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PEDS Advance Access originally published online on June 24, 2006
Protein Engineering Design and Selection 2006 19(9):401-408; doi:10.1093/protein/gzl024
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

Designing amino acid residues with single-conformations

Tran T. Tran1, Herbert Treutlein1 and Antony W. Burgess1,2

1 Ludwig Institute for Cancer Research and Cooperative Research Centre for Cellular and Growth Factors, Melbourne Victoria 3050, Australia

2To whom correspondence should be addressed. E-mail: Tony.Burgess{at}ludwig.edu.au

Drug design can benefit from the use of non-coded amino acids, such as {alpha}-amino isobutyric acids (Aib) or sarcosine (N-methyl-glycine). Non-coded amino acids can confer resistance to enzymatic degradation and increase the conformational stability of the peptides. We have simulated the conformational effects of combining N-methylation, bulky groups on the C{alpha} atom and/or thioamides using the class II CFF91 force field and our thioamide force field parameters. Although single amino acid substitutions (e.g. Aib) can restrict the available conformations, they do not necessarily lead to unique conformers, however, we predict that some of the amino acids described in this report will fold to a single {varphi}, {psi} conformation (e.g. N-methylated and thioamide penicillamine). Several other amino acid/thiopeptide combinations were designed, which are predicted to prefer only two conformations. Novel amino acids of this type should prove useful for designing peptides with defined conformations.

Keywords: conformationally restricted amino acids/N-methylation/penicillamine/protein engineering/thioamide

Received January 19, 2006; revised May 17, 2006; accepted May 30, 2006.


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