Limits...
Molecular Dynamics Study of Helicobacter pylori Urease.

Minkara MS, Ucisik MN, Weaver MN, Merz KM - J Chem Theory Comput (2014)

Bottom Line: Chem.An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products.Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, University of Florida , Gainesville, Florida 32611-8435, United States.

ABSTRACT
Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc. 2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine α322 residue were used to characterize flap motion. An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products. Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.

No MeSH data available.


Related in: MedlinePlus

Positions of the second active site flap (blue),the flap coveringthe active site (red) and the active site.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4020587&req=5

fig6: Positions of the second active site flap (blue),the flap coveringthe active site (red) and the active site.

Mentions: Figure 5 depicts the B factors from theX-ray structure of Ha et al.13 plottedagainst scaled RMSF values for the dimer that adopts the wide-openactive site flap conformation. The RMSF profile matches up quite wellwith the experimental B factors, which supports the reliability ofour molecular dynamics simulation. One of the particularly interestinghigh RMSF regions spanned residues α388−α395 (626–633)and this group of amino acids constitutes the loop portion of whathas been identified as a second mobile flap in the active site region(Figure 6). This flap has a profile similarto the experimental data for inhibitor complexes of B. pasteurii and S. pasteurii reported by Benini and co-workers.16 This flap consists of two α-helices spanningresidues α372−α387 (610–625) and α398−α410(636–648) and the loop portion, just as the flap that coversthe active site. One of the key differences observed in the two flapsduring the MD simulation was that while both α-helices wereobserved to lose α-helical character in the active site coveringflap, the helices are quite rigid in this second flap. This loop isobserved to be highly flexible in each of the 12 αβ dimersover the course of the simulation. This flap is positioned near oneof the vertices that allow direct access of molecules into the hollow,suggesting it may affect entrance into and egress from the internalcavity. While a number of hypotheses are possible we speculate thatthis flap may serve as an entrance/exhaust conduit that allows forthe exit of hydrolysis products from the active site. Analysis ofthe MD trajectory reveals one sodium ion clearly passing through thefirst flap (residues 771–791; α533−α553)and other ions briefly interacting. Due to the large accumulationof sodium ions in the hollow, the low occurrence of Na+ ion interaction with this flap may be a concentration issue andstudies underway with higher ion concentration (Na+ andNH4+) would be better able to support or rejectthe proposed conduit hypothesis.


Molecular Dynamics Study of Helicobacter pylori Urease.

Minkara MS, Ucisik MN, Weaver MN, Merz KM - J Chem Theory Comput (2014)

Positions of the second active site flap (blue),the flap coveringthe active site (red) and the active site.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4020587&req=5

fig6: Positions of the second active site flap (blue),the flap coveringthe active site (red) and the active site.
Mentions: Figure 5 depicts the B factors from theX-ray structure of Ha et al.13 plottedagainst scaled RMSF values for the dimer that adopts the wide-openactive site flap conformation. The RMSF profile matches up quite wellwith the experimental B factors, which supports the reliability ofour molecular dynamics simulation. One of the particularly interestinghigh RMSF regions spanned residues α388−α395 (626–633)and this group of amino acids constitutes the loop portion of whathas been identified as a second mobile flap in the active site region(Figure 6). This flap has a profile similarto the experimental data for inhibitor complexes of B. pasteurii and S. pasteurii reported by Benini and co-workers.16 This flap consists of two α-helices spanningresidues α372−α387 (610–625) and α398−α410(636–648) and the loop portion, just as the flap that coversthe active site. One of the key differences observed in the two flapsduring the MD simulation was that while both α-helices wereobserved to lose α-helical character in the active site coveringflap, the helices are quite rigid in this second flap. This loop isobserved to be highly flexible in each of the 12 αβ dimersover the course of the simulation. This flap is positioned near oneof the vertices that allow direct access of molecules into the hollow,suggesting it may affect entrance into and egress from the internalcavity. While a number of hypotheses are possible we speculate thatthis flap may serve as an entrance/exhaust conduit that allows forthe exit of hydrolysis products from the active site. Analysis ofthe MD trajectory reveals one sodium ion clearly passing through thefirst flap (residues 771–791; α533−α553)and other ions briefly interacting. Due to the large accumulationof sodium ions in the hollow, the low occurrence of Na+ ion interaction with this flap may be a concentration issue andstudies underway with higher ion concentration (Na+ andNH4+) would be better able to support or rejectthe proposed conduit hypothesis.

Bottom Line: Chem.An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products.Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, University of Florida , Gainesville, Florida 32611-8435, United States.

ABSTRACT
Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc. 2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine α322 residue were used to characterize flap motion. An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products. Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.

No MeSH data available.


Related in: MedlinePlus