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Abstract:

The acid-base behavior of amino acids is an important subject of study due to their prominent role in enzyme catalysis, substrate binding and protein structure. Due to interactions with the protein environment, their pKas can be shifted from their solution values and, if a protein has two stable conformations, it is possible for a residue to have different "microscopic", conformation-dependent pKa values. In those cases, interpretation of experimental measurements of the pKa is complicated by the coupling between pH, protonation state and protein conformation. We explored these issues using Nitrophorin 4 (NP4), a protein that releases NO in a pH sensitive manner. At pH 5.5 NP4 is in a closed conformation where NO is tightly bound, while at pH 7.5 Asp30 becomes deprotonated, causing the conformation to change to an open state from which NO can easily escape. Using constant pH molecular dynamics we found two distinct microscopic Asp30 pKas: 8.5 in the closed structure and 4.3 in the open structure. Using a four-state model, we then related the obtained microscopic values to the experimentally observed "apparent" pKa, obtaining a value of 6.5, in excellent agreement with experimental data. This value must be interpreted as the pH at which the closed to open population transition takes place. More generally, our results show that it is possible to relate microscopic structure dependent pKa values to experimentally observed ensemble dependent apparent pKas and that the insight gained in the relatively simple case of NP4 can be useful in several more complex cases involving a pH dependent transition, of great biochemical interest. © 2012 Di Russo et al.

Registro:

Documento: Artículo
Título:pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4
Autor:Di Russo, N.V.; Estrin, D.A.; Martí, M.A.; Roitberg, A.E.
Filiación:Quantum Theory Project and Department of Chemistry, University of Florida, Gainesville, FL, United States
Departamento de Quimica Inorganica, Analitica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
Palabras clave:aspartic acid; carrier protein; nitrophorin 4; unclassified drug; article; conformational transition; molecular dynamics; molecular model; pH; pKa; protein analysis; protein conformation; protein interaction; structure analysis; Animals; Aspartic Acid; Computational Biology; Computer Simulation; Hemeproteins; Hydrogen-Ion Concentration; Insect Proteins; Models, Chemical; Models, Molecular; Protein Conformation; Protein Folding; Rhodnius; Salivary Proteins and Peptides
Año:2012
Volumen:8
Número:11
DOI: http://dx.doi.org/10.1371/journal.pcbi.1002761
Título revista:PLoS Computational Biology
Título revista abreviado:PLoS Comput. Biol.
ISSN:1553734X
CAS:aspartic acid, 56-84-8, 6899-03-2; carrier protein, 80700-39-6; Aspartic Acid, 56-84-8; Hemeproteins; Insect Proteins; Salivary Proteins and Peptides; nitrophorin
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_1553734X_v8_n11_p_DiRusso

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Citas:

---------- APA ----------
Di Russo, N.V., Estrin, D.A., Martí, M.A. & Roitberg, A.E. (2012) . pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4. PLoS Computational Biology, 8(11).
http://dx.doi.org/10.1371/journal.pcbi.1002761
---------- CHICAGO ----------
Di Russo, N.V., Estrin, D.A., Martí, M.A., Roitberg, A.E. "pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4" . PLoS Computational Biology 8, no. 11 (2012).
http://dx.doi.org/10.1371/journal.pcbi.1002761
---------- MLA ----------
Di Russo, N.V., Estrin, D.A., Martí, M.A., Roitberg, A.E. "pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4" . PLoS Computational Biology, vol. 8, no. 11, 2012.
http://dx.doi.org/10.1371/journal.pcbi.1002761
---------- VANCOUVER ----------
Di Russo, N.V., Estrin, D.A., Martí, M.A., Roitberg, A.E. pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4. PLoS Comput. Biol. 2012;8(11).
http://dx.doi.org/10.1371/journal.pcbi.1002761