Search for: All records

ABSTRACT This study focuses on investigating the conformational structure and zinc(II) affinity of a zinc finger‐like motif (ZFM) peptide with the sequence acetyl‐His₁‐Cys₂‐Gly₃‐Pro₄‐Gly₅‐His₆‐Cys₇, where bold highlights the potential zinc(II) binding sites. Zinc fingers are crucial protein motifs known for their high specificity and affinity for zinc ions. The ZFM peptide's sequence contains the 2His‐2Cys zinc‐binding sites similar to those in natural zinc finger proteins but without the hydrophobic core, making it a valuable model for studying zinc(II)–peptide interactions. Previous research on related peptides showed that collision cross sections and B3LYP modeling predicted that the His‐2Cys‐carboxyl terminus coordination of zinc(II) was more stable than the 2His‐2Cys. Employing a comprehensive approach integrating ion mobility–mass spectrometry and theoretical modeling techniques, various zinc(II) binding modes of the ZFM have been thoroughly compared to ascertain their influence on the competitive threshold collision‐induced dissociation method for measuring the relative gas‐phase Zn(II) affinity of the ZFM peptide. The measured Zn(II) affinity of ZFM is greater than those measured recently for two peptides with similar primary structures, acetyl‐His₁‐Cys₂‐Gly₃‐Pro₄‐Gly₅‐Gly₆‐Cys₇and acetyl‐Asp₁‐His₂‐Gly₃‐Pro₄‐Gly₅‐Gly₆‐Cys₇, indicating the preference for the His₁‐Cys₂‐His₆‐Cys₇side groups for coordinating zinc(II) over the His‐2Cys‐carboxyl terminus or Asp‐His‐Cys‐carboxyl terminus in these related heptapeptides. 

Chemical dynamics simulations are performed to study the collision induced gas phase unimolecular fragmentation of a model peptide with the sequence acetyl-His 1 -Cys 2 -Gly 3 -Pro 4 -Tyr 5 -His 6 -Cys 7 (analogue methanobactin peptide-5, amb 5 ) and in particular to explore the role of zinc binding in reactivity. Fragmentation pathways, their mechanisms, and collision energy transfer are discussed. The probability distributions of the pathways are compared with the results of the experimental IM-MS, MS/MS spectrum and previous thermal simulations. Collisional activation gives both statistical and non-statistical fragmentation pathways with non-statistical shattering mechanisms accounting for a relevant percentage of reactive trajectories, becoming dominant at higher energies. The tetra-coordination of zinc changes qualitative and quantitative fragmentation, in particular the shattering. The collision energy threshold for the shattering mechanism was found to be 118.9 kcal mol −1 which is substantially higher than the statistical Arrhenius activation barrier of 35.8 kcal mol −1 identified previously during thermal simulations. This difference can be attributed to the tetra-coordinated zinc complex that hinders the availability of the sidechains to undergo direct collision with the Ar projectile.