1. Computational Biophys Fall 2004 Physics of Biological Macromolecules Fall 2004 PHY 320/620

2. Computational Biophys Fall 2004 Amino acid components of proteins http://wbiomed.curtin.edu.au/teach/biochem/tutorials/AAs/AA.html Link found on the Research Collaboratory for Structural Biology web site: www.rcsb.org/pdb/education.html See also Table 5.1 (Duane)

3. Computational Biophys Fall 2004 Nucleotides: components of nucleic acids http://ndbserver.rutgers.edu/NDB/archives/NAintro/ Link found on the Research Collaboratory for Structural Biology web site: www.rcsb.org/pdb/education.html See also Table 4.1 (Duane) http://www.web-books.com/MoBio/Free/Ch3A.htm

4. Computational Biophys Fall 2004 Examples of hydrogen bonds in biological molecules Donor- - - acceptorBond length (distance between heavy atoms; nm) Comment -O-H - - - O-H0.28 +/- 0.1H-bond in water -O-H - - - O=C0.28 +/- 0.1Bonding of water to other molecules -N-H - - - O-H0.29 +/- 0.1Bonding of water to other molecules -N-H - - - O=C0.29 +/- 0.1Common in protein and nucleic acids -N-H - - - N=0.31 +/- 0.2Common in protein and nucleic acids -N-H - - - S0.37Rare; weak Mathews and vanHolde, Biochemistry, p. 30

5. Computational Biophys Fall 2004 Thermodynamics: Definitions and terms System: part of universe under study Surroundings: all the of universe, except the system Open and closed systems: can exchange (or not) matter and energy with surroundings State function: value of function depends ONLY on state, not on how system got to that state Standard state: one mole of a pure substance at 298.15K (25ºC) and 1 bar pressure) U = energy within a system (measured as  U) Forms of energy transfer across boundary of system –q = heat (energy transfer due to temperature difference) transferred TO system –w = work (force acting to displace an object) done ON system H = enthalpy (heat absorbed by system at constant pressure) S = entropy (measure of disorder of a system)

6. Computational Biophys Fall 2004 Changes in thermodyamic parameters for protein unfolding

7. Computational Biophys Fall 2004 Wed Molecular Dynamics Lab Please preview: http://www.ks.uiuc.edu/Research/namd/