NMR paper Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

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[NMR paper] Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

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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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Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

Structure. 2015 Sep 9;

Authors: Courtney JM, Ye Q, Nesbitt AE, Tang M, Tuttle MD, Watt ED, Nuzzio KM, Sperling LJ, Comellas G, Peterson JR, Morrissey JH, Rienstra CM

Abstract
Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D (13)C-(13)C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins-GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor-and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25*kDa, COMPASS distinguished the correct fold, most often within 1.5*Å root-mean-square deviation of the reference structure.

PMID: 26365800 [PubMed - as supplied by publisher]

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