pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4
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 con...
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2012
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paper:paper_1553734X_v8_n11_p_DiRusso2023-06-08T16:23:09Z pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4 Estrin, Dario Ariel Martí, Marcelo Adrián 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 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. Fil:Estrin, D.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Martí, M.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2012 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_1553734X_v8_n11_p_DiRusso http://hdl.handle.net/20.500.12110/paper_1553734X_v8_n11_p_DiRusso |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
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 |
| spellingShingle |
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 Estrin, Dario Ariel Martí, Marcelo Adrián pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4 |
| topic_facet |
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 |
| description |
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. |
| author |
Estrin, Dario Ariel Martí, Marcelo Adrián |
| author_facet |
Estrin, Dario Ariel Martí, Marcelo Adrián |
| author_sort |
Estrin, Dario Ariel |
| title |
pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4 |
| title_short |
pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4 |
| title_full |
pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4 |
| title_fullStr |
pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4 |
| title_full_unstemmed |
pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4 |
| title_sort |
ph-dependent conformational changes in proteins and their effect on experimental pkas: the case of nitrophorin 4 |
| publishDate |
2012 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_1553734X_v8_n11_p_DiRusso http://hdl.handle.net/20.500.12110/paper_1553734X_v8_n11_p_DiRusso |
| work_keys_str_mv |
AT estrindarioariel phdependentconformationalchangesinproteinsandtheireffectonexperimentalpkasthecaseofnitrophorin4 AT martimarceloadrian phdependentconformationalchangesinproteinsandtheireffectonexperimentalpkasthecaseofnitrophorin4 |
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