surface burial in energy calc's

murphy kenneth p kpmurphy at
Mon Sep 19 16:32:50 EST 1994

In article <35kmdr$4kd at>,
John Kuszewski <johnk at> wrote:
>You should also have a look at Privalov and Makhatadze's
>papers last year (JMB 232. 639-659 and 660-779).  There
>is also another set of parameters from Murphy and Freire,
>but I don't have the reference in front of me (some 
>help, Kip?) that appeared recently.

Hi John!  Our basic approach is discussed in:

Murphy, K. P. & Freire, E. (1992). Thermodynamics of Structural Stability and 
Cooperative Folding Behavior in Proteins.  Adv. Protein Chem. 43, 313-361.

I've also written a review chapter which will be out fairly soon (I hope)

Murphy, K. P., "Noncovalent Forces Important to the Conformational Stability of
Protein Structures" in Protein Stability and Folding B. A. Shirley, Eds. (The 
Humana Press Inc., Clifton, NJ, 1994), in press.

>One major problem with comparing different solvation 
>parameters is that they model different thermodynamic
>processes:  eg., Murphy and Freire model the process of
>moving from protein interior to exposed sites, but 
>Privalov and Makhatadze model the process of moving 
>from gas to solvated liquid.  Thus, M&F's solvation
>parameters include energies such as making/breaking 
>van der Waals contacts, which P&M's model treats 
>Another problem is that different groups do their 
>analysis with different atom "classes":  Eisenberg
>et al. lump all carbons together (if I'm remembering
>correctly), but P&M treat aliphatic and aromatic 
>carbons separately.
>Werner Braun et al. (JMB 233. 275-292, 1993) published
>a paper that compares various solvation parameters 
>during torsion-angle-space energy minimization.  Ooi's, 
>Eisenberg's, and Scheraga's parameter sets were among 
>those examined.  None worked at all well, as the 
>gentleman from UCLA pointed out.
>If you want to learn about solvation in general,
>have a look at Ben-Naim's paper in Curr Op Struct
>Biol 4. 264-268 (1994).
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>John Kuszewski                     ||  |/  /|  ||      
>johnk at          ||  /  /||  ||
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>that's MISTER protein G to you!     |/__/|      |
>                                      /_________|

Dr. Kenneth P. Murphy				e-mail: k-murphy at
Department of Biochemistry			office: (319)335-8910
Univeristy of Iowa				lab:  (319)335-7936
Iowa City, IA 52242            		        FAX:  (319)335-9570

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