NMR paper The Residual Structure of Unfolded Proteins Was Elucidated From The Standard Deviation Of NMR Intensity Differences

		BioNMR > Educational resources > Journal club
[NMR paper] The Residual Structure of Unfolded Proteins Was Elucidated From The Standard Deviation Of NMR Intensity Differences

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

01-05-2023, 11:37 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,185

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

The Residual Structure of Unfolded Proteins Was Elucidated From The Standard Deviation Of NMR Intensity Differences

The Residual Structure of Unfolded Proteins Was Elucidated From The Standard Deviation Of NMR Intensity Differences

Introduction Sensitive methods are necessary to identify the residual structure in an unfolded protein, which may be similar to the functionally native structure. Signal intensity in NMR experiments is useful for analyzing the line width for a dynamic structure; however, another contribution is contained. Methods Here, the signal-intensity difference along the sequence was used for probability to calculate the standard deviation. Results The relative values of the standard deviations were 0.57,...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR. Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR. Related Articles Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR. Biophys J. 2020 Oct 14;: Authors: Yagi-Utsumi M, Chandak MS, Yanaka S, Hiranyakorn M, Nakamura T, Kato K, Kuwajima K Abstract The characterization of residual structures persistent in unfolded proteins in concentrated denaturant solution is currently an important issue in studies of protein folding because the residual structure...	nmrlearner	Journal club	0	11-04-2020 05:04 PM
[NMR paper] Distinct residual and disordered structures of alpha-synuclein analyzed by amide-proton exchange and NMR signal intensity. Distinct residual and disordered structures of alpha-synuclein analyzed by amide-proton exchange and NMR signal intensity. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Distinct residual and disordered structures of alpha-synuclein analyzed by amide-proton exchange and NMR signal intensity. Biochim Biophys Acta Proteins Proteom. 2020 Jun 01;:140464 Authors: Okuwaki R, Shinmura I, Morita S, Matsugami A, Hayashi F, Goto Y, Nishimura C Abstract ...	nmrlearner	Journal club	0	06-06-2020 04:36 PM
[NMR paper] NMR Characterization of the Near Native and Unfolded States of the PTB Domain of Dok1: Alternate Conformations and Residual Clusters. NMR Characterization of the Near Native and Unfolded States of the PTB Domain of Dok1: Alternate Conformations and Residual Clusters. Related Articles NMR Characterization of the Near Native and Unfolded States of the PTB Domain of Dok1: Alternate Conformations and Residual Clusters. PLoS One. 2014;9(2):e90557 Authors: Gupta S, Bhattacharjya S Abstract BACKGROUND: Phosphotyrosine binding (PTB) domains are critically involved in cellular signaling and diseases. PTB domains are categorized into three distinct structural classes namely...	nmrlearner	Journal club	0	03-04-2014 06:37 PM
[Question from NMRWiki Q&A forum] Macro available that can determine the standard deviation of the spectral noise for a many similar 2D spectra Macro available that can determine the standard deviation of the spectral noise for a many similar 2D spectra Hi ! I need a macro that can determine the standard deviation of the spectral noise for a manysimilar 2D spectra. I have 75 spectra obtained for an R1-rho experiment.Each spectra has an alteration for either of the varian parameter:deltadof2, dpwr2slock or ncyc. I use NMRPipe seriesTab to acquire the peak height for each spectrum.I use relax (http://nmr-relax.com) to perform the analysis.	nmrlearner	News from other NMR forums	0	09-16-2013 05:07 PM
Residual interactions in unfolded bile acid-binding protein by (19) F NMR. Residual interactions in unfolded bile acid-binding protein by (19) F NMR. Residual interactions in unfolded bile acid-binding protein by (19) F NMR. Protein Sci. 2011 Feb;20(2):327-35 Authors: Basehore HK, Ropson IJ The folding initiation mechanism of human bile acid-binding protein (BABP) has been examined by (19) F NMR. Equilibrium unfolding studies of BABP labeled with fluorine at all eight of its phenylalanine residues showed that at least two sites experience changes in solvent exposure at high denaturant concentrations. Peak...	nmrlearner	Journal club	0	02-02-2011 02:40 AM
Residual interactions in unfolded bile acid-binding protein by (19)F-NMR. Residual interactions in unfolded bile acid-binding protein by (19)F-NMR. Related Articles Residual interactions in unfolded bile acid-binding protein by (19)F-NMR. Protein Sci. 2010 Nov 29; Authors: Basehore HK, Ropson IJ The folding initiation mechanism of human bile acid-binding protein (BABP) has been examined by (19)F-NMR. Equilibrium unfolding studies of BABP labeled with fluorine at all eight of its phenylalanine residues showed that at least two sites experience changes in solvent exposure at high denaturant concentrations. Peak assignments...	nmrlearner	Journal club	0	12-01-2010 04:41 PM
[NMR paper] Probing residual interactions in unfolded protein states using NMR spin relaxation te Probing residual interactions in unfolded protein states using NMR spin relaxation techniques: an application to delta131delta. Related Articles Probing residual interactions in unfolded protein states using NMR spin relaxation techniques: an application to delta131delta. J Am Chem Soc. 2003 Oct 1;125(39):11988-92 Authors: Choy WY, Kay LE Residual interactions in delta131delta, a large disordered fragment of staphylococcal nuclease, have been probed at two different pHs using backbone (15)N and side-chain methyl (2)H NMR spin relaxation...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
Theoretical framework for NMR residual dipolar couplings in unfolded proteins Theoretical framework for NMR residual dipolar couplings in unfolded proteins O. I. Obolensky, Kai Schlepckow, Harald Schwalbe and A. V. Solov’yov Journal of Biomolecular NMR; 2007; 39(1) pp 1-16 Abstract: A theoretical framework for the prediction of nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) in unfolded proteins under weakly aligning conditions is presented. The unfolded polypeptide chain is modeled as a random flight chain while the alignment medium is represented by a set of regularly arranged obstacles. For the case of bicelles oriented perpendicular to...	stewart	Journal club	0	08-05-2008 02:26 AM

« 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