Related ArticlesUnraveling 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]
[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...
Unraveling the conformational landscape of ligand binding to Glucose/Galactose-binding protein by paramagnetic NMR and MD simulations.
Linear Mode
