Dataset Information

Large scale analysis of protein conformational transitions from aqueous to non-aqueous media.

ABSTRACT: BACKGROUND:Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. However, it is well established that the catalytic activity of proteins in organic solvents is much lower than in water. In order to explain this diminished activity and to further characterize the behaviour of proteins in non-aqueous environments, we performed a large-scale analysis (1737 proteins) of the conformational diversity of proteins crystallized in aqueous and co-crystallized or soaked in non-aqueous media. RESULTS:Using proteins' experimentally determined conformational diversity taken from CoDNaS database, we found that proteins in non-aqueous media display much lower conformational diversity when compared to the corresponding conformers obtained in water. When conformational diversity is compared between conformers obtained in different non-aqueous media, their structural differences are larger and mostly independent of the presence of cognate ligands. We also found that conformers corresponding to non-aqueous media have larger but less flexible cavities, lower number of disordered regions and lower active-site residue mobility. CONCLUSIONS:Our results show that non-aqueous media conformers have specific structural features and that they do not adopt extreme conformations found in aqueous media. This makes them clearly different from their corresponding aqueous conformers.

SUBMITTER: Rueda AJV

PROVIDER: S-EPMC5791380 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Large scale analysis of protein conformational transitions from aqueous to non-aqueous media.

Rueda Ana Julia Velez AJV Monzon Alexander Miguel AM Ardanaz Sebastián M SM Iglesias Luis E LE Parisi Gustavo G

BMC bioinformatics 20180130 1

<h4>Background</h4>Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. However, it is well established that the catalytic activity of proteins in organic solvents is much lower than in water. In order to explain this diminished activity and to furth ...[more]

PMID: 29382320

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Project description:BACKGROUND:Loneliness has become a public health problem described as an epidemic, and it has been argued that digital behavior such as social media posting affects loneliness. OBJECTIVE:The aim of this study is to expand knowledge of the determinants of loneliness by investigating online postings in a social media forum devoted to loneliness. Specifically, this study aims to analyze the temporal trends in loneliness and their associations with topics of interest, especially with those related to mental health determinants. METHODS:We collected a total of 19,668 postings from 11,054 users in the loneliness forum on Reddit. We asked seven crowdsourced workers to imagine themselves as writing 1 of 236 randomly chosen posts and to answer the short-form UCLA Loneliness Scale. After showing that these postings could provide an assessment of loneliness, we built a predictive model for loneliness scores based on the posts' text and applied it to all collected postings. We then analyzed trends in loneliness postings over time and their correlations with other topics of interest related to mental health determinants. RESULTS:We found that crowdsourced workers can estimate loneliness (interclass correlation=0.19) and that predictive models are correlated with reported loneliness scores (Pearson r=0.38). Our results show that increases in loneliness are strongly associated with postings to a suicidality-related forum (hazard ratio 1.19) and to forums associated with other detrimental behaviors such as depression and illicit drug use. Clustering demonstrates that people who are lonely come from diverse demographics and from a variety of interests. CONCLUSIONS:The results demonstrate that it is possible for unrelated individuals to assess people's social media postings for loneliness. Moreover, our findings show the multidimensional nature of online loneliness and its correlated behaviors. Our study shows the advantages of studying a hard-to-reach population through social media and suggests new directions for future studies.

Dataset Information

Large scale analysis of protein conformational transitions from aqueous to non-aqueous media.

Publications

Large scale analysis of protein conformational transitions from aqueous to non-aqueous media.

Similar Datasets

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