AI-driven mechanistic analysis of conformational dynamics in CNNM/CorC Mg2+ transporters

Jie Ma; Xingyu Song; Yosuke Funato; Xinyu Teng; Yichen Huang; Hiroaki Miki; Wenning Wang; Motoyuki Hattori

doi:10.1016/j.str.2024.10.021

AI-driven mechanistic analysis of conformational dynamics in CNNM/CorC Mg²⁺ transporters

Structure. 2024 Oct 29:S0969-2126(24)00456-8. doi: 10.1016/j.str.2024.10.021. Online ahead of print.

Authors

Jie Ma¹, Xingyu Song², Yosuke Funato³, Xinyu Teng¹, Yichen Huang¹, Hiroaki Miki⁴, Wenning Wang⁵, Motoyuki Hattori⁶

Affiliations

¹ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China.
² Department of Chemistry, Institutes of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China.
³ Laboratory of Biorecognition Chemistry, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.
⁴ Laboratory of Biorecognition Chemistry, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan. Electronic address: miki.hiroaki.4e@kyoto-u.ac.jp.
⁵ Department of Chemistry, Institutes of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China. Electronic address: wnwang@fudan.edu.cn.
⁶ State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China. Electronic address: hattorim@fudan.edu.cn.

PMID: 39510076
DOI: 10.1016/j.str.2024.10.021

Abstract

The CNNM/CorC Mg²⁺ transporters are widely conserved in eukaryotes (cyclin M [CNNM]) and prokaryotes (CorC) and participate in various biological processes. Previous structural analyses of the CorC transmembrane domain in the Mg²⁺-bound inward-facing conformation revealed the conserved Mg²⁺ recognition mechanism in the CNNM/CorC family; however, the conformational dynamics in the Mg²⁺ transport cycle remain unclear because structures in other conformations are unknown. Here, we used AlphaFold structure prediction to predict the occluded-like and outward-facing-like conformations of the CorC and CNNM proteins and identified conserved hydrophilic interactions close to the cytoplasmic side in these conformations. Molecular dynamics simulations and biochemical cross-linking showed that these conserved hydrophilic interactions are stable, especially in the outward-facing-like conformation. Furthermore, mutational analysis revealed that the residues involved in these hydrophilic interactions on the cytoplasmic side are important for Mg²⁺ transport in the CorC and CNNM proteins. Our work provides mechanistic insights into the transport cycle of the CNNM/CorC family.

Keywords: alphaFold; artificial intelligence; membrane proteins; structure prediction; transport cycle.