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Open AccessArticle

Effect of pH on the Supramolecular Structure of Helicobacter pylori Urease by Molecular Dynamics Simulations

Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, C/Martí i Franquès, 08028 Barcelona, Spain
Centro de Investigación en Ingeniería Molecular–CIIM, Vicerrectorado de Investigación, Universidad Católica de Santa María, Urb. San José s/n Umacollo, Arequipa 04013, Peru
Author to whom correspondence should be addressed.
Polymers 2020, 12(11), 2713;
Received: 28 October 2020 / Revised: 9 November 2020 / Accepted: 11 November 2020 / Published: 17 November 2020
The effect of pH on the supramolecular structure of Helicobacter pylori urease was studied by means of molecular dynamics simulations at seven different pHs. Appropriate urease charge distributions were calculated using a semi-grand canonical Monte Carlo (SGCMC) procedure that assigns each residue’s charge state depending on the assigned individual pKa obtained by PROPKA. The effect of pH on protein stability has been analyzed through root-mean-square deviation (RMSD), radius of gyration (RG), solvent-accessible surface area (SASA), hydrogen bonds (HB) and salt bridges (SB). Urease catalyses the hydrolysis of urea in 12 active sites that are covered by mobile regions that act like flaps. The mobility of these flaps is increased at acidic pHs. However, extreme acidic conditions cause urease to have the least number of stabilizing interactions. This initiates the process of denaturalization, wherein the four (αβ)3 subunits of the global structure ((αβ)3)4 of urease start to separate. View Full-Text
Keywords: molecular dynamics; semi-grand canonical; Monte Carlo; urease molecular dynamics; semi-grand canonical; Monte Carlo; urease
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MDPI and ACS Style

Barazorda-Ccahuana, H.L.; Gómez, B.; Mas, F.; Madurga, S. Effect of pH on the Supramolecular Structure of Helicobacter pylori Urease by Molecular Dynamics Simulations. Polymers 2020, 12, 2713.

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