QUESTIONS: alpha-helix "signals" in proteins

Simon Brocklehurst Bioc smb18 at mole.bio.cam.ac.uk
Tue Jul 5 12:29:40 EST 1994

Ken Prehoda <kenp at nmrfam.wisc.edu> writes:

>Since protein folding is believed to be thermodynamically controlled

Errr... NOT!

>(OK, see Agard, et al. for counterviews), this is really irrelevant
>to what you seem to be getting at.  Remember that G is a state function
>and is therefore independent of path.

 The bottom line is that folding pathway(s) is/are almost certainly 
 involved in getting to the _native_ state - so kinetics _are_
 I would bet money that anyone who says different is wrong!

  As for the original point about the relatiave importance of secondary 
  vs tertiary vs intrinsic interactions, for controlling formation of 
  (secondary) structure:

  Why can't they all be "equally" important???  That is, maybe in 
  one bit of a protein, intrinsic preferences are crucial for
  driving structure formation, whereas in a different bit, secondary
  interactions could be dominant.

  If this was true, then there would be different percentages
  of residues whose conformation was mainly determined by one of
  the above "things".  What these numbers would be is anyone's guess.

  But, it is worth remembering that the so-called "hydrophobic effect"
  is most likely to be the major driving force in structure formation.

  In the simplest model for considering this effect, there need be no 
  difference between secondary and tertiary interactions when considering
  this "effect".

  My guess is that, on average, secondary and tertiary interactions of 
  residues dominate over "intrinsic" residue preferences" in driving the 
  formation of secondary structure.

|  ,_ o     Simon M. Brocklehurst,
| /  //\,   Oxford Centre for Molecular Sciences,
|   \>> |   Department of Biochemistry, University of Oxford,
|    \\,    Oxford, UK.
|           E-mail: smb at bioch.ox.ac.uk

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