Geometry and Shape Analysis in Biological Sciences (8-9 June 2017)

Tutorial 1: Overview: Geometry and Topology in Biology

Venue: IMS, National University of Singapore

Organizers

• Joel Hass (University of California at Davis)
• Patrice Koehl (University of California at Davis)

Overview

Structural information on biological shapes can be obtained via a number of experimental techniques, including X-ray crystallography, NMR, and cryo-electron microscopy tomography for molecular systems, multiple microscopy and scanning techniques for larger biological shapes, and scanners for even larger shapes, to name only a few. However, it is the geometric and topological modeling that interprets and translates the data generated by those techniques into a meaningful model of the structure-function relationship for those systems, allowing the geometric information to be integrated into physical models that shed new light on the mechanisms of life. In this tutorial, we will introduce the different techniques for collecting data on biological objects, and describe geometric and topological problems that arise in attempting to analyze those data. We will focus on the geometric description of biomolecules, introducing the concepts of implicit solvent models and their use for predicting protein-drug interactions, and on bones and their use in 3D morphometrics.

Slides of the presentation

Visualizing biomolecular structures: a simple PDB viewer

DNAs: RNAs: Proteins: Representation:

Resources

Books and Review articles

1) Protein Structure:

• Introduction to Protein Structure, Branden, C. and Tooze, J. (1991) Garland Publishing, New York
• Proteins, Creighton, T.E. (1993) 2nd edition, W.H. Freeman & Co., New York
• Principles of Protein Structure, Schulz, G.E. and Schirmer, R.H. (1979) Springer-Verlag, New York


• Chothia, C., Levitt, M. and Richardson, D. (1977) Structure of proteins: Packing of alpha helices and beta sheets Proc. Natl. Acad. Sci. USA 74 4130-4134
• Chothia, C. (1984) Principles that determine the structure of proteins Ann. Rev. Biochem. 53 537-572
• Lesk, A.M. (1991) Protein architecture : a practical approach, IRL press, Oxford
• Rao, S.T. and Rossman, M.G. (1973) Comparison of super-secondary structures in proteins J. Mol. Biol. 76 241-256
• Richardson, J.S. (1981) The anatomy and taxonomy of protein structure Adv. Prot. Chem. 34 167-339
• Chothia, C, Hubbard, T, Brenner, S, Burns, H and Murzin, A. (1997) Protein folds in the all-beta and all-alpha classes Annu. Rev. Biophys. Biomol. Struct. 26 597-627
• Chao Zhang and S.H. Kim (2000) The anatomy of protein beta-sheet topology J. Mol. Biol. 299 1075-1089
• Chao Zhang and S.H. Kim (2000) A comprehensive analysis of the greek key motifs in protein beta-barrels and beta-sandwiches Proteins: Struct. Func. Genet. 40 409-419

2) Protein Structure Classification and Prediction

• Taylor, WR, May, ACW, Brown, NP and Aszodi, A (2001) Protein structure: geometry, topology and classification Rep. Prog. Phys. 64 517-590
• Ouzounis, CA, Coulson, RMR, Enright AJ, Kunin, V and Pereira-Leal, JB. (2003) Classification schemes for protein structure and function Nature Genetics 4 509-519

Useful links

• Databases
  
  • the Protein Data Bank (PDB)
• Visualization programs
  
  • RasMol
  • PyMol
  • Ramachandran Plot Explorer
• Protein Structures
  
  • Amino Acids (quizzes, ....)