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Introduction
Introduction
Protein allostery is one of the primary mechanisms for regulating biological function. It relies on long-range couplings between orthosteric and remote allosteric sites. Such couplings typically arise from transitions between macromolecular states with distinct structural and/or dynamic profiles. When allostery relies on subtle conformational or dynamical changes, as it is frequently the case, the underlying allosteric networks often remain elusive to traditional structural determination methods.
Protein NMR chemical shift perturbation is a robust approach to map otherwise elusive allosteric networks. Specifically, variations in 1H and 15N resonance frequencies are exquisitely sensitive not only to nearest-neighbor binding contacts, but also to subtle, yet functionally relevant, allosteric transitions underlying long-range effects. Using the CHEmical Shift Projection and Covariance Analyses (CHESPA and CHESCA), we have previously shown how to separate binding and allosteric contributions to 1H and 15N chemical shift changes.
We have designed an integrated software platform that offers a one-stop solution for the seamless transition from protein NMR spectra to allosteric network analysis and visualization through CHESPA and CHESCA plugins. It is now possible to semi-automate the transition from NMR data to CHESPA and CHESCA plots and matrices. To lower the learning barrier for CHESPA- and CHESCA- SPARKY, we prepared tutorial videos and example data sets with accompanying instructions. The new platform will enable the facile elucidation of allosteric mechanisms without having to export, compile, and analyze multiple peak lists and chemical shift data through several non-integrated scripts and software packages. Combined with the PINE-SPARKY.2 plugin, our CHESPA- and CHESCA- SPARKY software platform significantly lowers the barrier for non-NMR specialists to map protein allosteric networks by NMR spectroscopy.
NMR-based allosteric network analysis
NMR-based allosteric network analysis
Fig. 1: Outline of the CHESPA and CHESCA NMR chemical shift analysis methods to identify allosteric networks within a protein system. The blue rectangles illustrate the protein system of interest and the red triangle illustrates the ligands that bind to the protein. The purple circle and star illustrate an amino acid before and after site mutation, respectively. The oval shape of the protein illustrates the allosteric change caused by ligand binding and/or site mutation.
"Automated Workflow" to identify allosteric networks
"Automated Workflow" to identify allosteric networks
Fig. 2: Automated CHESPA and CHESCA workflow to identify the allosteric networks within an allosteric protein system.
Software Download
Software Download
Please download POKY. CHESCA- and CHESPA-SPARKY programs are pre-installed.
Link: https://poky.clas.ucdenver.edu [click to visit POKY web page]
Contact
Contact
Giuseppe Melacini (melacin@mcmaster.ca) or Woonghee Lee (woonghee.lee@ucdenver.edu)
Citation
Citation
Shao H, Boulton S, Olivieri C, Mohamed H, Akimoto M, Subrahmanian MV, Vegilia G, Markley JL, Melacini G, Lee W
CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery.
Bioinformatics. 2021 Apr. 15; 37(8):1176-77. https://doi.org/10.1093/bioinformatics/btaa781
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