Ultrahigh resolution protein structures using NMR chemical shift tensors [Biophysics and Computational Biology]

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Ultrahigh resolution protein structures using NMR chemical shift tensors [Biophysics and Computational Biology]

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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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10-12-2011, 06:37 AM

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Ultrahigh resolution protein structures using NMR chemical shift tensors [Biophysics and Computational Biology]

Ultrahigh resolution protein structures using NMR chemical shift tensors [Biophysics and Computational Biology]

Wylie, B. J., Sperling, L. J., Nieuwkoop, A. J., Franks, W. T., Oldfield, E., Rienstra, C. M....
Date: 2011-10-11

NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13C? and 15N (peptide backbone) groups in a protein, the ?1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13C? and 15N CSTs were measured using synchronously evolved recoupling experiments in which 13C and 15N tensors were projected onto the 1H-13C and 1H-15N vectors, respectively, and onto the 15N-13C vector in the case of 13C?. The orientations of the 13C? CSTs to the 1H-13C and 13C-15N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured 15N tensors exhibited larger reduced anisotropies in ?-helical versus ?-sheet regions, with very limited variation (18*±*4°) in the orientation of the z-axis of the 15N CST with respect to the 1H-15N vector. Incorporation of the 13C? CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance 13C-15N distances and vector angle restraints, improved the backbone rmsd to 0.16*Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51*Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and ?1/?2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination. Read More

PNAS:
Number: 41
Volume: 108

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