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Computational Biophys Fall 2004
Physics of Biological Macromolecules
Fall 2004
PHY 320/620
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)
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
Computational Biophys Fall 2004
Examples of hydrogen bonds in biological molecules
Donor- - - acceptor Bond length (distance between heavy atoms; nm)
Comment
-O-H - - - O-H 0.28 +/- 0.1 H-bond in water
-O-H - - - O=C 0.28 +/- 0.1 Bonding of water to other molecules
-N-H - - - O-H 0.29 +/- 0.1 Bonding of water to other molecules
-N-H - - - O=C 0.29 +/- 0.1 Common in protein and nucleic acids
-N-H - - - N= 0.31 +/- 0.2 Common in protein and nucleic acids
-N-H - - - S 0.37 Rare; weakMathews and vanHolde, Biochemistry, p. 30
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)
Computational Biophys Fall 2004
Changes in thermodyamic parameters for protein unfolding
Computational Biophys Fall 2004
Wed Molecular Dynamics Lab
• Please preview:
http://www.ks.uiuc.edu/Research/namd/