Structural Dynamics Couple Substrate-Induced Allosteric Responses with Domain Communication in Nonribosomal Peptide Synthetases

Abstract

Timely control of protein interactions is central to modulate biological activity such as gene activation, cell signaling or metabolism. Here, events such as post-translational modifications and substrate or protein binding affect proteins so as to govern their interactions with partner proteins and repress or promote activity. In spite of progress in identifying protagonists of molecular communication and predicting the outcome of molecular events, it has proven more challenging to determine how molecular responses within proteins translate into responses between proteins, particularly when remote sites are involved within proteins. Such challenges are inherent to understanding microbial, multi-domain enzymatic systems called nonribosomal peptide synthetases (NRPSs). NRPSs employ repeats of domains to covalently tether substrates onto carrier proteins (CP) and assemble them into complex products through intervening condensation or cyclization domains. The pharmaceutical properties of NRPS products (e.g. antibiotics) have spurred attempts at engineering NRPSs, but dynamics between domains have hampered progress, as it remains unclear whether and how synthesis drives domain communication. Using NMR, we demonstrate that large scale dynamics in a 52 kDa cyclization domain sense substrates tethered to partner CPs to promote binding and remodel binding sites for downstream partners, thus revealing a path for allosteric communication involving three partner domains. We provide a 3D structural description of the enzyme dynamics and demonstrate that mutations that impede catalysis injure the same dynamic allosteric network, suggesting that catalysis efficiency may be streamlined with productive domain communication and substrate recognition through dynamic responses. Our results demonstrate and describe substrate driven allosteric responses in NRPSs, and they exemplify how structural dynamics within proteins can couple substrate recognition with both local and remote protein communication.