Next Article in Journal
Quaternized Chitosan-Based Anion Exchange Membrane Composited with Quaternized Poly(vinylbenzyl chloride)/Polysulfone Blend
Previous Article in Journal
Preparation of a Cellulose Column for Enhancing the Sensing Efficiency of the Biocide 2-n-Octyl-4-Isothiazolin-3-One
Previous Article in Special Issue
Predicting Antibody Neutralization Efficacy in Hypermutated Epitopes Using Monte Carlo Simulations
Open AccessArticle

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

1
Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, C/Martí i Franquès, 08028 Barcelona, Spain
2
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; https://doi.org/10.3390/polym12112713
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
Show Figures

Graphical abstract

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.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Search more from Scilit
 
Search
Back to TopTop