Abstract
The development and application of
high-resolution NMR methods for protein structure determination was the topic
of the present thesis. Methods for calculating sequences of pulsed field
gradients for signal selection as well as the influence of diffusion on the
signal amplitudes were discussed in the first part, while the second part dealt
with the structure determination of the retinal environment of the integral
membrane protein bacteriorhodopsin based on a novel labelling strategy.
Pulsed field gradients are an
important tool for signal selection and artifact suppression in modern
high-resolution NMR. As part of the present work, the computer programs TRIPLE
GRADIENT and Z GRADIENT for the calculation of optimized sequences of pulsed
field gradients for arbitrary experiments were developed and tested. Signal
selection under consideration of rf-pulse imperfections was exemplified for the
HSQC experiment. The formalism on which the programs are based was extended to
include stochastic as well as deterministic translational motion of the
molecules. As a quantitative example, the influence of diffusion on the HQQC
experiment was discussed. It was shown that the diffusion coefficient of
ethanol can be reproduced correctly from an analysis of the line-widths in the
indirect dimension.
The integral membrane protein bacteriorhodopsin
was solubilized in dodecyl-maltoside micelles. Completely deuterated samples
with selectively protonated moieties of the protein detergent complex with a
molecular weight of more than 60 kDa were used to record 1H NOESY
spectra and to obtain sequence specific resonance assignments. Structures of
both forms of the dark-adapted protein were determined from distances between
protons in the retinal binding pocket. The theoretical analysis of the chemical
shifts as well as a comparison of the all-trans/15-anti NMR structure to
crystal structures shows the high accuracy of this method to obtain NMR
structures.
The high resolution structure of the
13-cis/15-syn form, now obtained for the first time, was able to reveal a
shorter distance between the protonated Schiff-base and its complex counterion
than found in the all-trans/15-anti form. The relative position of the retinal
carbon atoms to the neighboring tryptophan side-chains is almost identical to
that of an early intermediate of the photocycle, in which the retinal is in
13-cis/15-anti conformation. | 
