PMID: 10861935Jun 22, 2000Paper

Side-chain conformational entropy in protein unfolded states

Proteins
Trevor P Creamer

Abstract

The largest force disfavoring the folding of a protein is the loss of conformational entropy. A large contribution to this entropy loss is due to the side-chains, which are restricted, although not immobilized, in the folded protein. In order to accurately estimate the loss of side-chain conformational entropy that occurs upon folding it is necessary to have accurate estimates of the amount of entropy possessed by side-chains in the ensemble of unfolded states. A new scale of side-chain conformational entropies is presented here. This scale was derived from Monte Carlo computer simulations of small peptide models. It is demonstrated that the entropies are independent of host peptide length. This new scale has the advantage over previous scales of being more precise with low standard errors. Better estimates are obtained for long (e.g., Arg and Lys) and rare (e.g., Trp and Met) side-chains. Excellent agreement with previous side-chain entropy scales is achieved, indicating that further advancements in accuracy are likely to be small at best. Strikingly, longer side-chains are found to possess a smaller fraction of the theoretical maximum entropy available than short side-chains. This indicates that rotations about torsions after...Continue Reading

References

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Citations

Aug 7, 2002·Current Opinion in Structural Biology·Roland L Dunbrack
Oct 8, 2011·Journal of the American Chemical Society·Agustina Rodriguez-GranilloVikas Nanda
Feb 11, 2004·Journal of Biomolecular Structure & Dynamics·Ravindranath S Rathore, T Narasimhamurthy
Jun 21, 2011·Bioinformatics·Marcin J Mizianty, Lukasz Kurgan
Mar 3, 2006·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·David M AnstromS James Remington
Jul 27, 2002·Protein Science : a Publication of the Protein Society·Andrei L LomizeIrina D Pogozheva
May 22, 2002·Protein Science : a Publication of the Protein Society·Anton V FilikovBassil I Dahiyat
Mar 23, 2002·Protein Science : a Publication of the Protein Society·Adam L Rucker, Trevor P Creamer
Jan 1, 2011·Microbial Informatics and Experimentation·W Nicholson PriceJohn F Hunt
Dec 13, 2006·PLoS Computational Biology·Jinfeng Zhang, Jun S Liu
Mar 5, 2013·Annual Review of Biophysics·Zhixiu LiYaoqi Zhou
Dec 4, 2014·The Journal of Physical Chemistry. B·Amir NorouzyWerner M Nau
Oct 24, 2008·Journal of Computational Chemistry·Peng ZhouZhicai Shang
Nov 30, 2005·Proteins·Brian W Chellgren, Trevor P Creamer
May 8, 2013·Protein Science : a Publication of the Protein Society·Xiaoqiang HuangYushan Zhu
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Apr 5, 2002·Proteins·Themis LazaridisFrancois Gandolfo
Jun 21, 2018·Physical Biology·Ranjit RanbhorSusheel Durani
Jan 9, 2007·Proteins·Zhexin XiangBarry Honig
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Feb 20, 2008·Journal of Biomolecular Structure & Dynamics·Jeseong YoonSeokmin Shin
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May 5, 2006·The Journal of Physical Chemistry. B·Vibin RamakrishnanSusheel Durani
Oct 28, 2021·Journal of Chemical Information and Modeling·Yujin Wu, Charles L Brooks

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