Bioelectrochemistry is an area that studies electrochemical reactions and phenomena in organic molecules, such as proteins. Among several uses, this area stands out for having straight relations with medicine, biomedical engineering and with the comprehension of enzymatic kinetics. In this context, there are metalloproteins which act by performing electron transfer reactions, which are essential reactions for biological processes such as photosynthesis and cellular respiration. Among these proteins, this project targets Azurine and, in perspective, some types of cytochromes. The targets will be simulated freely and immobilized on inorganic supports that can act as electrodes (such as gold or graphene), immersed in environments with non-neutral pH and with redox potential applied. The simulations require several methods. The most important of them, is the recent method C(pH,E)MD (Constant pH and redox potential molecular dynamics), which can be seen as a hybrid between molecular dynamics and Monte Carlo methods that is able to simulate all the states and conformations of targets that are reactive to pH and redox potential (as is the case with metalloproteins). The method was developed for an AMBER force field. In addition to this main method, measures of interest for the complete study can be obtained with simulations using methods like Molecular Mechanics, Quantum Mechanics, QM / MM and with the Density Functional Theory. The immediate objectives of this project are: to study the behavior and catalytic activity of azurine in different environments with applied pH and redox potential (free and immobilized on an electrode), certify the applicability of the C(pH,E)MD method in the simulations and, as perspective, look for artificial enzymes that may have catalytic activity similar to that of Azurine in certain pH and potential ranges.
News published in Agência FAPESP Newsletter about the scholarship: