Molecular Dynamics Simulations Reveal the Proton:Peptide Coupling Mechanism in the Bacterial Proton-Coupled Oligopeptide Transporter YbgH

Nanda G. Aduri; Marco Montefiori; Ruqaiya Khalil; Michael Gajhede; Flemming Steen Jørgensen; Osman Mirza

doi:10.1021/acsomega.8b02131

Molecular Dynamics Simulations Reveal the Proton:Peptide Coupling Mechanism in the Bacterial Proton-Coupled Oligopeptide Transporter YbgH

Nanda G. Aduri, Marco Montefiori, Ruqaiya Khalil, Michael Gajhede, Flemming Steen Jørgensen, Osman Mirza

Abstract

Proton-coupled oligopeptide transporters (POTs) couple the inward movement of di- or tripeptides with the inward movement of protons. Experimentally, it has been shown that virtually all di- and tripeptides are recognized as substrates, which suggests that it is the backbone of the peptide that determines substrate affinity and specificity. We have previously shown that a conserved E₁XXE₂R motif is involved in the binding of the proton. Although the proposed protonation site is in close proximity to the peptide binding site, the mechanism by which the POTs couple protonation to peptide binding is not understood. Here, we have performed molecular dynamics simulations on the crystal structure of Escherichia coli POT YbgH in the absence and presence of a proton on the consensus E₂ (Glu21) and on both states in the absence and presence of a dipeptide. We observe that the highly conserved Lys118 is able to interact with Glu21 when Glu21 is not protonated but with the dipeptide C-terminus when Glu21 is protonated. Thus, Lys118 provides YbgH with a coupling mechanism sensor that ensures detection of protonation and peptide binding. Furthermore, we observe that the dipeptide initially interacts only with Glu391, with the rest of the peptide being flexible, and becomes stabilized upon interaction with Lys118. This suggests that the peptide binding is a two-step procedure and that the transition from the first to the second step depends upon protonation of Glu21. Finally, we observe occluded conformations of YbgH during the simulations. Most strikingly, in YbgH devoid of peptide, the highly conserved residues Tyr26 and Arg29 interact with Glu391, overlapping with the space that would otherwise be occupied by a bound peptide. This intramolecular substrate mimicry may explain how the apo transporter returns back into the outside-facing conformation.

Originalsprog	Engelsk
Tidsskrift	ACS Omega
Vol/bind	4
Udgave nummer	1
Sider (fra-til)	2040-2046
Antal sider	7
ISSN	2470-1343
DOI	https://doi.org/10.1021/acsomega.8b02131
Status	Udgivet - 25 jan. 2019

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10.1021/acsomega.8b02131Licens: CC BY-NC-ND

acsomega.8b02131Forlagets udgivne version, 4,49 MBLicens: CC BY-NC-ND

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title = "Molecular Dynamics Simulations Reveal the Proton:Peptide Coupling Mechanism in the Bacterial Proton-Coupled Oligopeptide Transporter YbgH",

abstract = "Proton-coupled oligopeptide transporters (POTs) couple the inward movement of di- or tripeptides with the inward movement of protons. Experimentally, it has been shown that virtually all di- and tripeptides are recognized as substrates, which suggests that it is the backbone of the peptide that determines substrate affinity and specificity. We have previously shown that a conserved E1XXE2R motif is involved in the binding of the proton. Although the proposed protonation site is in close proximity to the peptide binding site, the mechanism by which the POTs couple protonation to peptide binding is not understood. Here, we have performed molecular dynamics simulations on the crystal structure of Escherichia coli POT YbgH in the absence and presence of a proton on the consensus E2 (Glu21) and on both states in the absence and presence of a dipeptide. We observe that the highly conserved Lys118 is able to interact with Glu21 when Glu21 is not protonated but with the dipeptide C-terminus when Glu21 is protonated. Thus, Lys118 provides YbgH with a coupling mechanism sensor that ensures detection of protonation and peptide binding. Furthermore, we observe that the dipeptide initially interacts only with Glu391, with the rest of the peptide being flexible, and becomes stabilized upon interaction with Lys118. This suggests that the peptide binding is a two-step procedure and that the transition from the first to the second step depends upon protonation of Glu21. Finally, we observe occluded conformations of YbgH during the simulations. Most strikingly, in YbgH devoid of peptide, the highly conserved residues Tyr26 and Arg29 interact with Glu391, overlapping with the space that would otherwise be occupied by a bound peptide. This intramolecular substrate mimicry may explain how the apo transporter returns back into the outside-facing conformation.",

author = "Aduri, {Nanda G.} and Marco Montefiori and Ruqaiya Khalil and Michael Gajhede and J{\o}rgensen, {Flemming Steen} and Osman Mirza",

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T1 - Molecular Dynamics Simulations Reveal the Proton:Peptide Coupling Mechanism in the Bacterial Proton-Coupled Oligopeptide Transporter YbgH

AU - Aduri, Nanda G.

