Protein Folding

David F. Green dfgreen at lms.mit.edu
Thu Jan 15 09:01:16 EST 1998


Alan J. Robinson wrote:

> suggestions, please!  (The Ramachandran plot would make more sense if
> the allowed regions were merely preferred regions - energetically
> favorable.)
> 

That's exactly what they are!  You can think of a Ramachandran plot has
being a slice through a 3-D plot - the "allowed" regions, being areas of
low energy.  The relative energies of various regions of the
"disallowed" region differ between amino acids, with glycine generally
having the lowest energy disallowed region.  If you look at a
Ramachandran plot showing the positions of amino acids in a real protein
(e.g. Voet and Voet, "Biochemistry" 2nd ed. figure 7.8, Matthews and van
Holde, "Biochemistry" 2nd ed. figure 6.10 ) you will see that in most
proteins, there are amino acids with lie in "disallowed" regions of the
Ramachandran plot.

It's good that you posted this question - a lot of students have trouble
understanding exactly what a Ramachandran plot means, and why some amino
acids are allowed in the "disallowed" regions.  You seem to have a good
understanding of the concepts.  Good luck in your studies!

-- 
************************************************
David F. Green
Department of Chemistry
Massachusetts Institute of Technology
Cambridge, MA 02139

E-mail: dfgreen at lms.mit.edu
Phone: (617) 228-6229
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