Molecular basis for the ph dependent structural transition of nitrophorin 4
Allostery can be defined in a broad sense as a structural change in a protein. The theoretical framework for allostery includes several formulations. In the stereochemical view, the activation event causes a local conformational change that is propagated through residue-to-residue contacts to the re...
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todo:paper_15206106_v113_n7_p2135_Marti2023-10-03T16:20:19Z Molecular basis for the ph dependent structural transition of nitrophorin 4 Martí, M.A. Estrin, D.A. Roitberg, A.E. pH Porphyrins Activated conformations Allosteric transitions Allostery Conformational changes Conformational ensembles Conformational free energies Equilibrium state Free energy landscapes Heme proteins Md simulations Molecular basis Nitrophorin-4 Ph conditions pH dependents Protonation state Stable state Structural changes Structural transitions Theoretical frameworks Free energy hemoprotein nitrophorin saliva protein article chemical model chemistry computer simulation pH protein conformation Computer Simulation Hemeproteins Hydrogen-Ion Concentration Models, Chemical Protein Conformation Salivary Proteins and Peptides Allostery can be defined in a broad sense as a structural change in a protein. The theoretical framework for allostery includes several formulations. In the stereochemical view, the activation event causes a local conformational change that is propagated through residue-to-residue contacts to the rest of the protein through well-defined structural pathways. The thermodynamic, or population shift model, instead implies that the activated conformation is already present with non-negligible population in the nonactivated conformational ensemble, and therefore the activation merely shifts the equilibrium. Nitrophorins (NPs) are heme proteins that store and transport NO in a pH dependent manner, due to a conformational change. Using MD simulations, we show that the NP structural transition occurs in two different conformational free energy landscapes, each one corresponding to a pH condition and characterized by specific residue-residue interactions that characterize them. We also show that when the protonation state of the equilibrium state is modified the conformation becomes unstable and proceeds very fast to an intermediate stable state that is different for each pH condition. Finally, we will discuss that allosteric transition in NP4 does not occur due to a change in the relative population of both end states, but due to a drastic change in the free energy landscape of its conformational ensemble. © 2009 American Chemical Society. Fil:Martí, M.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Estrin, D.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_15206106_v113_n7_p2135_Marti |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
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R-134 |
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Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
pH Porphyrins Activated conformations Allosteric transitions Allostery Conformational changes Conformational ensembles Conformational free energies Equilibrium state Free energy landscapes Heme proteins Md simulations Molecular basis Nitrophorin-4 Ph conditions pH dependents Protonation state Stable state Structural changes Structural transitions Theoretical frameworks Free energy hemoprotein nitrophorin saliva protein article chemical model chemistry computer simulation pH protein conformation Computer Simulation Hemeproteins Hydrogen-Ion Concentration Models, Chemical Protein Conformation Salivary Proteins and Peptides |
| spellingShingle |
pH Porphyrins Activated conformations Allosteric transitions Allostery Conformational changes Conformational ensembles Conformational free energies Equilibrium state Free energy landscapes Heme proteins Md simulations Molecular basis Nitrophorin-4 Ph conditions pH dependents Protonation state Stable state Structural changes Structural transitions Theoretical frameworks Free energy hemoprotein nitrophorin saliva protein article chemical model chemistry computer simulation pH protein conformation Computer Simulation Hemeproteins Hydrogen-Ion Concentration Models, Chemical Protein Conformation Salivary Proteins and Peptides Martí, M.A. Estrin, D.A. Roitberg, A.E. Molecular basis for the ph dependent structural transition of nitrophorin 4 |
| topic_facet |
pH Porphyrins Activated conformations Allosteric transitions Allostery Conformational changes Conformational ensembles Conformational free energies Equilibrium state Free energy landscapes Heme proteins Md simulations Molecular basis Nitrophorin-4 Ph conditions pH dependents Protonation state Stable state Structural changes Structural transitions Theoretical frameworks Free energy hemoprotein nitrophorin saliva protein article chemical model chemistry computer simulation pH protein conformation Computer Simulation Hemeproteins Hydrogen-Ion Concentration Models, Chemical Protein Conformation Salivary Proteins and Peptides |
| description |
Allostery can be defined in a broad sense as a structural change in a protein. The theoretical framework for allostery includes several formulations. In the stereochemical view, the activation event causes a local conformational change that is propagated through residue-to-residue contacts to the rest of the protein through well-defined structural pathways. The thermodynamic, or population shift model, instead implies that the activated conformation is already present with non-negligible population in the nonactivated conformational ensemble, and therefore the activation merely shifts the equilibrium. Nitrophorins (NPs) are heme proteins that store and transport NO in a pH dependent manner, due to a conformational change. Using MD simulations, we show that the NP structural transition occurs in two different conformational free energy landscapes, each one corresponding to a pH condition and characterized by specific residue-residue interactions that characterize them. We also show that when the protonation state of the equilibrium state is modified the conformation becomes unstable and proceeds very fast to an intermediate stable state that is different for each pH condition. Finally, we will discuss that allosteric transition in NP4 does not occur due to a change in the relative population of both end states, but due to a drastic change in the free energy landscape of its conformational ensemble. © 2009 American Chemical Society. |
| format |
JOUR |
| author |
Martí, M.A. Estrin, D.A. Roitberg, A.E. |
| author_facet |
Martí, M.A. Estrin, D.A. Roitberg, A.E. |
| author_sort |
Martí, M.A. |
| title |
Molecular basis for the ph dependent structural transition of nitrophorin 4 |
| title_short |
Molecular basis for the ph dependent structural transition of nitrophorin 4 |
| title_full |
Molecular basis for the ph dependent structural transition of nitrophorin 4 |
| title_fullStr |
Molecular basis for the ph dependent structural transition of nitrophorin 4 |
| title_full_unstemmed |
Molecular basis for the ph dependent structural transition of nitrophorin 4 |
| title_sort |
molecular basis for the ph dependent structural transition of nitrophorin 4 |
| url |
http://hdl.handle.net/20.500.12110/paper_15206106_v113_n7_p2135_Marti |
| work_keys_str_mv |
AT martima molecularbasisforthephdependentstructuraltransitionofnitrophorin4 AT estrinda molecularbasisforthephdependentstructuraltransitionofnitrophorin4 AT roitbergae molecularbasisforthephdependentstructuraltransitionofnitrophorin4 |
| _version_ |
1807321879151640576 |