Synthetische und theoretische Methoden zur Bestimmung korrelierter Dynamiken in Miniproteinen

The purpose of the present work was to elucidate the correlated dynamics of various bioorganic systems with different time scales, using synthetic as well as analytical and theoretical methods. First, the characteristics of the motions of a dimeric tetradisulfide were established. Previous experimental studies postulated a directional hinge motion of the V-shaped structure composed of two β-hairpin motifs. NMR structure calculations followed by MD simulations allowed the initial capture of the overall dynamics. The dominant motions, opening and closing and twisting of the β-hairpins, were identified by principal component analysis. To overcome the limited sampling, collective variables were selected in analogy to the principal components and subsequently used in a wt-metadynamics to accelerate the exploration of the conformational space. The resulting free energy surface permitted the identification of a mechanism for the hinge-type motion. In addition to characterizing the dynamics of the isolated hinge peptide, this structural motif was simulated in a protein environment, the four-helix bundle. In the second chapter, the hydrophobic core dynamics of a zinc finger peptide was investigated by a combination of experimental and theoretical methods. Structure calculations and MD simulations revealed a restricted rotation of the central phenylalanine around χ2, which nevertheless allowed the formation of an AA'BB'C spin system in the NMR spectra. In order to accurately describe the orientation of the phenyl in the hydrophobic core, tolyl/xylyl derivatives were synthesized that led to a symmetry breaking of the degenerate rotation. This methyl hopping around the aromatic ring highlighted that ε-substitutions led to a single orientation, while modifications on the δ-position allowed a restricted rotation. The energy profile was again obtained by metadynamics and is in good agreement with the experimental results. Finally, the dynamics of β,β-diaryl-α-amino acids hybrids was investigated. NMR spectroscopy provided evidence for a dependent rotation of the side chains the so-called gearing. The combination of MD simulation and metadynamics revealed an increase in the energy barrier compared to the corresponding natural amino acid precursors, but the low interlocking of the aromatic rings prevented continuous gearing. Instead, gear slip was identified as the dominant form of motion. Based on ab initio calculations, substitution patterns within the side chain were postulated that not only feature adequate energy barriers and interlocking suitable for gearing but would also be synthetically accessible. The present work provides significant contributions for the characterization of correlated dynamics of bioorganic systems and thus extends the foundation for targeted design of structural motifs.