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 01-06-2018, 11:17 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 18,201
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 Integrating High-Resolution and Solid-State Magic Angle Spinning NMR Spectroscopy and a Transcriptomic Analysis of Soybean Tissues in Response to Water Deficiency.

Integrating High-Resolution and Solid-State Magic Angle Spinning NMR Spectroscopy and a Transcriptomic Analysis of Soybean Tissues in Response to Water Deficiency.

Related Articles Integrating High-Resolution and Solid-State Magic Angle Spinning NMR Spectroscopy and a Transcriptomic Analysis of Soybean Tissues in Response to Water Deficiency.

Phytochem Anal. 2017 Nov;28(6):529-540

Authors: Coutinho ID, Moraes TB, Mertz-Henning LM, Nepomuceno AL, Giordani W, Marcolino-Gomes J, Santagneli S, Colnago LA

Abstract
INTRODUCTION: Solid-state NMR (SSNMR) spectroscopy methods provide chemical environment and ultrastructural details that are not easily accessible by other non-destructive, high-resolution spectral techniques. High-resolution magic angle spinning (HR-MAS) has been widely used to obtain the metabolic profile of a heterogeneous sample, combining the resolution enhancement provided by MAS in SSNMR with the shimming and locking procedures in liquid-state NMR.
OBJECTIVE: In this work, we explored the feasibility of using the HR-MAS and SSNMR techniques to identify metabolic changes in soybean leaves subjected to water-deficient conditions.
METHODOLOGY: Control and water-deficient soybean leaves were analysed using one-dimensional (1D) HR-MAS and SSNMR. Total RNA was extracted from the leaves for the transcriptomic analysis.
RESULTS: The 1 H HR-MAS and CP-MAS 13 C{1 H} spectra of soybean leaves grown with and without water deficiency stress revealed striking differences in metabolites. A total of 30 metabolites were identified, and the impact of water deficiency on the metabolite profile of soybean leaves was to induce amino acid synthesis. High expression levels of genes required for amino acid biosynthesis were highly correlated with the compounds identified by 1 H HR-MAS.
CONCLUSIONS: The integration of the 1 H HR-MAS and SSNMR spectra with the transcriptomic data provided a complete picture of the major changes in the metabolic profile of soybeans in response to water deficiency. Copyright 2017 John Wiley & Sons, Ltd.


