Molecular Dynamics Study of Functionally Relevant Interdomain and Active Site Interactions in the Autotransporter Esterase EstA from Pseudomonas aeruginosa

Mrnjavac, Natalia (2015) Molecular Dynamics Study of Functionally Relevant Interdomain and Active Site Interactions in the Autotransporter Esterase EstA from Pseudomonas aeruginosa. Diploma thesis, Faculty of Science > Department of Biology.

[img]
Preview
PDF
Language: English

Download (5MB) | Preview

Abstract

The enzyme EstA is functionally a GDSL esterase. It is transferred through the outer membrane of Pseudomonas aeruginosa by the type Va or autotransporter mechanism, where the transfer of the catalytic domain (the passenger) to the cell exterior is aided by the β barrel domain (the autotransporter). In EstA the barrel remains membrane embedded with the passenger bound to it. The physiological substrate of EstA is unknown, although its activity is known to be related to bacterial cell motility, biofilm formation and rhamnogalacturonan production. As a GDSL hydrolase, the active site of EstA contains a catalytic triad and oxyanion hole. Relevant active site residues, including an active site hydrogen bond network, are described in this work. In addition, interdomain hydrogen bonds and hydrophobic interactions are characterised. Active site opening to fit the tetrahedral intermediate was observed in the isolated passenger domain, while a structural perturbation of the active site helix 6 was noticed when the tetrahedral intermediate was bound in full-length EstA. All results are based on 100 ns long molecular dynamics simulations of the passenger domain of EstA and full-length membrane embedded EstA, both with and without a bound tetrahedral intermediate.

Item Type: Thesis (Diploma thesis)
Keywords: GDSL hydrolases, passenger domain, autotransporter domain, molecular dynamics
Supervisor: Bertoša, Branimir
Date: 2015
Number of Pages: 82
Subjects: NATURAL SCIENCES > Biology
Divisions: Faculty of Science > Department of Biology
Depositing User: Silvana Šehić
Date Deposited: 04 Mar 2016 13:38
Last Modified: 04 Mar 2016 13:38
URI: http://digre.pmf.unizg.hr/id/eprint/4545

Actions (login required)

View Item View Item

Nema podataka za dohvacanje citata