1 A microscopic insight from conformational thermodynamics to functional ligand binding in proteins Samapan Sikdar a , J. Chakrabarti a, b * and Mahua Ghosh a * a Department of Chemical, Biological And Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700098, INDIA b Also at Unit of Nanoscience and Technology-II and The Thematic Unit of Excellence on Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700098, INDIA *Corresponding authors: E-mail: jaydeb@bose.res.in and mahuaghosh@bose.res.in Abstract We show that the thermodynamics of metal ion induced conformational changes aid to understand the functions of protein complexes. This is illustrated in case of a metalloprotein, alpha-lactalbumin (aLA), a divalent metal ion binding protein. We use the histograms of dihedral angles of the protein, generated from all-atom molecular dynamics simulations, to calculate the conformational thermodynamics. The thermodynamically destabilized and disordered residues in different conformational states of a protein are proposed to serve as binding sites for ligands. This is tested for β-1,4-galactosyltransferase (β4GalT) binding to the Ca 2+ -aLA complex where the binding residues are known. Among the binding residues,