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 08-21-2014, 06:43 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,652
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 NMR characterisation of the conformational fluctuations of the human lymphocyte function associated antigen-1 i domain

NMR characterisation of the conformational fluctuations of the human lymphocyte function associated antigen-1 i domain

Abstract

Lymphocyte function-associated antigen-1 (LFA-1) is an integrin protein that transmits information across the plasma membrane through the so-called ‘inside-out’ and ‘outside-in’ signalling mechanism. To investigate this mechanism, we carried out an NMR analysis of the dynamics of the LFA-1 I-domain, which has enabled us to characterise the motions of this domain on a broad range of timescales. We studied first the internal motions on the nanosecond timescale by spin relaxation measurements and model-free analysis. We then extended this analysis to the millisecond timescale motions by measuring 15N-1H residual dipolar couplings (RDCs) of the backbone amide groups. We analysed these results in the context of the three major conformational states of the I-domain using their corresponding X-ray crystallographic structures. Our results highlight the importance of the low-frequency motions of the LFA-1 I-domain in the inactive apo state. We found in particular that ?-helix 7 is in a position in the apo closed state that cannot be fully described by any of the existing X-ray structures, as it appears to be in dynamic exchange between different conformations. This type of motion seems to represent an inherent property of the LFA-1 I-domain and might be relevant for controlling the access to the allosteric binding pocket, as well as for the downward displacement of ?-helix 7 that is required for the activation of LFA-1.




More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Expression and structural characterization of anti-T-antigen single chain antibodies (scFvs) and analysis of their binding to T-antigen by surface plasmon resonance and NMR spectroscopy.
Expression and structural characterization of anti-T-antigen single chain antibodies (scFvs) and analysis of their binding to T-antigen by surface plasmon resonance and NMR spectroscopy. Expression and structural characterization of anti-T-antigen single chain antibodies (scFvs) and analysis of their binding to T-antigen by surface plasmon resonance and NMR spectroscopy. J Biochem. 2013 Oct 4; Authors: Yuasa N, Koyama T, Subedi GP, Yamaguchi Y, Matsushita M, Fujita-Yamaguchi Y Abstract T-antigen (Gal?1-3GalNAc?-1-Ser/Thr), also known as...
nmrlearner Journal club 0 10-08-2013 02:04 PM
The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation
The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation Available online 13 December 2012 Publication year: 2012 Source:Current Opinion in Structural Biology</br> </br> Historically it has been virtually impossible to experimentally determine the contribution of residual protein entropy to fundamental protein activities such as the binding of ligands. Recent progress has illuminated the possibility of employing NMR relaxation methods to quantitatively determine the role of changes in conformational...
nmrlearner Journal club 0 02-03-2013 10:13 AM
Pressure-induced chemical shifts as probes for conformational fluctuations in proteins
Pressure-induced chemical shifts as probes for conformational fluctuations in proteins Available online 19 January 2013 Publication year: 2013 Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br> </br> </br> </br></br>
nmrlearner Journal club 0 01-20-2013 07:56 PM
Structural Characterisation of a Histone Domain by Projection-Decomposition
Structural Characterisation of a Histone Domain by Projection-Decomposition Publication year: 2012 Source:Journal of Magnetic Resonance</br> Jonas Fredriksson, Wolfgang Bermel, Martin Billeter</br> We demonstrate that two projection experiments, a 15N-HSQC–NOESY–15N-HSQC and a 13C-HSQC–NOESY–15N-HSQC, recorded for a histone domain from yeast, contain enough information to support a structural characterisation of the protein. At the temperature used, 298K, the histone domain exhibits a very high extent of chemical shift degeneracy that is uncharacteristic for a fully...
nmrlearner Journal club 0 03-09-2012 09:16 AM
Structural Characterisation of a Histone Domain by Projection-Decomposition
Structural Characterisation of a Histone Domain by Projection-Decomposition Publication year: 2012 Source: Journal of Magnetic Resonance, Available online 23 February 2012</br> Jonas*Fredriksson, Wolfgang*Bermel, Martin*Billeter</br> We demonstrate that two projection experiments, aN-HSQC–NOESY–N-HSQC and aC-HSQC–NOESY–N-HSQC, recorded for a histone domain from yeast, contain enough information to support a structural characterisation of the protein. At the temperature used, 298K, the histone domain exhibits a very high extent of chemical shift degeneracy that is uncharacteristic for...
nmrlearner Journal club 0 02-25-2012 04:20 PM
[NMR paper] Metal-dependent conformational changes in a recombinant vWF-A domain from human facto
Metal-dependent conformational changes in a recombinant vWF-A domain from human factor B: a solution study by circular dichroism, fourier transform infrared and (1)H NMR spectroscopy. Related Articles Metal-dependent conformational changes in a recombinant vWF-A domain from human factor B: a solution study by circular dichroism, fourier transform infrared and (1)H NMR spectroscopy. J Mol Biol. 2000 Apr 21;298(1):135-47 Authors: Hinshelwood J, Perkins SJ Factor B is a key component of the alternative pathway of complement and is cleaved by...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] NMR solution structure of the inserted domain of human leukocyte function associated
NMR solution structure of the inserted domain of human leukocyte function associated antigen-1. Related Articles NMR solution structure of the inserted domain of human leukocyte function associated antigen-1. J Mol Biol. 2000 Feb 4;295(5):1251-64 Authors: Legge GB, Kriwacki RW, Chung J, Hommel U, Ramage P, Case DA, Dyson HJ, Wright PE The interaction between the leukocyte function-associated antigen-1 (LFA-1) and the intercellular adhesion molecule is thought to be mediated primarily via the inserted domain (I-domain) in the alpha-subunit. The...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] Contributions to conformational entropy arising from bond vector fluctuations measure
Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. J Mol Biol. 1996 Oct 25;263(2):369-82 Authors: Yang D, Kay LE The relation between order parameters derived from NMR...
nmrlearner Journal club 0 08-22-2010 02:20 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 07:41 AM.


Map