Exercise 11:Interface design

Interface design

● Step I: understand existing interface – detect “hotspots”

– Small set of residues that contribute most of the binding energy

– Performed via “alanine scanning” - remove side chain to understand its contribution

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Rosetta alanine scanning

● Robetta– Simple score-function:

– No structural flexibility

● RosettaScripts FlexDdG

– All-atom Rosetta score function (+constraints in minimization)

– Allow backbone flexibility

– Mutate and repack neighboring region to mutation

Robetta workflow

FlexDdG workflow

ScoreFunction: Talaris-2014 - Final ddG calculation dominated by: * Solvation * Hydrogen bonding and electrostatics * Lennard-Jones atomic packing interactions.

Built in a flexible manner - mutation set via a resfile, whose name is provided to the xml file via the commandline -script_vars flag

FoldX alanine scanning

● Score function:

● Simply remove atoms

(in mutations to alanine)

Gvdw van der Waals.

GsolvH / GsolvP solvation energy apolar/ polar

groupsGhbond hydrogen-bond energy

Gwb water bridges at the interface

Gel electrostatic energy

Smc entropy cost for fixing the backbone in the

folded state. (related to an amino acid's tendency to adopt certain dihedral angles)Ssc is the entropic cost of fixing a sidechain in a

particular conformation.

Energy scaled according to exposure.