA-arginine complex by NMR spectroscopy.

Related Articles Conformation of the TAR RNA-arginine complex by NMR spectroscopy.

Science. 1992 Jul 3;257(5066):76-80

Authors: Puglisi JD, Tan R, Calnan BJ, Frankel AD, Williamson JR

The messenger RNAs of human immunodeficiency virus-1 (HIV-1) have an RNA hairpin structure, TAR, at their 5' ends that contains a six-nucleotide loop and a three-nucleotide bulge. The conformations of TAR RNA and of TAR with an arginine analog specifically bound at the binding site for the viral protein, Tat, were characterized by nuclear magnetic resonance (NMR) spectroscopy. Upon arginine binding, the bulge changes conformation, and essential nucleotides for binding, U23 and A27.U38, form a base-triple interaction that stabilizes arginine hydrogen bonding to G26 and phosphates. Specificity in the arginine-TAR interaction appears to be derived largely from the structure of the RNA.

PMID: 1621097 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Solid-state NMR spectroscopy on complex biomolecules. Solid-state NMR spectroscopy on complex biomolecules. Solid-state NMR spectroscopy on complex biomolecules. Angew Chem Int Ed Engl. 2010 Nov 2;49(45):8346-57 Authors: Renault M, Cukkemane A, Baldus M Biomolecular applications of NMR spectroscopy are often merely associated with soluble molecules or magnetic resonance imaging. However, since the late 1970s, solid-state NMR (ssNMR) spectroscopy has demonstrated its ability to provide atomic-level insight into complex biomolecular systems ranging from lipid bilayers to complex biomaterials. In the...	nmrlearner	Journal club	0	02-15-2011 07:17 PM
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy Abstract Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of globular, modular and intrinsically disordered proteins, as well as proteinâ??protein and protein-DNA complexes. Here we characterized the conformation of a spin-label attached to the homodimeric protein CylR2 using a combination of X-ray crystallography, electron...	nmrlearner	Journal club	0	01-31-2011 06:03 AM
Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy. Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy. Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy. J Biomol NMR. 2011 Jan 28; Authors: Gruene T, Cho MK, Karyagina I, Kim HY, Grosse C, Giller K, Zweckstetter M, Becker S Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of...	nmrlearner	Journal club	0	01-29-2011 12:35 PM
[NMR paper] Study of the conformation of gamma-zeins in purified maize protein bodies by FTIR and NMR spectroscopy. Study of the conformation of gamma-zeins in purified maize protein bodies by FTIR and NMR spectroscopy. Related Articles Study of the conformation of gamma-zeins in purified maize protein bodies by FTIR and NMR spectroscopy. Anal Bioanal Chem. 2005 Sep;383(2):291-6 Authors: Bicudo TC, Forato LA, Batista LA, Colnago LA The gamma-zeins are a mixture of 16, 27, and 50-kDa polypeptides which are important in the formation and stabilization of protein bodies (PB). These organelles are used for deposition of zeins, the water-insoluble storage...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Towards a structure for a TSG-6.hyaluronan complex by modeling and NMR spectroscopy: Towards a structure for a TSG-6.hyaluronan complex by modeling and NMR spectroscopy: insights into other members of the link module superfamily. Related Articles Towards a structure for a TSG-6.hyaluronan complex by modeling and NMR spectroscopy: insights into other members of the link module superfamily. J Biol Chem. 2005 May 6;280(18):18189-201 Authors: Blundell CD, Almond A, Mahoney DJ, DeAngelis PL, Campbell ID, Day AJ The Link module from human TSG-6, a hyaladherin with roles in ovulation and inflammation, has a hyaluronan (HA)-binding...	nmrlearner	Journal club	0	11-24-2010 11:14 PM
Arginine interactions with anatase TiO(2) (100) surface and the perturbation of (49)T Arginine interactions with anatase TiO(2) (100) surface and the perturbation of (49)Ti NMR chemical shifts - a DFT investigation: relevance to Renu-Seeram bio solar cell. Related Articles Arginine interactions with anatase TiO(2) (100) surface and the perturbation of (49)Ti NMR chemical shifts - a DFT investigation: relevance to Renu-Seeram bio solar cell. J Mol Model. 2010 Sep 21; Authors: Koch R, Lipton AS, Filipek S, Renugopalakrishnan V Density functional theoretical calculations have been utilized to investigate the interaction of the amino...	nmrlearner	Journal club	0	09-22-2010 05:27 AM
[NMR paper] 1H-NMR spectroscopy of beta B2-crystallin from bovine eye lens. Conformation of the N 1H-NMR spectroscopy of beta B2-crystallin from bovine eye lens. Conformation of the N- and C-terminal extensions. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles 1H-NMR spectroscopy of beta B2-crystallin from bovine eye lens. Conformation of the N- and C-terminal extensions. Eur J Biochem. 1993 Apr 1;213(1):313-20 Authors: Carver JA, Cooper PG, Truscott RJ 1H-NMR spectroscopic studies of a 46-kDa homodimer, beta B2-crystallin,...	nmrlearner	Journal club	0	08-21-2010 11:53 PM
Solid-State NMR Spectroscopy of Membrane-Associated Myelin Basic Protein-Conformation Solid-State NMR Spectroscopy of Membrane-Associated Myelin Basic Protein-Conformation and Dynamics of an Immunodominant Epitope. Related Articles Solid-State NMR Spectroscopy of Membrane-Associated Myelin Basic Protein-Conformation and Dynamics of an Immunodominant Epitope. Biophys J. 2010 Aug 9;99(4):1247-1255 Authors: Ahmed MA, Bamm VV, Harauz G, Ladizhansky V Myelin basic protein (MBP) maintains the tight multilamellar compaction of the myelin sheath in the central nervous system through peripheral binding of adjacent lipid bilayers of...	nmrlearner	Journal club	0	08-18-2010 11:15 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