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Biochemical Reaction Gallery

Welcome to the Biochemical Reaction Gallery!

Below is a collection of images and movies of the biochemical reactions of interest to the York Group.

Density Functional Theory Image Gallery	Density Functional Theory Movie Gallery	QM/MM Simulations of Solution Reactions	QM/MM Simulations of Enzyme and Ribozyme Reactions
Molecular Simulations of RNA	Counterion Occupation in Linear and Bent DNA

Density Functional Theory Image Gallery

Transphosphorylation Thio Effects


Rate-controlling transition state for methanolysis of ethylene phosphate.	Rate-controlling transition state for methanolysis of thio-substituted (S:Op1) ethylene phosphate.	Rate-controlling transition state for methanolysis of thio-substituted (S:Op1Op2) ethylene phosphate.

Rate-controlling transition state for methanolysis of thio-substituted (S:O3') ethylene phosphate.	Rate-controlling transition state for methanolysis of thio-substituted (S:O2') ethylene phosphate.	Rate-controlling transition state for methanolysis of thio-substituted (S:O5') ethylene phosphate.

Density Functional Theory Movie Gallery

RNA Transphosphorylation and Migration


RNA transterification followed by exocyclic cleavage leading to a 3' ribose-phosphate transphosphorylation product.	RNA transesterification followed by pseudorotation and endocyclic cleavage leading to a 2' ribose-phosphate migration product.

QM/MM Simulations of Solution Reactions

Transphosphorylation Thio Effects


QM/MM simulation of model RNA transesterification of the native (unsubstituted) reaction in solution (Gregersen et al., 2004).	QM/MM simulation of model RNA transesterification of the thio-substituted S:Op1Op2 reaction in solution (Gregersen et al., 2004).

QM/MM simulation of model RNA transesterification of the thio-substituted S:O2' reaction in solution (Gregersen et al., 2004).	QM/MM simulation of model RNA transesterification of the thio-substituted S:O5' reaction in solution (Gregersen et al., 2004).

QM/MM Simulations of Enzyme and Ribozyme Reactions


QM/MM simulation of Phosphoglucomutase reaction.	QM/MM simulation of hammerhead ribozyme.

Molecular Dynamics Simulations of RNA

Molecular simulation of hammerhead ribozyme in a rhombododecahedral cell with explicit water and counterions.


Full-length hammmerhead ribozyme in solution	Late transition state (Mg initially at B-Site)

Late transition state (Mg initially at C-Site)	Proton transfer in transition state

Counterion Occupation in Linear and Bent DNA


Distribution of ion occupations as a function of ion load in a bent DNA model.	Distribution of ion occupations as a function of ion load in a linear DNA model.