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. 2024 Feb 29;20(8):1053–1065. doi: 10.1038/s41589-024-01568-7

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a, TPP-determined insolubility profile of E. coli lysate in the absence (gray) and presence (colors) of osmolytes. Plots show protein concentration in the soluble fraction scaled to the value at 37 °C. Shaded areas indicate the confidence interval of the fit. b, Comparison of protein stabilization analysis by LiP–MS and TPP. The plot shows the fraction of proteins reported stabilized by both methods (both), neither method (none) and one method (only LiP and only TPP). Only proteins defined as precipitators in TPP and detected in both datasets are included. c, Number of proteins significantly changed in abundance in the soluble fraction at low (37 °C and 42 °C) and high (68.2 °C, 72.5 °C and 76 °C) temperatures in TPP in the presence and absence of the indicated osmolytes. Significance was calculated separately for proteins with increased aggregation (+Aggreg.; fold change of <−1; dark gray) and decreased aggregation (–Aggreg.; fold change of >1; light gray) in the presence of osmolyte; adjusted P value of <0.05 (data were analyzed by two-sided t-test with a Benjamini–Hochberg correction). d, Heat map showing the most significantly different features (adjusted P value of <0.01; data were analyzed by t-test with a Benjamini–Hochberg correction) between proteins with increased aggregation in TMAO at high or low temperature (as in c) and all other detected proteins. Color indicates higher (red) or lower (blue) features in the increased aggregation group. Rg, radius of gyration; aIndex, aliphatic index. e, TPP profile for Frr in the absence (gray) and presence of the indicated osmolytes. The shaded area indicates the confidence interval of the fit. f, LiP–MS thermal profiles for two representative peptides from Frr for the indicated osmolytes. The top plot shows peptide positions along the Frr protein sequence. Top track, all detected peptides; blue, peptides with an increased aggregation profile under at least one condition; gray, peptides with no aggregation profile under any condition. Bottom track, predicted aggregation-prone regions (dark gray). The shaded area indicates the confidence interval of the fit.