Naslov
Računalne simulacije interakcija dviju domena autotransporterske esteraze EstA iz bakterije Pseudomonas aeruginosa
(Molecular Dynamics Study of Functionally Relevant Interdomain and Active Site Interactions in the Autotransporter Esterase EstA from Pseudomonas aeruginosa)

Autori
Natalia Mrnjavac

Vrsta, podvrsta i kategorija rada
Ocjenski radovi, diplomski rad, diplomski

Fakultet
Prirodoslovno-matematički fakultet

Mjesto
Zagreb

Datum
27.04

Godina
2015

Stranica
76

Mentor
Branimir Bertoša

Ključne riječi
GDSL hidrolaze ; katalitička domena ; autotransporterska domena ; molekulska dinamika
(GDSL hydrolases ; passenger domain ; autotransporter domain ; molecular dynamics)

Sažetak
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 theβ 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 catalytic triad and oxyanion hole. Relevant active site residues, including an active site hydrogen bond network, aredescribed in this work.In addition, interdomain hydrogen bonds and hydrophobic interactions arecharacterised. 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 the full length EstA. All results are based on the 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.

Izvorni jezik
Engleski

Znanstvena područja
Kemija, Biologija

POVEZANOST RADA