Limits...
Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics study.

Cáceres-Delpiano J, Teneb J, Mansilla R, García A, Salas-Burgos A - BMC Struct. Biol. (2015)

Bottom Line: We found different pH-dependent conformations of the urea transporter UreI from Helicobacter pylori, which are related to salt-bridge interactions in the periplasmic regions.The behaviour of every channel in the system is not independent, given the existance of a cooperative behaviour through the formation of salt-bridges between the subunits of the hexameric system.We believe that our results will be related to the generation of new eradication therapies using this transporter as an attractive target, denoting that the knowledge of the possible pH-dependent conformations adopted for this transporter are important for the development of rational drug design approximations.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology, School of Sciences, University of Concepción, Concepción, Chile. jcdelpiano@gmail.com.

ABSTRACT

Background: Helicobacter pylori is an important factor in the development of diseases such as ulcer and gastric cancer. This bacterium uses a periplasmic transporter, UreI, to deliver urea to the intracelullar space, where later it is transformed into ammonia by the cytoplasmic enzyme urease to survive the acidic condition of the human stomach. The UreI transporter presents a pH-dependent activity, where this pH-dependence remains unknown at a structural level. Althought the existance of several protonable residues in the periplasmic loops are related to the pH-dependent activity, we find interesting to have a clear view of the conformational changes involved in this phenomena through a molecular dynamic study.

Results: Molecular dynamic simulations of the UreI transporter at three different pH conditions were performed, revealing two main pH-dependent conformations, which we present as the open and close states. We find that salt bridges between the periplasmic loops are crucial interactions that stabilize these conformations. Besides, a cooperative behaviour exists between the six subunits of the system that is necessary to fulfill the activity of this transporter.

Conclusions: We found different pH-dependent conformations of the urea transporter UreI from Helicobacter pylori, which are related to salt-bridge interactions in the periplasmic regions. The behaviour of every channel in the system is not independent, given the existance of a cooperative behaviour through the formation of salt-bridges between the subunits of the hexameric system. We believe that our results will be related to the generation of new eradication therapies using this transporter as an attractive target, denoting that the knowledge of the possible pH-dependent conformations adopted for this transporter are important for the development of rational drug design approximations.

Show MeSH

Related in: MedlinePlus

Schematic representation of salt bridges. a Possible interaction between intra-loop residues and inter-chain residues at pH 2.0. b Interactions between inter-loop residues and inter-chain residues at pH 6.0. Red dashed lines represent which residues are interacting. The figures were rendered with the visualization software PyMol
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4482100&req=5

Fig3: Schematic representation of salt bridges. a Possible interaction between intra-loop residues and inter-chain residues at pH 2.0. b Interactions between inter-loop residues and inter-chain residues at pH 6.0. Red dashed lines represent which residues are interacting. The figures were rendered with the visualization software PyMol

Mentions: Based on the hypothesis of a possible interaction between the periplasmic loops, measuring of the distance between the periplasmic loops for every subunit of the full system will give us a quantitative view (Fig. 4), compare to the qualitative view in Fig. 3. The chosen residues were His70 for PL1 and Asp30 for PL2. Average values for the distance on every subunit were taken and graphed as shown (Fig. 4). The results are consistent with the expected for all simulations showing at pH 2.0 the average distance is ~27 Å, which is ~15 Å greater than the system at pH 6.0. These differences are also statistically significant, showing us that this event is probably due to pH condition, rather than a simple chance. There is no statistical significance difference between the obtained values for pH 7.4 and pH 6.0 simulations. It has to be noted that the behaviour of the system at pH 7.4 is different from others, showing an extreme value for one of the subunits. We interpreted this as a greater flexibility in the loop regions for this condition and to a loss in coherence of the system response against pH changes.Fig. 3


Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics study.

Cáceres-Delpiano J, Teneb J, Mansilla R, García A, Salas-Burgos A - BMC Struct. Biol. (2015)

Schematic representation of salt bridges. a Possible interaction between intra-loop residues and inter-chain residues at pH 2.0. b Interactions between inter-loop residues and inter-chain residues at pH 6.0. Red dashed lines represent which residues are interacting. The figures were rendered with the visualization software PyMol
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4482100&req=5

Fig3: Schematic representation of salt bridges. a Possible interaction between intra-loop residues and inter-chain residues at pH 2.0. b Interactions between inter-loop residues and inter-chain residues at pH 6.0. Red dashed lines represent which residues are interacting. The figures were rendered with the visualization software PyMol
Mentions: Based on the hypothesis of a possible interaction between the periplasmic loops, measuring of the distance between the periplasmic loops for every subunit of the full system will give us a quantitative view (Fig. 4), compare to the qualitative view in Fig. 3. The chosen residues were His70 for PL1 and Asp30 for PL2. Average values for the distance on every subunit were taken and graphed as shown (Fig. 4). The results are consistent with the expected for all simulations showing at pH 2.0 the average distance is ~27 Å, which is ~15 Å greater than the system at pH 6.0. These differences are also statistically significant, showing us that this event is probably due to pH condition, rather than a simple chance. There is no statistical significance difference between the obtained values for pH 7.4 and pH 6.0 simulations. It has to be noted that the behaviour of the system at pH 7.4 is different from others, showing an extreme value for one of the subunits. We interpreted this as a greater flexibility in the loop regions for this condition and to a loss in coherence of the system response against pH changes.Fig. 3

Bottom Line: We found different pH-dependent conformations of the urea transporter UreI from Helicobacter pylori, which are related to salt-bridge interactions in the periplasmic regions.The behaviour of every channel in the system is not independent, given the existance of a cooperative behaviour through the formation of salt-bridges between the subunits of the hexameric system.We believe that our results will be related to the generation of new eradication therapies using this transporter as an attractive target, denoting that the knowledge of the possible pH-dependent conformations adopted for this transporter are important for the development of rational drug design approximations.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology, School of Sciences, University of Concepción, Concepción, Chile. jcdelpiano@gmail.com.

ABSTRACT

Background: Helicobacter pylori is an important factor in the development of diseases such as ulcer and gastric cancer. This bacterium uses a periplasmic transporter, UreI, to deliver urea to the intracelullar space, where later it is transformed into ammonia by the cytoplasmic enzyme urease to survive the acidic condition of the human stomach. The UreI transporter presents a pH-dependent activity, where this pH-dependence remains unknown at a structural level. Althought the existance of several protonable residues in the periplasmic loops are related to the pH-dependent activity, we find interesting to have a clear view of the conformational changes involved in this phenomena through a molecular dynamic study.

Results: Molecular dynamic simulations of the UreI transporter at three different pH conditions were performed, revealing two main pH-dependent conformations, which we present as the open and close states. We find that salt bridges between the periplasmic loops are crucial interactions that stabilize these conformations. Besides, a cooperative behaviour exists between the six subunits of the system that is necessary to fulfill the activity of this transporter.

Conclusions: We found different pH-dependent conformations of the urea transporter UreI from Helicobacter pylori, which are related to salt-bridge interactions in the periplasmic regions. The behaviour of every channel in the system is not independent, given the existance of a cooperative behaviour through the formation of salt-bridges between the subunits of the hexameric system. We believe that our results will be related to the generation of new eradication therapies using this transporter as an attractive target, denoting that the knowledge of the possible pH-dependent conformations adopted for this transporter are important for the development of rational drug design approximations.

Show MeSH
Related in: MedlinePlus