Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases
The binding of diatomic ligands, such as O2, NO, and CO, to heme proteins is a process intimately related with their function. In this work, we analyzed by means of a combination of classical Molecular Dynamics (MD) and Hybrid Quantum-Classical (QM/MM) techniques the existence of multiple conformati...
| Autores principales: | , , , |
|---|---|
| Publicado: |
2007
|
| Materias: | |
| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_08873585_v68_n2_p480_Marti http://hdl.handle.net/20.500.12110/paper_08873585_v68_n2_p480_Marti |
| Aporte de: |
| id |
paper:paper_08873585_v68_n2_p480_Marti |
|---|---|
| record_format |
dspace |
| spelling |
paper:paper_08873585_v68_n2_p480_Marti2023-06-08T15:46:46Z Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases Martí, Marcelo Adrián Capece, Luciana Bikiel, Damian Ezequiel Estrin, Dario Ariel Heme protein Hydrogen bond Ligand binding Molecular dynamics QM/MM Structure carbon monoxide hemoglobin leghemoglobin nitric oxide oxygen article computer simulation enthalpy hydrogen bond molecular dynamics mutation nonhuman oxygen affinity Paramecium caudatum priority journal protein conformation quantum chemistry soybean Animals Binding Sites Computer Simulation Hemoglobins Kinetics Leghemoglobin Models, Molecular Oxygen Paramecium caudatum Plant Proteins Protein Conformation Protozoan Proteins Soybeans Glycine max Paramecium caudatum The binding of diatomic ligands, such as O2, NO, and CO, to heme proteins is a process intimately related with their function. In this work, we analyzed by means of a combination of classical Molecular Dynamics (MD) and Hybrid Quantum-Classical (QM/MM) techniques the existence of multiple conformations in the distal site of heme proteins and their influence on oxygen affinity regulation. We considered two representative examples: soybean leghemoglobin (Lba) and Paramecium caudatum truncated hemoglobin (PcHb). The results presented in this work provide a molecular interpretation for the kinetic, structural, and mutational data that cannot be obtained by assuming a single distal conformation. © 2007 Wiley-Liss, Inc. Fil:Martí, M.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Capece, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Bikiel, D.E. 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. 2007 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_08873585_v68_n2_p480_Marti http://hdl.handle.net/20.500.12110/paper_08873585_v68_n2_p480_Marti |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Heme protein Hydrogen bond Ligand binding Molecular dynamics QM/MM Structure carbon monoxide hemoglobin leghemoglobin nitric oxide oxygen article computer simulation enthalpy hydrogen bond molecular dynamics mutation nonhuman oxygen affinity Paramecium caudatum priority journal protein conformation quantum chemistry soybean Animals Binding Sites Computer Simulation Hemoglobins Kinetics Leghemoglobin Models, Molecular Oxygen Paramecium caudatum Plant Proteins Protein Conformation Protozoan Proteins Soybeans Glycine max Paramecium caudatum |
| spellingShingle |
Heme protein Hydrogen bond Ligand binding Molecular dynamics QM/MM Structure carbon monoxide hemoglobin leghemoglobin nitric oxide oxygen article computer simulation enthalpy hydrogen bond molecular dynamics mutation nonhuman oxygen affinity Paramecium caudatum priority journal protein conformation quantum chemistry soybean Animals Binding Sites Computer Simulation Hemoglobins Kinetics Leghemoglobin Models, Molecular Oxygen Paramecium caudatum Plant Proteins Protein Conformation Protozoan Proteins Soybeans Glycine max Paramecium caudatum Martí, Marcelo Adrián Capece, Luciana Bikiel, Damian Ezequiel Estrin, Dario Ariel Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases |
| topic_facet |
Heme protein Hydrogen bond Ligand binding Molecular dynamics QM/MM Structure carbon monoxide hemoglobin leghemoglobin nitric oxide oxygen article computer simulation enthalpy hydrogen bond molecular dynamics mutation nonhuman oxygen affinity Paramecium caudatum priority journal protein conformation quantum chemistry soybean Animals Binding Sites Computer Simulation Hemoglobins Kinetics Leghemoglobin Models, Molecular Oxygen Paramecium caudatum Plant Proteins Protein Conformation Protozoan Proteins Soybeans Glycine max Paramecium caudatum |
| description |
The binding of diatomic ligands, such as O2, NO, and CO, to heme proteins is a process intimately related with their function. In this work, we analyzed by means of a combination of classical Molecular Dynamics (MD) and Hybrid Quantum-Classical (QM/MM) techniques the existence of multiple conformations in the distal site of heme proteins and their influence on oxygen affinity regulation. We considered two representative examples: soybean leghemoglobin (Lba) and Paramecium caudatum truncated hemoglobin (PcHb). The results presented in this work provide a molecular interpretation for the kinetic, structural, and mutational data that cannot be obtained by assuming a single distal conformation. © 2007 Wiley-Liss, Inc. |
| author |
Martí, Marcelo Adrián Capece, Luciana Bikiel, Damian Ezequiel Estrin, Dario Ariel |
| author_facet |
Martí, Marcelo Adrián Capece, Luciana Bikiel, Damian Ezequiel Estrin, Dario Ariel |
| author_sort |
Martí, Marcelo Adrián |
| title |
Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases |
| title_short |
Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases |
| title_full |
Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases |
| title_fullStr |
Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases |
| title_full_unstemmed |
Oxygen affinity controlled by dynamical distal conformations: The soybean leghemoglobin and the Paramecium caudatum hemoglobin cases |
| title_sort |
oxygen affinity controlled by dynamical distal conformations: the soybean leghemoglobin and the paramecium caudatum hemoglobin cases |
| publishDate |
2007 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_08873585_v68_n2_p480_Marti http://hdl.handle.net/20.500.12110/paper_08873585_v68_n2_p480_Marti |
| work_keys_str_mv |
AT martimarceloadrian oxygenaffinitycontrolledbydynamicaldistalconformationsthesoybeanleghemoglobinandtheparameciumcaudatumhemoglobincases AT capeceluciana oxygenaffinitycontrolledbydynamicaldistalconformationsthesoybeanleghemoglobinandtheparameciumcaudatumhemoglobincases AT bikieldamianezequiel oxygenaffinitycontrolledbydynamicaldistalconformationsthesoybeanleghemoglobinandtheparameciumcaudatumhemoglobincases AT estrindarioariel oxygenaffinitycontrolledbydynamicaldistalconformationsthesoybeanleghemoglobinandtheparameciumcaudatumhemoglobincases |
| _version_ |
1768545056171491328 |