Water-mediated forces between the nucleotide binding domains generate the power stroke in an ABC transporter

Furukawa-Hagiya, Tomoka; Yoshida, Norio; Chiba, Shuntaro; Hayashi, Tomohiko; Furuta, Tadaomi; Saito, Yoshiro; Sakurai, Minoru

doi:10.1016/j.cplett.2014.10.038

Cited by 6 publications

(3 citation statements)

References 33 publications

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“…In other words, a strong attractive force is generated between MalK_A and MalK_B. Recently, we have applied the integral‐equation theory of liquids (3 D‐RISM) to analyze the NBD dimerization process in another ABC transporter (chloride ion channel CFTR) from the viewpoint of thermodynamics and revealed that a long‐range hydration force of enthalpic origin drives the 2 NBDs to approach from a large separation and the origin of short range attraction force is hydration entropy . This mechanism seems to be also applicable to maltose transporter because the amino acid sequence and tertiary structures of the NBDs are conserved well within and between bacterial and eukaryotic ABC transporters …”

Section: Discussionmentioning

confidence: 99%

The mechanism of nucleotide‐binding domain dimerization in the intact maltose transporter as studied by all‐atom molecular dynamics simulations

2017

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The Escherichia coli maltose transporter MalFGK -E belongs to the protein superfamily of ATP-binding cassette (ABC) transporters. This protein is composed of heterodimeric transmembrane domains (TMDs) MalF and MalG, and the homodimeric nucleotide-binding domains (NBDs) MalK . In addition to the TMDs and NBDs, the periplasmic maltose binding protein MalE captures maltose and shuttle it to the transporter. In this study, we performed all-atom molecular dynamics (MD) simulations on the maltose transporter and found that both the binding of MalE to the periplasmic side of the TMDs and binding of ATP to the MalK are necessary to facilitate the conformational change from the inward-facing state to the occluded state, in which MalK is completely dimerized. MalE binding suppressed the fluctuation of the TMDs and MalF periplasmic region (MalF-P2), and thus prevented the incorrect arrangement of the MalF C-terminal (TM8) helix. Without MalE binding, the MalF TM8 helix showed a tendency to intrude into the substrate translocation pathway, hindering the closure of the MalK . This observation is consistent with previous mutagenesis experimental results on MalF and provides a new point of view regarding the understanding of the substrate translocation mechanism of the maltose transporter.

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Section: Discussionmentioning

confidence: 99%

The mechanism of nucleotide‐binding domain dimerization in the intact maltose transporter as studied by all‐atom molecular dynamics simulations

2017

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“…This is because both thermodynamic and configuration integrals upon solvation can be performed analytically within the RISM framework. Due to these features, 1D- and 3D-RISM have been applied to various chemical reactions in solution, − molecular recognition, − ion permeation, , and aggregation. , …”

Section: Introductionmentioning

confidence: 99%

“…Due to these features, 1D-and 3D-RISM have been applied to various chemical reactions in solution, 6−11 molecular recognition, 12−14 ion permeation, 12,15 and aggregation. 16,17 To date, intensive efforts have been devoted to improving the accuracy of RISM methods. Palmer et al found that the error in the SFE of 3D-RISM strongly correlates with the partial molar volume (PMV) of solute molecules, 18 and they proposed the universal correction method using the PMV with empirical parameters.…”

Section: Introductionmentioning

confidence: 99%

Effect of Molecular Orientational Correlations on Solvation Free Energy Computed by Reference Interaction Site Model Theory

Tanimoto

Yoshida

Yamaguchi

et al. 2019

J. Chem. Inf. Model.

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The effect of molecular orientational correlations on the solvation free energy (SFE) of one-dimensional and three-dimensional reference interaction site models (1D-and 3D-RISM) is investigated. The repulsive bridge correction (RBC) and the partial wave (PW) expansion are representative approaches for accounting for the orientational correlation partially lacking in original 1D-and 3D-RISM. The SFEs of 1D-and 3D-RISM for a set of small organic molecules are compared with the simulation results. Accordingly, the SFE expressions, based on RBC and PW, provide more accurate results than those of the uncorrected HNC or KH SFE expressions, which indicates that accounting for molecular orientational dependencies significantly contributes to the improvement of the SFE. The SFE component analysis indicates that the nonpolar component mainly contributes to the correction. The dependence of the error in the RISM SFE on the number of solute sites is examined. In addition, we discuss the differences between 1D-and 3D-RISM through the effect of these corrections.

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Functional Mechanisms of ABC Transporters as Revealed by Molecular Simulations

Furuta

Sakurai

2018

The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery

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Water-mediated forces between the nucleotide binding domains generate the power stroke in an ABC transporter

Cited by 6 publications

References 33 publications

The mechanism of nucleotide‐binding domain dimerization in the intact maltose transporter as studied by all‐atom molecular dynamics simulations

The mechanism of nucleotide‐binding domain dimerization in the intact maltose transporter as studied by all‐atom molecular dynamics simulations

Effect of Molecular Orientational Correlations on Solvation Free Energy Computed by Reference Interaction Site Model Theory

Functional Mechanisms of ABC Transporters as Revealed by Molecular Simulations

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