Towards Biomimetic Phosphate Recovery: Molecular Dynamics Simulations of Phosphate Binding Proteins

Sigurd Friis Truelsen, Yong Wang, Kresten Lindorff-Larsen, Claus Hélix-Nielsen

Research output: Contribution to journalConference abstract in journalResearchpeer-review

Abstract

Phosphorous is a scarce and biologically-essential resource for sustaining the global food supply. Excess use, however, leads to eutrophication of rivers, lakes and oceans, and harms the natural environment. Thus, it is important to develop technologies for the extraction of phosphorous from e.g. waste water, enabling its reuse while limiting the environmental impact.

Employing highly specialized proteins could provide an efficient and effective starting point to develop a technology for phosphorous recovery. Phosphate Binding Proteins (PBPs) from Escherichia coli have an intrinsically high affinity and selectivity for phosphate over similar compounds such as the toxic arsenate. These properties makes PBPs a prime candidate for phosphate recovery in a biomimetic application. In order to utilize and improve these proteins for practical applications, we need to understand the molecular mechanisms by which these proteins bind and release phosphate.

PBPs have previously been extensively studied by experimental methods, with several identified crystal structures available in both phosphate-bound and unbound conformations. Yet little is known about the dynamical changes that result from binding and release, thus making it difficult to use molecular engineering to control these processes.

We have therefore used molecular dynamics simulations as a tool to probe protein-ligand interactions, and the resulting changes in the structure and dynamics of the PBPs. In particular, we have performed both unbiased and metadynamics-based, enhanced sampling molecular dynamics simulations of a PBP. We have investigated the free-energy landscape of domain-movements, phosphate binding and solvation of the binding pocket. Together with the known crystallographic-states of the protein these simulations provide new insights into the molecular mechanisms by which PBPs recognize, bind and release phosphate ions. With the information gained by this study we look further into various options for bioengineering of the PBPs for phosphate recovery.
Original languageEnglish
Article number297-Pos
JournalBIOPHYSICAL JOURNAL
Volume114
Issue numberIssue 3; Suppl. 1
Pages (from-to)57a
Number of pages1
ISSN0006-3495
DOIs
Publication statusPublished - 2018

Cite this

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title = "Towards Biomimetic Phosphate Recovery: Molecular Dynamics Simulations of Phosphate Binding Proteins",
abstract = "Phosphorous is a scarce and biologically-essential resource for sustaining the global food supply. Excess use, however, leads to eutrophication of rivers, lakes and oceans, and harms the natural environment. Thus, it is important to develop technologies for the extraction of phosphorous from e.g. waste water, enabling its reuse while limiting the environmental impact.Employing highly specialized proteins could provide an efficient and effective starting point to develop a technology for phosphorous recovery. Phosphate Binding Proteins (PBPs) from Escherichia coli have an intrinsically high affinity and selectivity for phosphate over similar compounds such as the toxic arsenate. These properties makes PBPs a prime candidate for phosphate recovery in a biomimetic application. In order to utilize and improve these proteins for practical applications, we need to understand the molecular mechanisms by which these proteins bind and release phosphate.PBPs have previously been extensively studied by experimental methods, with several identified crystal structures available in both phosphate-bound and unbound conformations. Yet little is known about the dynamical changes that result from binding and release, thus making it difficult to use molecular engineering to control these processes.We have therefore used molecular dynamics simulations as a tool to probe protein-ligand interactions, and the resulting changes in the structure and dynamics of the PBPs. In particular, we have performed both unbiased and metadynamics-based, enhanced sampling molecular dynamics simulations of a PBP. We have investigated the free-energy landscape of domain-movements, phosphate binding and solvation of the binding pocket. Together with the known crystallographic-states of the protein these simulations provide new insights into the molecular mechanisms by which PBPs recognize, bind and release phosphate ions. With the information gained by this study we look further into various options for bioengineering of the PBPs for phosphate recovery.",
author = "Truelsen, {Sigurd Friis} and Yong Wang and Kresten Lindorff-Larsen and Claus H{\'e}lix-Nielsen",
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language = "English",
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Towards Biomimetic Phosphate Recovery: Molecular Dynamics Simulations of Phosphate Binding Proteins. / Truelsen, Sigurd Friis; Wang, Yong; Lindorff-Larsen, Kresten; Hélix-Nielsen, Claus.

