PISA-SPARKY

PISA-SPARKY performs PISA-wheel modeling and analysis of oriented solid-state nuclear magnetic resonance (NMR) spectra to extract orientation and dynamic information for α-helical membrane proteins in aligned lipid bilayers.

Key Features:

• NMRFAM-SPARKY integration: Executes PISA-wheel simulations and fitting within the NMRFAM-SPARKY environment.
• Simulations and exhaustive fitting: Supports basic PISA-wheel simulations and exhaustive fitting of models against experimental spectra, including two-dimensional [15N-1H] separated local field data.
• Error analysis: Performs error analysis on fits to quantify uncertainty in model parameters.
• Dipolar and chemical shift plotting: Produces plots of dipolar and chemical shift waves for comparison with experimental spectra.
• Parameter handling: Accommodates parameters describing variable alignment and dynamic scaling relevant to magnetically aligned media.
• Restraints generation: Generates restraints for structure calculation based on fitted PISA-wheel parameters.
• PyMOL integration: Provides PyMOL integration for visualization of structural implications of fitted parameters.

Scientific Applications:

• Tilt and rotation determination: Determines tilt and rotation angles of α-helical segments within membrane proteins from oriented solid-state NMR data.
• Structure refinement: Produces restraints and quantitative fits that aid refinement of membrane protein structural models.
• Orientation and dynamics analysis: Extracts orientation and dynamic information of helical segments in magnetically aligned lipid bilayers.

Methodology:

Modeling of PISA-wheels applied to two-dimensional [15N-1H] separated local field solid-state NMR experiments, exhaustive fitting to experimental spectra, error analysis, plotting of dipolar and chemical shift waves, and generation of restraints for structure calculation.