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Oliver Smart

This section of the course concentrates on the nature of the interactions which underlie the structure of proteins. An attempt will be made to explain the fundamental principles for each effect and the mathematical forms which are conventionally used in computational representations of biomolecules. At each stage implications for protein structure are pointed out. The final parts of the section give a brief introduction to the application of simulation methods to proteins. In a number of places links are provided for advanced topics.

- Interactions, forces and energies
- Electromagnetic interactions dominate on the molecular scale
- The Born-Oppenheimer approximation
- Quantum chemistry can (theoretically) deal with all molecular interactions
- Advanced topic: A brief introduction to quantum chemistry
**.** - Advanced topic: The application of quantum chemistry to protein simulation.

- Electrostatic interactions:
salt bridges, hydrogen bonds, partial charges and induction - Dispersion
- Repulsion terms
- The Lennard-Jones potential and van der Waals Radii

- Dielectric effects
- The hydrophobic effect
- Advanced topic: "The hydrophobic effect and protein unfolding" (contribution from John Walshaw)

Start this section by looking at: Preliminary considerations unit.

This section was made possible by the generous support of the Wellcome Trust in the form of an Career Development Fellowship which provides my salary and the equipment used in its production. Figures were prepared using the programs: paint written by David Koalas (koblas@netcom.com), sigmaplot (product of Jandel Scientific), snapshot (SGI) and Quanta (a product of Molecular Simulations Inc.). Thanks to Drs John Walshaw, Raj Gill and John Mitchell for there help and advice. Most importantly, I should like to thank my wife Marisa for putting up with the amount of time that this project has taken!

One cannot avoid making mistakes if one tries to produce a set of words, or of mathematical formulae, to describe nature. Nature is more complicated than language or mathematics. Nevertheless, one must do one's best to produce a set of symbols which are not to discordant with the facts.

J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949