Paper Citing NAMD - Abstract
Negureanu, Lacramioara; Salsbury, Freddie R.
Insights into Protein - DNA Interactions, Stability and Allosteric Communications: A Computational Study of Muts alpha-DNA Recognition Complexes
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:757-776, FEB 2012
DNA mismatch repair proteins (MMR) maintain genetic stability by recognizing and repairing mismatched bases and insertion/deletion loops mistakenly incorporated during DNA replication, and initiate cellular response to certain types of DNA damage. Loss of MMR in mammalian cells has been linked to resistance to certain DNA damaging chemotherapeutic agents, as well as to increase risk of cancer. Mismatch repair pathway is considered to involve the concerted action of at least 20 proteins. The most abundant MMR mismatch-binding factor in eukaryotes, MutS alpha, recognizes and initiates the repair of base-base mismatches and small insertion/deletion. We performed molecular dynamics simulations on mismatched and damaged MutS alpha-DNA complexes. A comprehensive DNA binding site analysis of relevant conformations shows that MutS alpha proteins recognize the mismatched and platinum crosslinked DNA substrates in significantly different modes. Distinctive conformational changes associated with MutSa binding to mismatched and damaged DNA have been identified and they provide insight into the involvement of MMR proteins in DNA-repair and DNA-damage pathways. Stability and allosteric interactions at the heterodimer interface associated with the mismatch and damage recognition step allow for prediction of key residues in MMR cancer-causing mutations. A rigorous hydrogen bonding analysis for ADP molecules at the ATPase binding sites is also presented. Due to extended number of known MMR cancer causing mutations among the residues proved to make specific contacts with ADP molecules, recommendations for further studies on similar mutagenic effects were made.
