Applications in Biology
Structural Effects of Posttranslational Modifications
Posttranslational modifications play important roles in biological systems. In the case of polytheonamide B (pTB), which is one of the most heavily posttranslationally modified biomolecules known, the N-methylation of asparagine side chains were found to be crucial to stabilize the unusual β6.3-helical fold by forming an "exoskeleton" [1]. This channel-like function is required for the cytotoxic activity of the natural product. Reversion of the N-methylations led to a complete loss of the helical structure. Comparison with experimental data showed that the order in which the asparagine residues are N-methylated in nature parallels the build-up of the β-helical fold. The N-methylations alter the hydrogen-bonding preferences of the asparagine side chains towards intramolecular hydrogen bonds, which allows the formation of the "exoskeleton". These findings could lead to the establishment of a general strategy to stabilise special (β-)helical conformations of engineered peptides and peptidomimetics.
Effects of Glycans on Protein Structure and Dynamics
Glycosylation involves covalent attachement and trimming of branched oligosaccharids (glycans) at given sites on a glycoprotein. The enzymes facilitating trimming are located in closed cellular compartments in which the protein only spends a limited amount of time. Therefore, site-specific molecular interactions determine accessibility for glycosylation during generally time-limited, i.e., non-equilibrium, enzymatic reactions. In collaboration with the group of Markus Aebi, we studied protein disulfide isomerase (PDI) as a model protein with extensive MD simulations to investigate how glycans influence a glyco-protein’s flexibility and function, and which molecular interactions affect a generally site-specific glycosylation [2]. Conformational clustering revealed that glycans reduce PDI flexibility and stabilize the functional conformations of the protein. Our results confirm an interplay of glycosylation and protein architecture, indicating that glycans have a crucial functional role. The atomistic insights provided by MD simulations can be used to elucidate this role, but special care has to be taken regarding the choice of force field and water model [3].
[2] external pageMathew, Weiss, et al., RSC Chem. Biol. (2021), 2, 917.call_made
[3] external pageWeiss et al., J. Phys. Chem. B (2021), 125, 9467.call_made
Thermal Stability of Collagen Model Peptides
In collaboration with the group of Helma Wennemers, we studied the effect of different stuctural modifications on the thermal stability of collagen model peptides (CMP). In Ref. [4], we investigated two cross-links that differed only by the configuration of one stereocenter. The stark differences in thermal stability could be traced backed to different steric demands of the linkers. When alkyl chains are attached to the collagen strains, the thermal unfolding of the collagen triple helix is affected, influenced by unsaturation degree and chain length [5]. The MD simulations combined with experimental data indicate that the hydrophobic chains stabilize the collagen structure by interaction with the grooves of the triple helix and accelerate the folding and unfolding process by creating a molten globule-like intermediate.
[4] external pageHentzen et al., J. Am. Chem. Soc. (2017), 139, 12815.call_made
[5] external pageEgli et al., J. Am. Chem. Soc. (2021), 143, 5937.call_made
CMPs are composed of proline−hydroxyproline−glycine (POG) repeat units. Little attention has been paid so far to the effects arising from their terminal residues (i.e., P, O, or G). A combination of thermal denaturation, circular dichroism and NMR measurements, and MD simulations revealed that the stability differences between frame-shifted CMPs originate from the propensity of the peptide termini to preorganize into a polyproline-II helical structure [6]. A follow-up study on the effects of capping and pH on the thermal stability of the frame-shifted CMPs showed that these individual contributions are additive and allow for the prediction of the melting temperatures of CMP trimers [7].
[6] external pageFiala et al., J. Am. Chem. Soc. (2022), 144, 18642.call_made
[7] external pageFiala et al., Angew. Chem. Int. Ed. (2022), 62, e202214728.call_made