NMR paper Glassy dynamics of protein methyl groups revealed by deuteron NMR.

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[NMR paper] Glassy dynamics of protein methyl groups revealed by deuteron 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

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NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

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02-03-2013, 10:22 AM

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Glassy dynamics of protein methyl groups revealed by deuteron NMR.

Related Articles Glassy dynamics of protein methyl groups revealed by deuteron NMR.

J Phys Chem B. 2013 Jan 31;117(4):1051-61

Authors: Vugmeyster L, Ostrovsky D, Penland K, Hoatson GL, Vold RL

Abstract
We investigated site-specific dynamics of key methyl groups in the hydrophobic core of chicken villin headpiece subdomain (HP36) over the temperature range between 298 and 140 K using deuteron solid-state NMR longitudinal relaxation measurements. The relaxation of the longitudinal magnetization is weakly nonexponential (glassy) at high temperatures and exhibits a stronger degree of nonexponentiality below about 175 K. In addition, the characteristic relaxation times deviate from the simple Arrhenius law. We interpret this behavior via the existence of distribution of activation energy barriers for the three-site methyl jumps, which originates from somewhat different methyl environments within the local energy landscape. The width of the distribution of the activation barriers for methyl jumps is rather significant, about 1.4 kJ/mol. Our experimental results and modeling allow for the description of the apparent change at about 175 K without invoking a specific transition temperature. For most residues in the core, the relaxation behavior at high temperatures points to the existence of conformational exchange between the substates of the landscape, and our model takes into account the kinetics of this process. The observed dynamics are the same for dry and hydrated protein. We also looked at the effect of F58L mutation inside the hydrophobic core on the dynamics of one of the residues and observed a significant increase in its conformational exchange rate constant at high temperatures.

PMID: 23301823 [PubMed - in process]

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