Protonation States of Important Acidic Residues in the Central Ca2+ Ion Binding Sites of the Ca2+-ATPase: A Molecular Modeling Study.
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| Title: | Protonation States of Important Acidic Residues in the Central Ca2+ Ion Binding Sites of the Ca2+-ATPase: A Molecular Modeling Study. |
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| Authors: | Musgaard, Maria1,2, Thøgersen, Lea2,3, Schiøtt, Birgit1,4 birgit@chem.au.dk |
| Source: | Biochemistry. 12/27/2011, Vol. 50 Issue 51, p11109-11120. 12p. |
| Subjects: | Proton transfer reactions, Cell membranes, Cations, Amino acids, Endoplasmic reticulum, Protons |
| Abstract: | The P-type ATPases are responsible for the transport of cations across cell membranes. The sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions from the cytoplasm to the lumen of the sarco(endo)plasmic reticulum and countertransports two or three protons per catalytic cycle. Two binding sites for Ca2+ ions have been located via protein crystallography, including four acidic amino acid residues that are essential to the ion coordination. In this study, we present molecular dynamics (MD) simulations examining the protonation states of these amino acid residues in a Ca2+-free conformation of SERCA. Such knowledge will be important for an improved understanding of atomistic details of the transport mechanism of protons and Ca2+ ions. Eight combinations of the protonation of four central acidic residues, Glu309, Glu771, Asp800, and Glu908, are tested from 10 ns MD simulations with respect to protein stability and ability to maintain a structure similar to the crystal structure. The trajectories for the most prospective combinations of protonation states were elongated to 50 ns and subjected to more detailed analysis, including prediction of pKa values of the four acidic residues over the trajectories. From the simulations we find that the combination leaving only Asp800 as charged is most likely. The results are compared to available experimental data and explain the observed destabilization upon full deprotonation, resulting in the entry of cytoplasmic K+ ions into the Ca2+ binding sites during the simulation in which Ca2+ ions are absent. Furthermore, a hypothesis for the exchange of protons from the central binding cavity is proposed. [ABSTRACT FROM AUTHOR] |
| Copyright of Biochemistry is the property of American Chemical Society and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Protonation States of Important Acidic Residues in the Central Ca<superscript>2+</superscript> Ion Binding Sites of the Ca<superscript>2+</superscript>-ATPase: A Molecular Modeling Study. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Musgaard%2C+Maria%22">Musgaard, Maria</searchLink><relatesTo>1,2</relatesTo><br /><searchLink fieldCode="AR" term="%22Thøgersen%2C+Lea%22">Thøgersen, Lea</searchLink><relatesTo>2,3</relatesTo><br /><searchLink fieldCode="AR" term="%22Schiøtt%2C+Birgit%22">Schiøtt, Birgit</searchLink><relatesTo>1,4</relatesTo><i> birgit@chem.au.dk</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Biochemistry%22">Biochemistry</searchLink>. 12/27/2011, Vol. 50 Issue 51, p11109-11120. 12p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Proton+transfer+reactions%22">Proton transfer reactions</searchLink><br /><searchLink fieldCode="DE" term="%22Cell+membranes%22">Cell membranes</searchLink><br /><searchLink fieldCode="DE" term="%22Cations%22">Cations</searchLink><br /><searchLink fieldCode="DE" term="%22Amino+acids%22">Amino acids</searchLink><br /><searchLink fieldCode="DE" term="%22Endoplasmic+reticulum%22">Endoplasmic reticulum</searchLink><br /><searchLink fieldCode="DE" term="%22Protons%22">Protons</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: The P-type ATPases are responsible for the transport of cations across cell membranes. The sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions from the cytoplasm to the lumen of the sarco(endo)plasmic reticulum and countertransports two or three protons per catalytic cycle. Two binding sites for Ca2+ ions have been located via protein crystallography, including four acidic amino acid residues that are essential to the ion coordination. In this study, we present molecular dynamics (MD) simulations examining the protonation states of these amino acid residues in a Ca2+-free conformation of SERCA. Such knowledge will be important for an improved understanding of atomistic details of the transport mechanism of protons and Ca2+ ions. Eight combinations of the protonation of four central acidic residues, Glu309, Glu771, Asp800, and Glu908, are tested from 10 ns MD simulations with respect to protein stability and ability to maintain a structure similar to the crystal structure. The trajectories for the most prospective combinations of protonation states were elongated to 50 ns and subjected to more detailed analysis, including prediction of pKa values of the four acidic residues over the trajectories. From the simulations we find that the combination leaving only Asp800 as charged is most likely. The results are compared to available experimental data and explain the observed destabilization upon full deprotonation, resulting in the entry of cytoplasmic K+ ions into the Ca2+ binding sites during the simulation in which Ca2+ ions are absent. Furthermore, a hypothesis for the exchange of protons from the central binding cavity is proposed. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Biochemistry is the property of American Chemical Society and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1021/bi201164b Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 12 StartPage: 11109 Subjects: – SubjectFull: Proton transfer reactions Type: general – SubjectFull: Cell membranes Type: general – SubjectFull: Cations Type: general – SubjectFull: Amino acids Type: general – SubjectFull: Endoplasmic reticulum Type: general – SubjectFull: Protons Type: general Titles: – TitleFull: Protonation States of Important Acidic Residues in the Central Ca2+ Ion Binding Sites of the Ca2+-ATPase: A Molecular Modeling Study. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Musgaard, Maria – PersonEntity: Name: NameFull: Thøgersen, Lea – PersonEntity: Name: NameFull: Schiøtt, Birgit IsPartOfRelationships: – BibEntity: Dates: – D: 27 M: 12 Text: 12/27/2011 Type: published Y: 2011 Identifiers: – Type: issn-print Value: 00062960 Numbering: – Type: volume Value: 50 – Type: issue Value: 51 Titles: – TitleFull: Biochemistry Type: main |
| ResultId | 1 |
