Small ligand-globin interactions: Reviewing lessons derived from computer simulation
In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented...
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todo:paper_15709639_v1834_n9_p1722_Capece2023-10-03T16:26:53Z Small ligand-globin interactions: Reviewing lessons derived from computer simulation Capece, L. Boechi, L. Perissinotti, L.L. Arroyo-Mañez, P. Bikiel, D.E. Smulevich, G. Marti, M.A. Estrin, D.A. Computer simulation Globin Heme protein Molecular dynamics QM/MM amino acid cytochrome c globin heme hemoglobin ligand nitrite oxygen hemoprotein ligand amino acid composition article binding site computer simulation conformation controlled study crystal structure denitrifying bacterium dissociation equilibrium constant Escherichia coli experimental study hydrogen bond ligand binding molecular dynamics molecular mechanics nonhuman Paracoccus pantotrophus Paramecium caudatum point mutation priority journal protein protein interaction proton transport Pseudomonas aeruginosa quantum mechanics Raman spectrometry reduction kinetics site directed mutagenesis Wolinella succinogenes animal chemistry human metabolism QM/MM quantum theory review Computer simulation Globin Heme protein Molecular dynamics QM/MM Animals Computer Simulation Globins Humans Ligands Quantum Theory In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS-, F-, and NO2 - showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein-ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. © 2013 Elsevier B.V. All rights reserved. Fil:Capece, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Boechi, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Perissinotti, L.L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Arroyo-Mañez, P. 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:Marti, 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_15709639_v1834_n9_p1722_Capece |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Computer simulation Globin Heme protein Molecular dynamics QM/MM amino acid cytochrome c globin heme hemoglobin ligand nitrite oxygen hemoprotein ligand amino acid composition article binding site computer simulation conformation controlled study crystal structure denitrifying bacterium dissociation equilibrium constant Escherichia coli experimental study hydrogen bond ligand binding molecular dynamics molecular mechanics nonhuman Paracoccus pantotrophus Paramecium caudatum point mutation priority journal protein protein interaction proton transport Pseudomonas aeruginosa quantum mechanics Raman spectrometry reduction kinetics site directed mutagenesis Wolinella succinogenes animal chemistry human metabolism QM/MM quantum theory review Computer simulation Globin Heme protein Molecular dynamics QM/MM Animals Computer Simulation Globins Humans Ligands Quantum Theory |
| spellingShingle |
Computer simulation Globin Heme protein Molecular dynamics QM/MM amino acid cytochrome c globin heme hemoglobin ligand nitrite oxygen hemoprotein ligand amino acid composition article binding site computer simulation conformation controlled study crystal structure denitrifying bacterium dissociation equilibrium constant Escherichia coli experimental study hydrogen bond ligand binding molecular dynamics molecular mechanics nonhuman Paracoccus pantotrophus Paramecium caudatum point mutation priority journal protein protein interaction proton transport Pseudomonas aeruginosa quantum mechanics Raman spectrometry reduction kinetics site directed mutagenesis Wolinella succinogenes animal chemistry human metabolism QM/MM quantum theory review Computer simulation Globin Heme protein Molecular dynamics QM/MM Animals Computer Simulation Globins Humans Ligands Quantum Theory Capece, L. Boechi, L. Perissinotti, L.L. Arroyo-Mañez, P. Bikiel, D.E. Smulevich, G. Marti, M.A. Estrin, D.A. Small ligand-globin interactions: Reviewing lessons derived from computer simulation |
| topic_facet |
Computer simulation Globin Heme protein Molecular dynamics QM/MM amino acid cytochrome c globin heme hemoglobin ligand nitrite oxygen hemoprotein ligand amino acid composition article binding site computer simulation conformation controlled study crystal structure denitrifying bacterium dissociation equilibrium constant Escherichia coli experimental study hydrogen bond ligand binding molecular dynamics molecular mechanics nonhuman Paracoccus pantotrophus Paramecium caudatum point mutation priority journal protein protein interaction proton transport Pseudomonas aeruginosa quantum mechanics Raman spectrometry reduction kinetics site directed mutagenesis Wolinella succinogenes animal chemistry human metabolism QM/MM quantum theory review Computer simulation Globin Heme protein Molecular dynamics QM/MM Animals Computer Simulation Globins Humans Ligands Quantum Theory |
| description |
In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS-, F-, and NO2 - showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein-ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. © 2013 Elsevier B.V. All rights reserved. |
| format |
JOUR |
| author |
Capece, L. Boechi, L. Perissinotti, L.L. Arroyo-Mañez, P. Bikiel, D.E. Smulevich, G. Marti, M.A. Estrin, D.A. |
| author_facet |
Capece, L. Boechi, L. Perissinotti, L.L. Arroyo-Mañez, P. Bikiel, D.E. Smulevich, G. Marti, M.A. Estrin, D.A. |
| author_sort |
Capece, L. |
| title |
Small ligand-globin interactions: Reviewing lessons derived from computer simulation |
| title_short |
Small ligand-globin interactions: Reviewing lessons derived from computer simulation |
| title_full |
Small ligand-globin interactions: Reviewing lessons derived from computer simulation |
| title_fullStr |
Small ligand-globin interactions: Reviewing lessons derived from computer simulation |
| title_full_unstemmed |
Small ligand-globin interactions: Reviewing lessons derived from computer simulation |
| title_sort |
small ligand-globin interactions: reviewing lessons derived from computer simulation |
| url |
http://hdl.handle.net/20.500.12110/paper_15709639_v1834_n9_p1722_Capece |
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