Help for a rookie? (peptide sequences)

George A. Heavner gheavner at netaxs.com
Thu Sep 14 12:43:50 EST 1995


In the absence of any additional structural information (e.g. NMR)
for a linear pentapeptide, the answer to your question is, "what
would you like the 3D structure to be?"  Most small peptides are
confomationally flexible and can adopt a variety of conformations.
A search of the PDB files for a small peptide will give numerous
conformations of homologous sequences presented in the context of
large proteins.  While there are techniques to predict a structure
using preferred phi and psi angles as starting points, you will
generate several families of conformations.  Some experimental data
is necessary to decide which of these is "real".  Even then,
the conformation can change dramatically with solvent composition,
ionic strength and pH.

Any program that will draw a structure by entering the sequence
relies on operator input for the phi and psi angles or uses the
default values that the programmer decided.  Any similarity
between the results generated and reality is purely coincidental.


George A. Heavner
Senior Director, Peptide R&D
Centocor, Inc.




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