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 11-24-2010, 09:16 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,709
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 Probing solvent accessibility of transthyretin amyloid by solution NMR spectroscopy.

Probing solvent accessibility of transthyretin amyloid by solution NMR spectroscopy.

Related Articles Probing solvent accessibility of transthyretin amyloid by solution NMR spectroscopy.

J Biol Chem. 2004 Feb 13;279(7):5699-707

Authors: Olofsson A, Ippel JH, Wijmenga SS, Lundgren E, Ohman A

The human plasma protein transthyretin (TTR) may form fibrillar protein deposits that are associated with both inherited and idiopathic amyloidosis. The present study utilizes solution nuclear magnetic resonance spectroscopy, in combination with hydrogen/deuterium exchange, to determine residue-specific solvent protection factors within the fibrillar structure of the clinically relevant variant, TTRY114C. This novel approach suggests a fibril core comprised of the six beta-strands, A-B-E-F-G-H, which retains a native-like conformation. Strands C and D are dislocated from their native edge region and become solvent-exposed, leaving a new interface involving strands A and B open for intermolecular interactions. Our results further support a native-like intermolecular association between strands F-F' and H-H' with a prolongation of these beta-strands and, interestingly, with a possible shift in beta-strand register of the subunit assembly. This finding may explain previous observations of a monomeric intermediate preceding fibril formation. A structural model based on our results is presented.

PMID: 14604984 [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
Probing water-accessibility in HET-s(218-289) amyloid fibrils by solid-state NMR.
Probing water-accessibility in HET-s(218-289) amyloid fibrils by solid-state NMR. Probing water-accessibility in HET-s(218-289) amyloid fibrils by solid-state NMR. J Mol Biol. 2010 Nov 18; Authors: Van Melckebeke H, Schanda P, Gath J, Wasmer C, Verel R, Lange A, Meier BH, Böckmann A Despite its importance in the context of conformational diseases, structural information is still sparse for protein fibrils. Hydrogen/deuterium exchange measurements of backbone amides allow to identify hydrogen-bonding patterns and reveal pertinent information about...
nmrlearner Journal club 0 11-26-2010 05:32 PM
[NMR paper] Probing solvent accessibility of amyloid fibrils by solution NMR spectroscopy.
Probing solvent accessibility of amyloid fibrils by solution NMR spectroscopy. Related Articles Probing solvent accessibility of amyloid fibrils by solution NMR spectroscopy. Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8648-53 Authors: Ippel JH, Olofsson A, Schleucher J, Lundgren E, Wijmenga SS Amyloid is the result of an anomalous protein and peptide aggregation, leading to the formation of insoluble fibril deposits. At present, 18 human diseases have been associated with amyloid deposits-e.g., Alzheimer's disease and Prion-transmissible...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Probing proteins in solution by (129)Xe NMR spectroscopy.
Probing proteins in solution by (129)Xe NMR spectroscopy. Related Articles Probing proteins in solution by (129)Xe NMR spectroscopy. J Magn Reson. 2001 Jun;150(2):167-74 Authors: Locci E, Dehouck Y, Casu M, Saba G, Lai A, Luhmer M, Reisse J, Bartik K The interaction of xenon with different proteins in aqueous solution is investigated by (129)Xe NMR spectroscopy. Chemical shifts are measured in horse metmyoglobin, hen egg white lysozyme, and horse cytochrome c solutions as a function of xenon concentration. In these systems, xenon is in fast...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] Probing protein structure by solvent perturbation of NMR spectra: the surface accessi
Probing protein structure by solvent perturbation of NMR spectra: the surface accessibility of bovine pancreatic trypsin inhibitor. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Probing protein structure by solvent perturbation of NMR spectra: the surface accessibility of bovine pancreatic trypsin inhibitor. Biophys J. 1997 Jul;73(1):382-96 Authors: Molinari H,...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Evaluation of Solvent Accessibility to the [Fe(4)S(4)] Binding Pocket in Native and T
Evaluation of Solvent Accessibility to the Binding Pocket in Native and Tyr19 Mutant High Potential Iron Proteins by (1)H-(15)N HMQC and (19)F NMR Experiments. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Evaluation of Solvent Accessibility to the Binding Pocket in Native and Tyr19 Mutant High Potential Iron Proteins by (1)H-(15)N HMQC and (19)F NMR Experiments. Inorg Chem. 1996 Feb 28;35(5):1121-1125 Authors: Li D, Agarwal A, Cowan JA The solvent accessibility of Chromatium...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] Probing protein structure by solvent perturbation of NMR spectra. Photochemically ind
Probing protein structure by solvent perturbation of NMR spectra. Photochemically induced dynamic nuclear polarization and paramagnetic perturbation techniques applied to the study of the molten globule state of alpha-lactalbumin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Probing protein structure by solvent perturbation of NMR spectra. Photochemically induced dynamic nuclear polarization and paramagnetic perturbation techniques applied to the study of the...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] Probing protein structure by solvent perturbation of NMR spectra. A comparison with p
Probing protein structure by solvent perturbation of NMR spectra. A comparison with photochemically induced dynamic nuclear polarization techniques applied to native alpha-lactalbumin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Probing protein structure by solvent perturbation of NMR spectra. A comparison with photochemically induced dynamic nuclear polarization techniques applied to native alpha-lactalbumin. Eur J Biochem. 1995 Jan 15;227(1-2):78-86...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] Probing protein structure by solvent perturbation of NMR spectra. II. Determination o
Probing protein structure by solvent perturbation of NMR spectra. II. Determination of surface and buried residues in homologous proteins. Related Articles Probing protein structure by solvent perturbation of NMR spectra. II. Determination of surface and buried residues in homologous proteins. Biopolymers. 1993 May;33(5):839-46 Authors: Esposito G, Lesk AM, Molinari H, Motta A, Niccolai N, Pastore A The experimental assignment of most residues in a protein to the surface or interior is in principle possible without prior solution of a complete...
nmrlearner Journal club 0 08-21-2010 11:53 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 - 2017, 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 05:13 AM.


Map