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NMR processing:
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NMR assignment:
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Side-chains:
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NOEs:
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UNIO Candid
ASDP
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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:
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Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
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Secondary structure from chemical shifts:
CSI (via RCI server)
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MICS caps, β-turns
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Flexibility from chemical shifts:
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Interactions from chemical shifts:
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Chemical shifts re-referencing:
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UNIO Shiftinspector
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RDCs:
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Protein geomtery:
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Methyl S2
B-factor
Molecular dynamics:
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From structure:
Shiftx2
Sparta+
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CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
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Camcoil
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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
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Isotope labeling:
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Solid-state NMR:
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Default Site-Resolved Backbone and Side-Chain Intermediate Dynamics in a Carbohydrate-Binding Module Protein Studied by Magic-Angle Spinning NMR Spectroscopy.

Site-Resolved Backbone and Side-Chain Intermediate Dynamics in a Carbohydrate-Binding Module Protein Studied by Magic-Angle Spinning NMR Spectroscopy.

Site-Resolved Backbone and Side-Chain Intermediate Dynamics in a Carbohydrate-Binding Module Protein Studied by Magic-Angle Spinning NMR Spectroscopy.

Chemistry. 2015 Jun 12;

Authors: Ivanir-Dabora H, Nimerovsky E, Madhu PK, Goldbourt A

Abstract
Magic-angle spinning solid-state NMR spectroscopy has been applied to study the dynamics of CBM3b-Cbh9A from Clostridium thermocellum (ctCBM3b), a cellulose binding module protein. This 146-residue protein has a nine-stranded ?-sandwich fold, in which 35 % of the residues are in the ?-sheet and the remainder are composed of loops and turns. Dynamically averaged (1) H-(13) C dipolar coupling order parameters were extracted in a site-specific manner by using a pseudo-three-dimensional constant-time recoupled separated-local-field experiment (dipolar-chemical shift correlation experiment; DIPSHIFT). The backbone-C? and C? order parameters indicate that the majority of the protein, including turns, is rigid despite having a high content of loops; this suggests that restricted motions of the turns stabilize the loops and create a rigid structure. Water molecules, located in the crystalline interface between protein units, induce an increased dynamics of the interface residues thereby lubricating crystal water-mediated contacts, whereas other crystal contacts remain rigid.


PMID: 26073185 [PubMed - as supplied by publisher]



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