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

Daniel K. Weber, Songlin Wang, John L. Markley, Gianluigi Veglia, Gianluigi Veglia, Woonghee Lee

Research output: Contribution to journalArticlepeer-review

Abstract

Motivation: Two-dimensional [15N-1H] separated local field solid-state nuclear magnetic resonance (NMR) experiments of membrane proteins aligned in lipid bilayers provide tilt and rotation angles for a-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.

Original languageEnglish (US)
Pages (from-to)2915-2916
Number of pages2
JournalBioinformatics
Volume36
Issue number9
DOIs
StatePublished - May 1 2020

Bibliographical note

Funding Information:
This work has been supported the National Science Foundation [DBI 1902076 to J.L.M. and W.L.], and partially by the National Institutes of Health [R01 GM 64742 and HL 144130 to G.V.; P41 GM 103399 to J.L.M.] and the American Heart Association [19POST34420009 to D.K.W.]. Part of this work was carried out using hardware provided by the University of Minnesota Supercomputing Institute.

Publisher Copyright:
© 2020 The Author(s). Published by Oxford University Press.

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

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