Applications of molecular modeling to flavoproteins

Insights and challenges

Emil Sjulstok, Ilia A. Solov'yov, Peter L. Freddolino*

*Kontaktforfatter for dette arbejde

Publikation: Bidrag til bog/antologi/rapport/konference-proceedingBidrag til bog/antologiForskningpeer review

Resumé

The general field of molecular simulation provides a wide spectrum of methods for studying the structure and function of biomolecules. Depending on the scale and question of interest, appropriate approaches may range from ab initio quantum mechanical calculations (when detailed aspects of and changes in electronic structure must be considered) to Brownian dynamics and coarse-grained molecular dynamics (to track large scale conformational motions, diffusion, and inter-molecular interactions). The entire range of molecular simulation methods has been fruitfully applied to a range of flavoenzymes, allowing researchers to address everything from the specific intermediates involved in the photoreactions of flavin chromophore-containing light sensors, to the very long timescale motions induced by covalent modifications to bound flavin. The unique challenge posed by flavoproteins to all types of molecular simulation arises from the chemistry of the flavin isoalloxazine moiety, which presents an unusually large delocalized electron system which must be carefully treated in order to represent its contributions to the overall behavior of the system. Here we outline the particular considerations required for appropriate treatment of flavoproteins in simulations ranging from electronic structure calculations to long-timescale modeling of flavoprotein conformational transitions.

OriginalsprogEngelsk
TitelMethods in Enzymology
RedaktørerBruce A. Palfey
ForlagAcademic Press
Publikationsdato1. jan. 2019
Sider277-314
ISBN (Trykt)9780128168295
DOI
StatusUdgivet - 1. jan. 2019
NavnMethods in Enzymology
Vol/bind620
ISSN0076-6879

Fingeraftryk

Flavoproteins
Molecular Dynamics Simulation
Research Personnel
Electrons
4,6-dinitro-o-cresol

Citer dette

Sjulstok, E., Solov'yov, I. A., & Freddolino, P. L. (2019). Applications of molecular modeling to flavoproteins: Insights and challenges. I B. A. Palfey (red.), Methods in Enzymology (s. 277-314). Academic Press. Methods in Enzymology, Bind. 620 https://doi.org/10.1016/bs.mie.2019.03.014
Sjulstok, Emil ; Solov'yov, Ilia A. ; Freddolino, Peter L. / Applications of molecular modeling to flavoproteins : Insights and challenges. Methods in Enzymology. red. / Bruce A. Palfey. Academic Press, 2019. s. 277-314 (Methods in Enzymology, Bind 620).
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Sjulstok, E, Solov'yov, IA & Freddolino, PL 2019, Applications of molecular modeling to flavoproteins: Insights and challenges. i BA Palfey (red.), Methods in Enzymology. Academic Press, Methods in Enzymology, bind 620, s. 277-314. https://doi.org/10.1016/bs.mie.2019.03.014

Applications of molecular modeling to flavoproteins : Insights and challenges. / Sjulstok, Emil; Solov'yov, Ilia A.; Freddolino, Peter L.

Methods in Enzymology. red. / Bruce A. Palfey. Academic Press, 2019. s. 277-314 (Methods in Enzymology, Bind 620).

Publikation: Bidrag til bog/antologi/rapport/konference-proceedingBidrag til bog/antologiForskningpeer review

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T2 - Insights and challenges

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AU - Freddolino, Peter L.

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N2 - The general field of molecular simulation provides a wide spectrum of methods for studying the structure and function of biomolecules. Depending on the scale and question of interest, appropriate approaches may range from ab initio quantum mechanical calculations (when detailed aspects of and changes in electronic structure must be considered) to Brownian dynamics and coarse-grained molecular dynamics (to track large scale conformational motions, diffusion, and inter-molecular interactions). The entire range of molecular simulation methods has been fruitfully applied to a range of flavoenzymes, allowing researchers to address everything from the specific intermediates involved in the photoreactions of flavin chromophore-containing light sensors, to the very long timescale motions induced by covalent modifications to bound flavin. The unique challenge posed by flavoproteins to all types of molecular simulation arises from the chemistry of the flavin isoalloxazine moiety, which presents an unusually large delocalized electron system which must be carefully treated in order to represent its contributions to the overall behavior of the system. Here we outline the particular considerations required for appropriate treatment of flavoproteins in simulations ranging from electronic structure calculations to long-timescale modeling of flavoprotein conformational transitions.

AB - The general field of molecular simulation provides a wide spectrum of methods for studying the structure and function of biomolecules. Depending on the scale and question of interest, appropriate approaches may range from ab initio quantum mechanical calculations (when detailed aspects of and changes in electronic structure must be considered) to Brownian dynamics and coarse-grained molecular dynamics (to track large scale conformational motions, diffusion, and inter-molecular interactions). The entire range of molecular simulation methods has been fruitfully applied to a range of flavoenzymes, allowing researchers to address everything from the specific intermediates involved in the photoreactions of flavin chromophore-containing light sensors, to the very long timescale motions induced by covalent modifications to bound flavin. The unique challenge posed by flavoproteins to all types of molecular simulation arises from the chemistry of the flavin isoalloxazine moiety, which presents an unusually large delocalized electron system which must be carefully treated in order to represent its contributions to the overall behavior of the system. Here we outline the particular considerations required for appropriate treatment of flavoproteins in simulations ranging from electronic structure calculations to long-timescale modeling of flavoprotein conformational transitions.

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Sjulstok E, Solov'yov IA, Freddolino PL. Applications of molecular modeling to flavoproteins: Insights and challenges. I Palfey BA, red., Methods in Enzymology. Academic Press. 2019. s. 277-314. (Methods in Enzymology, Bind 620). https://doi.org/10.1016/bs.mie.2019.03.014