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NMR processing:
MDD
NMR assignment:
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MARS
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PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
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UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
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Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
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RPF scores
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Chemical shifts:
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Vasco
iCing
RDCs:
DC
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Pseudocontact shifts:
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Protein geomtery:
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PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
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MetaMQAPII
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STAN
Ramachandran Plot
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ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
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V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
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Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
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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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Default Site-Specific Internal Motions in GB1 Protein Microcrystals Revealed by 3D (2)H-(13)C-(13)C Solid-State NMR Spectroscopy.

Site-Specific Internal Motions in GB1 Protein Microcrystals Revealed by 3D (2)H-(13)C-(13)C Solid-State NMR Spectroscopy.

Related Articles Site-Specific Internal Motions in GB1 Protein Microcrystals Revealed by 3D (2)H-(13)C-(13)C Solid-State NMR Spectroscopy.

J Am Chem Soc. 2016 Feb 5;

Authors: Shi X, Rienstra CM

Abstract
(2)H quadrupolar line shapes deliver rich information about protein dynamics. A newly designed 3D (2)H-(13)C-(13)Csolid-state NMR magic angle spinning (MAS) experiment is presented and demonstrated on the microcrystalline ?1 immunoglobulin binding domain of protein G (GB1). The implementation of (2)H-(13)C adiabatic rotor-echo-short-pulse-irradiation cross polarization (RESPIRATION CP) ensures the accuracy of the extracted line shapes and provides enhanced sensitivity relative to conventional CP methods. The 3D (2)H-(13)C-(13)C spectrum reveals 2H line shapes for 140 resolved aliphatic deuterium sites. Motional averaged (2)H quadrupolar parameters obtained from the line shape fitting identify side chain motions. Restricted side chain dynamics are observed for a number of polar residues including K13, D22, E27, K31, D36, N37, D46, D47, K50, and E56, which we attribute to the effects of salt bridges and hydrogen bonds. In contrast, we observe significantly enhanced side chain flexibility for Q2, K4, K10, E15, E19, N35, N40, and E42, due to solvent exposure and low packing density. T11, T16 and T17 side chains exhibit motions with larger amplitudes than other Thr residues due to solvent interactions. The side chains of L5, V54 and V29 are highly rigid because they are packed in the core of the protein.High correlations were demonstrated between GB1 side chain dynamics and its biological function. Large-amplitude side chain motions are observed for regions contacting and interacting with immunoglobulin G (IgG). In contrast, rigid side chains are primarily found for residues in the structural core of the protein that are absent from protein binding and interactions.


PMID: 26849428 [PubMed - as supplied by publisher]



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