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Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin

Soloviov, Maksym and Meuwly, Markus. (2015) Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin. Journal of Chemical Physics, 143 (10). p. 105103.

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Abstract

Multidimensional potential energy surfaces based on reproducing kernel-interpolation are employed to explore the energetics and dynamics of free and bound nitric oxide in myoglobin (Mb). Combining a force field description for the majority of degrees of freedom and the higher-accuracy representation for the NO ligand and the Fe out-of-plane motion allows for a simulation approach akin to a mixed quantum mechanics/molecular mechanics treatment. However, the kernel-representation can be evaluated at conventional force-field speed. With the explicit inclusion of the Fe-out-of-plane (Fe-oop) coordinate, the dynamics and structural equilibrium after photodissociation of the ligand are correctly described compared to experiment. Experimentally, the Fe-oop coordinate plays an important role for the ligand dynamics. This is also found here where the isomerization dynamics between the Fe-ON and Fe-NO state is significantly affected whether or not this co-ordinate is explicitly included. Although the Fe-ON conformation is metastable when considering only the bound (2)A state, it may disappear once the (4)A state is included. This explains the absence of the Fe-ON state in previous experimental investigations of MbNO.
Faculties and Departments:05 Faculty of Science > Departement Chemie > Chemie > Physikalische Chemie (Meuwly)
UniBasel Contributors:Meuwly, Markus
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:AIP Publishing
ISSN:0021-9606
Note:Publication type according to Uni Basel Research Database: Journal article -- The final publication is available at AIP, see DOI link.
Language:English
Identification Number:
Last Modified:07 Dec 2016 15:07
Deposited On:25 Apr 2016 12:16

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