On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins

Abstract

Asparagine (Asn) is a powerful turn-inducer residue, with a large propensity to occupy the second position in the central region of β-turns of proteins. The present work aims at investigating the role of a local anchoring between the Asn side chain and the main chain in this remarkable property. For this purpose, the H-bonding patterns of an asparagine residue in an isolated protein chain fragment forming a γ- or a β-turn have been determined using IR/UV double resonance gas phase spectroscopy on laser-desorbed, jet-cooled short models in conjunction with relevant quantum chemistry calculations. These gas phase data provide evidence for an original double anchoring linking the Asn primary amide side chain (SC), which adopts a gauche+ rotameric form, to its main chain (MC) local environment. From both IR spectroscopic evidence (H-bond induced red shifts) and quantum chemistry, Asn SC is found to behave as a stronger H-bond acceptor than donor, resulting in stronger MC→SC H-bonds than SC→MC ones. These gas phase structural data, relevant to a hydrophobic environment, have been used as a reference to assess the anchoring taking place in high resolution crystallized proteins of the Protein Data Bank. This approach reveals that, when the SC adopts a gauche+ orientation, the stronger MC→SC bonds are preserved in many cases whereas the SC→MC bonds are always disrupted, in qualitative agreement with the gas phase ranking of these interactions. Most interestingly, when Asn occupies the second position of central part of a β-turn (i.e., the very turn-inducer position), the MC→SC H-bonds are also disrupted and replaced by a water-mediated SC to MC anchoring. Owing to the specific features of the hydrated Asn side chain, we propose that it could be a turn precursor structure, able to facilitate turn formation in the early events of the folding process.

Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues

“…The bbSC H-bonds (6  ) are found to be stronger than the SCbb bonds (cf. Table 6, Section 6), in agreement with both the spectral shifts 82 and the calculated H-bonding distances. 79,82 With the longer side chain of glutamine, -type folding appears as an exception favoured by extra interactions: in one of the conformers of the Ac-Gln-NHBn molecule, a  H-bond occuring between the Gln side chain amide and the NHBn cap enables the formation of a compact 7  (  8- Bn )-7 network.…”

“…above) are indicated by 'Cn' or simply 'n'; a free NH group is labelled with 'f'; an interaction with a π-system with 'π'. A more complex nomenclature is needed when SCs are involved in H-bonding [77][78][79][80][81][82][83] : the size of the ring formed is again denoted with 'n', but the way the bb/SC nature of the bonding is indicated differs. Some authors simply mention them separately from the previous backbone bonds; [77][78][79] others adopt a more sophisticated nomenclature, 81,82 which enables distinction between a donor or an acceptor SC, the position of the side chain group relative to its α-C-atom being given by Greek letters (e.g.…”

“…It should be noted that the same spectroscopic trick applies to the carboxamide groups of the asparagine and glutamine side chains 77,78,82 , as well as to the N-terminal amino groups of uncapped peptides, although less used in this latter case. ) and one Hbonded, red-shifted (the redshift being taken as a measure of the H-bond strength) are coupled according to a coupling constant independent of the H-bond.…”

Interactions of aggregating peptides probed by IR-UV action spectroscopy

“…17 Studying peptide aggregation under neutral conditions might provide more insights into non-charge driven aggregation interactions, such as dispersion interactions, NH-p and p-p stacking, and intra-and intermolecular hydrogen bond interactions. [23][24][25][26] For example, the p-p interactions are expected to play a directing role by stabilizing the hydrophobic domains crucial for the development of amyloid structures. 24,[27][28][29][30][31] Although cluster formation between (bio)molecules and solvent molecules, such as water or methanol, is rather straightforward by co-expanding the solvent molecules with the seed gas, [32][33][34][35] the formation of aggregates of neutral peptides is not.…”

Interactions of Aggregating Peptides Probed by IR-UV Action Spectroscopy

“…Studying peptide aggregation under neutral conditions might provide more insights into non-charge driven aggregation interactions such as dispersion interactions such as NH-π and π −π stacking, and intra-and intermolecular hydrogen bond interactions. [23][24][25][26] As for example, the π −π interactions are expected to play a directing role by stabilizing hydrophobic domains crucial for the development of amyloid structures. 24,[27][28][29][30][31] Although cluster formation between (bio)molecules and solvent molecules such as water or methanol are rather straightforward by co-expanding the solvent molecules with the seed gas [32][33][34][35] , the formation of aggregates of neutral peptides is not.…”