NMR paper Refinement of the geometry of the retinal binding pocket in dark-adapted bacteriorhod

		BioNMR > Educational resources > Journal club
[NMR paper] Refinement of the geometry of the retinal binding pocket in dark-adapted bacteriorhod

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

11-19-2010, 08:29 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,184

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

Refinement of the geometry of the retinal binding pocket in dark-adapted bacteriorhod

Refinement of the geometry of the retinal binding pocket in dark-adapted bacteriorhodopsin by heteronuclear solid-state NMR distance measurements.

Related Articles Refinement of the geometry of the retinal binding pocket in dark-adapted bacteriorhodopsin by heteronuclear solid-state NMR distance measurements.

Biochemistry. 2000 Aug 22;39(33):10066-71

Authors: Helmle M, Patzelt H, Ockenfels A, Gärtner W, Oesterhelt D, Bechinger B

The bacterial proton pump bacteriorhodopsin (BR) is a 26.5 kDa seven-transmembrane helical protein. Several structural models have been published at > or =1.55 A resolution. The initial cis-trans isomerization of the retinal moiety involves structural changes within

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] CORCEMA refinement of the bound ligand conformation within the protein binding pocket CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities. Related Articles CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities. J Magn Reson. 2004 May;168(1):36-45 Authors: Jayalakshmi V, Rama Krishna N We describe an intensity-restrained optimization procedure for refining approximate structures of ligands within the protein binding pockets using STD-NMR...	nmrlearner	Journal club	0	11-24-2010 09:51 PM
[NMR paper] Irreversible conformational change of bacterio-opsin induced by binding of retinal du Irreversible conformational change of bacterio-opsin induced by binding of retinal during its reconstitution to bacteriorhodopsin, as studied by (13)C NMR. Related Articles Irreversible conformational change of bacterio-opsin induced by binding of retinal during its reconstitution to bacteriorhodopsin, as studied by (13)C NMR. J Biochem. 2000 May;127(5):861-9 Authors: Yamaguchi S, Tuzi S, Tanio M, Naito A, Lanyi JK, Needleman R, Saitô H We compared (13)C NMR spectra of Ala- and Val-labeled bacterio-opsin (bO), produced either by bleaching bR...	nmrlearner	Journal club	0	11-18-2010 09:15 PM
[NMR paper] Probing the agonist binding pocket in the nicotinic acetylcholine receptor: a high-re Probing the agonist binding pocket in the nicotinic acetylcholine receptor: a high-resolution solid-state NMR approach. Related Articles Probing the agonist binding pocket in the nicotinic acetylcholine receptor: a high-resolution solid-state NMR approach. Biochemistry. 1998 Jul 28;37(30):10854-9 Authors: Williamson PT, Gröbner G, Spooner PJ, Miller KW, Watts A Acetylcholine, the agonist for the nicotinic acetylcholine receptor, has been observed directly when bound specifically to its binding site in the fully functional receptor-enriched...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
[NMR paper] Evaluation of Solvent Accessibility to the [Fe(4)S(4)] Binding Pocket in Native and T Evaluation of Solvent Accessibility to the Binding Pocket in Native and Tyr19 Mutant High Potential Iron Proteins by (1)H-(15)N HMQC and (19)F NMR Experiments. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Evaluation of Solvent Accessibility to the Binding Pocket in Native and Tyr19 Mutant High Potential Iron Proteins by (1)H-(15)N HMQC and (19)F NMR Experiments. Inorg Chem. 1996 Feb 28;35(5):1121-1125 Authors: Li D, Agarwal A, Cowan JA The solvent accessibility of Chromatium...	nmrlearner	Journal club	0	08-22-2010 02:27 PM
[NMR paper] Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations. J Mol Biol. 1995 Apr 7;247(4):689-700 Authors: van Tilborg MA, Bonvin AM, HÃ¥rd K, Davis AL, Maler B, Boelens R, Yamamoto KR, Kaptein R The solution structure of the glucocorticoid...	nmrlearner	Journal club	0	08-22-2010 03:41 AM
[NMR paper] Determination of membrane protein structure by rotational resonance NMR: bacteriorhod Determination of membrane protein structure by rotational resonance NMR: bacteriorhodopsin. Related Articles Determination of membrane protein structure by rotational resonance NMR: bacteriorhodopsin. Science. 1991 Feb 15;251(4995):783-6 Authors: Creuzet F, McDermott A, Gebhard R, van der Hoef K, Spijker-Assink MB, Herzfeld J, Lugtenburg J, Levitt MH, Griffin RG Rotationally resonant magnetization exchange, a new nuclear magnetic resonance (NMR) technique for measuring internuclear distances between like spins in solids, was used to determine...	nmrlearner	Journal club	0	08-21-2010 11:16 PM
[NMR paper] Solid-state 13C NMR study of tyrosine protonation in dark-adapted bacteriorhodopsin. Solid-state 13C NMR study of tyrosine protonation in dark-adapted bacteriorhodopsin. Related Articles Solid-state 13C NMR study of tyrosine protonation in dark-adapted bacteriorhodopsin. Biochemistry. 1990 Jun 12;29(23):5567-74 Authors: Herzfeld J, Das Gupta SK, Farrar MR, Harbison GS, McDermott AE, Pelletier SL, Raleigh DP, Smith SO, Winkel C, Lugtenburg J Solid-state 13C MAS NMR spectra were obtained for dark-adapted bacteriorhodopsin (bR) labeled with Tyr. Difference spectra (labeled minus natural abundance) taken at pH values between 2 and...	nmrlearner	Journal club	0	08-21-2010 10:48 PM
[NMR paper] Location of a cation-binding site in the loop between helices F and G of bacteriorhod Location of a cation-binding site in the loop between helices F and G of bacteriorhodopsin as studied by 13C NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Location of a cation-binding site in the loop between helices F and G of bacteriorhodopsin as studied by 13C NMR. Biophys J. 1999 Mar;76(3):1523-31 Authors: Tuzi S, Yamaguchi S, Tanio M, Konishi H, Inoue S, Naito A,...	nmrlearner	Journal club	0	08-21-2010 04:03 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