BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 11-17-2010, 11:15 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 18,077
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default NMR solution structure of type II human cellular retinoic acid binding protein: impli

NMR solution structure of type II human cellular retinoic acid binding protein: implications for ligand binding.

Related Articles NMR solution structure of type II human cellular retinoic acid binding protein: implications for ligand binding.

Biochemistry. 1998 Sep 15;37(37):12727-36

Authors: Wang L, Li Y, Abildgaard F, Markley JL, Yan H

The structure of human apo-cellular retinoic acid binding protein II (apo-CRABPII) in solution at pH 7.3 has been determined by NMR spectroscopy. The sequential assignments of the 1H, 13C, and 15N resonances of apo-CRABPII were established by multinuclear, multidimensional NMR spectroscopy. The solution structure of apo-CRABPII was derived from 2382 experimental NMR restraints using a hybrid distance geometry-simulated annealing protocol. The root-mean-square deviation of the ensemble of 25 refined conformers that represent the structure from the mean coordinate set derived from them was 0.54 +/- 0.18 and 0.92 +/- 0.20 A for the backbone atoms and all heavy atoms, respectively, of all residues except Ala32-Pro39 and Thr57-Glu62, which are in disordered regions. The solution structure of apo-CRABPII is similar to the crystal structure of holo-CRABPII [Kleywegt, G. J., Bergfors, T., Senn, H., Le Motte, P., Gsell, B., Shudo, K., and Jones, T. A. (1994) Structure 2, 1241-1258] except the ligand entrance, which is sufficiently enlarged in the apoprotein to be readily accessible to retinoic acid. The enlargement of the ligand entrance of apo-CRABPII relative to that of holo-CRABPII is due mainly to a concerted conformational change in three structural elements, namely, the second helix, the betaC-betaD loop, and the betaE-betaF loop. Furthermore, the ligand-binding pocket of apo-CRABPII showed evidence of dynamic disorder; among the 21 residues that constitute this pocket, 16 residues had weak or no detectable cross-peaks in the two-dimensional 1H-15N HSQC spectrum recorded under conditions of minimal water saturation or dephasing. Apo-CRABPII is largely monomeric in solution, with no evidence for the dimeric structure shown in the crystal structure of apo-CRABPI which was suggested to be a prerequisite for ligand entry [Thompson, J. R., Bratt, J. M., and Banaszak, L. J. (1995) J. Mol. Biol. 252, 433-446]. Thus, the widening of the ligand entrance required for entry of retinoic acid appears to be a property of monomeric apo-CRABPII.

PMID: 9737849 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function.
Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function. Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function. Proteins. 2011 Oct;79(10):2988-91 Authors: Aramini JM, Rossi P, Fischer M, Xiao R, Acton TB, Montelione GT Abstract Protein domain family PF09905 (DUF2132) is a family of small domains of unknown function that are conserved in a wide range of bacteria. Here we describe the solution NMR structure of the 80-residue VF0530 protein from Vibrio fischeri,...
nmrlearner Journal club 0 09-10-2011 06:51 PM
Solution NMR structure of MED25(391-543) comprising the activator-interacting domain (ACID) of human mediator subunit 25.
Solution NMR structure of MED25(391-543) comprising the activator-interacting domain (ACID) of human mediator subunit 25. Solution NMR structure of MED25(391-543) comprising the activator-interacting domain (ACID) of human mediator subunit 25. J Struct Funct Genomics. 2011 Jul 23; Authors: Eletsky A, Ruyechan WT, Xiao R, Acton TB, Montelione GT, Szyperski T The solution NMR structure of protein MED25(391-543), comprising the activator interacting domain (ACID) of subunit 25 of the human mediator, is presented along with the measurement of...
nmrlearner Journal club 0 07-26-2011 09:30 PM
[NMR paper] Validation of the binding site structure of the cellular retinol-binding protein (CRB
Validation of the binding site structure of the cellular retinol-binding protein (CRBP) by ligand NMR chemical shift perturbations. Related Articles Validation of the binding site structure of the cellular retinol-binding protein (CRBP) by ligand NMR chemical shift perturbations. J Am Chem Soc. 2005 Apr 20;127(15):5310-1 Authors: Wang B, Merz KM We have calculated proton chemical shift perturbations (CSPs) of retinol in the cellular retinol-binding protein (CRBP) through the use of a recently developed computational approach (Wang et al. J....
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] NMR study of the binding of all-trans-retinoic acid to type II human cellular retinoi
NMR study of the binding of all-trans-retinoic acid to type II human cellular retinoic acid binding protein. Related Articles NMR study of the binding of all-trans-retinoic acid to type II human cellular retinoic acid binding protein. Biochim Biophys Acta. 1999 Aug 17;1433(1-2):240-52 Authors: Wang L, Yan H Cellular RA binding proteins are thought to play important roles in the (RA), a hormonally active metabolite of vitamin A that has profound effects on cell growth, + differentiation and morphogenesis. Binding of RA to type II human cellular...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] The NMR solution structure of intestinal fatty acid-binding protein complexed with pa
The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm. J Mol Biol. 1996 Dec 6;264(3):585-602 Authors: Hodsdon ME, Ponder JW, Cistola DP The three-dimensional solution structure of rat...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] NMR solution structure of the RNA-binding peptide from human immunodeficiency virus (
NMR solution structure of the RNA-binding peptide from human immunodeficiency virus (type 1) Rev. Related Articles NMR solution structure of the RNA-binding peptide from human immunodeficiency virus (type 1) Rev. Biochemistry. 1995 Jul 4;34(26):8242-9 Authors: Scanlon MJ, Fairlie DP, Craik DJ, Englebretsen DR, West ML NMR spectroscopy has been used to solve the three-dimensional solution structure of a minimal RNA-binding domain of the Rev protein from the human immunodeficiency virus (type 1), an essential regulatory protein for viral...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] Solution structure of human type-alpha transforming growth factor determined by heter
Solution structure of human type-alpha transforming growth factor determined by heteronuclear NMR spectroscopy and refined by energy minimization with restraints. Related Articles Solution structure of human type-alpha transforming growth factor determined by heteronuclear NMR spectroscopy and refined by energy minimization with restraints. Biochemistry. 1993 Jul 27;32(29):7334-53 Authors: Moy FJ, Li YC, Rauenbuehler P, Winkler ME, Scheraga HA, Montelione GT Human type-alpha transforming growth factor (hTGF alpha) is a small mitogenic protein...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] The structure of the human retinoic acid receptor-beta DNA-binding domain determined
The structure of the human retinoic acid receptor-beta DNA-binding domain determined by NMR. Related Articles The structure of the human retinoic acid receptor-beta DNA-binding domain determined by NMR. Nucleic Acids Symp Ser. 1992;(27):65-6 Authors: Katahira M, Knegtel R, Schilthius J, Boelens R, Eib D, van der Saag P, Kaptein R The solution structure of the DNA-binding domain (DBD) of the human retinoic acid receptor-beta (hRAR-beta) has been determined by nuclear magnetic resonance (NMR) spectroscopy and distance geometry (DG). The...
nmrlearner Journal club 0 08-21-2010 11:41 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2017, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 04:52 PM.


Map