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1,2-Dichloroethane in Haloalkane Dehalogenase Protein and in Water Solvent: A Case Study of the Confinement Effect on Structural and Dynamical Properties
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).ORCID iD: 0000-0003-0185-5724
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).ORCID iD: 0000-0002-1763-9383
2009 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 11, 3257-3263 p.Article in journal (Refereed) Published
Abstract [en]

The structural and dynamical properties of an individual molecule is much affected by changes in a surrounding solvent or protein environment. The focus of the present study is to investigate such changes between proteins and solvents, using as an illustrating example the structure and dynamics of 1,2-dichloroethane (DCE) within haloalkane dehalogenase (HAD) as protein and within water as solvent. We have studied DCE within HAD using Car-Parrinello molecular dynamics calculations in a quantum mechanics/molecular mechanics set-up. We find that the C-Cl bond length is shorter in HAD when compared to solution phase value, whereas the net atomic charges and dipole moment are significantly larger than the solution phase values. In contradiction to the usual trend that molecules in the vicinity of the proteins are less polar, we report the observation that the protein environment indeed polarizes the DCE solute more than the water solvent. Furthermore, within the protein environment we do not observe any conformational transition between gauche and trans conformers, and the DCE remains in the more polar gauche conformer during the entire simulation time scale. However, the trans conformer interconverts to the gauche conformer spontaneously within 0.4 ps, which clearly indicates that the trans conformer is unstable within the HAD protein. In contrast, the scatter diagram of total Kohn-Sham energy and dihedral angle between Cl-C-C-Cl atoms shows that the gauche and trans conformers have comparable energies in water. Overall, the present calculations show the within the protein not only the structure of DCE is altered but also that the conformational interconversion dynamics is affected very much. To investigate the confinement effect on the conformational equilibrium, we have also carried out force-field molecular dynamics calculations which show that the population of trans conformer is significantly lower within the protein when compared to that in water solvent.

Place, publisher, year, edition, pages
2009. Vol. 113, no 11, 3257-3263 p.
Keyword [en]
nucleophilic-substitution reaction, xanthobacter-autotrophicus gj10, molecular-dynamics, crystal-structure, biological water, aqueous-solution, dependence, density, femtosecond, simulations
National Category
Chemical Sciences
URN: urn:nbn:se:kth:diva-18239DOI: 10.1021/jp808647cISI: 000264111200001ScopusID: 2-s2.0-65249110484OAI: diva2:336285

QC 20100525

Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2013-03-14Bibliographically approved

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Natarajan Arul, MuruganÅgren, Hans
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Theoretical Chemistry (closed 20110512)
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