Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase {alpha}-aminoacrylate intermediate [Biophysics and Computational Biology]

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Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase {alpha}-aminoacrylate intermediate [Biophysics and Computational Biology]

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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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01-08-2022, 02:36 AM

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Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase {alpha}-aminoacrylate intermediate [Biophysics and Computational Biology]

Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase {alpha}-aminoacrylate intermediate [Biophysics and Computational Biology]

Jacob B. Holmes, Viktoriia Liu, Bethany G. Caulkins, Eduardo Hilario, Rittik K. Ghosh, Victoria N. Drago, Robert P. Young, Jennifer A. Romero, Adam D. Gill, Paul M. Bogie, Joana Paulino, Xiaoling Wang, Gwladys Riviere, Yuliana K. Bosken, Jochem Struppe, Alia Hassan, Jevgeni Guidoulianov, Barbara Perrone, Frederic Mentink-Vigier, Chia-en A. Chang, Joanna R. Long, Richard J. Hooley, Timothy C. Mueser, Michael F. Dunn, Leonard J. Mueller...
Date: 2022-01-07

NMR-assisted crystallography—the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry—holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach... Read More

PNAS:
Number: 2
Volume: 119

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