Structure-function relationship of archaeal rhodopsin proteins analyzed by continuum electrostatics

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