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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 04-27-2013, 01:56 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,732
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 Volumetric properties underlying ligand binding in a monomeric hemoglobin: A high-pressure NMR study.

Volumetric properties underlying ligand binding in a monomeric hemoglobin: A high-pressure NMR study.

Related Articles Volumetric properties underlying ligand binding in a monomeric hemoglobin: A high-pressure NMR study.

Biochim Biophys Acta. 2013 Apr 22;

Authors: Dellarole M, Roumestand C, Royer C, Lecomte JT

Abstract
The 2/2 hemoglobin of the cyanobacterium Synechococcus sp. PCC 7002, GlbN, coordinates the heme iron with two histidines and exists either with a b heme or with a covalently attached heme. The binding of exogenous ligands displaces the distal histidine and induces a conformational rearrangement involving the reorganization of internal void volumes. The formation of passageways within the resulting conformation is thought to facilitate ligand exchange and play a functional role. Here we monitored the perturbation induced by pressure on the ferric bis-histidine and cyanide-bound states of GlbN using (1)H-(15)N HSQC NMR spectroscopy. We inspected the outcome with a statistical analysis of 170 homologous 2/2 hemoglobin sequences. We found that the compression landscape of GlbN, as represented by the variation of an average chemical shift parameter, was highly sensitive to ligand swapping and heme covalent attachment. Stabilization of rare conformers was observed at high pressures and consistent with cavity redistribution upon ligand binding. In all states, the EF loop was found to be exceptionally labile to pressure, suggesting a functional role as a semi-flexible hinge between the adjacent helices. Finally, coevolved clusters presented a common pattern of compensating pressure responses. The high-pressure dissection combined with protein sequence analysis established locations with volumetric signatures relevant to residual communication of 2/2 hemoglobins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.


PMID: 23619242 [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
A Delicate Interplay of Structure, Dynamics, and Thermodynamics for Function: A High Pressure NMR Study of Outer Surface Protein A
A Delicate Interplay of Structure, Dynamics, and Thermodynamics for Function: A High Pressure NMR Study of Outer Surface Protein A 22 February 2012 Publication year: 2012 Source:Biophysical Journal, Volume 102, Issue 4</br> </br> Outer surface protein A (OspA) is a crucial protein in the infection of Borrelia burgdorferi causing Lyme disease. We studied conformational fluctuations of OspA with high-pressure 15N/1H two-dimensional NMR along with high-pressure fluorescence spectroscopy. We found evidence within folded, native OspA for rapid local fluctuations of the...
nmrlearner Journal club 0 02-03-2013 10:13 AM
[NMR paper] High pressure nmr study of dihydrofolate reductase from a deep-sea bacterium Moritell
High pressure nmr study of dihydrofolate reductase from a deep-sea bacterium Moritella profunda. Related Articles High pressure nmr study of dihydrofolate reductase from a deep-sea bacterium Moritella profunda. Cell Mol Biol (Noisy-le-grand). 2004 Jun;50(4):311-6 Authors: Hata K, Kono R, Fujisawa M, Kitahara R, Kamatari YO, Akasaka K, Xu Y We have investigated the effect of pressure and temperature on the structural and thermodynamic stability of a protein dihydrofolate reductase from a deep-sea bacterium Moritella profunda in its folate-bound...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] High-pressure NMR study of the complex of a GTPase Rap1A with its effector RalGDS. A
High-pressure NMR study of the complex of a GTPase Rap1A with its effector RalGDS. A conformational switch in RalGDS revealed from non-linear pressure shifts. Related Articles High-pressure NMR study of the complex of a GTPase Rap1A with its effector RalGDS. A conformational switch in RalGDS revealed from non-linear pressure shifts. FEBS Lett. 2001 Oct 12;506(3):180-4 Authors: Inoue K, Maurer T, Yamada H, Herrmann C, Horn G, Kalbitzer HR, Akasaka K Unusually large non-linear 1H and 15N nuclear magnetic resonance chemical shifts against...
nmrlearner Journal club 0 11-19-2010 08:44 PM
[NMR paper] High pressure NMR study of a small protein, gurmarin.
High pressure NMR study of a small protein, gurmarin. Related Articles High pressure NMR study of a small protein, gurmarin. J Biomol NMR. 1998 Nov;12(4):535-41 Authors: Inoue K, Yamada H, Imoto T, Akasaka K The effect of pressure on the structure of gurmarin, a globular, 35-residue protein from Gymnema sylvestre, was studied in aqueous environment (95% 1H2O/5% 2H2O, pH 2.0) with an on-line variable pressure NMR system operating at 750 MHz. Two-dimensional TOCSY and NOESY spectra were measured as functions of pressure between 1 and 2000 bar at...
nmrlearner Journal club 0 11-17-2010 11:15 PM
[NMR paper] An NMR study of ligand binding by maltodextrin binding protein.
An NMR study of ligand binding by maltodextrin binding protein. Related Articles An NMR study of ligand binding by maltodextrin binding protein. Biochem Cell Biol. 1998;76(2-3):189-97 Authors: Gehring K, Zhang X, Hall J, Nikaido H, Wemmer DE Proton NMR spectra of maltodextrin binding protein from Escherichia coli were used to monitor conformational changes that accompany ligand binding. Chemical shift changes associated with the binding of different maltodextrins to maltodextrin binding protein were studied using one-dimensional difference...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[NMR paper] Thermodynamics of unfolding of ribonuclease A under high pressure. A study by proton
Thermodynamics of unfolding of ribonuclease A under high pressure. A study by proton NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Thermodynamics of unfolding of ribonuclease A under high pressure. A study by proton NMR. J Mol Biol. 1995 Jul 28;250(5):689-94 Authors: Yamaguchi T, Yamada H, Akasaka K Thermodynamic stability of ribonuclease A (6.2 mM pH 1.0, 0.15 M KCl, in 2H2O) has been studied in the pressure range of 1 to 2000 atm and in the temperature range...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] High-resolution NMR study of the pressure-induced unfolding of lysozyme.
High-resolution NMR study of the pressure-induced unfolding of lysozyme. Related Articles High-resolution NMR study of the pressure-induced unfolding of lysozyme. Biochemistry. 1992 Sep 1;31(34):7773-8 Authors: Samarasinghe SD, Campbell DM, Jonas A, Jonas J The pressure-induced reversible unfolding of lysozyme was investigated by high-resolution proton magnetic resonance spectroscopy by following the proton spectra of the following residues: His-15 epsilon 1, Trp-28 epsilon 3, Leu-17 delta 2, Cys-64 alpha, and Trp-108 epsilon 3. The...
nmrlearner Journal club 0 08-21-2010 11:45 PM
[NMR paper] High resolution NMR for screening ligand/protein binding.
High resolution NMR for screening ligand/protein binding. Related Articles High resolution NMR for screening ligand/protein binding. Curr Opin Drug Discov Devel. 1999 Jul;2(4):396-400 Authors: Shapiro MJ, Wareing JR High resolution NMR spectroscopy has provided a versatile tool for assessing ligand/receptor interactions. NMR-based methods are currently being investigated which may prove valuable for compound screening. These techniques include the use of chemical shift perturbations, the monitoring of translational diffusion and the...
nmrlearner Journal club 0 08-21-2010 04:03 PM



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 02:37 AM.


Map