Effects of Secondary Structure on Solid-State Hydrogen-Deuterium Exchange in Model α-Helix and β-Sheet Peptides

The effects of peptide secondary structure on the rate and extent of deuterium incorporation in solid-state hydrogen deuterium exchange mass spectrometry (ssHDX-MS) were assessed. Unstructured poly-d,l-alanine (PDLA) peptides, an α-helical model peptide (peptide A) and a β-sheet model peptide (peptide B), were co-lyophilized with various excipients. Peptide structures were confirmed in solution using circular dichroism (CD) spectroscopy and in the solid state with Fourier transform infrared (FTIR) spectroscopy. ssHDX-MS was conducted at two relative humidities (11 and 23% RH D₂O) and deuterium uptake kinetics were monitored over 10 days. The relative contributions of peptide secondary structure and matrix interactions to deuteration incorporation were evaluated by comparing the ssHDX-MS kinetic data of peptide A and peptide B with PDLA of similar molecular weight. The results demonstrate that both peptide secondary structure and interactions with the solid matrix contribute to the protection from exchange in ssHDX-MS. A quantitative data analysis and interpretation method is presented, in which the number of protected amide bonds is calculated as the difference between the maximum deuterium incorporation in solution and in solid samples.