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 07-23-2020, 11:23 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 NMR Lineshape Analysis of Intrinsically Disordered Protein Interactions.

NMR Lineshape Analysis of Intrinsically Disordered Protein Interactions.

Related Articles NMR Lineshape Analysis of Intrinsically Disordered Protein Interactions.

Methods Mol Biol. 2020;2141:477-504

Authors: Waudby CA, Christodoulou J

Abstract
Interactions of intrinsically disordered proteins are central to their cellular functions, and solution-state NMR spectroscopy provides a powerful tool for characterizing both structural and mechanistic aspects of such interactions. Here we focus on the analysis of IDP interactions using NMR titration measurements. Changes in resonance lineshapes in two-dimensional NMR spectra upon titration with a ligand contain rich information on structural changes in the protein and the thermodynamics and kinetics of the interaction, as well as on the microscopic association mechanism. Here we present protocols for the optimal design of titration experiments, data acquisition, and data analysis by two-dimensional lineshape fitting using the TITAN software package.


PMID: 32696373 [PubMed - in process]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Rapid Quantification of Protein-Ligand Binding via 19F NMR Lineshape Analysis.
Rapid Quantification of Protein-Ligand Binding via 19F NMR Lineshape Analysis. Related Articles Rapid Quantification of Protein-Ligand Binding via 19F NMR Lineshape Analysis. Biophys J. 2020 Apr 15;: Authors: Stadmiller SS, Aguilar JS, Waudby CA, Pielak GJ Abstract Fluorine incorporation is ideally suited to many NMR techniques, and incorporation of fluorine into proteins and fragment libraries for drug discovery has become increasingly common. Here, we use one-dimensional 19F NMR lineshape analysis to quantify the kinetics and...
nmrlearner Journal club 0 04-30-2020 02:58 PM
[NMR paper] Direct Detection of Carbon and Nitrogen Nuclei for High-Resolution Analysis of Intrinsically Disordered Proteins using NMR Spectroscopy.
Direct Detection of Carbon and Nitrogen Nuclei for High-Resolution Analysis of Intrinsically Disordered Proteins using NMR Spectroscopy. Direct Detection of Carbon and Nitrogen Nuclei for High-Resolution Analysis of Intrinsically Disordered Proteins using NMR Spectroscopy. Methods. 2018 Jan 13;: Authors: Gibbs EB, Kriwacki RW Abstract Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique for characterizing the structural and dynamic properties of intrinsically disordered proteins and protein regions (IDPs &...
nmrlearner Journal club 0 01-18-2018 12:41 PM
Direct Detection of Carbon and Nitrogen Nuclei for High-Resolution Analysis of Intrinsically Disordered Proteins using NMR Spectroscopy
Direct Detection of Carbon and Nitrogen Nuclei for High-Resolution Analysis of Intrinsically Disordered Proteins using NMR Spectroscopy Publication date: Available online 16 January 2018 Source:Methods</br> Author(s): E.B. Gibbs, R.W. Kriwacki</br> Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique for characterizing the structural and dynamic properties of intrinsically disordered proteins and protein regions (IDPs & IDRs). However, the application of NMR to IDPs has been limited by poor chemical shift dispersion in two-dimensional (2D) 1H-15N...
nmrlearner Journal club 0 01-17-2018 07:00 PM
[NMR paper] Common molecular pathogenesis of disease-related intrinsically disordered proteins revealed by NMR analysis.
Common molecular pathogenesis of disease-related intrinsically disordered proteins revealed by NMR analysis. Common molecular pathogenesis of disease-related intrinsically disordered proteins revealed by NMR analysis. J Biochem. 2017 Sep 11;: Authors: Shigemitsu Y, Hiroaki H Abstract Intrinsically disordered proteins (IDPs) are either completely unstructured or contain large disordered regions in their native state; they have drawn much attention in the field of molecular pathology. Some of them substantially tend to form...
nmrlearner Journal club 0 10-11-2017 10:37 AM
Role of Electrostatic Interactions in Binding of Peptidesand Intrinsically Disordered Proteins to Their Folded Targets. 1.NMR and MD Characterization of the Complex between the c-Crk N-SH3 Domain and the PeptideSos
Role of Electrostatic Interactions in Binding of Peptidesand Intrinsically Disordered Proteins to Their Folded Targets. 1.NMR and MD Characterization of the Complex between the c-Crk N-SH3 Domain and the PeptideSos http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi500904f/20141007/images/medium/bi-2014-00904f_0012.gif Biochemistry DOI: 10.1021/bi500904f http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/uw_59WsXyRU More...
nmrlearner Journal club 0 10-08-2014 04:17 AM
[NMR paper] The role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between c-Crk N SH3 domain and peptide Sos.
The role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between c-Crk N SH3 domain and peptide Sos. Related Articles The role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between c-Crk N SH3 domain and peptide Sos. Biochemistry. 2014 Sep 10; Authors: Xue Y, Yuwen T, Zhu F, Skrynnikov NR Abstract ...
nmrlearner Journal club 0 09-11-2014 02:54 PM
[NMR paper] Tyrosine Phosphorylation within the Intrinsically Disordered Cytosolic Domains of the B-Cell Receptor: An NMR-Based Structural Analysis.
Tyrosine Phosphorylation within the Intrinsically Disordered Cytosolic Domains of the B-Cell Receptor: An NMR-Based Structural Analysis. Related Articles Tyrosine Phosphorylation within the Intrinsically Disordered Cytosolic Domains of the B-Cell Receptor: An NMR-Based Structural Analysis. PLoS One. 2014;9(4):e96199 Authors: Rosenlöw J, Isaksson L, Mayzel M, Lengqvist J, Orekhov VY Abstract Intrinsically disordered proteins are found extensively in cell signaling pathways where they often are targets of posttranslational...
nmrlearner Journal club 0 04-29-2014 12:04 PM
4D Non-uniformly sampled HCBCACON and 1J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins
4D Non-uniformly sampled HCBCACON and 1J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins Abstract A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit 13C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (Hα, and Hβ) and carbon (Cα, Cβ) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient...
nmrlearner Journal club 0 05-17-2012 08:40 AM


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 - 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 12:18 PM.


Map