A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT
- 25 March 2008
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 105 (12), 4615-4620
- https://doi.org/10.1073/pnas.0708058105
Abstract
O(6)-alkylguanine-DNA alkyltransferase (AGT) repairs damage to the human genome by flipping guanine and thymine bases into its active site for irreversible transfer of alkyl lesions to Cys-145, but how the protein identifies its targets has remained unknown. Understanding molecular recognition in this system, which can serve as a paradigm for the many nucleotide-flipping proteins that regulate genes and repair DNA in all kingdoms of life, is particularly important given that inhibitors are in clinical trials as anticancer therapeutics. Computational approaches introduced recently for harvesting and statistically characterizing trajectories of molecularly rare events now enable us to elucidate a pathway for nucleotide flipping by AGT and the forces that promote it. In contrast to previously proposed flipping mechanisms, we observe a two-step process that promotes a kinetic, rather than a thermodynamic, gate-keeping strategy for lesion discrimination. Connection is made to recent single-molecule studies of DNA-repair proteins sliding on DNA to understand how they sense subtle chemical differences between bases efficiently.Keywords
This publication has 39 references indexed in Scilit:
- Enzymatic capture of an extrahelical thymine in the search for uracil in DNANature, 2007
- Activation Mechanism of a Signaling Protein at Atomic Resolution from Advanced ComputationsJournal of the American Chemical Society, 2007
- Reaction coordinate of an enzymatic reaction revealed by transition path samplingProceedings of the National Academy of Sciences of the United States of America, 2007
- Interactions of Human O6-Alkylguanine-DNA Alkyltransferase (AGT) with Short Single-stranded DNAsPublished by Elsevier BV ,2007
- A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNAProceedings of the National Academy of Sciences of the United States of America, 2006
- A general method for the covalent labeling of fusion proteins with small molecules in vivoNature Biotechnology, 2002
- Investigation of the Role of Tyrosine-114 in the Activity of Human O6-Alkylguanine-DNA AlkyltranferaseBiochemistry, 1998
- All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of ProteinsThe Journal of Physical Chemistry B, 1998
- Targeted Molecular Dynamics Simulation of Conformational Change-Application to the T ↔ R Transition in InsulinMolecular Simulation, 1993
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry, 1983