ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values.

Area of Science:

• Biophysics
• Structural Biology
• Computational Chemistry

Background:

• Nuclear magnetic resonance (NMR) spectroscopy is crucial for studying protein behavior in solution.
• NMR chemical shifts provide detailed insights into local atomic environments, amino acid residue dynamics, and protein conformation.
• Analyzing the complex, multi-dimensional information within chemical shifts is challenging.

Purpose of the Study:

• To introduce the ShiftCrypt web server, a tool for simplifying NMR chemical shift analysis.
• To make the ShiftCrypt method, which compresses chemical shift data, easily accessible to researchers.
• To enable biophysically-based protein alignment using ShiftCrypt values.

Main Methods:

• The ShiftCrypt method utilizes a neural network auto-encoder architecture.
• The web server accepts chemical shift data in NMR Exchange Format (NEF) or NMR-STAR.
• Protein alignment is performed using Dynamic Time Warping on ShiftCrypt values, with optional inclusion of amino acid information.

Main Results:

• ShiftCrypt compresses per-amino acid chemical shift information into a single, interpretable, amino acid-type independent value.
• The web server visualizes ShiftCrypt results and provides API access.
• The server facilitates pairwise protein alignment, particularly for disordered regions.

Conclusions:

• The ShiftCrypt web server provides a user-friendly platform for analyzing complex NMR chemical shift data.
• The method and server offer novel applications in protein biophysical characterization and sequence alignment.
• The ShiftCrypt approach enhances the interpretability of NMR data for structural biology research.