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. 2014 Sep 3:7:602.
doi: 10.1186/1756-0500-7-602.

On methods for determining solvent accessible surface area for proteins in their unfolded state

Shennon Lu, Amy S Wagaman  1
Affiliations

On methods for determining solvent accessible surface area for proteins in their unfolded state

Shennon Lu et al. BMC Res Notes. .

Abstract

Background: There are many different methods for estimating solvent accessible surface area for proteins in their unfolded states. In this article, we compare eight methods, assessing whether or not they lead to different estimates of total accessible surface area as well as their impact on relationships with thermodynamic variables.

Findings: Our results demonstrate that most pairs of compared methods do result in different unfolded estimates of accessible surface area (only four pairs of methods do not yield significantly different estimates). However, we do not see a significant impact on the relationship between accessible surface area and thermodynamic parameters across the different methods.

Conclusions: We advocate the use of the Gong and Rose transition midpoint method for computing solvent accessible surface area due to its computational ease, physical basis, and performance in terms of relationships with thermodynamic parameters.

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Figures

Figure 1
Figure 1
Boxplots of unfolded solvent accessible surface area. Unfolded ASA values are provided for comparison across methods for the set of 51 proteins.
Figure 2
Figure 2
Boxplots of change in solvent accessible surface area. Changes in ASA values are provided for comparison across methods including tripeptide results for the subset of 44 proteins.
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