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 08-22-2010, 03:41 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 Characterization of the N-terminal half-saturated state of calbindin D9k: NMR studies

Characterization of the N-terminal half-saturated state of calbindin D9k: NMR studies of the N56A mutant.

Related Articles Characterization of the N-terminal half-saturated state of calbindin D9k: NMR studies of the N56A mutant.

Protein Sci. 1995 Jun;4(6):1045-55

Authors: Wimberly B, Thulin E, Chazin WJ

Calbindin D9k is a small EF-hand protein that binds two calcium ions with positive cooperativity. The molecular basis of cooperativity for the binding pathway where the first ion binds in the N-terminal site (1) is investigated by NMR experiments on the half-saturated state of the N56A mutant, which exhibits sequential yet cooperative binding (Linse S, Chazin WJ, 1995, Protein Sci 4:1038-1044). Analysis of calcium-induced changes in chemical shifts, amide proton exchange rates, and NOEs indicates that ion binding to the N-terminal binding loop causes significant changes in conformation and/or dynamics throughout the protein. In particular, all three parameters indicate that the hydrophobic core undergoes a change in packing to a conformation very similar to the calcium-loaded state. These results are similar to those observed for the (Cd2+)1 state of the wild-type protein, a model for the complementary half-saturated state with an ion bound in the C-terminal site (II). Thus, with respect to cooperativity in either of the binding pathways, binding of the first ion drives the conformation and dynamics of the protein far toward the (Ca2+)2 state, thereby facilitating binding of the second ion. Comparison with the half-saturated state of the analogous E65Q mutant confirms that mutation of this critical bidentate calcium ligand at position 12 of the consensus EF-hand binding loop causes very significant structural perturbations. This result has important implications regarding numerous studies that have utilized mutation of this critical residue for site deactivation.

PMID: 7549869 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain.
Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain. Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain. Biochimie. 2011 Sep 22; Authors: Galea CA, Mobli M, McNeil KA, Mulhern TD, Wallace JC, King GF, Forbes BE, Norton RS Abstract The insulin-like growth factor binding proteins are a family of six proteins (IGFBP-1 to 6) that bind insulin-like growth factors-I and -II (IGF-I/II) with high affinity. In addition...
nmrlearner Journal club 0 09-30-2011 06:00 AM
Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain.
Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain. Insulin-like growth factor binding protein-2: NMR analysis and structural characterization of the N-terminal domain. Biochimie. 2011 Sep 22; Authors: Galea CA, Mobli M, McNeil KA, Mulhern TD, Wallace JC, King GF, Forbes BE, Norton RS Abstract The insulin-like growth factor binding proteins are a family of six proteins (IGFBP-1 to 6) that bind insulin-like growth factors-I and -II (IGF-I/II) with high affinity. In...
nmrlearner Journal club 0 09-30-2011 05:59 AM
[NMR paper] NMR characterization of the interaction between the C-terminal domain of interferon-g
NMR characterization of the interaction between the C-terminal domain of interferon-gamma and heparin-derived oligosaccharides. Related Articles NMR characterization of the interaction between the C-terminal domain of interferon-gamma and heparin-derived oligosaccharides. Biochem J. 2004 Nov 15;384(Pt 1):93-9 Authors: Vanhaverbeke C, Simorre JP, Sadir R, Gans P, Lortat-Jacob H Interferons are cytokines that play a complex role in the resistance of mammalian hosts to pathogens. IFNgamma (interferon-gamma) is secreted by activated T-cells and...
nmrlearner Journal club 0 11-24-2010 10:03 PM
[NMR paper] Low temperature solid-state NMR experiments of half-integer quadrupolar nuclides: cav
Low temperature solid-state NMR experiments of half-integer quadrupolar nuclides: caveats and data analysis. Related Articles Low temperature solid-state NMR experiments of half-integer quadrupolar nuclides: caveats and data analysis. J Magn Reson. 2004 May;168(1):66-74 Authors: Lipton AS, Heck RW, Sears JA, Ellis PD Solid-state NMR spectroscopy of half-integer quadrupolar nuclides has received a lot of interest recently with the advent of new methodologies and higher magnetic fields. We present here the extension of our previous low...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] NMR structural characterization of the N-terminal domain of the adenylyl cyclase-asso
NMR structural characterization of the N-terminal domain of the adenylyl cyclase-associated protein (CAP) from Dictyostelium discoideum. Related Articles NMR structural characterization of the N-terminal domain of the adenylyl cyclase-associated protein (CAP) from Dictyostelium discoideum. J Biomol NMR. 2004 May;29(1):73-84 Authors: Mavoungou C, Israel L, Rehm T, Ksiazek D, Krajewski M, Popowicz G, Noegel AA, Schleicher M, Holak TA Cyclase-associated proteins (CAPs) are highly conserved, ubiquitous actin binding proteins that are involved in...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Solution structure of the carboxyl-terminal domain of RAP74 and NMR characterization
Solution structure of the carboxyl-terminal domain of RAP74 and NMR characterization of the FCP1-binding sites of RAP74 and human TFIIB. Solution structure of the carboxyl-terminal domain of RAP74 and NMR characterization of the FCP1-binding sites of RAP74 and human TFIIB. Biochemistry. 2003 Feb 18;42(6):1460-9 Authors: Nguyen BD, Chen HT, Kobor MS, Greenblatt J, Legault P, Omichinski JG FCP1 (TFIIF-associated CTD phosphatase) is the only known phosphatase specific for the phosphorylated CTD of RNAP II. The phosphatase activity of FCP1 is...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] NMR solution structure of calcium-saturated skeletal muscle troponin C.
NMR solution structure of calcium-saturated skeletal muscle troponin C. Related Articles NMR solution structure of calcium-saturated skeletal muscle troponin C. Biochemistry. 1995 Dec 12;34(49):15953-64 Authors: Slupsky CM, Sykes BD Troponin C (TnC) is an 18 kDa (162-residue) thin-filament calcium-binding protein responsible for triggering muscle contraction upon the release of calcium from the sarcoplasmic reticulum. The structure of TnC with two calcium ions bound has previously been solved by X-ray methods. Shown here is the solution...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[U. of Ottawa NMR Facility Blog] Solid State NMR of Half Integer Quadrupolar Nuclei
Solid State NMR of Half Integer Quadrupolar Nuclei Many students who do liquid state NMR or solid state NMR of spin I=1/2 nuclei have very little appreciation for the information content and complexity of the solid state NMR spectra of spin I = n/2 quadrupolar nuclei (n= 3, 5, 7....). In part, I think this may be due to the mathematics involved with explaining the important effects. With this post, I attempt to describe the NMR spectrum of an I = 5/2 nucleus in the soild state without resorting to mathematics. I hope that this post helps to boost the understanding and appreciation for the...
nmrlearner News from NMR blogs 0 08-21-2010 08:15 PM


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 08:17 PM.


Map