Protein Secondary Structure of Green Lynx Spider Dragline Silk Investigated by Solid-state NMR and X-ray Diffraction

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$Protein Secondary Structure of Green Lynx Spider Dragline Silk Investigated by Solid-state NMR and X-ray Diffraction$ Protein Secondary Structure of Green Lynx Spider Dragline Silk Investigated by Solid-state NMR and X-ray Diffraction

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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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07-30-2015, 01:34 PM

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Protein Secondary Structure of Green Lynx Spider Dragline Silk Investigated by Solid-state NMR and X-ray Diffraction

Protein Secondary Structure of Green Lynx Spider Dragline Silk Investigated by Solid-state NMR and X-ray Diffraction

Publication date: Available online 29 July 2015
Source:International Journal of Biological Macromolecules

Author(s): Dian Xu, Xiangyan Shi, Forrest Thompson, Warner S. Weber, Qiushi Mou, Jeffery L. Yarger

In this study, the secondary structure of the major ampullate silk from Peucetia viridans (Green Lynx) spiders is characterized by X-ray diffraction and solid-state NMR spectroscopy. From X-ray diffraction measurement, ?-sheet nanocrystallites were observed and found to be highly oriented along the fiber axis, with an orientational order, f _ c ? 0.98. The size of the nanocrystallites was determined to be on average 2.5nm x 3.3nm x 3.8nm. Besides a prominent nanocrystalline region, a partially oriented amorphous region was also observed with an f _ a ? 0.89. Two-dimensional 13C-13C through-space and through-bond solid-state NMR experiments were employed to elucidate structure details of Peucetia viridans silk proteins. It reveals that ?-sheet nanocrystallites constitutes 40.0±1.2% of the protein and are dominated by alanine-rich repetitive motifs. Furthermore, based upon the NMR data, 18±1% of alanine, 60±2% glycine and 54±2% serine are incorporated into helical conformations.

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