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 04-27-2018, 05:00 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,033
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 High-dimensional NMR methods for intrinsically disordered proteins studies

High-dimensional NMR methods for intrinsically disordered proteins studies

Publication date: Available online 27 April 2018
Source:Methods

Author(s): Katarzyna Grudzi??, Anna Zawadzka-Kazimierczuk, Wiktor Ko?mi?ski

Intrinsically disordered proteins (IDPs) are getting more and more interest of the scientific community. Nuclear magnetic resonance (NMR) is often a technique of choice for these studies, as it provides atomic-resolution information on structure, dynamics and interactions of IDPs. Nonetheless, NMR spectra of IDPs are typically extraordinary crowded, comparing to those of structured proteins. To overcome this problem, high-dimensional NMR experiments can be used, which allow for a better peak separation. In the present review different aspects of such experiments are discussed, from data acquisition and processing to analysis, focusing on experiments for resonance assignment.







More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Application of NMR to studies of intrinsically disordered proteins.
Application of NMR to studies of intrinsically disordered proteins. Related Articles Application of NMR to studies of intrinsically disordered proteins. Arch Biochem Biophys. 2017 May 11;: Authors: Gibbs EB, Cook EC, Showalter SA Abstract The prevalence of intrinsically disordered protein regions, particularly in eukaryotic proteins, and their clear functional advantages for signaling and gene regulation have created an imperative for high-resolution structural and mechanistic studies. NMR spectroscopy has played a central role...
nmrlearner Journal club 0 05-16-2017 10:27 PM
A six-dimensional alpha proton detection-based APSY experiment for backbone assignment of intrinsically disordered proteins
A six-dimensional alpha proton detection-based APSY experiment for backbone assignment of intrinsically disordered proteins Abstract Sequence specific resonance assignment is the prerequisite for the NMR-based analysis of the conformational ensembles and their underlying dynamics of intrinsically disordered proteins. However, rapid solvent exchange in intrinsically disordered proteins often complicates assignment strategies based on HN-detection. Here we present a six-dimensional alpha proton detection-based automated projection spectroscopy (APSY)...
nmrlearner Journal club 0 11-04-2014 01:02 AM
[NMR paper] Novel methods based on 13C detection to study intrinsically disordered proteins
Novel methods based on 13C detection to study intrinsically disordered proteins Publication date: April 2014 Source:Journal of Magnetic Resonance, Volume 241</br> Author(s): Isabella C. Felli , Roberta Pierattelli</br> Intrinsically disordered proteins (IDPs) are characterized by highly flexible solvent exposed backbones and can sample many different conformations. These properties confer them functional advantages, complementary to those of folded proteins, which need to be characterized to expand our view of how protein structural and dynamic features affect...
nmrlearner Journal club 0 03-22-2014 01:28 AM
[NMR paper] Enhancing the resolution of multi-dimensional heteronuclear NMR spectra of intrinsically disordered proteins by homonuclear broadband decoupling.
Enhancing the resolution of multi-dimensional heteronuclear NMR spectra of intrinsically disordered proteins by homonuclear broadband decoupling. Related Articles Enhancing the resolution of multi-dimensional heteronuclear NMR spectra of intrinsically disordered proteins by homonuclear broadband decoupling. Chem Commun (Camb). 2013 Dec 23; Authors: Helge Meyer N, Zangger K Abstract Limited spectral resolution in the proton dimension of NMR spectra is a severe problem in intrinsically disordered proteins. Here we show that homonuclear...
nmrlearner Journal club 0 12-25-2013 03:39 PM
[NMR paper] Generating NMR Chemical Shift Assignments of Intrinsically Disordered Proteins Using Carbon-Detect NMR Methods.
Generating NMR Chemical Shift Assignments of Intrinsically Disordered Proteins Using Carbon-Detect NMR Methods. Related Articles Generating NMR Chemical Shift Assignments of Intrinsically Disordered Proteins Using Carbon-Detect NMR Methods. Anal Biochem. 2013 Dec 9; Authors: Sahu D, Bastidas M, Showalter S Abstract There is an extraordinary need to describe the structures of intrinsically disordered proteins (IDPs) due to their role in various biological processes involved in signaling and transcription. However, general study of IDPs...
nmrlearner Journal club 0 12-18-2013 04:00 PM
Generating NMR Chemical Shift Assignments of Intrinsically Disordered Proteins Using Carbon-Detect NMR Methods
Generating NMR Chemical Shift Assignments of Intrinsically Disordered Proteins Using Carbon-Detect NMR Methods Publication date: Available online 10 December 2013 Source:Analytical Biochemistry</br> Author(s): Debashish Sahu , Monique Bastidas , Scott Showalter</br> There is an extraordinary need to describe the structures of intrinsically disordered proteins (IDPs) due to their role in various biological processes involved in signaling and transcription. However, general study of IDPs by NMR spectroscopy is limited by the poor 1H-amide chemical shift dispersion...
nmrlearner Journal club 0 12-10-2013 04:48 AM
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins Abstract Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using δ subunit (20 kDa) of Bacillus subtilis RNA polymerase...
nmrlearner Journal club 0 02-21-2012 03:40 AM
Paramagnetic relaxation enhancement to improve sensitivity of fast NMR methods: application to intrinsically disordered proteins
Paramagnetic relaxation enhancement to improve sensitivity of fast NMR methods: application to intrinsically disordered proteins Abstract We report enhanced sensitivity NMR measurements of intrinsically disordered proteins in the presence of paramagnetic relaxation enhancement (PRE) agents such as Ni2+-chelated DO2A. In proton-detected 1H-15N SOFAST-HMQC and carbon-detected (H-flip)13CO-15N experiments, faster longitudinal relaxation enables the usage of even shorter interscan delays. This results in higher NMR signal intensities per units of experimental time, without adverse line...
nmrlearner Journal club 0 10-21-2011 10:04 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 - 2020, 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 09:03 PM.


Map