Proton Transfer Networks and the Mechanism of Long Range Proton Transfer in Proteins
type: CreativeWork
description: The main energy providing reaction systems in living cells, for example the photosynthesis or the respiratory chain, are based on long range proton transfer (LRPT) reactions. Even since these LRPT reactions have been heavily investigated in the last decades, the mechanism of these reactions is still not completely understood. The reaction kinetics of the LRPT are under heavy discussion and it is not clear, whether the reorientation of the hydrogen bond network (HBN)or the electrostatic barrier for the charge transfer is rate limiting. The main purpose of this work is to investigate the dynamics of chemical reactions inside of proteins, focused on long range proton transfer reactions. Electron transfer reactions, rotations of water molecules or conformational changes of the protein are also considered. The developed sequential dynamical Monte Carlo (SDMC) method is applicable to almost all kinds of chemical reactions. For all proton transfer reactions, the HBN of a protein plays a major role. Protons are transferred along such hydrogen bonds. Therefore, knowledge about the hydrogen bond network of a protein is crucial for the simulation of LRPT systems. The HBN can be calculated from the protein structure and the rotational state of the amino acid side chains. The reaction rate can be calculated from the electrostatic energies of the participating proton donor and acceptor groups. These two criteria are combined for the decision if a proton transfer between two molecules is possible and how fast this transfer would happen. While the calculation of electrostatic energies of protonatable amino acid side chains or relevant cofactors in proteins (among them also water molecules) is already solved - implemented in various programs - the remaining tasks - calculating the hydrogen bond network followed by calculating the reaction rates - were solved during this work. Before the hydrogen bond network and the electrostatic energies could be calculated, the lack of water posit…
abstract: The main energy providing reaction systems in living cells, for example the photosynthesis or the respiratory chain, are based on long range proton transfer (LRPT) reactions. Even since these LRPT reactions have been heavily investigated in the last decades, the mechanism of these reactions is still not completely understood. The reaction kinetics of the LRPT are under heavy discussion and it is not clear, whether the reorientation of the hydrogen bond network (HBN)or the electrostatic barrier for the charge transfer is rate limiting. The main purpose of this work is to investigate the dynamics of chemical reactions inside of proteins, focused on long range proton transfer reactions. Electron transfer reactions, rotations of water molecules or conformational changes of the protein are also considered. The developed sequential dynamical Monte Carlo (SDMC) method is applicable to almost all kinds of chemical reactions. For all proton transfer reactions, the HBN of a protein plays a major role. Protons are transferred along such hydrogen bonds. Therefore, knowledge about the hydrogen bond network of a protein is crucial for the simulation of LRPT systems. The HBN can be calculated from the protein structure and the rotational state of the amino acid side chains. The reaction rate can be calculated from the electrostatic energies of the participating proton donor and acceptor groups. These two criteria are combined for the decision if a proton transfer between two molecules is possible and how fast this transfer would happen. While the calculation of electrostatic energies of protonatable amino acid side chains or relevant cofactors in proteins (among them also water molecules) is already solved - implemented in various programs - the remaining tasks - calculating the hydrogen bond network followed by calculating the reaction rates - were solved during this work. Before the hydrogen bond network and the electrostatic energies could be calculated, the lack of water posit…
author: Till, Mirco
date published: 2010-06-21
date modified: 2026-07-27T18:49:12Z
provider: Universität Bayreuth
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: Universität Bayreuth