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 11-01-2017, 07:49 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 The conformation of the Congo-red ligand bound to amyloid fibrils HET-s(218â??289): a solid-state NMR study

The conformation of the Congo-red ligand bound to amyloid fibrils HET-s(218â??289): a solid-state NMR study

Abstract

We have previously shown that Congo red (CR) binds site specifically to amyloid fibrils formed by HET-s(218â??289) with the long axis of the CR molecule almost parallel to the fibril axis. HADDOCK docking studies indicated that CR adopts a roughly planar conformation with the torsion angle Ï? characterizing the relative orientation of the two phenyl rings being a few degrees. In this study, we experimentally determine the torsion angle Ï? at the center of the CR molecule when bound to HET-s(218â??289) amyloid fibrils using solid-state NMR tensor-correlation experiments. The method described here relies on the site-specific 13C labeling of CR and on the analysis of the two-dimensional magic-angle spinning tensor-correlation spectrum of 13C2-CR. We determined the torsion angle Ï? to be 19°.



Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Emerging Structural Understanding of Amyloid Fibrils by Solid-State NMR.
Emerging Structural Understanding of Amyloid Fibrils by Solid-State NMR. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif Related Articles Emerging Structural Understanding of Amyloid Fibrils by Solid-State NMR. Trends Biochem Sci. 2017 Oct;42(10):777-787 Authors: Meier BH, Riek R, Böckmann A Abstract Amyloid structures at atomic resolution have remained elusive mainly because of their extensive polymorphism and because their polymeric properties have hampered...
nmrlearner Journal club 0 10-12-2017 02:58 PM
[NMR paper] Structural Polymorphism of Alzheimer's ?-Amyloid Fibrils as Controlled by an E22 Switch: A Solid-State NMR Study.
Structural Polymorphism of Alzheimer's ?-Amyloid Fibrils as Controlled by an E22 Switch: A Solid-State NMR Study. Structural Polymorphism of Alzheimer's ?-Amyloid Fibrils as Controlled by an E22 Switch: A Solid-State NMR Study. J Am Chem Soc. 2016 Jul 14; Authors: Elkins MR, Wang T, Nick M, Jo H, Lemmin T, Prusiner SB, DeGrado WF, Stoehr J, Hong M Abstract The amyloid-? (A?) peptide of the Alzheimer's disease (AD) forms polymorphic fibrils on the micrometer scale and molecular scale. Various fibril growth conditions have been...
nmrlearner Journal club 0 07-16-2016 04:54 AM
[NMR paper] Preparation of Amyloid Fibrils for Magic-Angle Spinning Solid-State NMR Spectroscopy.
Preparation of Amyloid Fibrils for Magic-Angle Spinning Solid-State NMR Spectroscopy. Related Articles Preparation of Amyloid Fibrils for Magic-Angle Spinning Solid-State NMR Spectroscopy. Methods Mol Biol. 2016;1345:173-83 Authors: Tuttle MD, Courtney JM, Barclay AM, Rienstra CM Abstract Solid-state NMR spectroscopy (SSNMR) is an established and invaluable tool for the study of amyloid fibril structure with atomic-level detail. Optimization of the homogeneity and concentration of fibrils enhances the resolution and sensitivity...
nmrlearner Journal club 0 10-12-2015 01:04 AM
[NMR paper] Capturing a reactive state of amyloid aggregates: NMR-based characterization of copper-bound Alzheimer disease amyloid ?-fibrils in a redox cycle.
Capturing a reactive state of amyloid aggregates: NMR-based characterization of copper-bound Alzheimer disease amyloid ?-fibrils in a redox cycle. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_final.gif Related Articles Capturing a reactive state of amyloid aggregates: NMR-based characterization of copper-bound Alzheimer disease amyloid ?-fibrils in a redox cycle. J Biol Chem. 2014 Apr 4;289(14):9998-10010 Authors: Parthasarathy S, Yoo B, McElheny D, Tay W,...
nmrlearner Journal club 0 05-31-2014 01:57 PM
Atomic-resolution three-dimensional structure of HET-s(218-289) amyloid fibrils by solid-state NMR spectroscopy.
Atomic-resolution three-dimensional structure of HET-s(218-289) amyloid fibrils by solid-state NMR spectroscopy. Atomic-resolution three-dimensional structure of HET-s(218-289) amyloid fibrils by solid-state NMR spectroscopy. J Am Chem Soc. 2010 Oct 6;132(39):13765-75 Authors: Van Melckebeke H, Wasmer C, Lange A, Ab E, Loquet A, Böckmann A, Meier BH We present a strategy to solve the high-resolution structure of amyloid fibrils by solid-state NMR and use it to determine the atomic-resolution structure of the prion domain of the fungal prion HET-s...
nmrlearner Journal club 0 01-21-2011 12:00 PM
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
High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation an
High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation and Implications for Protofilament Assembly and Structure http://pubs.acs.org//appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi100864t/aop/images/medium/bi-2010-00864t_0004.gifBiochemistry, Volume 0, Issue 0, Articles ASAP (As Soon As Publishable). More...
nmrlearner Journal club 0 08-18-2010 12:19 AM
High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation an
High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation and Implications for Protofilament Assembly and Structure . Related Articles High-Resolution MAS NMR Analysis of PI3-SH3 Amyloid Fibrils: Backbone Conformation and Implications for Protofilament Assembly and Structure . Biochemistry. 2010 Aug 13; Authors: Bayro MJ, Maly T, Birkett NR, Macphee CE, Dobson CM, Griffin RG The SH3 domain of the PI3 kinase (PI3-SH3 or PI3K-SH3) readily aggregates into fibrils in vitro and has served as an important model system in the...
nmrlearner Journal club 0 08-17-2010 01:53 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 - 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 06:52 PM.


Map