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A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes
Published on: May 4, 2020
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Exploring the Heterogeneous Structural Dynamics of Class II Lanthipeptide Synthetases with Hydrogen-Deuterium
Kevin A Uggowitzer1, Annie R Q Shao1, Yeganeh Habibi1
1Department of Chemistry, McGill University, 801 Sherbrooke St., Montreal, Quebec H3A0B8, Canada.
Biochemistry
|September 12, 2022
Summary
Class II lanthipeptide synthetases (LanM enzymes) use AlphaFold and HDX-MS to study how precursor peptides (LanA) bind. This reveals conserved dynamics in the LanM dehydratase domain but variable cyclase domain dynamics, impacting biosynthesis.
Area of Science:
- Biochemistry
- Structural Biology
- Natural Product Biosynthesis
Background:
- Class II lanthipeptide synthetases (LanM enzymes) are crucial for producing macrocyclic lanthipeptides, a diverse group of bioactive natural products.
- These enzymes catalyze the formation of multiple thioether bridges in precursor peptides (LanA), creating complex structures.
- The precise mechanisms governing LanM enzyme specificity and catalytic outcome are not fully understood, but involve enzyme-substrate interactions and conformational changes.
Purpose of the Study:
- To investigate the conformational dynamics of LanM enzymes and their precursor peptides (LanA) during the biosynthesis of lanthipeptides.
- To explore the role of intermolecular interactions and intramolecular conformational changes in the [LanM:LanA] complex.
- To assess the utility of combining AlphaFold modeling with hydrogen-deuterium exchange mass spectrometry (HDX-MS) for studying enzyme dynamics.
Main Methods:
- Utilized AlphaFold for protein structure prediction, specifically modeling protein-peptide interactions.
- Employed hydrogen-deuterium exchange mass spectrometry (HDX-MS) to analyze the conformational dynamics of LanM/LanA systems.
- Studied a small set of divergent LanM/LanA systems to compare dynamic properties.
Main Results:
- LanA precursor peptide binding induced conserved changes in the structural dynamics of the LanM dehydratase domain across different enzymes.
- This suggests a conserved binding mode for the leader peptide within the LanM family.
- In contrast, the dynamics of the LanM cyclase domain showed significant variability, indicating diverse peptide-cyclase interactions or allosteric regulation mechanisms.
Conclusions:
- The study supports a conserved leader peptide binding mechanism in Class II lanthipeptide synthetases.
- Variability in cyclase domain dynamics suggests distinct mechanisms for cyclization and allosteric activation.
- The integrated approach of AlphaFold modeling and HDX-MS is a powerful tool for investigating enzyme conformational dynamics in natural product biosynthesis.
