Amino acid deprotonation rates from classical force fields
| العنوان: | Amino acid deprotonation rates from classical force fields |
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| المؤلفون: | Themis Lazaridis, Aliasghar Sepehri |
| المصدر: | The Journal of Chemical Physics. 157:085101 |
| بيانات النشر: | AIP Publishing, 2022. |
| سنة النشر: | 2022 |
| مصطلحات موضوعية: | Aspartic Acid, Kinetics, Bacteriorhodopsins, General Physics and Astronomy, Amino Acids, Hydrogen-Ion Concentration, Protons, Physical and Theoretical Chemistry |
| الوصف: | Acid ionization constants (pKa’s) of titratable amino acid side chains have received a large amount of experimental and theoretical attention. In many situations, however, the rates of protonation and deprotonation, kon and koff, may also be important, for example, in understanding the mechanism of action of proton channels or membrane proteins that couple proton transport to other processes. Protonation and deprotonation involve the making and breaking of covalent bonds, which cannot be studied by classical force fields. However, environment effects on the rates should be captured by such methods. Here, we present an approach for estimating deprotonation rates based on Warshel’s extension of Marcus’s theory of electron transfer, with input from molecular simulations. The missing bond dissociation energy is represented by a constant term determined by fitting the pKa value in solution. The statistics of the energy gap between protonated and deprotonated states is used to compute free energy curves of the two states and, thus, free energy barriers, from which the rate can be deduced. The method is applied to Glu, Asp, and His in bulk solution and select membrane proteins: the M2 proton channel, bacteriorhodopsin, and cytochrome c oxidase. |
| تدمد: | 1089-7690 0021-9606 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9b0d4c7aa0fb4fc289ecab00245679a2Test https://doi.org/10.1063/5.0101960Test |
| رقم الانضمام: | edsair.doi.dedup.....9b0d4c7aa0fb4fc289ecab00245679a2 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 10897690 00219606 |
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