Observation of acetyl phosphate formation in mammalian mitochondria using real-time in-organelle NMR metabolomics [Biochemistry]

		BioNMR > Educational resources > Journal club
Observation of acetyl phosphate formation in mammalian mitochondria using real-time in-organelle NMR metabolomics [Biochemistry]

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

04-18-2018, 01:27 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Observation of acetyl phosphate formation in mammalian mitochondria using real-time in-organelle NMR metabolomics [Biochemistry]

Observation of acetyl phosphate formation in mammalian mitochondria using real-time in-organelle NMR metabolomics [Biochemistry]

Wen Jun Xu, He Wen, Han Sun Kim, Yoon-Joo Ko, Seung-Mo Dong, In-Sun Park, Jong In Yook, Sunghyouk Park...
Date: 2018-04-17

Recent studies point out the link between altered mitochondrial metabolism and cancer, and detailed understanding of mitochondrial metabolism requires real-time detection of its metabolites. Employing heteronuclear 2D NMR spectroscopy and 13C3-pyruvate, we propose in-organelle metabolomics that allows for the monitoring of mitochondrial metabolic changes in real time. The approach identified... Read More

PNAS:
Number: 16
Volume: 115

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Observation by Real-Time NMR and Interpretation of Length- and Location-Dependent Deamination Activity of APOBEC3B. Observation by Real-Time NMR and Interpretation of Length- and Location-Dependent Deamination Activity of APOBEC3B. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Observation by Real-Time NMR and Interpretation of Length- and Location-Dependent Deamination Activity of APOBEC3B. ACS Chem Biol. 2017 Nov 17;12(11):2704-2708 Authors: Wan L, Nagata T, Morishita R, Takaori-Kondo A, Katahira M Abstract Human APOBEC3B (A3B) deaminates a cytosine into a...	nmrlearner	Journal club	0	12-20-2017 10:12 PM
[NMR paper] Real-Time Observation of the Interaction between Thioflavin T and an Amyloid Protein by Using High-Sensitivity Rheo-NMR. Real-Time Observation of the Interaction between Thioflavin T and an Amyloid Protein by Using High-Sensitivity Rheo-NMR. Real-Time Observation of the Interaction between Thioflavin T and an Amyloid Protein by Using High-Sensitivity Rheo-NMR. Int J Mol Sci. 2017 Oct 28;18(11): Authors: Iwakawa N, Morimoto D, Walinda E, Kawata Y, Shirakawa M, Sugase K Abstract Amyloid fibril formation is associated with numerous neurodegenerative diseases. To elucidate the mechanism of fibril formation, the thioflavin T (ThT) fluorescence assay is...	nmrlearner	Journal club	0	11-17-2017 12:42 PM
Real-time pure shift 15 N HSQC of proteins: a real improvement in resolution and sensitivity Real-time pure shift 15 N HSQC of proteins: a real improvement in resolution and sensitivity Abstract Spectral resolution in proton NMR spectroscopy is reduced by the splitting of resonances into multiplets due to the effect of homonuclear scalar couplings. Although these effects are often hidden in protein NMR spectroscopy by low digital resolution and routine apodization, behind the scenes homonuclear scalar couplings increase spectral overcrowding. The possibilities for biomolecular NMR offered by new pure shift NMR methods are illustrated here....	nmrlearner	Journal club	0	03-04-2015 08:56 AM
[NMR paper] NMR methods for metabolomics of Mammalian cell culture bioreactors. NMR methods for metabolomics of Mammalian cell culture bioreactors. Related Articles NMR methods for metabolomics of Mammalian cell culture bioreactors. Methods Mol Biol. 2014;1104:223-36 Authors: Aranibar N, Reily MD Abstract Metabolomics has become an important tool for measuring pools of small molecules in mammalian cell cultures expressing therapeutic proteins. NMR spectroscopy has played an important role, largely because it requires minimal sample preparation, does not require chromatographic separation, and is quantitative. The...	nmrlearner	Journal club	0	12-04-2013 03:12 PM
NMR profiling of histone deacetylase and acetyl-transferase activities in real time. NMR profiling of histone deacetylase and acetyl-transferase activities in real time. NMR profiling of histone deacetylase and acetyl-transferase activities in real time. ACS Chem Biol. 2011 May 20;6(5):419-24 Authors: Dose A, Liokatis S, Theillet FX, Selenko P, Schwarzer D Abstract Histone deacetylases (HDACs) and histone acetyl-transferases (HATs) are universal regulators of eukaryotic transcriptional activity and emerging therapeutic targets for human diseases. Here we describe the generation of isotope-labeled deacetylation and...	nmrlearner	Journal club	0	09-07-2011 06:28 PM
NMR-based metabolomics of mammalian cell and tissue cultures NMR-based metabolomics of mammalian cell and tissue cultures Abstract NMR spectroscopy was used to evaluate growth media and the cellular metabolome in two systems of interest to biomedical research. The first of these was a Chinese hamster ovary cell line engineered to express a recombinant protein. Here, NMR spectroscopy and a quantum mechanical total line shape analysis were utilized to quantify 30 metabolites such as amino acids, Krebs cycle intermediates, activated sugars, cofactors, and others in both media and cell extracts. The impact of bioreactor scale and addition of...	nmrlearner	Journal club	0	03-09-2011 04:19 AM
NMR-based metabolomics of mammalian cell and tissue cultures. NMR-based metabolomics of mammalian cell and tissue cultures. NMR-based metabolomics of mammalian cell and tissue cultures. J Biomol NMR. 2011 Mar 4; Authors: Aranibar N, Borys M, Mackin NA, Ly V, Abu-Absi N, Abu-Absi S, Niemitz M, Schilling B, Li ZJ, Brock B, Russell RJ, Tymiak A, Reily MD NMR spectroscopy was used to evaluate growth media and the cellular metabolome in two systems of interest to biomedical research. The first of these was a Chinese hamster ovary cell line engineered to express a recombinant protein. Here, NMR spectroscopy and a...	nmrlearner	Journal club	0	03-05-2011 01:02 PM
NMR-based stable isotope resolved metabolomics in systems biochemistry NMR-based stable isotope resolved metabolomics in systems biochemistry Abstract An important goal of metabolomics is to characterize the changes in metabolic networks in cells or various tissues of an organism in response to external perturbations or pathologies. The profiling of metabolites and their steady state concentrations does not directly provide information regarding the architecture and fluxes through metabolic networks. This requires tracer approaches. NMR is especially powerful as it can be used not only to identify and quantify metabolites in an unfractionated mixture such...	nmrlearner	Journal club	0	03-03-2011 02:06 AM

« Previous Thread | Next 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