Analysis of Protein Geometry, Particularly Related to Packingat the Protein Surface

Analysis of Protein Geometry, Particularly Related to Packingat the Protein Surface

What is Protein Geometry?

Packing at Interfaces

Classic Papers

Lego

Packing ~ VDW force

Close-packing is Default

Water v. Argon

Voronoi Volumes

Voronoi Volumes, the Natural Way to Measure Packing

Delauney Triangulation, the Natural Way to Define Packing Neighbors

Standard Residue Volumes

Clustering into a set of Atom Types

Atoms have different sizes

Set of VDW Radii

Standard Core Volumes (Prelim.)

PPT Slide

PPT Slide

Small Packing Changes Significant

ALREADY MADE:Apply Voronoi Polyhedra to Protein Surface

ALREADY MADE:Surface Volume Increase in 20 High Resolution Structures

ALREADY MADE:Simulation

ALREADY MADE:picture of PTI simulation

Ways of Rationalizing Packing

ALREADY MADE:Compressibility

ALREADY MADE PICTURE:[C19: 7rsa.surfcv.cont.rgb.gz]

ALREADY MADE:Structural Hydrophobicity

ALREADY MADE:Expansion of Surface Grooves

Packing defines the “Correct Definition” of the Protein Surface

Defining Surfaces from Packing: Convex Hull and Layers of Waters

Defining a Surface from the Faces of Voronoi Polyhedra

Accessible Surface as a Time-averaged Water Layer

The Hydration Surface: Trying to Model Real Water

ALREADY MADE:Toy System

Second Solvent Shell:Water v LJ Liquid

ALREADY MADE:helical projections

Hydration Surface

Packing at Interfaces

Credits

References

18 (or 11) different atom types

Compare Volumes: Core v. Amino Acid Crystals

ALREADY MADE: Compare standard volumes with amino acids SOLUTION volumes

SKIP:Compare standard residue volumes with those amino acids occupy in solution (Detail)

SKIP:Paradoxabout protein folding

SKIP:Our ResultsResolve this Paradox