PMID: 273217Feb 1, 1978Paper

On the formation of protein tertiary structure on a computer

Proceedings of the National Academy of Sciences of the United States of America
A T Hagler, B Honig

Abstract

In this paper we carry out computer simulation studies of some of the factors responsible for protein tertiary structure. We show that it is possible to obtain (fold) a compact globular conformation from a sequence of amino acids consisting of only glycines and alanines. Our results indicate that glycines play a central role in stabilizing globular structures by facilitating the formation of turns and by destabilizing helical structures. Using this simple two-amino-acid representation, which serves as a control experiment, we are able to obtain a conformation that resembles the native structure of pancreatic trypsin inhibitor, as closely as any obtained previously in folding studies. However, careful examination reveals that the true chain topology has not been reproduced here or in previous studies. We suggest that the discrepancies between calculated and observed structures are more significant than the similarities. The implications of these results for the validity of models for protein folding, the use of pancreatic trypsin inhibitor in folding studies, and the possible role of glycine in the evolution of protein structure are discussed.

References

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Citations

Dec 1, 1990·Biopolymers·R E Bruccoleri, M Karplus
May 1, 1993·Protein Science : a Publication of the Protein Society·S Sun
Aug 1, 1993·Journal of Computer-aided Molecular Design·A GodzikJ Skolnick
Jan 1, 1987·Progress in Biophysics and Molecular Biology·S J WodakJ Janin
Jan 1, 1993·Progress in Biophysics and Molecular Biology·A A Rashin
Apr 1, 1997·Current Opinion in Structural Biology·S VajdaJ Novotny
Dec 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·T Head-GordonD M Gay
Dec 2, 1998·Journal of Biomolecular Structure & Dynamics·J SkolnickA R Ortiz
Sep 14, 2013·The Journal of Chemical Physics·W G Noid
Nov 3, 2010·Annual Review of Physical Chemistry·Shina C L KamerlinArieh Warshel
Jul 1, 1989·Trends in Biochemical Sciences·G D Fasman
Aug 25, 1984·Journal of Molecular Biology·J NovotnýM Karplus
Apr 1, 1980·Journal of Molecular Biology·F E Cohen, M J Sternberg
Jul 1, 1993·Current Biology : CB·J SkolnickA Rey
Nov 5, 1983·Journal of Molecular Biology·M Levitt
Jan 1, 1983·CRC Critical Reviews in Biochemistry·B Robson
Jun 23, 2016·Chemical Reviews·Sebastian KmiecikAndrzej Kolinski
Jan 1, 1980·CRC Critical Reviews in Biochemistry·C Toniolo
Jan 1, 1989·Proteins·L S Reid, J M Thornton
Jun 4, 2017·Journal of Biological Physics·Konda Mani Saravanan, Samuel Selvaraj
Jan 12, 2010·Journal of Chemical Theory and Computation·Jérome HéninMichael L Klein
Nov 13, 2004·Journal of Molecular Recognition : JMR·Mono PirunFred J Stevens

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