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Bioinformatics. 2020 Jan 13. pii: btaa019. doi: 10.1093/bioinformatics/btaa019. [Epub ahead of print]

PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins.

Author information

1
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
2
National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA.
3
Department of Chemistry, University of Minnesota, Minneapolis, MN, USA.

Abstract

MOTIVATION:

Two-dimensional [15N-1H] separated local field (SLF) solid-state NMR experiments of membrane proteins aligned in lipid bilayers provide tilt and rotation angles for α-helical segments using Polar Index Slant Angle (PISA) wheel models. No integrated software has been made available for data analysis and visualization.

RESULTS:

We have developed the PISA-SPARKY plugin to seamlessly integrate PISA-wheel modeling into the NMRFAM-SPARKY platform. The plugin performs basic simulations, exhaustive fitting against experimental spectra, error analysis and dipolar and chemical shift wave plotting. The plugin also supports PyMOL integration and handling of parameters that describe variable alignment and dynamic scaling encountered with magnetically aligned media, ensuring optimal fitting and generation of restraints for structure calculation.

AVAILABILITY:

PISA-SPARKY is freely available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org) and to subscribers of the SBGrid (https://sbgrid.org). The pisa.py script is available and documented on GitHub (https://github.com/weberdak/pisa.py) along with a tutorial video and sample data.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

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