Particularly Related to Packing at the Protein Surface
Table of ContentsAnalysis of Protein Geometry, Particularly Related to Packing at the Protein Surface Analysis of Protein Geometry, Particularly Related to Packing at 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: Paradox about protein folding SKIP: Our Results Resolve this Paradox |
Author: Mark Gerstein
Email: Mark.Gerstein@Yale.edu Home Page: http://bioinfo.csb.yale.edu/Geometry Other information: |