Rerun of essentials of week one From Rotamers to Models and back via the Entropy of Water

Protein structure bioinformatics Predict mutations Analyse mutations Understand biology Design medicines (etc) Homology modelling for the above

Mutations and rotamers ‘Rotamer’ is an abused word. It both means any side chain conformation and preferred side chain conformation.

Improbable things

©CMBI 2006 β-branched prefers β-strand

Common sense and tau… Valine, Isoleucine, and Threonine are β-branched. Common sense dictates to treat their tau angles special. Their γ-atoms bulldozer into their own backbone, and that is why β -branched residues prefer β -strands

Tau angle

Rotamers So, there is much we don’t understand

Rotamers Predict mutations Analyse mutations Help with docking Homology modelling Structure validation

Model! 1: Template recognition and initial alignment 2: Alignment correction 3: Backbone generation 4: Loop modeling 5: Sidechain modeling 6: Model optimization 7: Model validation 8: Iteration

MUTANT DESIGN BIO- INFORMATICS QUESTION ‘MOLECULAR BIOLOGY’ BIOPHYSICS

Mutations Protein stability Enzyme activity Enzyme specificity Antigenicity Validate/falsify hypotheses Etcetera

PROTEIN STABILITY Δ G = Δ H - T Δ S Δ G = -RT ln(K) K = [Folded] / [Unfolded] So, you can interfere either with the folded, or with the unfolded form. Choosing between Δ H and Δ S will be much more difficult, because Δ G is a property of the complete system, including H 2 O….

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 A bluffer’s guide to Thermodynamic Equilibrium, by Alan Cooper

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

Both enthalpy and entropy are integral functions of heat capacity... ….from which  G =  H - T.  S So  C p is the key - if we can understand heat capacity effects, then we can understand everything else.

So, what is the role of water? So  C p is the key - if we can understand heat capacity effects, then we can understand everything else. And  C p 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!

Stability engineering Entropic versus enthalpic Folded versus unfolded form Thermodynamic versus kinetic Always compensatory