Molecular Dynamics Simulation to Explore Functional Regions Involving Pho4 Interaction with Co-Activator and PHO5 Promoter

Abstract

The PHO pathway is essential for the transcriptional response to inorganic phosphate starvation, and the core components are evolutionarily conserved across fungi. Pho4 and its co-activator Pho2 control the PHO5 gene expression and serve as a paradigm for understanding chromatin remodelling and the evolution of combinatorial transcriptional control. Protein sequence alignment and structural modelling reveal that Pho4 homologs contain a large proportion of intrinsically disordered regions (IDRs). Using molecular dynamics (MD) simulations, we monitored the behaviors of the yeast Saccharomyces cerevisiae Pho4 protein (ScPho4), which includes the DNA Binding Domain (DBD), and the Pho2 Interaction Domain (P2ID), an IDR, in complex with the PHO5 promoter (ScPHO5), both in the presence and absence of the Pho2 protein (ScPho2). The ScPho2-ScPho4 dimer formed a more stable complex at ScPHO5, as reflected by a lower RMSD and greater binding energy, compared to ScPho4 alone. This dimer also induced more structural changes in promoter DNA. Notably, the P2ID of ScPho4 adopted an open conformation when interacting with ScPho2, and a closed conformation in its absence. In human pathogenic yeast Candida glabrata, MD simulations revealed dynamic IDR movements in Pho4 homologs. Unlike other previous studies, our approach enables direct visualization and quantification of conformational changes in protein-DNA complex over simulation time. These findings highlight the value of MD simulation as a routine complement to experimental methods, advancing our knowledge of structure-motion-function.

Keywords

molecular dynamics simulation / Pho2 / Pho4 / yeasts / Saccharomyces cerevisiae / Candida glabrata

Supplementary Materials

The additional data and information can be downloaded at: https://media.sciltp.com/articles/others/2509220950069856/Supplemental-Materials.zip. Table S1: Total number of counterions added to the system.

Author Contributions

T.W. and M.P. conceived and supervised the study; T.W., N.K., and M.P. performed the MD simulations; T.W., N.K., and M.P. analyzed data and generated the figures and tables; T.W., N.K., and M.P. wrote the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This research was financially supported by the Faculty of Medicine Research Fund, grant no. 138-2568 to T.W. and no. 046-2566 to M.P.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The protein ID and sequences (Supplemental Data S1) as well as the 3D coordinate files (Supplemental Data S2-S4), used to generate figures in this manuscript, are available in the supporting materials.

Acknowledgments

We would like to thank ERAWAN HPC, Information Technology Service Center (ITSC) of Chiang Mai University, for their support in the high-performance computing resources.

Conflicts of Interest

The authors declare no competing interests.

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