Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER.

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• Nuclear Magnetic Resonance (NMR) spectroscopy is crucial for determining protein structures.
• Sequence-specific NMR assignment is a fundamental step in protein structure determination.
• Ambiguities in NMR assignments can hinder the analysis of large or complex proteins.

Purpose of the Study:

• To introduce MAPPER, a novel semiautomatic program for sequence-specific NMR assignment in proteins.
• To leverage global mapping of protein fragments for improved assignment accuracy.
• To resolve otherwise intractable ambiguities in NMR spectral analysis.

Main Methods:

• MAPPER utilizes short fragments of sequentially neighboring residues as input.
• Input fragments are assembled based on sequential NMR connectivities.
• The program incorporates 13C chemical shifts or amino acid type data for fragment identification.
• MAPPER performs an exhaustive search for self-consistent mappings onto the protein sequence.

Main Results:

• MAPPER successfully obtained virtually complete sequence-specific assignments for a 110 kDa homooctameric protein.
• The global mapping approach significantly resolved assignment ambiguities compared to individual fragment mapping.
• The program demonstrated effectiveness on a complex biological system, Staphylococcus aureus 7,8-dihydroneopterin aldolase.

Conclusions:

• MAPPER provides a powerful tool for semiautomatic, sequence-specific NMR assignment.
• The global mapping strategy enhances the reliability and completeness of protein NMR assignments.
• This approach facilitates the structural analysis of large and challenging protein targets.