Illuminating ligand-induced dynamics in nuclear receptors through MD simulations

Yu, Tracy; Sudhakar, Nishanti; Okafor, C. Denise

doi:10.1016/j.bbagrm.2024.195025

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

2024

DOI: 10.1016/j.bbagrm.2024.195025

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Illuminating ligand-induced dynamics in nuclear receptors through MD simulations

Tracy Yu,

Nishanti Sudhakar,

C. Denise Okafor

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2024

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Cited by 2 publications

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Impact of Replicas and Simulation Length on In Silico Behaviors of a Protein Domain

Biswas,

Eisert‐Sasse,

Okafor

2024

ChemPhysChem

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Molecular dynamics (MD) simulations are a powerful tool for life sciences, valuable for their ability to capture atomic‐level behavior of molecules over time. To advance knowledge on reasonable timescales, researchers must optimize the amount of useful information extracted from simulation data while frugally managing computational resources. They must balance trajectory lengths and number of replicas, with the aim of maximizing conformational sampling. Identifying this balance is not always intuitive, and lack of standardization among researchers produces variability in results from MD measurements. We investigate how changes in simulation length and replica numbers impact this variability. Using a 231‐residue domain, we compare measurements from independent trajectories to a benchmark trajectory of 3x1000‐ns replicates. We simulate 27 protein‐ligand complexes, allowing us to compare ligand‐specific rankings of complexes across replicas. We reveal that some MD measurements are reliably ranked by single trajectories, while others are not. We uncover similar variability in the effects of trajectory lengths on measurements. Our findings suggest that a one‐size‐fits‐all approach to MD simulations is not ideal, and depending on the intended measurements and research question, it is sometimes advantageous to prioritize longer trajectories over multiple replicas. This work provides important considerations for researchers while designing simulation studies.

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Impact of Replicas and Simulation Length on In Silico Behaviors of a Protein Domain

Biswas,

Eisert‐Sasse,

Okafor

2024

ChemPhysChem

View full text Add to dashboard Cite

show abstract

Simulations Reveal Unique Roles for the FXR Hinge in the FXR–RXR Nuclear Receptor Heterodimer

Yu,

Biswas,

Dube

et al. 2024

ACS Bio Med Chem Au

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Illuminating ligand-induced dynamics in nuclear receptors through MD simulations

Cited by 2 publications

References 44 publications

Impact of Replicas and Simulation Length on In Silico Behaviors of a Protein Domain

Impact of Replicas and Simulation Length on In Silico Behaviors of a Protein Domain

Simulations Reveal Unique Roles for the FXR Hinge in the FXR–RXR Nuclear Receptor Heterodimer

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