Quantitative measurement of exchange dynamics in proteins via 13 C relaxation dispersion of 13 CHD 2 -labeled samples

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Quantitative measurement of exchange dynamics in proteins via 13 C relaxation dispersion of 13 CHD 2 -labeled samples

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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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06-02-2016, 02:11 AM

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Quantitative measurement of exchange dynamics in proteins via 13 C relaxation dispersion of 13 CHD 2 -labeled samples

Quantitative measurement of exchange dynamics in proteins via 13 C relaxation dispersion of 13 CHD 2 -labeled samples

Abstract

Methyl groups have emerged as powerful probes of protein dynamics with timescales from picoseconds to seconds. Typically, studies involving high molecular weight complexes exploit 13CH3- or 13CHD2-labeling in otherwise highly deuterated proteins. The 13CHD2 label offers the unique advantage of providing 13C, 1H and 2H spin probes, however a disadvantage has been the lack of an experiment to record 13C Carrâ??Purcellâ??Meiboomâ??Gill relaxation dispersion that monitors millisecond time-scale dynamics, implicated in a wide range of biological processes. Herein we develop an experiment that eliminates artifacts that would normally result from the scalar coupling between 13C and 2H spins that has limited applications in the past. The utility of the approach is established with a number of applications, including measurement of ms dynamics of a disease mutant of a 320Â*kDa p97 complex.

Source: Journal of Biomolecular NMR

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