Presentation Title

COMPUTATIONAL MECHANICAL STUDIES ON E. COLI TYPE-1 PILI ADHESION WITH HOMOGENEOUS SURFACES

Faculty Mentor

Eileen M. Spain

Start Date

17-11-2018 12:30 PM

End Date

17-11-2018 2:30 PM

Location

CREVELING 23

Session

POSTER 2

Type of Presentation

Poster

Subject Area

physical_mathematical_sciences

Abstract

Prior research [Xu, H. et al. Langmuir, 2013, 29 (9), pp 3000–3011] showed that E. coli adhered to distinct, chemically well-characterized homogeneous surfaces at various strengths using atomic force microscopy. In this work, the interactions between the E. coli FimH pili protein and various surfaces are modeled and simulated to understand the chemical mechanisms of the adhesion. Scripps Research Institute’s AutoDock Vina software was used to screen for the optimal binding sites and these data are subsequently used in steered molecular dynamics to replicate Xu et al.’s experiment in silico. From the docking data, we observed major binding sites for fluorosilane, polyethylene glycol, aminosilane, and methyl α-D-mannopyranoside (MADM), and subsequently hypothesized a mechanism of which MADM inhibits fluorosilane adhesion. With these binding conformation data in hand, CHARMM General Force Field data was modified to parameterize physical interactions within the surface ligands. Using a constant force pull in Nanoscale Molecular Dynamics (NAMD) software to simulate a fast-paced version of what happens when E. coli detaches from the surface, mechanisms were observed such that single or multiple strands of the surface detach from the protein. Data generated by steered molecular dynamics experiments were reminiscent of measurements obtained by Xu et al., particularly the pull-off features. These findings indicated that there was accuracy and precision in replicating E. Coli-surface binding in silico, and allowed further step-by-step analysis of these mechanics and processes.

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Nov 17th, 12:30 PM Nov 17th, 2:30 PM

COMPUTATIONAL MECHANICAL STUDIES ON E. COLI TYPE-1 PILI ADHESION WITH HOMOGENEOUS SURFACES

CREVELING 23

Prior research [Xu, H. et al. Langmuir, 2013, 29 (9), pp 3000–3011] showed that E. coli adhered to distinct, chemically well-characterized homogeneous surfaces at various strengths using atomic force microscopy. In this work, the interactions between the E. coli FimH pili protein and various surfaces are modeled and simulated to understand the chemical mechanisms of the adhesion. Scripps Research Institute’s AutoDock Vina software was used to screen for the optimal binding sites and these data are subsequently used in steered molecular dynamics to replicate Xu et al.’s experiment in silico. From the docking data, we observed major binding sites for fluorosilane, polyethylene glycol, aminosilane, and methyl α-D-mannopyranoside (MADM), and subsequently hypothesized a mechanism of which MADM inhibits fluorosilane adhesion. With these binding conformation data in hand, CHARMM General Force Field data was modified to parameterize physical interactions within the surface ligands. Using a constant force pull in Nanoscale Molecular Dynamics (NAMD) software to simulate a fast-paced version of what happens when E. coli detaches from the surface, mechanisms were observed such that single or multiple strands of the surface detach from the protein. Data generated by steered molecular dynamics experiments were reminiscent of measurements obtained by Xu et al., particularly the pull-off features. These findings indicated that there was accuracy and precision in replicating E. Coli-surface binding in silico, and allowed further step-by-step analysis of these mechanics and processes.