ArticlePloS one2012
Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass.Scientific reports · 2017Article
- Network topology of NaV1.7 mutations in sodium channel-related painful disorders.BMC systems biology · 2017Article
- Dissecting protein architecture with communication blocks and communicating segment pairs.BMC bioinformatics · 2016Article
- The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer.Frontiers in molecular biosciences · 2016Article
- Molecular dynamics simulations of acylpeptide hydrolase bound to chlorpyrifosmethyl oxon and dichlorvos.International journal of molecular sciences · 2015Article
- Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.Frontiers in molecular biosciences · 2015Article
- Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops.PLoS computational biology · 2014Article
- Gates of enzymes.Chemical reviews · 2013Review
- Does changing the predicted dynamics of a phospholipase C alter activity and membrane binding?Biophysical journal · 2013Article
- The impact of a ligand binding on strand migration in the SAM-I riboswitch.PLoS computational biology · 2013Article
- On the role of aggregation prone regions in protein evolution, stability, and enzymatic catalysis: insights from diverse analyses.PLoS computational biology · 2013Article
- Reciprocal influence of protein domains in the cold-adapted acyl aminoacyl peptidase from Sporosarcina psychrophila.PloS one · 2013Article
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3 authors.
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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.
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