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 03-25-2011, 06:34 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,714
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 Sequence-Dependent Enrichment of a Model Phosphopeptide: A Combined MALDI-TOF and NMR Study.

Sequence-Dependent Enrichment of a Model Phosphopeptide: A Combined MALDI-TOF and NMR Study.

Sequence-Dependent Enrichment of a Model Phosphopeptide: A Combined MALDI-TOF and NMR Study.

Anal Chem. 2011 Mar 23;

Authors: Lucre?ce M, Emmanuelle S, Fabienne B, Sandrine S, Olivier L, Ge?rard B

The goal of this study was to detect and quantify by MALDI-TOF MS the phosphorylation of a peptide containing the recognition motif of the Protein Kinase C (PKC). Such model peptide can be used as a phosphorylation probe to follow intracellular kinase/phosphatase activities. This study allowed us to establish relationships between sequence specificities and affinity for TiO(2) or IMAC media. The peptide has the sequence biotin-GGGGCFRTPSFLKK-NH(2) in which the serine residue can be phosphorylated. Enrichment of the corresponding phosphopeptide, by the dedicated IMAC and TiO(2) affinity chromatography methods, proved inefficient. By combining MALDI-TOF and NMR data, we first showed that the lack of affinity of the phosphopeptide for TiO(2) was partly related to the basic property of its peptide sequence. Furthermore, the peptide shows local structuration around the P(9)- S(10) segment, with formation of a salt bridge between the guanidinium group of the R(7) side chain and the phosphate moiety. In conjunction with an inadequate position of the {biotin-G(4)} N-terminal tag, this local structure could shield the phosphate group, preventing interaction with TiO(2). To improve TiO(2) affinity, the peptide sequence was modified accordingly. The new sequences retained the biological properties while their enrichment by IMAC or TiO(2) became possible.

PMID: 21428305 [PubMed - as supplied by publisher]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study.
Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study. Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study. J Phys Chem B. 2011 May 2; Authors: Hwang S, Shao Q, Williams H, Hilty C, Gao YQ A combined simulation and experimental study was performed to investigate how methanol affects the structure of a model peptide BBA5. BBA5 forms a stable ?-hairpin-?-helix structure in aqueous solutions....
nmrlearner Journal club 0 05-04-2011 04:14 PM
[NMR paper] Sequence-dependent correction of random coil NMR chemical shifts.
Sequence-dependent correction of random coil NMR chemical shifts. Related Articles Sequence-dependent correction of random coil NMR chemical shifts. J Am Chem Soc. 2001 Apr 4;123(13):2970-8 Authors: Schwarzinger S, Kroon GJ, Foss TR, Chung J, Wright PE, Dyson HJ Random coil chemical shifts are commonly used to detect secondary structure elements in proteins in chemical shift index calculations. While this technique is very reliable for folded proteins, application to unfolded proteins reveals significant deviations from measured random coil...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] Sequence-dependent bending of DNA induced by cisplatin: NMR structures of an A.T-rich
Sequence-dependent bending of DNA induced by cisplatin: NMR structures of an A.T-rich 14-mer duplex. Related Articles Sequence-dependent bending of DNA induced by cisplatin: NMR structures of an A.T-rich 14-mer duplex. Chemistry. 2000 Oct 2;6(19):3636-44 Authors: Parkinson JA, Chen Y, del Socorro Murdoch P, Guo Z, Berners-Price SJ, Brown T, Sadler PJ The NMR solution structure of the A.T rich DNA 14-mer duplex d(ATACATGGTACATA).d(TATGTACCATGTAT) is reported. This is compared with the NMR structure of the same duplex intrastrand cross-linked at...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] DNA bending and sequence-dependent backbone conformation NMR and computer experiments
DNA bending and sequence-dependent backbone conformation NMR and computer experiments. Related Articles DNA bending and sequence-dependent backbone conformation NMR and computer experiments. Eur J Biochem. 1999 Oct 1;265(1):35-53 Authors: Ojha RP, Dhingra MM, Sarma MH, Shibata M, Farrar M, Turner CJ, Sarma RH Although DNA bending plays a crucial role in several biological processes, very little is known experimentally about the relationship between sugar phosphate conformation and sequence directed bending. In this paper, we determine the...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] Solvent polarity-dependent structural refolding: a CD and NMR study of a 15 residue p
Solvent polarity-dependent structural refolding: a CD and NMR study of a 15 residue peptide. Related Articles Solvent polarity-dependent structural refolding: a CD and NMR study of a 15 residue peptide. Proteins. 1995 Oct;23(2):196-203 Authors: Graf von Stosch A, Jiménez MA, Kinzel V, Reed J A close association between the HIV surface protein gp120 and the CD4 T cell receptor initiates the viral multiplication cycle. A 15 amino acid peptide (LAV) within the CD4 binding domain of gp 120 has been shown to retain receptor binding ability. The...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] 19F-NMR study on the pH-dependent regioselectivity and rate of the ortho-hydroxylatio
19F-NMR study on the pH-dependent regioselectivity and rate of the ortho-hydroxylation of 3-fluorophenol by phenol hydroxylase from Trichosporon cutaneum. Implications for the reaction mechanism. 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 19F-NMR study on the pH-dependent regioselectivity and rate of the ortho-hydroxylation of 3-fluorophenol by phenol hydroxylase from Trichosporon cutaneum. Implications for the reaction mechanism. Eur J Biochem. 1993...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger o
Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR structure of the complex with the Psi-site analog, dACGCC. 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 Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR...
nmrlearner Journal club 0 08-21-2010 11:53 PM
[NMR paper] 13C magic angle spinning NMR study of the light-induced and temperature-dependent cha
13C magic angle spinning NMR study of the light-induced and temperature-dependent changes in Rhodobacter sphaeroides R26 reaction centers enriched in tyrosine. Related Articles 13C magic angle spinning NMR study of the light-induced and temperature-dependent changes in Rhodobacter sphaeroides R26 reaction centers enriched in tyrosine. Biochemistry. 1992 Nov 17;31(45):11038-49 Authors: Fischer MR, de Groot HJ, Raap J, Winkel C, Hoff AJ, Lugtenburg J Solid-state 13C magic angle spinning (MAS) NMR has been used to investigate...
nmrlearner Journal club 0 08-21-2010 11:45 PM



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 05:26 PM.


Map