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 08-21-2010, 11:04 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 1H NMR studies of the glucocorticoid receptor DNA-binding domain: sequential assignme

1H NMR studies of the glucocorticoid receptor DNA-binding domain: sequential assignments and identification of secondary structure elements.

Related Articles 1H NMR studies of the glucocorticoid receptor DNA-binding domain: sequential assignments and identification of secondary structure elements.

Biochemistry. 1990 Sep 25;29(38):9015-23

Authors: Härd T, Kellenbach E, Boelens R, Kaptein R, Dahlman K, Carlstedt-Duke J, Freedman LP, Maler BA, Hyde EI, Gustafsson JA

Two protein fragments containing the DNA-binding domain (DBD) of the glucocorticoid receptor (GR) have been studied by two-dimensional 1H NMR spectroscopy. The two peptides (93 and 115 residues, respectively) contain a common segment corresponding to residues C440-I519 of the rat GR or residues C421-I500 of the human GR and include two Zn-binding "finger" domains. The structures of this segment are almost identical in the two protein fragments, as judged from chemical shifts and sequential NOE connectivities. More than 90% of all observable 1H resonances within a 71-residue segment encompassing C440-R510 (rat GR) could be sequentially assigned by standard techniques, and stereospecific assignments could be made for the methyl groups in four valine residues within this segment. Sequential NOE connectivities indicate several elements of secondary structure including two alpha-helical segments consisting of residues S459-E469 and P493-G504, a type I reverse turn between residues R479 and C482, a type II reverse turn between residues L475 and G478, and several regions of extended peptide conformation. No evidence for alpha-helical conformation was found within the two putative zinc-finger domains, indicating that the structures of these domains differ from that of TFIIIA-type zinc fingers. The observation of some very slowly exchanging amide protons in the N-terminal (CI) domain of the DBD in combination with slow rotation of the Y452 aromatic ring indicates that this domain has a restricted conformational flexibility compared to the C-terminal (CII) domain. We also observe several long-range NOE connectivities within C440-R510, suggesting that the sequential assignments presented here will provide a basis for a complete structure determination of this segment of the GR.

PMID: 2271574 [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
[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] Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignme
Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments. Related Articles Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments. J Biomol NMR. 2003 Dec;27(4):313-21 Authors: Slupsky CM, Boyko RF, Booth VK, Sykes BD Complete and accurate NMR spectral assignment is a prerequisite for high-throughput automated structure determination of biological macromolecules. However, completely automated assignment procedures generally encounter difficulties for all but the most ideal data...
nmrlearner Journal club 0 11-24-2010 09:16 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, Hård 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] NMR studies of the POU-specific DNA-binding domain of Oct-1: sequential 1H and 15N as
NMR studies of the POU-specific DNA-binding domain of Oct-1: sequential 1H and 15N assignments and secondary structure. Related Articles NMR studies of the POU-specific DNA-binding domain of Oct-1: sequential 1H and 15N assignments and secondary structure. Biochemistry. 1993 Jun 15;32(23):6032-40 Authors: Cox M, Dekker N, Boelens R, Verrijzer CP, van der Vliet PC, Kaptein R The 1H and 15N resonances of the POU-specific DNA-binding domain of transcription factor Oct-1 have been assigned sequentially using two-dimensional homo- and heteronuclear...
nmrlearner Journal club 0 08-21-2010 11:53 PM
[NMR paper] Sequential 1H NMR assignments and secondary structure of an IgG-binding domain from p
Sequential 1H NMR assignments and secondary structure of an IgG-binding domain from protein G. Related Articles Sequential 1H NMR assignments and secondary structure of an IgG-binding domain from protein G. Biochemistry. 1991 Jun 4;30(22):5335-40 Authors: Lian LY, Yang JC, Derrick JP, Sutcliffe MJ, Roberts GC, Murphy JP, Goward CR, Atkinson T Protein G is a member of a class of cell surface bacterial proteins from Streptococcus that bind IgG with high affinity. A fragment of molecular mass 6988, which retains IgG-binding activity, has been...
nmrlearner Journal club 0 08-21-2010 11:16 PM
[NMR paper] 1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA
1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA binding domain with a half-site response element. Related Articles 1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA binding domain with a half-site response element. Biochemistry. 1991 Dec 17;30(50):11620-4 Authors: Remerowski ML, Kellenbach E, Boelens R, van der Marel GA, van Boom JH, Maler BA, Yamamoto KR, Kaptein R The complex of the rat glucocorticoid receptor (GR) DNA binding domain (DBD) and half-site sequence of the...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] 1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA
1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA binding domain with a half-site response element. Related Articles 1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA binding domain with a half-site response element. Biochemistry. 1991 Dec 17;30(50):11620-4 Authors: Remerowski ML, Kellenbach E, Boelens R, van der Marel GA, van Boom JH, Maler BA, Yamamoto KR, Kaptein R The complex of the rat glucocorticoid receptor (GR) DNA binding domain (DBD) and half-site sequence of the...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] Cadmium-113 NMR studies of the DNA binding domain of the mammalian glucocorticoid rec
Cadmium-113 NMR studies of the DNA binding domain of the mammalian glucocorticoid receptor. Related Articles Cadmium-113 NMR studies of the DNA binding domain of the mammalian glucocorticoid receptor. Biochemistry. 1990 Oct 2;29(39):9218-25 Authors: Pan T, Freedman LP, Coleman JE The DNA binding domain of the mammalian glucocorticoid hormone receptor (GR) contains nine highly conserved cysteine residues, a conservation shared by the superfamily of steroid and thyroid hormone receptors. A fragment consisting of GR residues 407-556, containing...
nmrlearner Journal club 0 08-21-2010 11:04 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 - 2024, 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 09:27 PM.


Map