Show simple item record

Files in this item

Cover for Reduction Potential Properties of Electron Transfer Proteins
dc.contributor.advisorIchiye, Toshiko
dc.creator
dc.date.accessioned2018-06-22T13:35:59Z
dc.date.available2018-06-22T13:35:59Z
dc.date.created2018
dc.date.issued
dc.date.submitted01/01/2018
dc.identifier.otherAPT-BAG: georgetown.edu.10822_1050744.tar;APT-ETAG: 5000b4cc0d548e871846cb4958e99680; APT-DATE: 2019-03-18_08:43:04en_US
dc.identifier.uri
dc.descriptionPh.D.
dc.description.abstractElectron transfer reactions play an important role in biological processes such as photosynthesis, respiration, and nitrogen fixation. Here, the electron transfer properties of iron-sulfur (Fe-S) proteins and blue copper proteins are investigated. The reduction potentials of these proteins determine the driving forces for their electron transfer. The most important determinant of the reduction potential is the primary coordination sphere, or the type and number of metal ion(s) and the geometry of the redox site with its coordinating ligands. However, for a given redox site, the reduction potentials can vary by ~1 V for non-homologous proteins and ~0.3 V for homologous proteins. Therefore, the protein matrix and solvent environment around the redox site are important factors that are responsible for tuning the reduction potential to serve a variety of biological functions.
dc.description.abstractHere, a method for calculating the reduction potentials of metalloproteins is presented in which the redox site or inner sphere contribution is calculated by density functional theory (DFT) and the protein and solvent environment or outer sphere contribution is calculated by Poisson-Boltzmann (PB) continuum electrostatics. Reduction potentials calculated using the DFT+PB method are in good agreement with the experimental values for and the nine Fe-S clusters in respiratory complex I. Moreover, the method used here is a useful computational tool to study other questions about complex I. In addition, the method is being extended to the blue copper proteins.
dc.description.abstractThe protein matrix and surrounding solution are investigated in a long 10 microsecond molecular dynamics simulation of 2[4Fe-4S] ferredoxin, a small electron shuttle protein, at very dilute ionic concentration (~0.04 M KCl) similar to the conditions of the rate measurement. The potassium ions form a “cloud” favoring the product due to the arrangement of negatively charged groups of the protein, which suggests a possible mechanism for an electron shuttle protein. Finally, since most of the computer time for molecular dynamics simulations is spent calculating water-water interactions, a fast and efficient water model was developed for biological simulations.
dc.formatPDF
dc.format.extent166 leaves
dc.languageen
dc.publisherGeorgetown University
dc.sourceGeorgetown University-Graduate School of Arts & Sciences
dc.sourceChemistry
dc.subject.otherComputational chemistry
dc.titleReduction Potential Properties of Electron Transfer Proteins
dc.typethesis
dc.identifier.orcid0000-0003-1952-5600


This item appears in the following Collection(s)

Show simple item record