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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 08-22-2010, 03:03 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,700
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, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary struct

1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.

Related Articles 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.

J Biomol NMR. 1997 Feb;9(2):167-80

Authors: Yu J, Simplaceanu V, Tjandra NL, Cottam PF, Lukin JA, Ho C

1H, 13C, and 15N NMR assignments of the backbone atoms and beta-carbons have been made for liganded glutamine-binding protein (GlnBP) of Escherichia coli, a monomeric protein with 226 amino acid residues and a molecular weight of 24935 Da. GlnBP is a periplasmic binding protein which plays an essential role in the active transport of L-glutamine through the cytoplasmic membrane. The assignments have been obtained from three-dimensional triple-resonance NMR experiments on a 13C, 15N uniformly labeled sample as well as specifically labeled samples. Results from the 3D triple-resonance experiments, HNCO, HN(CO)CA, HN(COCA)HA, HNCA, HN(CA)HA, HN(CA)CO, and CBCA(CO)NH, are the main sources used to make the resonance assignments. Other 3D experiments, such as HNCACB, COCAH, HCACO, HCACON, and HOHAHA-HMQC, have been used to confirm the resonance assignments and to extend connections where resonance peaks are missing in some of the experiments mentioned above. We have assigned more than 95% of the polypeptide backbone resonances of GlnBP. The result of the standard manual assignment is in agreement with that predicted by an automated probailistic method developed in our laboratory. A solution secondary structure of the GlnBP-Gln complex has been proposed based on chemical shift deviations from random coil values. Eight alpha-helices and 10 beta-strands are derived using the Chemical Shift Index method.

PMID: 9090131 [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
VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy
VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy Abstract Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR...
nmrlearner Journal club 0 12-22-2011 06:50 AM
Backbone and Ile-?1, Leu, Val Methyl (1)H, (13)C and (15)N NMR chemical shift assignments for human interferon-stimulated gene 15 protein.
Backbone and Ile-?1, Leu, Val Methyl (1)H, (13)C and (15)N NMR chemical shift assignments for human interferon-stimulated gene 15 protein. Backbone and Ile-?1, Leu, Val Methyl (1)H, (13)C and (15)N NMR chemical shift assignments for human interferon-stimulated gene 15 protein. Biomol NMR Assign. 2011 May 5; Authors: Yin C, Aramini JM, Ma LC, Cort JR, Swapna GV, Krug RM, Montelione GT Human interferon-stimulated gene 15 protein (ISG15), also called ubiquitin cross-reactive protein (UCRP), is the first identified ubiquitin-like protein containing...
nmrlearner Journal club 0 05-06-2011 12:02 PM
NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived fr
NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived from the C-terminus of Daxx. Related Articles NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived from the C-terminus of Daxx. Biomol NMR Assign. 2010 Oct 7; Authors: Naik MT, Chang CC, Naik NM, Kung CC, Shih HM, Huang TH Small Ubiquitin-like MOdifiers (SUMOs) are ubiquitin-like proteins known to covalently modify large number of cellular proteins. The mammalian SUMO family includes four paralogues, SUMO-1 through SUMO-4....
nmrlearner Journal club 0 10-12-2010 02:52 PM
[NMR paper] 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary struct
1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli. Related Articles 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli. J Biomol NMR. 1997 Feb;9(2):167-80 Authors: Yu J, Simplaceanu V, Tjandra NL, Cottam PF, Lukin JA, Ho C 1H, 13C, and 15N NMR assignments of the backbone atoms and beta-carbons have been made for liganded glutamine-binding protein (GlnBP) of Escherichia...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronu
Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronuclear NMR spectroscopy. Related Articles Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronuclear NMR spectroscopy. J Biomol NMR. 1996 Mar;7(2):89-98 Authors: Wang YS, Frederick AF, Senior MM, Lyons BA, Black S, Kirschmeier P, Perkins LM, Wilson O The growth factor receptor-bound protein-2 (Grb-2) is an adaptor protein that mediates signal transduction pathways. Chemical shift assignments were obtained for the SH2 domain of...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnes
1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnesium-binding characteristics of the Bacillus subtilis response regulator, Spo0F, determined by heteronuclear high-resolution NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] 1H, 13C and 15N NMR backbone assignments and secondary structure of the 269-residue p
1H, 13C and 15N NMR backbone assignments and secondary structure of the 269-residue protease subtilisin 309 from Bacillus lentus. Related Articles 1H, 13C and 15N NMR backbone assignments and secondary structure of the 269-residue protease subtilisin 309 from Bacillus lentus. J Biomol NMR. 1994 Mar;4(2):257-78 Authors: Remerowski ML, Domke T, Groenewegen A, Pepermans HA, Hilbers CW, van de Ven FJ 1H, 13C and 15N NMR assignments of the backbone atoms of subtilisin 309, secreted by Bacillus lentus, have been made using heteronuclear 3D NMR...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] 1H, 13C and 15N NMR backbone assignments and secondary structure of the 269-residue p
1H, 13C and 15N NMR backbone assignments and secondary structure of the 269-residue protease subtilisin 309 from Bacillus lentus. Related Articles 1H, 13C and 15N NMR backbone assignments and secondary structure of the 269-residue protease subtilisin 309 from Bacillus lentus. J Biomol NMR. 1994 Mar;4(2):257-78 Authors: Remerowski ML, Domke T, Groenewegen A, Pepermans HA, Hilbers CW, van de Ven FJ 1H, 13C and 15N NMR assignments of the backbone atoms of subtilisin 309, secreted by Bacillus lentus, have been made using heteronuclear 3D NMR...
nmrlearner Journal club 0 08-22-2010 03:33 AM



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 08:58 PM.


Map