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 06-03-2018, 01:03 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 Spectral Comparisons of Mammalian Cells and Intact Organelles by Solid-State NMR.

Spectral Comparisons of Mammalian Cells and Intact Organelles by Solid-State NMR.

Related Articles Spectral Comparisons of Mammalian Cells and Intact Organelles by Solid-State NMR.

J Struct Biol. 2018 May 30;:

Authors: Werby SH, Cegelski L

Abstract
Whole-cell protein profiling, spatial localization, and quantification of activities such as gene transcription and protein translation are possible with modern biochemical and biophysical techniques. Yet, addressing questions of overall compositional changes within a cell - capturing the relative amounts of protein and ribosomal RNA levels and lipid content simultaneously - would require numerous extractions and purifications with caveats due to isolation yields and detection methods. A holistic view of cellular composition would aid in the study of cellular composition and function. Here, solid state NMR is used to identify 13C NMR signatures for cellular organelles in HeLa cells, without the use of any isotopic labeling. Comparisons are made with carbon spectra of subcellular assemblies including DNA, lipids, ribosomes, nuclei and mitochondria. Whole-cell comparisons are made with different mammalian cells lines, with red blood cells that lack nuclei and organelles, and with Gram-negative and Gram-positive bacteria. Furthermore, treatment of mammalian cells with cycloheximide, a commonly used protein synthesis inhibitor, revealed unanticipated changes consistent with a significant increase in protein glycosylation, obvious at the whole cell level. Thus, we demonstrate that solid-state NMR serves as a unique analytical tool to catalog and compare the ratios of distinct carbon types in cells and serves as a discovery tool to reveal the workings of inhibitors such as cycloheximide on whole-cell biochemistry.


PMID: 29859329 [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
[NMR paper] Preparation of highly and generally enriched mammalian tissues for solid state NMR.
Preparation of highly and generally enriched mammalian tissues for solid state NMR. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Preparation of highly and generally enriched mammalian tissues for solid state NMR. J Biomol NMR. 2015 Oct;63(2):119-23 Authors: Wong VW, Reid DG, Chow WY, Rajan R, Green M, Brooks RA, Duer MJ Abstract An appreciable level of isotope labelling is essential for future NMR structure elucidation of...
nmrlearner Journal club 0 07-02-2016 07:23 PM
[NMR paper] A Genetically Encoded ?-Lactamase Reporter for Ultrasensitive (129) Xe NMR in Mammalian Cells.
A Genetically Encoded ?-Lactamase Reporter for Ultrasensitive (129) Xe NMR in Mammalian Cells. Related Articles A Genetically Encoded ?-Lactamase Reporter for Ultrasensitive (129) Xe NMR in Mammalian Cells. Angew Chem Int Ed Engl. 2016 Jun 15; Authors: Wang Y, Roose BW, Palovcak EJ, Carnevale V, Dmochowski IJ Abstract Molecular imaging holds considerable promise for elucidating biological processes in normal physiology as well as disease states, but requires noninvasive methods for identifying analytes at sub-micromolar...
nmrlearner Journal club 0 06-16-2016 12:06 PM
[NMR paper] Characterization of proteins by in-cell NMR spectroscopy in cultured mammalian cells.
Characterization of proteins by in-cell NMR spectroscopy in cultured mammalian cells. Characterization of proteins by in-cell NMR spectroscopy in cultured mammalian cells. Nat Protoc. 2016 Jun;11(6):1101-1111 Authors: Barbieri L, Luchinat E, Banci L Abstract
nmrlearner Journal club 0 05-20-2016 03:04 PM
[NMR paper] Algal autolysate medium to label proteins for NMR in mammalian cells.
Algal autolysate medium to label proteins for NMR in mammalian cells. Related Articles Algal autolysate medium to label proteins for NMR in mammalian cells. J Biomol NMR. 2016 Apr 22; Authors: Fuccio C, Luchinat E, Barbieri L, Neri S, Fragai M Abstract In-cell NMR provides structural and functional information on proteins directly inside living cells. At present, the high costs of the labeled media for mammalian cells represent a limiting factor for the development of this methodology. Here we report a protocol to prepare a...
nmrlearner Journal club 0 04-24-2016 10:29 PM
Algal autolysate medium to label proteins for NMR in mammalian cells
Algal autolysate medium to label proteins for NMR in mammalian cells Abstract In-cell NMR provides structural and functional information on proteins directly inside living cells. At present, the high costs of the labeled media for mammalian cells represent a limiting factor for the development of this methodology. Here we report a protocol to prepare a homemade growth medium from Spirulina platensis autolysate, suitable to express uniformly labeled proteins inside mammalian cells at a reduced cost-per-sample. The human proteins SOD1 and Mia40 were...
nmrlearner Journal club 0 04-22-2016 08:45 PM
[NMR paper] Fluorine NMR-based assay in living mammalian cells.
Fluorine NMR-based assay in living mammalian cells. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Fluorine NMR-based assay in living mammalian cells. Anal Biochem. 2015 Dec 11; Authors: Veronesi M, Giacomina F, Romeo E, Castellani B, Ottonello G, Lambruschini C, Garau G, Scarpelli R, Bandiera T, Piomelli D, Dalvit C Abstract Nuclear Magnetic Resonance (NMR)-based screening has been recognized as a powerful approach for the identification...
nmrlearner Journal club 0 12-28-2015 12:26 AM
Preparation of highly and generally enriched mammalian tissues for solid state NMR
Preparation of highly and generally enriched mammalian tissues for solid state NMR Abstract An appreciable level of isotope labelling is essential for future NMR structure elucidation of mammalian biomaterials, which are either poorly expressed, or unexpressable, using micro-organisms. We present a detailed protocol for high level 13C enrichment even in slow turnover murine biomaterials (fur keratin), using a customized diet supplemented with commercial labelled algal hydrolysate and formulated as a gel to minimize wastage, which female mice...
nmrlearner Journal club 0 09-26-2015 05:13 AM
[NMR paper] Detection of fructose-3-phosphokinase activity in intact mammalian lenses by 31P NMR
Detection of fructose-3-phosphokinase activity in intact mammalian lenses by 31P NMR spectroscopy. Related Articles Detection of fructose-3-phosphokinase activity in intact mammalian lenses by 31P NMR spectroscopy. J Biol Chem. 1993 Apr 15;268(11):7763-7 Authors: Lal S, Szwergold BS, Kappler F, Brown T Recently we have identified two novel phosphorylated metabolites in the lenses of diabetic rats as sorbitol 3-phosphate (Sor-3-P) and fructose 3-phosphate (Fru-3-P). The latter compound is of particular interest since it is a potent glycating...
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 - 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 04:54 AM.


Map