NMR paper In situ characterization of advanced glycation end products (AGEs) in collagen and model extracellular matrix by solid state NMR.

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[NMR paper] In situ characterization of advanced glycation end products (AGEs) in collagen and model extracellular matrix by solid state NMR.

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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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12-02-2017, 02:54 PM

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In situ characterization of advanced glycation end products (AGEs) in collagen and model extracellular matrix by solid state NMR.

In situ characterization of advanced glycation end products (AGEs) in collagen and model extracellular matrix by solid state NMR.

In situ characterization of advanced glycation end products (AGEs) in collagen and model extracellular matrix by solid state NMR.

Chem Commun (Camb). 2017 Dec 01;:

Authors: Li R, Rajan R, Wong WCV, Reid DG, Duer MJ, Somovilla VJ, Martinez-Saez N, Bernardes GJL, Hayward R, Shanahan CM

Abstract
Non-enzymatic glycation of extracellular matrix with (U-13C5)-d-ribose-5-phosphate (R5P), enables in situ 2D ssNMR identification of many deleterious protein modifications and crosslinks, including previously unreported oxalamido and hemiaminal (CH3-CH(OH)NHR) substructures. Changes in charged residue proportions and distribution may be as important as crosslinking in provoking and understanding harmful tissue changes.

PMID: 29192920 [PubMed - as supplied by publisher]

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