Artículo

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" (2013) Biochimica et Biophysica Acta - Proteins and Proteomics. 1834(9):1722-1738
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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 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.

Registro:

Documento: Artículo
Título:Small ligand-globin interactions: Reviewing lessons derived from computer simulation
Autor:Capece, L.; Boechi, L.; Perissinotti, L.L.; Arroyo-Mañez, P.; Bikiel, D.E.; Smulevich, G.; Marti, M.A.; Estrin, D.A.
Filiación:Departamento de Quimica Inorganica, Analitica, y Quimica Fisica/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellon 2, C1428EHA Buenos Aires, Argentina
Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellon 2, C1428EHA Buenos Aires, Argentina
Department of Chemistry and Biochemistry, University of California San Diego, 92093 - LaJoya, CA, United States
Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary AB T2N1N4, Canada
Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
Dipartimento di Chimica Ugo Schiff, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
Palabras clave: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
Año:2013
Volumen:1834
Número:9
Página de inicio:1722
Página de fin:1738
DOI: http://dx.doi.org/10.1016/j.bbapap.2013.02.038
Título revista:Biochimica et Biophysica Acta - Proteins and Proteomics
Título revista abreviado:Biochim. Biophys. Acta Proteins Proteomics
ISSN:15709639
CODEN:BBAPB
CAS:amino acid, 65072-01-7; cytochrome c, 9007-43-6, 9064-84-0; heme, 14875-96-8; hemoglobin, 9008-02-0; nitrite, 14797-65-0; oxygen, 7782-44-7; Globins, 9004-22-2; Ligands
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15709639_v1834_n9_p1722_Capece

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Citas:

---------- APA ----------
Capece, L., Boechi, L., Perissinotti, L.L., Arroyo-Mañez, P., Bikiel, D.E., Smulevich, G., Marti, M.A.,..., Estrin, D.A. (2013) . Small ligand-globin interactions: Reviewing lessons derived from computer simulation. Biochimica et Biophysica Acta - Proteins and Proteomics, 1834(9), 1722-1738.
http://dx.doi.org/10.1016/j.bbapap.2013.02.038
---------- CHICAGO ----------
Capece, L., Boechi, L., Perissinotti, L.L., Arroyo-Mañez, P., Bikiel, D.E., Smulevich, G., et al. "Small ligand-globin interactions: Reviewing lessons derived from computer simulation" . Biochimica et Biophysica Acta - Proteins and Proteomics 1834, no. 9 (2013) : 1722-1738.
http://dx.doi.org/10.1016/j.bbapap.2013.02.038
---------- MLA ----------
Capece, L., Boechi, L., Perissinotti, L.L., Arroyo-Mañez, P., Bikiel, D.E., Smulevich, G., et al. "Small ligand-globin interactions: Reviewing lessons derived from computer simulation" . Biochimica et Biophysica Acta - Proteins and Proteomics, vol. 1834, no. 9, 2013, pp. 1722-1738.
http://dx.doi.org/10.1016/j.bbapap.2013.02.038
---------- VANCOUVER ----------
Capece, L., Boechi, L., Perissinotti, L.L., Arroyo-Mañez, P., Bikiel, D.E., Smulevich, G., et al. Small ligand-globin interactions: Reviewing lessons derived from computer simulation. Biochim. Biophys. Acta Proteins Proteomics. 2013;1834(9):1722-1738.
http://dx.doi.org/10.1016/j.bbapap.2013.02.038