Polypeptide Chain Growth Mechanisms and Secondary Structure Formation in Glycine Gas-Phase Deposition on Silica Surfaces

Abstract

Peptide formation by amino acids condensation represents a crucial reaction in the quest of the origins of life as well as in synthetic chemistry. However, it is still poorly understood in terms of efficiency and reaction mechanism. In the present work, peptide formation has been investigated through thermal condensation of gas-phase glycine in fluctuating silica environments as a model of prebiotic environments. In-situ IR spectroscopy measurements under a controlled atmosphere reveal that a humidity fluctuating system subjected to both temperature and water activity variations results in the formation of more abundant peptides compared to a dehydrated system subjected only to temperature fluctuations cycles. A model is proposed in which hydration steps result in the hydrolysis and redistribution of the oligomers formed during previous deposition in dry conditions. This results in the formation of self-assembled aggregates with well-defined secondary structures (especially β-sheets). Upon further monomers feeding, structural elements are conserved in newly growing chains, with indications of templated polymerization. The structural dynamics of peptides were also evaluated. Rigid self-assembled structures with a high resistance to further wetting/drying cycles and inaccessibility to isotopic exchange were present in the humidity fluctuating system compared to more flexible structures in the dehydrated system. The resistance and growth of self-assembled structures were also investigated for an extended duration of Gly deposition using isotope labeling.

Cyclic or Linear? Parameters Determining the Outcome of Glycine Polymerization in Silica Surface Prebiotic Scenarios

“…Intermediate steps of 2.5 h Gly CVD were applied in a specific IR cell for in situ measurements, as described in our previously published papers (Figure S4). [37,38] The results obtained in this setting are coherent with those obtained after ex situ thermal treatments and displayed in Figure 3. In particular, amide I, amide II, amide A bands and surface esters progressively increase during the 20 h CVD on A50, either untreated (Figure S4, panel A) or precalcined at 450 °C (Figure S4, panel B).…”

“…These observations are in line with previously observed behavior on the support A50. [37][38][39] However, when the A50 and A200 silicas were calcined at 700 °C (G/A50 (700) and G/A200 (700) ; Figure 3, Panel A and B respectively, curves c), the amide I and amide II bands after 20 h CVD exhibited a significant decrease with respect to supports pretreated at lower temperatures and the band related to the surface esters disappeared. Thus, high-temperature pretreatment somehow "quenches" glycine polymerization reactivity on both samples.…”

“…In contrast, silanol densities in the 1.4 to 2.7 range seem favorable for linear peptide formation; samples with such densities include the pristine A50, which was used in our previous studies. [14,37,38] Gas-phase glycine can be grafted on these surfaces, forming ester groups, and rather long linear peptides grow from these over several tens of hours at 160 °C. Finally, on the sample with the highest density of silanols (A380 (rt) , 4.5 nm À 2 ), a large amount of DKP is formed (this is still observed on A380 (450) , with 2 silanols nm À 2 ).…”

Controlling Solvent Polarity to Regulate Protein Self-Assembly Morphology and Its Universal Insight for Fibrillation Mechanism

“…Therefore, the addition of excess ethanol reduced the polarity of the aqueous solution and thus inhibited the unfolding and hydrolysis of proteins, which in turn caused a decrease in the hydrophobic interactions between proteins in the solution. 25 39,53 Among them, the amide I band is the most sensitive to the secondary structures of proteins and is commonly used to analyze the secondary structure changes of proteins. 54 The change in the broad peak of 3400−3200 cm −1 (amide A, from the stretching vibration of N−H) indicates the formation of hydrogen bonds in the proteins that are actually in selfassembled aggregates, 29,55,56 and that of the 3000−2800 cm −1 peak (amide B, from the stretching vibration of C−H) is associated with the hydrophobic interaction formed between the methyl groups (−CH 3 ).…”

“…Each spectrum was scanned 512 times with 4 cm –1 resolution in the wavenumber range of 4000–500 cm –1 . The peaks in the FTIR spectra with a high wavenumber ranging from 4000 to 2500 cm –1 were used to investigate the molecular interactions in the protein samples, including the hydrophobic interaction and hydrogen bonding, while the band from 1700 to 1600 cm –1 refers to the amide I band, which is a characteristic band of peptides and proteins and was used to analyze the secondary structures of the protein samples by calculating the second-order derivative of the peaks . The area at different wavenumbers obtained by the second derivative fitting was used to calculate the proportion of secondary structures in the formed protein self-assembly structures.…”