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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.

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Related in: MedlinePlus

The different orientations of the periplasmic loop. a UreI at pH 2.0 and a zoom to the trapped conformation, facing the adjacent chain against clockwise. b Conformation of UreI at pH 6.0 and enlargement of the conformation observed related to the movement of PL1 loop toward PL2 (c) Orientation of PL1 loop at pH 7.4. It is observed that the PL1 loop loses coherence within the system, showing no pattern in their orientation. At the right, the covariance values are annoted for each pair of conditions
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Fig2: The different orientations of the periplasmic loop. a UreI at pH 2.0 and a zoom to the trapped conformation, facing the adjacent chain against clockwise. b Conformation of UreI at pH 6.0 and enlargement of the conformation observed related to the movement of PL1 loop toward PL2 (c) Orientation of PL1 loop at pH 7.4. It is observed that the PL1 loop loses coherence within the system, showing no pattern in their orientation. At the right, the covariance values are annoted for each pair of conditions

Mentions: Different changes can be seen in the structure of the hpUreI system that is mainly involved in the movement of the periplasmic loops, especially in the periplasmic loop PL1 (Fig. 2). The PL1 loop at pH 2.0 is in a "trapped" like conformation towards the interior of the complex, and adjacent to the next subunit in a counter clockwise direction (Fig. 2a). This, in comparison to the structure at pH 6.0, shows a release of this trapped conformation of PL1, now oriented towards the PL2 loop of the same subunit (Fig. 2b). In contrast, the structure at pH 7.4 shows no coherence between each of the subunits, where further analyses are required (Fig. 2c). In order to evidence how these variables change in concordance with one each other, we decide to make covariance analysis between pair of conditions. The calculate values of covariance between pH2 and pH6 (covariance = −10.2) and the pH6 and pH7 pair (covariance = −1.41), presents a negative value, suggesting an opposite behaviour, which in our case is related to an open or a closed state of the channel given by the distance between periplasmic loops. It is interesting to see that the value of covariance between pH2 and pH7 presents a positive sign (covariance = 4.1) that might be interpreted as a similar behaviour in both conditions, suggesting that in both condition an open conformation exists.Fig. 2


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)

The different orientations of the periplasmic loop. a UreI at pH 2.0 and a zoom to the trapped conformation, facing the adjacent chain against clockwise. b Conformation of UreI at pH 6.0 and enlargement of the conformation observed related to the movement of PL1 loop toward PL2 (c) Orientation of PL1 loop at pH 7.4. It is observed that the PL1 loop loses coherence within the system, showing no pattern in their orientation. At the right, the covariance values are annoted for each pair of conditions
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: The different orientations of the periplasmic loop. a UreI at pH 2.0 and a zoom to the trapped conformation, facing the adjacent chain against clockwise. b Conformation of UreI at pH 6.0 and enlargement of the conformation observed related to the movement of PL1 loop toward PL2 (c) Orientation of PL1 loop at pH 7.4. It is observed that the PL1 loop loses coherence within the system, showing no pattern in their orientation. At the right, the covariance values are annoted for each pair of conditions
Mentions: Different changes can be seen in the structure of the hpUreI system that is mainly involved in the movement of the periplasmic loops, especially in the periplasmic loop PL1 (Fig. 2). The PL1 loop at pH 2.0 is in a "trapped" like conformation towards the interior of the complex, and adjacent to the next subunit in a counter clockwise direction (Fig. 2a). This, in comparison to the structure at pH 6.0, shows a release of this trapped conformation of PL1, now oriented towards the PL2 loop of the same subunit (Fig. 2b). In contrast, the structure at pH 7.4 shows no coherence between each of the subunits, where further analyses are required (Fig. 2c). In order to evidence how these variables change in concordance with one each other, we decide to make covariance analysis between pair of conditions. The calculate values of covariance between pH2 and pH6 (covariance = −10.2) and the pH6 and pH7 pair (covariance = −1.41), presents a negative value, suggesting an opposite behaviour, which in our case is related to an open or a closed state of the channel given by the distance between periplasmic loops. It is interesting to see that the value of covariance between pH2 and pH7 presents a positive sign (covariance = 4.1) that might be interpreted as a similar behaviour in both conditions, suggesting that in both condition an open conformation exists.Fig. 2

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