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The effect of a Pro28Thr point mutation on the local structure and stability of human galactokinase enzyme—a theoretical study

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Abstract

Galactokinase is responsible for the phosphorylation of α-d-galactose, which is an important step in the metabolism of the latter. Malfunctioning of galactokinase due to a single point mutation causes cataracts and, in serious cases, blindness. This paper reports a study of the Pro28Thr point mutation using a variety of theories including molecular dynamics (MD), MM-PBSA/GBSA calculations and AIM analysis. Altered H-bonding networks were detected based on geometric and electron density criteria that resulted in local unfolding of the β-sheet secondary structure. Another consequence was the decrease in stability (5–7 kcal mol−1) around this region, as confirmed by ΔGbind calculations for the extracted part of the whole system. Local unfolding was verified by several other MD simulations performed with different duration, initial velocities and force field. Based on the results, we propose a possible mechanism for the unfolding caused by the Pro28Thr point mutation.

The role of Thr28 and a water molecule in the local unfolding process around the point mutation of human galactokinase

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Abbreviations

MD:

Molecular dynamics

WT:

Wild-type form of galactokinase

MT:

Point-mutated form of galactokinase

GALK:

Galactokinase

WTA:

Chain A of wild-type galactokinase

WTB:

Chain B of wild-type galactokinase

MTA:

Chain A of point-mutated galactokinase

MTB:

Chain B of point-mutated galactokinase

AIM:

Atoms in molecules theory

a.u.:

Atomic unit

bcp:

Bond critical points

PM:

Point mutation

ΔGbind :

Binding free energy

MTA2, MTA3, MTA4, MTA5:

Shorter (6 ns long) MD simulation of the MTA using different initial velocities

n.p.:

Not possible

ΔΔGbind :

Relative binding free energy

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Acknowledgments

This work was supported by “Társadalmi Megújulás Operatív Program” (TÁMOP-4.2.1/B-09/1/KONV-2010-0005). The authors thank M. Labádi for technical support at the High Performance Computing Centre of the University of Szeged. The help of Methos L. Müller in the preparation of the graphics is acknowledged.

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Authors and Affiliations

  1. Department of Chemical Informatics, University of Szeged, Boldogasszony sgt. 6, Szeged, 6725, Hungary

    Balázs Jójárt, Milán Szőri, Róbert Izsák, István Marsi, Imre G. Csizmadia & Béla Viskolcz

  2. Department of Pediatrics, Albert Szent-Györgyi Medical Center, University of Szeged, Korányi fasor 14-15, Szeged, 6725, Hungary

    Aranka László

  3. Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada

    Imre G. Csizmadia

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  1. Balázs Jójárt
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  2. Milán Szőri
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Correspondence to Balázs Jójárt.

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Jójárt, B., Szőri, M., Izsák, R. et al. The effect of a Pro28Thr point mutation on the local structure and stability of human galactokinase enzyme—a theoretical study. J Mol Model 17, 2639–2649 (2011). https://doi.org/10.1007/s00894-011-0958-y

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