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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Vydáno v:Biochimica et biophysica acta Ročník 1834; číslo 9; s. 1722 - 1738
Hlavní autoři: Capece, Luciana, Boechi, Leonardo, Perissinotti, Laura L., Arroyo-Mañez, Pau, Bikiel, Damián E., Smulevich, Giulietta, Marti, Marcelo A., Estrin, Dario A.
Médium: Journal Article
Jazyk:angličtina
Vydáno: Netherlands Elsevier B.V 01.09.2013
Témata:
amino acids
Animals
carbon monoxide
Computer Simulation
fluorides
Globin
Globins - chemistry
Globins - metabolism
heme
Heme protein
Humans
Ligands
Molecular dynamics
nitric oxide
nitrites
oxygen
proteins
QM/MM
Quantum Theory
Globin
Molecular dynamics
Heme protein
QM/MM
Computer simulation
ISSN:1570-9639, 0006-3002, 1878-1454
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Abstract 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 proteinligand 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. •We review the use of simulation tools to study ligand interactions with globins.•We describe ligand migration, entry and exit to/from the active site.•We describe, for different ligands, how the metalligand bond can be modulated.
AbstractList 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 proteinligand 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.
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.
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 proteinligand 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.
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.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.
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 proteinligand 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. •We review the use of simulation tools to study ligand interactions with globins.•We describe ligand migration, entry and exit to/from the active site.•We describe, for different ligands, how the metalligand bond can be modulated.
Author Boechi, Leonardo
Marti, Marcelo A.
Bikiel, Damián E.
Arroyo-Mañez, Pau
Smulevich, Giulietta
Capece, Luciana
Perissinotti, Laura L.
Estrin, Dario A.
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  surname: Capece
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  organization: Departamento de Química Inorgánica, Analítica, y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
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  givenname: Leonardo
  surname: Boechi
  fullname: Boechi, Leonardo
  organization: Department of Chemistry and Biochemistry, University of California San Diego, 92093 — La Joya, CA United States
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  givenname: Laura L.
  surname: Perissinotti
  fullname: Perissinotti, Laura L.
  organization: Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW Calgary, Alberta T2N1N4, Canada
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  givenname: Pau
  surname: Arroyo-Mañez
  fullname: Arroyo-Mañez, Pau
  organization: Departamento de Química Inorgánica, Analítica, y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
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  givenname: Damián E.
  surname: Bikiel
  fullname: Bikiel, Damián E.
  organization: Departamento de Química Inorgánica, Analítica, y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
– sequence: 6
  givenname: Giulietta
  surname: Smulevich
  fullname: Smulevich, Giulietta
  organization: Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
– sequence: 7
  givenname: Marcelo A.
  surname: Marti
  fullname: Marti, Marcelo A.
  email: marcelo@qi.fcen.uba.ar
  organization: Departamento de Química Inorgánica, Analítica, y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
– sequence: 8
  givenname: Dario A.
  surname: Estrin
  fullname: Estrin, Dario A.
  email: dario@qi.fcen.uba.ar
  organization: Departamento de Química Inorgánica, Analítica, y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
BackLink https://www.ncbi.nlm.nih.gov/pubmed/23470499$$D View this record in MEDLINE/PubMed
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Keywords Globin
Molecular dynamics
Heme protein
QM/MM
Computer simulation
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Snippet In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction...
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SubjectTerms amino acids
Animals
carbon monoxide
Computer Simulation
fluorides
Globin
Globins - chemistry
Globins - metabolism
heme
Heme protein
Humans
Ligands
Molecular dynamics
nitric oxide
nitrites
oxygen
proteins
QM/MM
Quantum Theory
Title Small ligand–globin interactions: Reviewing lessons derived from computer simulation
URI https://dx.doi.org/10.1016/j.bbapap.2013.02.038
https://www.ncbi.nlm.nih.gov/pubmed/23470499
https://www.proquest.com/docview/1415599912
https://www.proquest.com/docview/1753432521
Volume 1834
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