Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation.

PloS One
Elena PapaleoMatteo Tiberti

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 cata...Continue Reading

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Citations

Apr 8, 2014·Journal of Chemical Information and Modeling·Matteo TibertiElena Papaleo
May 25, 2013·PLoS Computational Biology·Wei HuangFareed Aboul-ela
Jun 23, 2012·Journal of Chemical Information and Modeling·Marco PasiElena Papaleo
Jun 19, 2012·Physical Chemistry Chemical Physics : PCCP·Elena PapaleoLuca De Gioia
Mar 21, 2015·International Journal of Molecular Sciences·Hanyong JinWeiwei Han
Jan 8, 2016·Chemical Reviews·Andre A S T Ribeiro, Vanessa Ortiz
Apr 27, 2013·Chemical Reviews·Artur GoraJiri Damborsky
Nov 18, 2015·Journal of Chemical Theory and Computation·Matteo TibertiElena Papaleo
Sep 5, 2014·PLoS Computational Biology·Gaetano InvernizziElena Papaleo
Jan 30, 2016·BMC Bioinformatics·Yasaman KaramiAlessandra Carbone
Feb 27, 2017·BMC Systems Biology·Dimos KapetisUNKNOWN PROPANE Study Group
Dec 27, 2016·Frontiers in Molecular Biosciences·Mads NygaardElena Papaleo
Mar 12, 2015·Acta Crystallographica. Section D, Biological Crystallography·Dóra Karancsiné MenyhárdVeronika Harmat
Apr 14, 2021·The Journal of Physical Chemistry. B·Valentina SoraElena Papaleo
Jan 22, 2013·Biophysical Journal·Jiongjia ChengAnne Gershenson

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Methods Mentioned

BETA
nuclear magnetic resonance
NMR
X-ray
PCA
electron microscopy

Software Mentioned

DCCM
Mutant
Protorp
PoPMuSiC
DSSP
GROMACS
FoldX
PSN
PIC
FlexServ

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