AU - Montefiori, Marco

AU - Khalil, Ruqaiya

AU - Gajhede, Michael

AU - Jørgensen, Flemming Steen

AU - Mirza, Osman

PY - 2019/1/25

Y1 - 2019/1/25

N2 - Proton-coupled oligopeptide transporters (POTs) couple the inward movement of di- or tripeptides with the inward movement of protons. Experimentally, it has been shown that virtually all di- and tripeptides are recognized as substrates, which suggests that it is the backbone of the peptide that determines substrate affinity and specificity. We have previously shown that a conserved E1XXE2R motif is involved in the binding of the proton. Although the proposed protonation site is in close proximity to the peptide binding site, the mechanism by which the POTs couple protonation to peptide binding is not understood. Here, we have performed molecular dynamics simulations on the crystal structure of Escherichia coli POT YbgH in the absence and presence of a proton on the consensus E2 (Glu21) and on both states in the absence and presence of a dipeptide. We observe that the highly conserved Lys118 is able to interact with Glu21 when Glu21 is not protonated but with the dipeptide C-terminus when Glu21 is protonated. Thus, Lys118 provides YbgH with a coupling mechanism sensor that ensures detection of protonation and peptide binding. Furthermore, we observe that the dipeptide initially interacts only with Glu391, with the rest of the peptide being flexible, and becomes stabilized upon interaction with Lys118. This suggests that the peptide binding is a two-step procedure and that the transition from the first to the second step depends upon protonation of Glu21. Finally, we observe occluded conformations of YbgH during the simulations. Most strikingly, in YbgH devoid of peptide, the highly conserved residues Tyr26 and Arg29 interact with Glu391, overlapping with the space that would otherwise be occupied by a bound peptide. This intramolecular substrate mimicry may explain how the apo transporter returns back into the outside-facing conformation.

AB - Proton-coupled oligopeptide transporters (POTs) couple the inward movement of di- or tripeptides with the inward movement of protons. Experimentally, it has been shown that virtually all di- and tripeptides are recognized as substrates, which suggests that it is the backbone of the peptide that determines substrate affinity and specificity. We have previously shown that a conserved E1XXE2R motif is involved in the binding of the proton. Although the proposed protonation site is in close proximity to the peptide binding site, the mechanism by which the POTs couple protonation to peptide binding is not understood. Here, we have performed molecular dynamics simulations on the crystal structure of Escherichia coli POT YbgH in the absence and presence of a proton on the consensus E2 (Glu21) and on both states in the absence and presence of a dipeptide. We observe that the highly conserved Lys118 is able to interact with Glu21 when Glu21 is not protonated but with the dipeptide C-terminus when Glu21 is protonated. Thus, Lys118 provides YbgH with a coupling mechanism sensor that ensures detection of protonation and peptide binding. Furthermore, we observe that the dipeptide initially interacts only with Glu391, with the rest of the peptide being flexible, and becomes stabilized upon interaction with Lys118. This suggests that the peptide binding is a two-step procedure and that the transition from the first to the second step depends upon protonation of Glu21. Finally, we observe occluded conformations of YbgH during the simulations. Most strikingly, in YbgH devoid of peptide, the highly conserved residues Tyr26 and Arg29 interact with Glu391, overlapping with the space that would otherwise be occupied by a bound peptide. This intramolecular substrate mimicry may explain how the apo transporter returns back into the outside-facing conformation.

UR - http://pubs.acs.org/doi/10.1021/acsomega.8b02131

UR - http://www.mendeley.com/research/molecular-dynamics-simulations-reveal-protonpeptide-coupling-mechanism-bacterial-protoncoupled-oligo

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DO - 10.1021/acsomega.8b02131

M3 - Journal article

SN - 2470-1343

VL - 4

SP - 2040

EP - 2046

JO - ACS Omega

JF - ACS Omega

IS - 1

ER -

Molecular Dynamics Simulations Reveal the Proton:Peptide Coupling Mechanism in the Bacterial Proton-Coupled Oligopeptide Transporter YbgH

Abstract

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