NDLI: Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model

Content Provider	PubMed Central
Author	Gong, Haipeng Rose, George D.
Abstract	We present a physically rigorous method to calculate solvent-dependent accessible surface areas (ASAs) of amino acid residues in unfolded proteins. ASA values will be larger in a good solvent, where solute–solvent interactions dominate and promote chain extension. Conversely, they will be smaller in a poor solvent, where solute–solute interactions dominate and promote chain collapse. In the method described here, these solvent-dependent effects are modeled by Boltzmann-weighting a simulated ensemble for solvent quality—good or poor. Solvent quality is parameterized as intramolecular hydrogen bond strength, using a “hydrogen bond dial” that can be varied from “off” to “high” (i.e., from 0 to −6 kcal/mol per hydrogen bond). When plotted as a function of hydrogen bond strength, the Boltzmann-weighted distribution of conformers describes a sigmoidal curve, with a transition midpoint near 1.5 kcal/mol per hydrogen bond. ASA tables for the 20 residues are provided under good solvent conditions and at this transition midpoint. For the backbone, these midpoint ASA values are found to be in good agreement with the earlier estimate of unfolded state ASA given by the mean of Creamer's upper and lower bounds [Creamer TP, et al. (1997) Biochemistry 36:2832–2835], a gratifying result in that cosolvents of experimental interest, such as urea (good solvent) and trimethylamine N-oxide (poor solvent), are known to affect the backbone predominantly. Unanticipated results from our simulations predict that a significant population of three-residue, hydrogen-bonded turns (inverse γ-turns) will be detectable in blocked polyalanyl heptamers in poor solvent—an experimentally verifiable conjecture.
Related Links	http://dx.doi.org/10.1073/pnas.0712240105
Starting Page	3321
File Format	PDF
ISSN	10916490
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	9
Volume Number	105
Language	English
Publisher	National Academy of Sciences
Publisher Date	2008-03-04
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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