Explanation of a tertiary structure

Shaun D. Black SHAUN at JASON.UTHCT.EDU
Tue Sep 26 08:49:27 EST 1995


Dear Colleagues,

     Minnesota.Coal.Company at net.bio.net asked about how weak interactions
contribute to protein structure.  His professor required that he answer this
without mentioning "secondary structure".  After defining all the weak
forces, he was given no credit for his answer.

     Well, it depends a lot on what your professor was getting at.  Granted,
it is important to know that ionic bonds (approx 5-10 kcal/mol), hydrogen
bonds (approx 1-5 kcal/mol), and van der Waals forces (approx 0.03 kcal/mol)
contribute to the folded state of a protein.  However, you might also want
to discuss the "hydrophobic effect", currently viewed as the dominant force
in protein folding.  Folding results from the inability of non-polar moiteies
in the protein to interact with strongly hydrogen-bonded water in the bulk
medium.  The net effect is that it is more energetically favorable for such
greasy groups to bond weakly with each other (van der Waals, pi-pi stacking,
induced dipoles, etc.) than to interact unfavorably with water; the overall
effect is worth about 3 kcal/mol and sums to a potent force.  This effect
collectively results in a "hydrophobic collapse" during initial stages of
protein folding.  Thus, all the weak forces work cooperatively to promote
the tertiary structure of a protein.  In other words, many weak, non-covalent,
forces work locally (short-range) to promote a network of bonding interactions
in an aqueous medium to promote and stabilize protein folding.

     I hope that helps you a bit.  But then again, maybe I will get no
credit for my answer too ;)  .  Best regards,  Shaun

  =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 
  = Shaun D. Black, PhD   | Internet address:     shaun at jason.uthct.edu = 
  = Dept. of Biochemistry | University of Texas Health Center, at Tyler = 
  = World Wide Web:    http://pegasus.uthct.edu/UTHCT-Home/Welcome.html =
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