NDLI: Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal -helix in an acylaminoacyl peptidase.

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Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal -helix in an acylaminoacyl peptidase.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Papaleo, Elena Renzetti, Giulia
Description	Country affiliation: Italy Author Affiliation: Papaleo E ( Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 20126 Milan, Italy. elena.papaleo@unimib.it)
Abstract	Acylaminoacyl peptidase (AAP) subfamily belongs to the prolyl oligopeptidase (POP) family of serine-proteases. There is a great interest in the definition of molecular mechanisms related to the activity and substrate recognition of these complex multi-domain enzymes. The active site relies at the interface between the C-terminal catalytic domain and the ß-propeller domain, whose N-terminal region acts as a bridge to the hydrolase domain. In AAP, the N-terminal extension is characterized by a structurally conserved 1-helix, which is known to affect thermal stability and thermal dependence of the catalytic activity. In the present contribution, results from hundreds nanosecond all-atom molecular dynamics simulations, along with analyses of the networks of cross-correlated motions of a member of the AAP subfamily are discussed. The MD investigation identifies a tunnel that from the surrounding of the N-terminal 1-helix bring to the catalytic site. This cavity seems to be regulated by conformational changes of the 1-helix itself during the dynamics. The evidence here provided can be a useful guide for a better understanding of the mechanistic aspects related to AAP activity, but also for drug design purposes.
File Format	HTM / HTML
ISSN	10933263
Volume Number	38
e-ISSN	18734243
Journal	Journal of Molecular Graphics and Modelling
Language	English
Publisher	Elsevier
Publisher Date	2012-09-01
Publisher Place	United States
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Discipline Molecular Biology Aeropyrum Chemistry Archaeal Proteins Molecular Dynamics Simulation Peptide Hydrolases Enzymology Catalytic Domain Databases, Protein Hydrophobic And Hydrophilic Interactions Kinetics Protein Stability Protein Structure, Secondary Protein Structure, Tertiary Static Electricity Temperature Thermodynamics Journal Article Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Computer Graphics and Computer-Aided Design Spectroscopy Materials Chemistry Physical and Theoretical Chemistry

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