Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

		BioNMR > Educational resources > Journal club
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

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:

Thread Tools

Search this Thread

Rate Thread

Display Modes

06-06-2011, 12:53 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

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

Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

Abstract Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residueâ??s effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict 13C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve the identification of small populations of transient structure in disordered proteins.

Content Type Journal Article
Pages 1-9
DOI 10.1007/s10858-011-9508-2
Authors
- Magnus Kjaergaard, Department of Biology, University of Copenhagen, Ole MaalÃ¸es Vej 5, 2200 Copenhagen, Denmark
- Flemming M. Poulsen, Department of Biology, University of Copenhagen, Ole MaalÃ¸es Vej 5, 2200 Copenhagen, Denmark

- Journal Journal of Biomolecular NMR
- Online ISSN 1573-5001
- Print ISSN 0925-2738

Source: Journal of Biomolecular NMR

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
RCI - Random Coil Index for predicting protein flexibility from chemical shifts RCI website RCI method predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts and predicting values of model-free order parameters as well as per-residue RMSF of NMR and MD ensembles from the Random Coil Index. The key advantages of this protocol over existing methods of studying protein flexibility are (i) it does not require prior knowledge of a protein's tertiary structure, (ii) it is not sensitive to the protein's overall tumbling and (iii) it does not require additional NMR measurements beyond the standard experiments for backbone...	markber	NMR software	0	02-02-2012 11:36 PM
Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH Abstract Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970â??2978, 2001). The chemical shifts are...	nmrlearner	Journal club	0	01-17-2011 02:40 AM
[NMR paper] Proline-directed random-coil chemical shift values as a tool for the NMR assignment o Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites. Related Articles Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites. Chembiochem. 2004 Jan 3;5(1):73-8 Authors: Lippens G, Wieruszeski JM, Leroy A, Smet C, Sillen A, Buée L, Landrieu I NMR spectroscopy of the full-length neuronal Tau protein has proved to be difficult due to the length of the protein and the unfavorable amino acid composition. We show that the...	nmrlearner	Journal club	0	11-24-2010 09:25 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] Correction of the NMR structure of the ETS1/DNA complex. Correction of the NMR structure of the ETS1/DNA complex. Related Articles Correction of the NMR structure of the ETS1/DNA complex. J Biomol NMR. 1997 Dec;10(4):317-28 Authors: Werner MH, Clore GM, Fisher CL, Fisher RJ, Trinh L, Shiloach J, Gronenborn AM The ETS family of transcription factors consists of a group of proteins that share a highly conserved 85 amino acid DNA-binding domain (DBD). This family recognizes a consensus sequence rich in purine bases with a central GGAA motif. A comparison of the published three-dimensional structures of...	nmrlearner	Journal club	0	08-22-2010 05:08 PM
Sequential nearest-neighbor effects on computed 13CÎ± chemical shifts Abstract To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of 13CÎ± chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue Î±/Î² protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed 13CÎ± chemical...	nmrlearner	Journal club	0	08-14-2010 04:19 AM
CheckShift: automatic correction of inconsistent chemical shift referencing CheckShift: automatic correction of inconsistent chemical shift referencing Simon W. Ginzinger, Fabian Gerick, Murray Coles and Volker Heun Journal of Biomolecular NMR; 2007; 39(3); pp 223-227 Abstract: The construction of a consistent protein chemical shift database is an important step toward making more extensive use of this data in structural studies. Unfortunately, progress in this direction has been hampered by the quality of the available data, particularly with respect to chemical shift referencing, which is often either inaccurate or inconsistently annotated. Preprocessing of...	Deano	Journal club	0	08-14-2008 09:57 PM
Chemical shift prediction in random coil peptides Please check this program and let me know if it does work for your random coil peptides. http://bloch.anu.edu.au/cgi-bin/shiftpred/shiftpred.cgi Thank you, Bogdan Bancia bbancia@yahoo.com	bbancia	NMR software	2	04-13-2007 03:54 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