Abstract
Protein dynamics and the underlying networks of intramolecular interactions and communicating residues within the three-dimensional (3D) structure are known to influence protein function and stability, as well as to modulate conformational changes and allostery. Acylaminoacyl peptidase (AAP) subfamily of enzymes belongs to a unique class of serine proteases, the prolyl oligopeptidase (POP) family, which has not been thoroughly investigated yet. POPs have a characteristic multidomain three-dimensional architecture with the active site at the interface of the C-terminal catalytic domain and a β-propeller domain, whose N-terminal region acts as a bridge to the hydrolase domain. In the present contribution, protein dynamics signatures of a hyperthermophilic acylaminoacyl peptidase (AAP) of the prolyl oligopeptidase (POP) family, as well as of a deletion variant and alanine mutants (I12A, V13A, V16A, L19A, I20A) are reported. In particular, we aimed at identifying crucial residues for long range communications to the catalytic site or promoting the conformational changes to switch from closed to open ApAAP conformations. Our investigation shows that the N-terminal α1-helix mediates structural intramolecular communication to the catalytic site, concurring to the maintenance of a proper functional architecture of the catalytic triad. Main determinants of the effects induced by α1-helix are a subset of hydrophobic residues (V16, L19 and I20). Moreover, a subset of residues characterized by relevant interaction networks or coupled motions have been identified, which are likely to modulate the conformational properties at the interdomain interface.
Highlights
The current scenario on enzyme function and mechanisms reveals that conformational dynamics is indispensable for protein function, as well as that conformational transitions can involve mechanisms of conformational selection and induced fit, which can be considered as a special case in the catalytic network [1]
We focus our attention on protein dynamics signatures of acylaminoacyl peptidase (AAP), which belong to the prolyl oligopeptidase (POP) family [28]
In silico alanine Scanning and Networks of Hydrophobic Interactions of the N-terminal a1-helix Residues Support a Role for Hydrophobic Interactions in Mediating Intramolecular Communication and Protein Stability a1-helix has been demonstrated crucial for ApAAP structure and stability, even if the mutations of its charged residues alone did not mimic the deletion of the whole a1-helix, as demonstrated by Feng’s group [32], suggesting that the determinants of the effects transmitted by the a1-helix has to be found in other interactions that the helix can exploit
Summary
The current scenario on enzyme function and mechanisms reveals that conformational dynamics is indispensable for protein function, as well as that conformational transitions can involve mechanisms of conformational selection and induced fit, which can be considered as a special case in the catalytic network [1]. In light of the above observations, the present contribution, by in silico alanine scanning, hundreds nanoseconds all-atom molecular dynamics (MD) simulations of wild type, deleted and mutant ApAAP variants (Table 1), provides a description of coupled motions and networks of intramolecular interactions and their dynamical communications, with particular attention to the Nterminal a1-helix and other interdomain interface regions.
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