NMR paper Investigating the Dynamics of Destabilized Nucleosomes Using Methyl-TROSY NMR.

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[NMR paper] Investigating the Dynamics of Destabilized Nucleosomes Using Methyl-TROSY 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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03-29-2018, 07:42 PM

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Investigating the Dynamics of Destabilized Nucleosomes Using Methyl-TROSY NMR.

Investigating the Dynamics of Destabilized Nucleosomes Using Methyl-TROSY NMR.

Investigating the Dynamics of Destabilized Nucleosomes Using Methyl-TROSY NMR.

J Am Chem Soc. 2018 Mar 28;:

Authors: Kitevski-LeBlanc JL, Yuwen T, Dyer PN, Rudolph J, Luger K, Kay LE

Abstract
The nucleosome core particle (NCP), comprised of histone proteins wrapped with ~146 base pairs of DNA, provides both protection and controlled access to DNA so as to regulate vital cellular processes. High-resolution structures of nucleosomes and nucleosome complexes have afforded a clear understanding of the structural role of NCPs, but a detailed description of the dynamical properties that facilitate DNA-templated processes is only beginning to emerge. Using methyl-TROSY NMR approaches we evaluate the effect of point mutations designed to perturb key histone interfaces that become destabilized during nucleosome remodeling in an effort to probe NCP plasticity. Notably the NCP retains its overall structural integrity, yet relaxation experiments of mutant nucleosomes reveal significant dynamics within a central histone interface associated with alternative NCP conformations populated to as much as 15% under low salt conditions. This work highlights the inherent plasticity of NCPs and establishes methyl-TROSY NMR as a valuable compliment to current single molecule methods in quantifying NCP dynamic properties.

PMID: 29589929 [PubMed - as supplied by publisher]

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