A HitchHikers Guide to Molecular Thermodynamics What really makes proteins fold and ligands bind

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A Hitch-Hikers Guide to Molecular
ThermodynamicsWhat really makes proteins fold
and ligands bind
Alan Cooper
Chemistry Department Joseph Black Building,
Glasgow University Glasgow G12 8QQ, Scotland
Amsterdam November 2002
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Concepts and tools for medicinal chemists
What makes this protein fold, and what controls
its stability ?
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Concepts and tools for medicinal chemists
What makes this protein fold, and what controls
its stability ?
What are the thermodynamic forces responsible for
ligand binding ? Can we use them to design better
ligands ?
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Concepts and tools for medicinal chemists
Thermodynamic homeostasis, compensation
hydrogen-bonded lattices ...the role of water
in biomolecular interactions
Microcalorimetry analytical uses for
biomolecular interactions and stability
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A bluffers guide to Thermodynamic Equilibrium
There is a natural tendency for all things (even
atoms molecules) to roll downhill - to fall to
lower energy. ?H wants to be negative
This is opposed (at the molecular level) by the
equally natural tendency for thermal/Brownian
motion (otherwise known as entropy) to make
things go the other way and this effect gets
bigger as the temperature increases. T.?S wants
to be positive
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Thermodynamic Equilibrium, expressed in terms of
the Gibbs Free Energy change, reflects just the
balance between these opposing tendencies ?G
?H - T?S Equilibrium is reached when these
two forces just balance (?G 0). The standard
free energy change, ?G?, is just another way of
expressing the equilibrium constant, or affinity
(K) for any process, on a logarithmic scale ?G?
-RTlnK
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Both enthalpy and entropy are integral functions
of heat capacity...
.from which DG DH - T.DS
So DCp is the key - if we can understand heat
capacity effects, then we can understand
everything else.
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Calorimetric techniques...

• Differential scanning calorimetry (DSC)
• Isothermal titration calorimetry (ITC)
• Pressure perturbation calorimetry (PPC)

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So, what is the role of water?
So DCp is the key - if we can understand heat
capacity effects, then we can understand
everything else. And DCp is largely determined by
the interactions between water and the
macromolecule(s). In figure b many more waters
are free than in a. And free waters are happy
waters!
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DGDH-TDS DG-RTln(K)
? G must negative for a reaction to take place.
?G 1.38 kCal/Mole means a factor 10 difference
in an equilibrium. Example A ltgt B A
B ? G17.2 (it is impossible to know that
DG17.2, but lets pretend) If we make ? G18.6
(so, ? ? G 1.38) then B becomes 10 times
bigger than A.
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DGDH-TDS
Good for ? H 1) Contacts in protein (H-bonds,
Van der Waals interactions, salt bridges,
aromatic stacking, etc). 2) H-bonds between water
molecules Bad for ? H 1) H-bonds between water
and part of protein that gets buried.
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DGDH-TDS
Good for ? S Entropy of water. Bad for ? S
Entropy of protein.