PMID: 28722224 [PubMed - indexed for MEDLINE]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] The effects of high concentrations of ionic liquid on GB1 protein structure and dynamics probed by high-resolution magic-angle-spinning NMR spectroscopy.
The effects of high concentrations of ionic liquid on GB1 protein structure and dynamics probed by high-resolution magic-angle-spinning NMR spectroscopy. Related Articles The effects of high concentrations of ionic liquid on GB1 protein structure and dynamics probed by high-resolution magic-angle-spinning NMR spectroscopy. Biochem Biophys Rep. 2016 Dec;8:75-80 Authors: Warner L, Gjersing E, Follett SE, Elliott KW, Dzyuba SV, Varga K Abstract Ionic liquids have great potential in biological applications and biocatalysis, as some...
nmrlearner Journal club 0 07-20-2017 08:40 AM
The effects of high concentrations of ionic liquid on GB1 protein structure and dynamics probed by high-resolution magic-angle-spinning NMR spectroscopy
The effects of high concentrations of ionic liquid on GB1 protein structure and dynamics probed by high-resolution magic-angle-spinning NMR spectroscopy Publication date: Available online 11 August 2016 Source:Biochemistry and Biophysics Reports</br> Author(s): Lisa Warner, Erica Gjersing, Shelby E. Follett, K. Wade Elliott, Sergei V. Dzyuba, Krisztina Varga</br> Ionic liquids have great potential in biological applications and biocatalysis, as some ionic liquids can stabilize proteins and enhance enzyme activity, while others have the opposite effect....
nmrlearner Journal club 0 08-11-2016 07:03 PM
[NMR paper] A Novel High-Resolution and Sensitivity-Enhanced Three-Dimensional Solid-State NMR Experiment Under Ultrafast Magic Angle Spinning Conditions.
A Novel High-Resolution and Sensitivity-Enhanced Three-Dimensional Solid-State NMR Experiment Under Ultrafast Magic Angle Spinning Conditions. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.nature.com-images-lo_npg.gif http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.ncbi.nlm.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles A Novel High-Resolution and Sensitivity-Enhanced Three-Dimensional Solid-State NMR Experiment Under Ultrafast Magic Angle Spinning Conditions. Sci Rep. 2015;5:11810 ...
nmrlearner Journal club 0 08-03-2016 04:58 AM
[NMR paper] Relative merits of rCW(A) and XiX heteronuclear spin decoupling in solid-state magic-angle-spinning NMR spectroscopy: A bimodal Floquet analysis.
Relative merits of rCW(A) and XiX heteronuclear spin decoupling in solid-state magic-angle-spinning NMR spectroscopy: A bimodal Floquet analysis. Relative merits of rCW(A) and XiX heteronuclear spin decoupling in solid-state magic-angle-spinning NMR spectroscopy: A bimodal Floquet analysis. J Magn Reson. 2016 Jan 6;263:55-64 Authors: Equbal A, Leskes M, Nielsen NC, Madhu PK, Vega S Abstract We present a bimodal Floquet analysis of the recently introduced refocused continuous wave (rCW) solid-state NMR heteronuclear dipolar...
nmrlearner Journal club 0 01-17-2016 12:06 PM
[NMR paper] Restoring Resolution in Biological Solid-State NMR under Conditions of Off-Magic-Angle Spinning.
Restoring Resolution in Biological Solid-State NMR under Conditions of Off-Magic-Angle Spinning. Related Articles Restoring Resolution in Biological Solid-State NMR under Conditions of Off-Magic-Angle Spinning. J Phys Chem Lett. 2015 Dec 7;:5040-5044 Authors: Sarkar R, Rodriguez Camargo DC, Pintacuda G, Reif B Abstract Spin-state-selective excitation (S3E) experiments allow the selection of individual transitions in a coupled two spin system. We show that in the solid state, the dipole-dipole interaction (DD) between (15)N and...
nmrlearner Journal club 0 12-08-2015 08:28 PM
[NMR paper] Correlating high-resolution magic angle spinning NMR spectroscopy and gene analysis in osteoarthritic cartilage.
Correlating high-resolution magic angle spinning NMR spectroscopy and gene analysis in osteoarthritic cartilage. Correlating high-resolution magic angle spinning NMR spectroscopy and gene analysis in osteoarthritic cartilage. NMR Biomed. 2015 Mar 12; Authors: Tufts L, Shet Vishnudas K, Fu E, Kurhanewicz J, Ries M, Alliston T, Li X Abstract Osteoarthritis (OA) is a common multifactorial and heterogeneous degenerative joint disease, and biochemical changes in cartilage matrix occur during the early stages of OA before...
nmrlearner Journal club 0 03-13-2015 12:31 PM
[NMR paper] High-resolution paramagnetically enhanced solid-state NMR spectroscopy of membrane proteins at fast magic angle spinning.
High-resolution paramagnetically enhanced solid-state NMR spectroscopy of membrane proteins at fast magic angle spinning. Related Articles High-resolution paramagnetically enhanced solid-state NMR spectroscopy of membrane proteins at fast magic angle spinning. J Biomol NMR. 2013 Dec 13; Authors: Ward ME, Wang S, Krishnamurthy S, Hutchins H, Fey M, Brown LS, Ladizhansky V Abstract Magic angle spinning nuclear magnetic resonance (MAS NMR) is well suited for the study of membrane proteins in membrane mimetic and native membrane...
nmrlearner Journal club 0 12-18-2013 04:00 PM
[NMR paper] Resonance assignments and secondary structure analysis of E. coli thioredoxin by magic angle spinning solid-state NMR spectroscopy.
Resonance assignments and secondary structure analysis of E. coli thioredoxin by magic angle spinning solid-state NMR spectroscopy. Related Articles Resonance assignments and secondary structure analysis of E. coli thioredoxin by magic angle spinning solid-state NMR spectroscopy. J Phys Chem B. 2005 Sep 29;109(38):18135-45 Authors: Marulanda D, Tasayco ML, Cataldi M, Arriaran V, Polenova T De novo site-specific 13C and 15N backbone and sidechain resonance assignments are presented for uniformly enriched E. coli thioredoxin, established using...
nmrlearner Journal club 0 12-01-2010 06:56 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 - 2018, 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 04:40 AM.


Map