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Essential Role of Loop Dynamics in Type II NRPS Biomolecular Recognition
Joshua C Corpuz1, Ashay Patel1, Tony D Davis1
1Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States.
ACS Chemical Biology
|September 29, 2022
Summary
Engineering non-ribosomal peptide synthetases (NRPSs) is key for new therapeutics. This study used chemical biology and structural methods to understand protein interactions in NRPSs, enabling rational engineering for novel drug discovery.
Area of Science:
- Biochemistry
- Structural Biology
- Chemical Biology
Background:
- Non-ribosomal peptides are crucial clinical therapeutics.
- Engineering non-ribosomal peptide synthetases (NRPSs) via combinatorial biosynthesis offers access to diverse chemical structures.
- Limited success in NRPS engineering is attributed to poor protein-protein interactions between non-cognate components.
Purpose of the Study:
- To elucidate binding specificities between peptidyl carrier proteins (PCPs) and adenylation (A) domains.
- To enable rational re-engineering of NRPSs for non-cognate interactions.
- To understand the structural and dynamic basis of PCP-A domain interactions.
Main Methods:
- X-ray crystallography of crosslinked PCP-A domain complexes.
- Molecular dynamics (MD) simulations of PCP-A domain complexes.
- Biochemical studies and gain-of-function mutation analysis.
Main Results:
- Determined crystal structures of cognate (PigG-PigI) and non-cognate (PigG-PltF) PCP-A domain complexes.
- Identified large interfaces with hydrophobic and electrostatic interactions critical for substrate delivery.
- MD simulations confirmed the role of a PCP loop in recognition and revealed dynamic interactions.
- Demonstrated that modifying PCP loop 1 interactions controls binding specificity.
Conclusions:
- PCP loop conformational preferences and dynamics drive specific PCP-A domain interactions.
- Rational re-engineering of NRPSs for non-cognate interactions is achievable.
- Integrated crystallographic, biochemical, and computational approaches are powerful for NRPS engineering.
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