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 02-23-2018, 03:44 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,916
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 Site-Specific Studies of Nucleosome Interactions by Solid-State NMR.

Site-Specific Studies of Nucleosome Interactions by Solid-State NMR.

Related Articles Site-Specific Studies of Nucleosome Interactions by Solid-State NMR.

Angew Chem Int Ed Engl. 2018 Feb 21;:

Authors: Xiang S, le Paige UB, Horn V, Houben K, Baldus M, van Ingen H

Abstract
Chromatin function depends on a dense network of interactions between nucleosomes and wide range of proteins. A detailed description of these protein-nucleosome interactions is required to reach a full molecular understanding of chromatin function in both genetics and epigenetics. Here, we show that the structure, dynamics and interactions of nucleosomes can be interrogated in a residue-specific manner using state-of-the-art solid-state NMR. Using sedimented nucleosomes, high-resolution spectra are obtained for both flexible histone tails and the non-mobile histone core. Through co-sedimentation of a nucleosome-binding peptide, we demonstrate that protein binding sites on the nucleosome surface can be determined. We believe that this approach holds great promise as it is generally applicable, extendable to include the structure and dynamics of the bound proteins, and scalable to interactions of proteins with higher-order chromatin structures, including isolated or cellular chromatin.


PMID: 29465771 [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
Site-Specific Protein Internal Motions Revealed by 2H Solid-State NMR Spectroscopy
Site-Specific Protein Internal Motions Revealed by 2H Solid-State NMR Spectroscopy Publication date: 16 February 2016 Source:Biophysical Journal, Volume 110, Issue 3, Supplement 1</br> Author(s): Xiangyan Shi, Deborah A. Berthold, Chad M. Rienstra</br> </br></br> </br></br> More...
nmrlearner Journal club 0 02-17-2016 07:50 PM
[NMR paper] Site-Specific Internal Motions in GB1 Protein Microcrystals Revealed by 3D (2)H-(13)C-(13)C Solid-State NMR Spectroscopy.
Site-Specific Internal Motions in GB1 Protein Microcrystals Revealed by 3D (2)H-(13)C-(13)C Solid-State NMR Spectroscopy. Related Articles Site-Specific Internal Motions in GB1 Protein Microcrystals Revealed by 3D (2)H-(13)C-(13)C Solid-State NMR Spectroscopy. J Am Chem Soc. 2016 Feb 5; Authors: Shi X, Rienstra CM Abstract (2)H quadrupolar line shapes deliver rich information about protein dynamics. A newly designed 3D (2)H-(13)C-(13)Csolid-state NMR magic angle spinning (MAS) experiment is presented and demonstrated on the...
nmrlearner Journal club 0 02-06-2016 03:10 PM
[NMR paper] Visualizing specific Cross-Protomer Interactions in the Homo-Oligomeric Membrane Protein Proteorhodopsin by DNP-enhanced Solid-state NMR.
Visualizing specific Cross-Protomer Interactions in the Homo-Oligomeric Membrane Protein Proteorhodopsin by DNP-enhanced Solid-state NMR. Visualizing specific Cross-Protomer Interactions in the Homo-Oligomeric Membrane Protein Proteorhodopsin by DNP-enhanced Solid-state NMR. J Am Chem Soc. 2015 Jun 23; Authors: Maciejko J, Mehler M, Kaur J, Lieblein T, Morgner N, Ouari O, Tordo P, Becker-Baldus J, Glaubitz C Abstract Membrane proteins often form oligomeric complexes within the lipid bilayer but factors controlling their assembly...
nmrlearner Journal club 0 06-24-2015 01:08 PM
[NMR paper] Site-Specific Solid-State NMR Studies of "Trigger Factor" in Complex with the Large Ribosomal Subunit 50S.
Site-Specific Solid-State NMR Studies of "Trigger Factor" in Complex with the Large Ribosomal Subunit 50S. Related Articles Site-Specific Solid-State NMR Studies of "Trigger Factor" in Complex with the Large Ribosomal Subunit 50S. Angew Chem Int Ed Engl. 2015 Feb 5; Authors: Barbet-Massin E, Huang CT, Daebel V, Hsu ST, Reif B Abstract Co-translational protein folding is not yet well understood despite the availability of high-resolution ribosome crystal structures. We present first solid-state NMR data on non-mobile regions of a...
nmrlearner Journal club 0 02-08-2015 01:21 AM
[NMR paper] Site-specific identification of an a? fibril-heparin interaction site by using solid-state NMR spectroscopy.
Site-specific identification of an a? fibril-heparin interaction site by using solid-state NMR spectroscopy. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary-Button_120x27px_FullText.gif Related Articles Site-specific identification of an a? fibril-heparin interaction site by using solid-state NMR spectroscopy. Angew Chem Int Ed Engl. 2012 Dec 21;51(52):13140-3 Authors: Madine J, Pandya MJ, Hicks MR, Rodger A, Yates EA, Radford SE, Middleton DA Abstract At the...
nmrlearner Journal club 0 06-12-2013 11:42 AM
Site-Specific Solid-State NMR Detection of Hydrogen-Deuterium Exchange Reveals Conformational Changes in a 7-Helical Transmembrane Protein.
Site-Specific Solid-State NMR Detection of Hydrogen-Deuterium Exchange Reveals Conformational Changes in a 7-Helical Transmembrane Protein. Site-Specific Solid-State NMR Detection of Hydrogen-Deuterium Exchange Reveals Conformational Changes in a 7-Helical Transmembrane Protein. Biophys J. 2011 Aug 3;101(3):L23-L25 Authors: Wang S, Shi L, Kawamura I, Brown LS, Ladizhansky V Solid-state NMR spectroscopy is an efficient tool for following conformational dynamics of membrane proteins at atomic resolution. We used this technique for the site-specific...
nmrlearner Journal club 0 08-03-2011 12:00 PM
[NMR paper] Site-specific backbone dynamics from a crystalline protein by solid-state NMR spectro
Site-specific backbone dynamics from a crystalline protein by solid-state NMR spectroscopy. Related Articles Site-specific backbone dynamics from a crystalline protein by solid-state NMR spectroscopy. J Am Chem Soc. 2004 Sep 22;126(37):11422-3 Authors: Giraud N, Böckmann A, Lesage A, Penin F, Blackledge M, Emsley L Site-specific nitrogen-15 longitudinal relaxation rates are measured for the microcrystalline dimeric form of the protein Crh using multidimensional high-resolution solid-state NMR methods. The measured rates are used to provide a...
nmrlearner Journal club 0 11-24-2010 10:01 PM
[NMR paper] Probing site-specific interactions in protein-DNA complexes using heteronuclear NMR s
Probing site-specific interactions in protein-DNA complexes using heteronuclear NMR spectroscopy and molecular modeling: binding of Cro repressor to OR3. Related Articles Probing site-specific interactions in protein-DNA complexes using heteronuclear NMR spectroscopy and molecular modeling: binding of Cro repressor to OR3. J Biomol Struct Dyn. 1998 Aug;16(1):13-20 Authors: Edwards CA, Tung CS, Silks LA, Gatewood JM, Fee JA, Mariappan SV In this paper, a general method is developed to study site-specific interactions in DNA-protein complexes...
nmrlearner Journal club 0 11-17-2010 11:15 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 - 2020, 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 10:16 AM.


Map