Understanding the role of dynamics in the iron sulfur cluster molecular machine

• Published in: Biochimica et biophysica acta Vol. 1861; no. 1; pp. 3154 - 3163
• Main Authors: di Maio, Danilo, Chandramouli, Balasubramanian, Yan, Robert, Brancato, Giuseppe, Pastore, Annalisa
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2017; Elsevier Pub. Co
• Subjects: bacterial proteins; Biocatalysis; Carbon-Sulfur Lyases - chemistry; Carbon-Sulfur Lyases - metabolism; crystal structure; CyaY; Escherichia coli - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Frataxin; Iron-sulfur cluster biogenesis; Iron-Sulfur Proteins - chemistry; Iron-Sulfur Proteins - metabolism; Magnetic Resonance Spectroscopy; Molecular dynamics; nuclear magnetic resonance spectroscopy; prostheses; Protein Stability; Protein Structure, Secondary; Static Electricity; Structure; sulfur; NMR; Iron-sulfur cluster biogenesis; Frataxin; MD; RMSF; Molecular dynamics; RMSD; Structure; CyaY; PCA; ED
• ISSN: 0304-4165; 0006-3002; 1872-8006; 1878-2434
• DOI: 10.1016/j.bbagen.2016.07.020

The bacterial proteins IscS, IscU and CyaY, the bacterial orthologue of frataxin, play an essential role in the biological machine that assembles the prosthetic FeS cluster groups on proteins. They form functionally binary and ternary complexes both in vivo and in vitro. Yet, the mechanism by which they work remains unclear. We carried out extensive molecular dynamics simulations to understand the nature of their interactions and the role of dynamics starting from the crystal structure of a IscS-IscU complex and the experimentally-based model of a ternary IscS-IscU-CyaY complex and used nuclear magnetic resonance to experimentally test the interface. We show that, while being firmly anchored to IscS, IscU has a pivotal motion around the interface. Our results also describe how the catalytic loop of IscS can flip conformation to allow FeS cluster assembly. This motion is hampered in the ternary complex explaining its inhibitory properties in cluster formation. We conclude that the observed ‘fluid’ IscS-IscU interface provides the binary complex with a functional adaptability exploited in partner recognition and unravels the molecular determinants of the reported inhibitory action of CyaY in the IscS-IscU-CyaY complex explained in terms of the hampering effect on specific IscU-IscS movements. Our study provides the first mechanistic basis to explain how the IscS-IscU complex selects its binding partners and supports the inhibitory role of CyaY in the ternary complex. [Display omitted] •IscU protomers show a pivotal motion around the interface with IscS, in complex.•Both IscS catalytic loop and IscU motion seem correlated with FeS cluster assembly.•Shuttling of the IscS catalytic loop is accompanied by a structural transition.•CyaY inhibits cluster formation by hampering the dynamics of the IscS-IscU complex.