- DEE (1) (remove)
- Structure-function relationship of archaeal rhodopsin proteins analyzed by continuum electrostatics (2009)
- Rhodopsin proteins perform two cellular key functions: signaling of external stimuli and ion transport. Examples of both functional types are found in the family of archaeal rhodopsins, namely the proton pump bacteriorhodopsin, the chloride pump halorhodopsin and the photoreceptor sensory rhodopsin II. For these three membrane proteins, high-resolution X-ray structures are available, allowing a theoretical investigation in atomic detail. In this thesis, calculations are presented based on a continuum electrostatics approach using a finite-difference discretization of the Poisson-Boltzmann equation. The results can be divided into three parts. One of the interesting features of rhodopsin proteins is the extreme range over which the absorption maximum of their chromophore retinal is tuned. This characteristic and the precision of the tuning mechanism is a fundamental requirement for color vision. Using the archaeal rhodopsins as model systems, this work aims at advancing the understanding of the inter-protein absorption shift. The presented results demonstrate that the electrostatic interactions of the protein with the retinal are a major determinant of the inter-protein shift. The differences in electrostatic potential that the proteins cause at the retinal could be assigned to seven residues. A generalized model of a quantum mechanical particle in a box including the electrostatic potential as a parameter allows a qualitative description of the absorption maxima. Bacteriorhodopsin has become one of the most important model systems in the field of bioenergetics. This is due to its relative simplicity making it amenable to experimental and theoretical studies. Here, the probability of functionally relevant protonation states is calculated to characterize the available structures. The protonation behavior of the key residues of proton transfer and the correlation between the protonation of these residues is analyzed. The results show that with respect to the protonation the bR, K, L and M1 intermediate state are well represented by the available structures, while the M2, N and O intermediate state are less well represented. An algorithm is introduced that determines a gap-free list of the lowest energy states. Such a list allows to analyze the ensemble of states accessible to a system in a certain energy range and, thus, can provide useful insight into the functional mechanism. The newly developed algorithm, termed X-DEE, is based on the dead-end elimination theorem. The X-DEE algorithm is applicable to a wide range of problems, for instance in protein design attempts. Here, X-DEE is successfully applied to bacteriorhodopsin to obtain gap-free lists of the lowest energy protonation states.