PMID: 19140326Jan 15, 2009Paper

The relationship between protein accessible surface area and number of native contacts in its structure

Molekuliarnaia biologiia
N S Bogatyreva, D N Ivankov

Abstract

The degree of folding for a protein is usually characterized by either solvent-accessible surface area or by number of formed native contacts. It is clearly that these two values must be coupled with each other, since the decrease in solvent-accessible surface area must be accompanied with the corresponding increase in the number of native contacts. In this study we show that this relationship does exist and is excellent (correlation coefficient is higher than 99%), which can be used for accurate and fast estimate of accessible surface area by means of number of native contacts. Among commonly used methods for native contacts calculation thebest correlation is observed for atom-atom scheme, if hydrogen atoms are taken into account and cutoff value for the distance between atoms' centers is 8 angstroms. The latter means that for hiding protein interior from water two layers of surface atoms are necessary.

References

Feb 14, 1971·Journal of Molecular Biology·B Lee, F M Richards
Feb 1, 1995·Current Opinion in Structural Biology·A R Fersht
Jan 1, 1996·Folding & Design·J N OnuchicP G Wolynes
May 30, 1998·Journal of Molecular Biology·K W PlaxcoD Baker
Aug 26, 1998·Folding & Design·S E Jackson
Sep 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·O V Galzitskaya, A V Finkelstein
Sep 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·E Alm, D Baker
Dec 26, 2001·Biophysical Journal·Hongyi Zhou, Yaoqi Zhou
Oct 5, 2002·Protein Engineering·Uttamkumar SamantaPinak Chakrabarti
Feb 6, 2004·Journal of Molecular Biology·Sergiy O GarbuzynskiyOxana V Galzitskaya
Sep 19, 2007·Proteins·Oxana V GalzitskayaSergiy O Garbuzynskiy

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Citations

Jun 23, 2016·International Journal for Ion Mobility Spectrometry : Official Publication of the International Society for Ion Mobility Spectrometry·Emily R SchenkFrancisco Fernandez-Lima
Feb 19, 2015·Journal of the American Society for Mass Spectrometry·Emily R SchenkFrancisco Fernandez-Lima

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