Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization

Area of Science:

• Biochemistry and Molecular Biology
• Computational Biology

Background:

• Lanthipeptides are ribosomally synthesized and post-translationally modified peptides.
• Class II lanthipeptide synthetases, like ProcM, exhibit broad substrate tolerance, posing a challenge in understanding their site-selectivity.
• Previous research suggested substrate sequence, not the enzyme, determines lanthionine formation selectivity.

Purpose of the Study:

• To investigate how substrate sequence and solution structure influence site-selective lanthipeptide biosynthesis.
• To explore the correlation between predicted substrate solution structure and final product formation.
• To determine the role of secondary structure in lanthipeptide ring pattern determination.

Main Methods:

• Molecular dynamic simulations were performed on ProcA3.3, ProcA1.1, and ProcA2.8 variants.
• Simulations predicted the solution structure of precursor peptides.
• Correlated predicted solution structures with experimental outcomes for ring formation patterns.

Main Results:

• Substrate secondary structure is crucial for determining the final product's ring pattern.
• The dehydration step does not affect the site-selectivity of ring formation.
• Simulations for ProcA1.1 and ProcA2.8 indicated a higher likelihood of C-terminal ring formation, consistent with experimental data.

Conclusions:

• Substrate sequence and its solution structure, particularly secondary structure, can predict lanthipeptide site-selectivity and ring formation order.
• These findings enhance understanding of lanthipeptide biosynthetic mechanisms.
• The results will aid in accelerating bioengineering efforts for lanthipeptide-derived products.