Nitric oxide reactivity with globins as investigated through computer simulation

TitleNitric oxide reactivity with globins as investigated through computer simulation
Publication TypeJournal Article
Year of Publication2008
AuthorsMarti, MA, Capece L, Bidon-Chanal A, Crespo A, Guallar V, Luque FJ, Estrin DA
JournalMethods in enzymology
Pagination477 - 498
Date Published2008///
KeywordsBiomechanics; Computer Simulation; Energy Metabolism; Globins/chemistry/metabolism; Heme/chemistry; Kinetics; Metabolic Detoxication, Drug; Models, Molecular; Models, Theoretical; Mycobacterium tuberculosis; Myoglobin/chemistry/metabolism; Nitric Oxide/chemistry/metabolism/pharmacokinetics; Oxygen/metabolism/pharmacology; Protein Binding; Protein Folding; Quantum Theory; Signal Transduction; Substrate Specificity; Trun
AbstractThis chapter reviews the application of classical and quantum-mechanical atomistic simulation tools used in the investigation of several relevant issues in nitric oxide reactivity with globins and presents different simulation strategies based on classical force fields: standard molecular dynamics, essential dynamics, umbrella sampling, multiple steering molecular dynamics, and a novel technique for exploring the protein energy landscape. It also presents hybrid quantum-classical schemes as a tool to obtain relevant information regarding binding energies and chemical reactivity of globins. As illustrative examples, investigations of the structural flexibility, ligand migration profiles, oxygen affinity, and reactivity toward nitric oxide of truncated hemoglobin N of Mycobacterium tuberculosis are presented.