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/