Extend-NMR: Extending NMR for Functional and Structural Genomics
TopSpin MDD PRODECOMP AUREMOL CCPN ARIA ISD HADDOCK CING Deposition
Partner 5A:University of Gothenburg
People involved:Martin Billeter, Doroteya K. Staykova, Jonas Fredriksson
Website:www.lundberg.gu.se/nmr/software.php?program=PRODECOMP

PRODECOMP: Analysis of 'Fast' NMR Data

Proteins pose a variety of challenges in NMR studies in terms of their size, native disorder, stability etc. 'Fast' NMR is motivated by the resulting, but contradicting, requirements on spectrum dimensionality, resolution and experiment time.

Projection spectroscopy may speed up the recording of very high-dimensional data (4-7 D) by factors of a thousand or more while maintaining high resolution. Decompositions provide an optimal tool to analyze 2D projections of high-dimensional experiments (Fig. A, B): signal-to-noise is not compromised, projections from several experiments can be combined (Fig. C), and the output is well suited for automated interpretation, e.g. assignment by the SHABBA protocol (Fig. D top), and structure determination (Fig. D bottom).

The PRODECOMP tool for decomposition of NMR projections is based on a solid mathematical procedure, warranting its robustness and efficiency. PRODECOMP is tightly interweaved with the TopSpin (Bruker) recording and processing software, and fully integrated into the CCPN data model. Its Python code is freely available.


A) Examples of 2D projections recorded instead of high-dimensional spectra (the latter are represented by dotted 3D cubes). The colors indicate two different experiments, e.g. based on scalar coupling only (red) or including NOE transfers (blue). B) Each stack of projections may be analyzed separately, but more efficient and informative is a simultaneous analysis of projections from several experiments.
C) Decompositions for the DNA-binding protein histone G1 using projections from 5 experiments (including those in A) yield 15-dimensional data, illustrated here by the component for Phe 66. The chemical shifts provided on the left allow for a straightforward sequential assignment, while the right side (lower 4 panels) provides distance restraints for structure calculations.

Features

  • 'Fast' NMR data
  • No loss of sensitivity
  • Very high-dimensional (~15D)
  • Simultaneous analysis of different experiments
  • Automated further processing (e.g. assignment)
  • User-friendly
  • CCPN integrated

D) Typical goals for the combination of projection spectroscopy and decomposition analysis: resonance assignments (top) or 3D structures (bottom: azurin structure from projection data only).