Theoretical Photobiology Enzyme Activity and Mechanisms

Theoretical Photobiology : Fluorescent Proteins

Because of their many applications in biomedicine as in vivo markers, fluorescent proteins are hot topics in current research: The most renowned member of the family, the Green Fluorescent Protein (GFP), afforded to its discoverers and developers the 2008 Nobel Prize in Chemistry. In recent years, many more proteins have joined the cast, differing in specific properties like wavelengths of excitation or fluorescence, stability, quantum yield and mechanism of operation.

Proteins or else: the basic operational principle is similar to that of other fluorescent molecules. Under certain conditions, the protein –or rather, its cromophore- absorbs radiation and undergoes an electronic transition to an excited state. Triggered by the ensuing electronic redistribution, a (usually very fast) chemical reaction takes place in the photoactive state rendering a product that, eventually, radiates to the ground electronic state. This coveted fluorescence is the indispensible ingredient of these proteins’ technical applications.

This simple picture is misleading: Reactivity in excited states is far less understood than ground state reactivity and the mechanisms operating are often unknown, reactivity is not thermally activated, non-adiabaticity is often encountered and is suspected of decreasing the quantum yield of the overall photocycle, and last but not least, it often includes transfer of light atoms and quantum effects pervade the field.

Our interest lies in some of the hottest members of the family of fluorescent proteins: GFP itself, and many members of the Red Fluorescent Protein (RFP) family: the Keima and Kate families. The latter have specific technological interest as possible fluorescent tags for multimode imaging. We have a strong background in theoretical chemistry, and we use its powerful tools to study these wonderfully complex systems and provide answers to questions:

  • What is the structure of these systems? How stable is it?
  • How does the structure correlate with the spectroscopic properties of the protein? What changes can be attempted to produce variants with specific properties?
  • What mechanism operates within? How fast is it?
  • Are there non-radiative relaxation pathways?

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Enzyme Activity and Mechanisms

Theoretical Chemistry and Simulation techniques are used and developed for the study of enzyme activity: substrate binding, enzyme-substrate interactions and, mainly, enzyme catalysis. The main purpose of our work is the molecular-level understanding of these phenomena for the systems under study and, with this knowledge, contribute to the design of inhibitors or the design of new enzymes. The enzymes studied are therefore of biomedical and/or biotechnological interest.

The methodology used by the group include hybrid quantum mechanics and molecular mechanics methods (QM/MM), molecular dynamics simulations, free energy calculations (thermodynamics integration, FEP, umbrella sampling) and calculation of quantum nuclear effects (EA-VTST), being the latter one of the expertises of the group.

The current research lines focus on the following systems:

  1. Lipoxygenases. Mammalian 15-LO
  2. Serine-Threonine Kinases
  3. Glycosyltransferases (GTs). GTs are responsible for the highly specific biosynthesis of glycosidic bonds that give rise to a great diversity of glycoderivatives (glycans), which participate in a variety of biological functions and processes.
  4. Glutamate Racemases
  5. Flavoproteins


6 / 3 / 2012

The new web of the dynamics group has been released.