What are computational methods used for in the context of enzyme catalysis?
testing hypothesized reaction mechanisms
discussing the origin of catalysis in an enzyme
e.g. LBHBs
identifying intermediates
help interpret crystal data
Why can’t we perfectly describe chemical reactions with computational methods?
Theoretically, the fundamental laws to describe chemical reactions are known and we should be able to describe them.
Practically, real systems are so complex (number of interactions) that we do not have the computational power to describe them in a reasonable time.
—> approximations
What are the two approaches to describe the behaviour of a molecule?
Molecular mechanics:
model: atoms behave like balls connected with springs
bonds cannot break!
good way to describe conformational changes
(Molecular mechanics uses harmonic oscillator approximation (black), therefore, no bond breakage possible)
Quantum mechanics:
model: atoms have nuclei and electrons
more precise but still an approximation
approach to describe a molecule: combine wave functions of orbitals, minimize energy (that is your bond)
problem: even equations with relatively few atoms can take a long time to be solved
only used for up to a few hundred atoms
To describe proteins/enzyme mechanisms, both approaches are combined (MM for conformational changes, movements of substrates, ions, water, QM for the actual catalysis)
What properties of a bond can be described with molecular mechanics?
(formulas do not need to be memorized)
bond stretching: 1 bond
angle bending: 2 bonds involved
torsion: 3 bonds involved
non-bonded terms: describe interaction of atoms that are several bonds apart
electrostatic interactions
vdW interactions
What are periodic boundary conditions?
During computational simulations of chemical reactions, periodic boundary conditions are used to restrict the area you have to consider.
The theoretical reaction vessel is divided into cubes that contain the relevant molecules.
Molecules can leave the space but enter at the same time from the opposite direction.
Why might it be difficult to computationally model metalloenzymes with molecular mechanics?
difficult to describe coordination
d-orbitals of transition metals are difficult to calculate
exchange of ligands (bond breakage) cannot be modelled
What experimental approaches could one use to assess whether electrostatic stabilization is the main catalysis factor?
For many systems, it has been postulated that the origin of catalysis comes from electrostatic transition state stabilization. Choose one example from previous lectures and discuss how this stabilization is specific to the TS. Can you find one or more reasons why this should be a particularly dominant feature in enzymatic catalysis?
Give an example of an experimental method to track intermediates of an enzymatic reaction, and list its limitations.
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