ACCEPT-NMR: A New Tool for the Analysis of Crystal Contacts and Their Links to NMR Chemical Shift Perturbations

Abstract

We have developed an open-source cross-platform software toolkit entitled ACCEPT-NMR (Automated Crystal Contact Extrapolation/Prediction Toolkit for NMR) as a helpful tool to automate many of the complex tasks required to find and visualize crystal contacts in structures of biomolecules and biomolecular assemblies. This toolkit provides many powerful features geared toward NMR spectroscopy and related disciplines, such as isotopic labeling, advanced visualization options, and reporting tools. Using this software, we have undertaken a survey of available chemical shift data in the literature and deposited in the BMRB, and show that the mere presence of one or more crystal contacts to a residue confers an approximately 65% likelihood of significant chemical shift perturbations (relative to solution NMR chemical shifts). The presence of each additional crystal contact subsequently increases this probability, resulting in predictive accuracies in excess of 80% in many cases. Conversely, the presence of a significant experimental chemical shift perturbation indicates a >60% likelihood of finding one or more crystal contacts to a particular residue. Pinpointing sites likely to experience large CSPs is critical to mapping solution NMR chemical shifts onto solid-state NMR data as a basis for preliminary assignments, and can thus simplify the assignment process for complex biomolecules. Mapping observed CSPs onto the molecular structure, on the other hand, can indicate the presence of crystal interfaces where no crystal structure is available. Finally, by detecting sites critical to intermolecular interfaces, ACCEPT-NMR can help guide experimental approaches (e.g. isotopic labeling schemes) to detect and probe specific inter-subunit interactions.