New paper in PLOS Computational Biology


Our paper ‘Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases’ was published in PLOS Computational Biology. We employed chain-of-replicas path optimization strategy to determine a minimum energy path (MEP) for flipping out a 3-methyl adenine lesion by the DNA glycosylase AlkD. The path showed that AlkD acts by sculpting the global DNA conformation to achieve lesion expulsion. From the MEP we computed an effective free energy profile and delineated the energetics of base extrusion.