Abstract
Molecular dynamics simulations have been applied to unbind biological ligands from their receptors [1–5]. Conformation changes are observed in the biomolecules during unbinding, but there exists no systematic method to detect these conformation changes. In this work, we have used `essential dynamics' (ED) [6–7] and projection to latent structures (PLS) [8] to investigate the conformation changes of the bovine serum retinol-binding protein when retinol unbinds from its receptor site. The results of these analyses characterise a large proportion of the movements that occur during unbinding. We find that the loop regions of retinol-binding protein exhibit the largest movements during unbinding. The sudden changes in unbinding speed during the unbinding process appear not to be caused by sudden changes in protein structure.
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Chau, PL., Howe, P. Analysis methods for identifying coordinated movements during ligand unbinding. J Comput Aided Mol Des 16, 755–765 (2002). https://doi.org/10.1023/A:1022475832253
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DOI: https://doi.org/10.1023/A:1022475832253