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bioRxiv · 10.1101/2023.04.28.538683

Fluctuation dominated ligand binding in molten globule protein

Moulick, A. G.·Chakrabarti, J.
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Abstract

A molten globule (MG) state is an intermediate state of protein observed during the unfolding of the native structure. In MG states, milk protein -Lactalbumin (aLA) binds to oleic acid (OLA). This MG-aLA-OLA complex, popularly known as XAM-LET performs cytotoxic activities against cancer cell lines. However, the microscopic understanding of ligand recognition ability in MG state of protein is not yet explored. Motivated by this, we explore binding of bovine aLA with OLA (BAMLET) using all atom molecular dynamics(MD) simulations. We find the binding mode between MG-aLA and OLA using the conformational thermodynamics method. We also estimate the binding free energy using the umbrella sampling (US) method for both MG state and neutral state. We find that the binding free energy obtained from US is comparable with earlier experimental results. We characterize the dihedral fluctuations as the ligand is liberated from the active site of the protein using steered molecular dynamics. The long-live fluctuations occur near the ligand binding site, which eventually transfers towards Ca2+ binding site as the ligand is taken away from the protein. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/538683v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1e374f7org.highwire.dtl.DTLVardef@142d1aorg.highwire.dtl.DTLVardef@9d3636org.highwire.dtl.DTLVardef@152542b_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Moulick, A. G., Chakrabarti, J.. 2023-04-28. Fluctuation dominated ligand binding in molten globule protein. https://doi.org/10.1101/2023.04.28.538683

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