In: BIOPHYSICAL JOURNAL, Vol. 114, No. Issue 3; Suppl. 1, 297-Pos, 2018, p. 57a.

Research output: Contribution to journalConference abstract in journalResearchpeer-review

TY - ABST

T1 - Towards Biomimetic Phosphate Recovery: Molecular Dynamics Simulations of Phosphate Binding Proteins

AU - Truelsen, Sigurd Friis

AU - Wang, Yong

AU - Lindorff-Larsen, Kresten

AU - Hélix-Nielsen, Claus

PY - 2018

Y1 - 2018

N2 - Phosphorous is a scarce and biologically-essential resource for sustaining the global food supply. Excess use, however, leads to eutrophication of rivers, lakes and oceans, and harms the natural environment. Thus, it is important to develop technologies for the extraction of phosphorous from e.g. waste water, enabling its reuse while limiting the environmental impact.Employing highly specialized proteins could provide an efficient and effective starting point to develop a technology for phosphorous recovery. Phosphate Binding Proteins (PBPs) from Escherichia coli have an intrinsically high affinity and selectivity for phosphate over similar compounds such as the toxic arsenate. These properties makes PBPs a prime candidate for phosphate recovery in a biomimetic application. In order to utilize and improve these proteins for practical applications, we need to understand the molecular mechanisms by which these proteins bind and release phosphate.PBPs have previously been extensively studied by experimental methods, with several identified crystal structures available in both phosphate-bound and unbound conformations. Yet little is known about the dynamical changes that result from binding and release, thus making it difficult to use molecular engineering to control these processes.We have therefore used molecular dynamics simulations as a tool to probe protein-ligand interactions, and the resulting changes in the structure and dynamics of the PBPs. In particular, we have performed both unbiased and metadynamics-based, enhanced sampling molecular dynamics simulations of a PBP. We have investigated the free-energy landscape of domain-movements, phosphate binding and solvation of the binding pocket. Together with the known crystallographic-states of the protein these simulations provide new insights into the molecular mechanisms by which PBPs recognize, bind and release phosphate ions. With the information gained by this study we look further into various options for bioengineering of the PBPs for phosphate recovery.

AB - Phosphorous is a scarce and biologically-essential resource for sustaining the global food supply. Excess use, however, leads to eutrophication of rivers, lakes and oceans, and harms the natural environment. Thus, it is important to develop technologies for the extraction of phosphorous from e.g. waste water, enabling its reuse while limiting the environmental impact.Employing highly specialized proteins could provide an efficient and effective starting point to develop a technology for phosphorous recovery. Phosphate Binding Proteins (PBPs) from Escherichia coli have an intrinsically high affinity and selectivity for phosphate over similar compounds such as the toxic arsenate. These properties makes PBPs a prime candidate for phosphate recovery in a biomimetic application. In order to utilize and improve these proteins for practical applications, we need to understand the molecular mechanisms by which these proteins bind and release phosphate.PBPs have previously been extensively studied by experimental methods, with several identified crystal structures available in both phosphate-bound and unbound conformations. Yet little is known about the dynamical changes that result from binding and release, thus making it difficult to use molecular engineering to control these processes.We have therefore used molecular dynamics simulations as a tool to probe protein-ligand interactions, and the resulting changes in the structure and dynamics of the PBPs. In particular, we have performed both unbiased and metadynamics-based, enhanced sampling molecular dynamics simulations of a PBP. We have investigated the free-energy landscape of domain-movements, phosphate binding and solvation of the binding pocket. Together with the known crystallographic-states of the protein these simulations provide new insights into the molecular mechanisms by which PBPs recognize, bind and release phosphate ions. With the information gained by this study we look further into various options for bioengineering of the PBPs for phosphate recovery.

U2 - 10.1016/j.bpj.2017.11.364

DO - 10.1016/j.bpj.2017.11.364

M3 - Conference abstract in journal

VL - 114

SP - 57a

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - Issue 3; Suppl. 1

M1 - 297-Pos

ER -