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 05-10-2018, 01:31 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 3D Structures of Plant Phytochrome A as Pr and Pfr From Solid-State NMR: Implications for Molecular Function.

3D Structures of Plant Phytochrome A as Pr and Pfr From Solid-State NMR: Implications for Molecular Function.

Related Articles 3D Structures of Plant Phytochrome A as Pr and Pfr From Solid-State NMR: Implications for Molecular Function.

Front Plant Sci. 2018;9:498

Authors: Song C, Mroginski MA, Lang C, Kopycki J, Gärtner W, Matysik J, Hughes J

Abstract
We present structural information for oat phyA3 in the far-red-light-absorbing (Pfr) signaling state, to our knowledge the first three-dimensional (3D) information for a plant phytochrome as Pfr. Solid-state magic-angle spinning (MAS) NMR was used to detect interatomic contacts in the complete photosensory module [residues 1-595, including the NTE (N-terminal extension), PAS (Per/Arnt/Sim), GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) and PHY (phytochrome-specific) domains but with the C-terminal PAS repeat and transmitter-like module deleted] auto-assembled in vitro with 13C- and 15N-labeled phycocyanobilin (PCB) chromophore. Thereafter, quantum mechanics/molecular mechanics (QM/MM) enabled us to refine 3D structural models constrained by the NMR data. We provide definitive atomic assignments for all carbon and nitrogen atoms of the chromophore, showing the Pfr chromophore geometry to be periplanar ZZEssa with the D -ring in a ?-facial disposition incompatible with many earlier notions regarding photoconversion yet supporting circular dichroism (CD) data. The Y268 side chain is shifted radically relative to published Pfr crystal structures in order to accommodate the ?-facial ring D . Our findings support a photoconversion sequence beginning with Pr photoactivation via an anticlockwise D -ring Za->Ea photoflip followed by significant shifts at the coupling of ring A to the protein, a B -ring propionate partner swap from R317 to R287, changes in the C -ring propionate hydrogen-bonding network, breakage of the D272-R552 salt bridge accompanied by sheet-to-helix refolding of the tongue region stabilized by Y326-D272-S554 hydrogen bonding, and binding of the NTE to the hydrophobic side of ring A . We discuss phyA photoconversion, including the possible roles of mesoscopic phase transitions and protonation dynamics in the chromophore pocket. We also discuss possible associations between structural changes and translocation and signaling processes within the cell.


PMID: 29740459 [PubMed]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
MembraneInsertion of a Dinuclear Polypyridylruthenium(II)Complex Revealed by Solid-State NMR and Molecular Dynamics Simulation:Implications for Selective Antibacterial Activity
MembraneInsertion of a Dinuclear Polypyridylruthenium(II)Complex Revealed by Solid-State NMR and Molecular Dynamics Simulation:Implications for Selective Antibacterial Activity Daniel K. Weber, Marc-Antoine Sani, Matthew T. Downton, Frances Separovic, F. Richard Keene and J. Grant Collins http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.6b09996/20161109/images/medium/ja-2016-099965_0009.gif Journal of the American Chemical Society DOI: 10.1021/jacs.6b09996 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
nmrlearner Journal club 0 11-19-2016 08:35 PM
Multidimensional solid-state NMR spectroscopy of plant cell walls #DNPNMR
From The DNP-NMR Blog: Multidimensional solid-state NMR spectroscopy of plant cell walls #DNPNMR p.p1 {margin: 0.0px 0.0px 0.0px 36.0px; text-indent: -36.0px; font: 12.0px Helvetica} Wang, T., P. Phyo, and M. Hong, Multidimensional solid-state NMR spectroscopy of plant cell walls. Solid State Nuclear Magnetic Resonance, 2016. 78: p. 56-63. http://www.sciencedirect.com/science/article/pii/S0926204016300595
nmrlearner News from NMR blogs 0 11-19-2016 08:35 PM
[NMR paper] Multidimensional solid-state NMR spectroscopy of plant cell walls.
Multidimensional solid-state NMR spectroscopy of plant cell walls. Multidimensional solid-state NMR spectroscopy of plant cell walls. Solid State Nucl Magn Reson. 2016 Aug 13;78:56-63 Authors: Wang T, Phyo P, Hong M Abstract Plant biomass has become an important source of bio-renewable energy in modern society. The molecular structure of plant cell walls is difficult to characterize by most atomic-resolution techniques due to the insoluble and disordered nature of the cell wall. Solid-state NMR (SSNMR) spectroscopy is uniquely...
nmrlearner Journal club 0 08-24-2016 04:39 PM
[NMR paper] Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.
Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography. J Phys Chem B. 2014 Mar 27;118(12):3298-309 Authors: Pawlak T, Potrzebowski MJ Abstract This paper presents a methodology that allows the fine refinement of the crystal and molecular structure...
nmrlearner Journal club 0 11-14-2014 08:40 PM
[NMR paper] Sensitivity-enhanced solid-state NMR detection of expansin's target in plant cell walls.
Sensitivity-enhanced solid-state NMR detection of expansin's target in plant cell walls. Related Articles Sensitivity-enhanced solid-state NMR detection of expansin's target in plant cell walls. Proc Natl Acad Sci U S A. 2013 Sep 24; Authors: Wang T, Park YB, Caporini MA, Rosay M, Zhong L, Cosgrove DJ, Hong M Abstract Structure determination of protein binding to noncrystalline macromolecular assemblies such as plant cell walls (CWs) poses a significant structural biology challenge. CWs are loosened during growth by expansin proteins,...
nmrlearner Journal club 0 09-27-2013 03:28 AM
[NMR paper] Water scaffolding in collagen: Implications on protein dynamics as revealed by solid-state NMR.
Water scaffolding in collagen: Implications on protein dynamics as revealed by solid-state NMR. Water scaffolding in collagen: Implications on protein dynamics as revealed by solid-state NMR. Biopolymers. 2013 Jun 19; Authors: Aliev AE, Courtier-Murias D Abstract Solid-state NMR studies of collagen samples of various origin confirm that the amplitude of collagen backbone and sidechain motions increases significantly on increasing the water content. This conclusion is supported by the changes observed in three different NMR...
nmrlearner Journal club 0 06-21-2013 01:10 PM
Ultra-high resolution in MAS solid-state NMR of perdeuterated proteins: Implications for structure and dynamics
Ultra-high resolution in MAS solid-state NMR of perdeuterated proteins: Implications for structure and dynamics Publication year: 2012 Source:Journal of Magnetic Resonance, Volume 216</br> Bernd Reif</br> High resolution proton spectra are obtained in MAS solid-state NMR in case samples are prepared using perdeuterated protein and D2O in the recrystallization buffer. Deuteration reduces drastically 1H, 1H dipolar interactions and allows to obtain amide proton line widths on the order of 20 Hz. Similarly, high-resolution proton spectra of aliphatic groups can be obtained...
nmrlearner Journal club 0 03-13-2012 03:33 PM
Ultra-high resolution in MAS solid-state NMR of perdeuterated proteins: Implications for Structure and Dynamics
Ultra-high resolution in MAS solid-state NMR of perdeuterated proteins: Implications for Structure and Dynamics Publication year: 2012 Source: Journal of Magnetic Resonance, Available online 5 January 2012</br> Bernd*Reif</br> http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S1090780711005969-fx1.sml</br></br></br> Source: Journal of Magnetic Resonance
nmrlearner Journal club 0 01-07-2012 03:12 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 01:30 PM.


Map