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 Rating: Thread Rating: 1 votes, 5.00 average. Display Modes
  #1  
Unread 09-15-2017, 08:41 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 The thermodynamic basis of the fuzzy interaction of an intrinsically disordered protein

The thermodynamic basis of the fuzzy interaction of an intrinsically disordered protein


Many intrinsically disordered proteins (IDP) that fold upon binding retain conformational heterogeneity in IDP-target complexes. The thermodynamics of such fuzzy interactions is poorly understood. Here we introduce a thermodynamic framework, based on analysis of ITC and CD spectroscopy data, that provides experimental description of IDP association in terms of folding and binding contributions which can be predicted using sequence folding propensities and molecular modeling. We show how IDP can modulate the entropy and enthalpy by adapting their bound-state structural ensemble to achieve optimal binding. This is explained in terms of a free energy landscape that provides the relationship between free energy, sequence folding propensity and disorder. The observed "fuzzy" behavior is possible not only because of IDP flexibility but also because backbone and side chain interactions are, to some extent, energetically decoupled allowing IDP to minimize energetically unfavorable folding.

More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP
A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP Abstract Intrinsically disordered proteins (IDPs) are multi-conformational polypeptides that lack a single stable three-dimensional structure. It has become increasingly clear that the versatile IDPs play key roles in a multitude of biological processes, and, given their flexible nature, NMR is a leading method to investigate IDP behavior on the molecular level. Here we present an IDP-tailored J-modulated experiment designed to...
nmrlearner Journal club 0 11-19-2016 08:35 PM
[NMR paper] Identification of Dynamic Modes in an Intrinsically Disordered Protein using Temperature-dependent NMR Relaxation.
Identification of Dynamic Modes in an Intrinsically Disordered Protein using Temperature-dependent NMR Relaxation. Related Articles Identification of Dynamic Modes in an Intrinsically Disordered Protein using Temperature-dependent NMR Relaxation. J Am Chem Soc. 2016 Apr 26; Authors: Abyzov A, Salvi N, Schneider R, Maurin D, Ruigrok RW, Jensen MR, Blackledge M Abstract
nmrlearner Journal club 0 04-27-2016 01:51 PM
NMR-Based Molecular view of the Biology and Biophysics of WIP, An Intrinsically Disordered Protein
NMR-Based Molecular view of the Biology and Biophysics of WIP, An Intrinsically Disordered Protein Publication date: 16 February 2016 Source:Biophysical Journal, Volume 110, Issue 3, Supplement 1</br> Author(s): Eva Rozentur-Shkop, Hadassa Shaked, Jordan Chill</br> </br></br> </br></br> More...
nmrlearner Journal club 0 02-17-2016 07:50 PM
[NMR paper] A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR.
A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR. Related Articles A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR. Int J Mol Sci. 2015;16(7):15743-15760 Authors: Goda N, Shimizu K, Kuwahara Y, Tenno T, Noguchi T, Ikegami T, Ota M, Hiroaki H Abstract Intrinsically disordered proteins (IDPs) that lack stable conformations and are highly flexible have attracted the attention of biologists. Therefore, the development of a systematic method to identify...
nmrlearner Journal club 0 07-18-2015 08:46 PM
[NMR paper] NMR assignment of intrinsically disordered self-processing module of the FrpC protein of Neisseria meningitidis.
NMR assignment of intrinsically disordered self-processing module of the FrpC protein of Neisseria meningitidis. NMR assignment of intrinsically disordered self-processing module of the FrpC protein of Neisseria meningitidis. Biomol NMR Assign. 2015 Jul 3; Authors: Kubá? V, Nová?ek J, Bumba L, Žídek L Abstract The self-processing module (SPM) is an internal segment of the FrpC protein (P415-F591) secreted by the pathogenic Gram-negative bacterium Neisseria meningitidis during meningococcal infection of human upper respiratory...
nmrlearner Journal club 0 07-05-2015 02:07 AM
[NMR paper] Visualizing the molecular recognition trajectory of an intrinsically disordered protein using multinuclear relaxation dispersion NMR.
Visualizing the molecular recognition trajectory of an intrinsically disordered protein using multinuclear relaxation dispersion NMR. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Visualizing the molecular recognition trajectory of an intrinsically disordered protein using multinuclear relaxation dispersion NMR. J Am Chem Soc. 2014 Dec 31; Authors: Schneider R, Maurin D, Communie G, Kragelj J, Hansen DF, Ruigrok RW, Jensen MR, Blackledge M Abstract Despite playing...
nmrlearner Journal club 0 01-01-2015 11:00 PM
[NMR paper] Dynamics of the Intrinsically Disordered C-Terminal Domain of the Nipah Virus Nucleoprotein and Interaction with the X Domain of the Phosphoprotein as Unveiled by NMR Spectroscopy.
Dynamics of the Intrinsically Disordered C-Terminal Domain of the Nipah Virus Nucleoprotein and Interaction with the X Domain of the Phosphoprotein as Unveiled by NMR Spectroscopy. Related Articles Dynamics of the Intrinsically Disordered C-Terminal Domain of the Nipah Virus Nucleoprotein and Interaction with the X Domain of the Phosphoprotein as Unveiled by NMR Spectroscopy. Chembiochem. 2014 Dec 9; Authors: Baronti L, Erales J, Habchi J, Felli IC, Pierattelli R, Longhi S Abstract We provide an atomic-resolution description...
nmrlearner Journal club 0 12-11-2014 11:22 PM
Deuterium isotope shifts for backbone 1H, 15N and 13C nuclei in intrinsically disordered protein α-synuclein
Deuterium isotope shifts for backbone 1H, 15N and 13C nuclei in intrinsically disordered protein α-synuclein Abstract Intrinsically disordered proteins (IDPs) are abundant in nature and characterization of their potential structural propensities remains a widely pursued but challenging task. Analysis of NMR secondary chemical shifts plays an important role in such studies, but the output of such analyses depends on the accuracy of reference random coil chemical shifts. Although uniform perdeuteration of IDPs can dramatically increase spectral resolution, a feature particularly...
nmrlearner Journal club 0 09-10-2012 01:48 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 09:35 AM.


Map