NMR paper NMR studies of retinoid-protein interactions: the conformation of [13C]-beta-ionones

		BioNMR > Educational resources > Journal club
[NMR paper] NMR studies of retinoid-protein interactions: the conformation of [13C]-beta-ionones

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, 04:03 PM

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

NMR studies of retinoid-protein interactions: the conformation of [13C]-beta-ionones

NMR studies of retinoid-protein interactions: the conformation of [13C]-beta-ionones bound to beta-lactoglobulin B.

Related Articles NMR studies of retinoid-protein interactions: the conformation of [13C]-beta-ionones bound to beta-lactoglobulin B.

Pharm Res. 1999 May;16(5):651-9

Authors: Curley RW, Sundaram AK, Fowble JW, Abildgaard F, Westler WM, Markley JL

PURPOSE: Vitamin A (retinol) and its metabolites comprise the natural retinoids. While the biological action of these molecules are thought to be primarily mediated by ca. 55 kDa nuclear retinoic acid receptors, a number of structurally similar 15-20 kDa proteins are involved in the transport, and possibly metabolism, of these compounds. The milk protein beta-lactoglobulin B (beta-LG) is an 18 kDa protein which binds retinol and may be involved in oral delivery of retinol to neonates. beta-LG also binds drugs and other natural products and is of potential interest as a protective delivery vehicle. METHODS: To examine the conformation of the model retinoid beta-ionone both in solution and when bound to beta-LG, NMR and computational methods have been employed. RESULTS: Taken together, NMR studies of beta-ionone in solution measuring scalar and dipolar coupling, as well as CHARMm calculations, suggest beta-ionone prefers a slightly twisted 6-s-cis conformation. Isotope-edited NMR studies of 13C-labeled beta-ionones bound to beta-LG, primarily employing the HMQC-NOE experiment, suggest beta-ionone also binds to beta-LG in its 6-s-cis conformation. CONCLUSIONS: The methods employed here allow estimates of protein-bound ligand conformation. However, additional sites of ligand labeling will be necessary to aid in binding site localization.

PMID: 10350006 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR thesis] NMR Studies of Protein-DNA Interactions : Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions NMR Studies of Protein-DNA Interactions : Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions Sun, Yun (1992) NMR Studies of Protein-DNA Interactions : Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions. Dissertation (Ph.D.), California Institute of Technology. http://resolver.caltech.edu/CaltechTHESIS:09132011-160134197 More...	nmrlearner	NMR theses	0	09-16-2011 10:02 PM
[NMR paper] NMR studies for identifying phosphopeptide ligands of the HIV-1 protein Vpu binding to the F-box protein beta-TrCP. NMR studies for identifying phosphopeptide ligands of the HIV-1 protein Vpu binding to the F-box protein beta-TrCP. Related Articles NMR studies for identifying phosphopeptide ligands of the HIV-1 protein Vpu binding to the F-box protein beta-TrCP. Peptides. 2006 Jan;27(1):194-210 Authors: Evrard-Todeschi N, Gharbi-Benarous J, Bertho G, Coadou G, Megy S, Benarous R, Girault JP The human immunodeficiency virus type 1 (HIV-1) Vpu enhances viral particle release and, its interaction with the ubiquitin ligase SCF-beta-TrCP triggers the HIV-1...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Cell-free protein synthesis in an autoinduction system for NMR studies of protein-protein interactions. Cell-free protein synthesis in an autoinduction system for NMR studies of protein-protein interactions. Related Articles Cell-free protein synthesis in an autoinduction system for NMR studies of protein-protein interactions. J Biomol NMR. 2005 Jul;32(3):235-41 Authors: Ozawa K, Jergic S, Crowther JA, Thompson PR, Wijffels G, Otting G, Dixon NA Cell-free protein synthesis systems provide facile access to proteins in a nascent state that enables formation of soluble, native protein-protein complexes even if one of the protein components is prone...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] STD and TRNOESY NMR studies on the conformation of the oncogenic protein beta-catenin STD and TRNOESY NMR studies on the conformation of the oncogenic protein beta-catenin containing the phosphorylated motif DpSGXXpS bound to the beta-TrCP protein. Related Articles STD and TRNOESY NMR studies on the conformation of the oncogenic protein beta-catenin containing the phosphorylated motif DpSGXXpS bound to the beta-TrCP protein. J Biol Chem. 2005 Aug 12;280(32):29107-16 Authors: Megy S, Bertho G, Gharbi-Benarous J, Evrard-Todeschi N, Coadou G, Ségéral E, Iehle C, Quéméneur E, Benarous R, Girault JP beta-TrCP is the F-box protein...	nmrlearner	Journal club	0	11-25-2010 08:21 PM
[NMR paper] NMR studies of restriction enzyme-DNA interactions: role of conformation in sequence NMR studies of restriction enzyme-DNA interactions: role of conformation in sequence specificity. Related Articles NMR studies of restriction enzyme-DNA interactions: role of conformation in sequence specificity. Biochemistry. 2005 Apr 5;44(13):5065-74 Authors: Dupureur CM Sequence specific DNA binding proteins are thought to adopt distinct conformations when binding to target (cognate) and nontarget (noncognate) sequences. There is both biochemical and crystallographic evidence that this behavior is important in mediating sequence recognition...	nmrlearner	Journal club	0	11-25-2010 08:21 PM
[NMR paper] Conformation of a beta-adrenoceptor-derived signal transducing peptide as inferred by Conformation of a beta-adrenoceptor-derived signal transducing peptide as inferred by circular dichroism and 1H NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Conformation of a beta-adrenoceptor-derived signal transducing peptide as inferred by circular dichroism and 1H NMR spectroscopy. Biochemistry. 1996 May 21;35(20):6399-405 Authors: Jung H, Windhaber R, Palm D, Schnackerz KD The peptide T345-359 representing the fourth intracellular loop of the avian...	nmrlearner	Journal club	0	08-22-2010 02:27 PM
[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
[NMR paper] The solution conformation of tubulin-beta(422-434)-NH2 and its Nac-DATADEQG-NH2 fragm The solution conformation of tubulin-beta(422-434)-NH2 and its Nac-DATADEQG-NH2 fragment based on NMR. Related Articles The solution conformation of tubulin-beta(422-434)-NH2 and its Nac-DATADEQG-NH2 fragment based on NMR. Biopolymers. 1991 Mar;31(4):449-58 Authors: Otter A, Scott PG, Maccioni RB, Kotovych G The solution conformation of tubulin-beta(422-434)-NH2 (YQQYQDATADEQG-NH2) and its Nac-DATADEQG-NH2 fragment has been studied by two-dimensional 1H-nmr spectroscopy in CD3OH/H2O (90/10 v/v) at neutral and low pH. The 13 amino acid peptide...	nmrlearner	Journal club	0	08-21-2010 11:16 PM

« 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