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 05-25-2016, 02:33 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,165
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 Unraveling the conformational landscape of ligand binding to Glucose/Galactose-binding protein by paramagnetic NMR and MD simulations.

Unraveling the conformational landscape of ligand binding to Glucose/Galactose-binding protein by paramagnetic NMR and MD simulations.

Related Articles Unraveling the conformational landscape of ligand binding to Glucose/Galactose-binding protein by paramagnetic NMR and MD simulations.

ACS Chem Biol. 2016 May 24;

Authors: Unione L, Ortega G, Mallagaray A, Corzana F, Perez-Castells J, Canales A, Jimenez-Barbero J, Millet O

Abstract
Protein dynamics related to function can be nowadays structurally well characterized (i. e. instances obtained by high resolution structures) but they are still ill-defined energetically and the energy landscapes are only accessible computationally. This is the case for glucose galactose binding protein (GGBP), where the crystal structures of the apo and holo states provide structural information for the domain rearrangement upon ligand binding, while the time scale and the energetic determinants for such concerted dynamics have been so far elusive. Here we use GGBP as a paradigm to define a functional conformational landscape, both structurally and energetically, by using an innovative combination of paramagnetic NMR experiments and MD simulations. Anisotropic NMR parameters induced by self-alignment of paramagnetic metal ions was used to characterize the ensemble of conformations adopted by the protein in solution while the rate of interconversion between conformations was elucidated by long molecular dynamic simulation on two states of GGBP, the closed-liganded (holo_cl) and open-unloaded (apo_op). Our results demonstrate that, in its apo state, the protein coexists between open-like (68%) and closed-like (32%) conformations, with an exchange rate around 25ns. Despite such conformational heterogeneity, the presence of the ligand is the ultimate driving force to unbalance the equilibrium towards the holo_cl form, in a mechanism largely governed by a conformational selection mechanism.


PMID: 27219646 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding.
NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding. Related Articles NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding. Phys Chem Chem Phys. 2014 Mar 7; Authors: Cembran A, Kim J, Gao J, Veglia G Abstract Proteins exist as an ensemble of conformers that are distributed on free energy landscapes resembling folding funnels. While the most stable conformers populate low energy basins, protein function is often...
nmrlearner Journal club 0 03-10-2014 10:35 AM
[NMR paper] Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies.
Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies. Related Articles Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies. Biochim Biophys Acta. 2013 Dec 26; Authors: Bernini A, De Angelis LH, Morandi E, Spiga O, Santucci A, Assfalg M, Molinari H, Pillozzi S, Arcangeli A, Niccolai N Abstract Hotspot delineation on protein surfaces represents a fundamental step for targeting protein-protein interfaces....
nmrlearner Journal club 0 01-01-2014 03:05 PM
Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies
Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies Publication date: Available online 27 December 2013 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics</br> Author(s): Andrea Bernini , Lucia Henrici De Angelis , Edoardo Morandi , Ottavia Spiga , Annalisa Santucci , Michael Assfalg , Henriette Molinari , Serena Pillozzi , Annarosa Arcangeli , Neri Niccolai</br> Hotspot delineation on protein surfaces represents a fundamental step for targeting protein-protein interfaces....
nmrlearner Journal club 0 12-27-2013 11:54 AM
[NMR paper] Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations.
Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations. Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations. PLoS One. 2013;8(9):e74040 Authors: Huan X, Shi J, Lim L, Mitra S, Zhu W, Qin H, Pasquale EB, Song J Abstract The 16 EphA and EphB receptors represent the largest family of receptor tyrosine kinases, and their interactions...
nmrlearner Journal club 0 10-03-2013 03:31 PM
[NMR paper] Low 13C-background for NMR-based studies of ligand binding using 13C-depleted glucose
Low 13C-background for NMR-based studies of ligand binding using 13C-depleted glucose as carbon source for microbial growth: 13C-labeled glucose and 13C-forskolin binding to the galactose-H+ symport protein GalP in Escherichia coli. Related Articles Low 13C-background for NMR-based studies of ligand binding using 13C-depleted glucose as carbon source for microbial growth: 13C-labeled glucose and 13C-forskolin binding to the galactose-H+ symport protein GalP in Escherichia coli. J Am Chem Soc. 2004 Jan 14;126(1):86-7 Authors: Patching SG, Herbert RB,...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein
Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange. Biochemistry. 1997 Feb 25;36(8):2278-90 Authors: Hodsdon ME, Cistola DP The backbone dynamics of the liganded (holo) and unliganded (apo) forms of Escherichia...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein
Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange. Biochemistry. 1997 Feb 25;36(8):2278-90 Authors: Hodsdon ME, Cistola DP The backbone dynamics of the liganded (holo) and unliganded (apo) forms of Escherichia...
nmrlearner Journal club 0 08-22-2010 03:03 PM
[NMR paper] An investigation of the ligand-binding site of the glutamine-binding protein of Esche
An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR. Related Articles An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR. Biochemistry. 1994 Jul 26;33(29):8651-61 Authors: Hing AW, Tjandra N, Cottam PF, Schaefer J, Ho C Glutamine-binding protein (GlnBP) is an essential component of the glutamine transport system in Escherichia coli. Rotational-echo double-resonance...
nmrlearner Journal club 0 08-22-2010 03:29 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 - 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 03:09 AM.


Map