| Full text | |
| Author(s): |
Total Authors: 3
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| Affiliation: | [1] Univ Florida, Dept Chem, Gainesville, FL 32611 - USA
[2] Univ Estadual Paulista, Inst Quim, Dept Fis Quim, UNESP, Araraquara, SP - Brazil
Total Affiliations: 2
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| Document type: | Journal article |
| Source: | Journal of the American Chemical Society; v. 142, n. 8, p. 3823-3835, FEB 26 2020. |
| Web of Science Citations: | 0 |
| Abstract | |
Coupled redox and pH-driven processes are at the core of many important biological mechanisms. As the distribution of protonation and redox states in a system is associated with the pH and redox potential of the solution, having efficient computational tools that can simulate under these conditions becomes very important. Such tools have the potential to provide information that complement and drive experiments. In previous publications we have presented the implementation of the constant pH and redox potential molecular dynamics (C(pH,E)MD) method in AMBER and we have shown how multidimensional replica exchange can be used to significantly enhance the convergence efficiency of our simulations. In the current work, after an improvement in our C(pH,E)MD approach that allows a given residue to be simultaneously pH- and redox-active, we have employed our methodologies to study five different systems of interest in the literature. We present results for capped tyrosine dipeptide, two maquette systems containing one pH- and redox-active tyrosine (alpha Y-3 and peptide A), and two proteins that contain multiple heme groups (diheme cytochrome c from Rhodobacter sphaeroides and Desulfovibrio vulgaris Hildenborough cytochrome c(3)). We show that our results can provide new insights into previous theoretical and experimental findings by using a fully force-field based and GPU-accelerated approach, which allows the simulations to be executed with high computational performance. (AU) | |
| FAPESP's process: | 17/13401-4 - Computational simulation of redox processes in complex environments |
| Grantee: | Gustavo Troiano Feliciano |
| Support Opportunities: | Regular Research Grants |