NMR paper Metabolic variations among low grade and high grade gliomas - profiling by 1h nmr spectroscopy.

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[NMR paper] Metabolic variations among low grade and high grade gliomas - profiling by 1h nmr spectroscopy.

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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:

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05-13-2020, 09:14 PM

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Metabolic variations among low grade and high grade gliomas - profiling by 1h nmr spectroscopy.

METABOLIC VARIATIONS AMONG LOW GRADE AND HIGH GRADE GLIOMAS - PROFILING BY 1H NMR SPECTROSCOPY.

Related Articles METABOLIC VARIATIONS AMONG LOW GRADE AND HIGH GRADE GLIOMAS - PROFILING BY 1H NMR SPECTROSCOPY.

J Proteome Res. 2020 May 11;:

Authors: Jothi J, Vanisree AJ, Krishnaswamy R

Abstract
Altered cellular metabolism is one of the crucial hallmarks of glioma that deserves an exploration, as the metabolites act as direct indicators of protein function and genetic variations. The current study focused on metabolomic profiling of patients, from whom glioma specimens were obtained for identification of specific metabolites that could distinguish the low grade and high grade. In the current study 1 H NMR spectroscopy has carried out and the data were analysed by partial least squares discriminant analysis (PLS-DA) and orthogonal projection to latent structure with discriminant analysis (OPLS-DA). Pathway analysis was done to associate characteristic metabolites with the grades of sample using MetaboAnalyst 4.0 software based on KEGG metabolic pathways database. Distinctive metabolic profile among low and high grade gliomas with top fifteen characteristic metabolites that could discriminate these grades were identified on the basis of their VIP scores from the OPLS-DA model. The major altered metabolic pathways include: choline, taurine & hypotaurine, glutamate/glutamine, glutathione, and phenyl alanine/tyrosine which were found to be consistent with the particular grade of a sample. Our study clearly demonstrated a characteristic metabolic profile of an individual grades of glioma suggesting that an altered metabolism are consistent to the specific grades of glioma appreciation and which could lead to devise novel treatment strategies.

PMID: 32393032 [PubMed - as supplied by publisher]

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