Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A

<p>Abstract</p> <p>Background</p> <p>The Lipase Engineering Database (LED) integrates information on sequence, structure and function of lipases, esterases and related proteins with the α/β hydrolase fold. A new superfamily for <it>Candida antarctica </it>lipase A (CALA) was introduced including the recently published crystal structure of CALA. Since CALA has a highly divergent sequence in comparison to other α/β hydrolases, the Lipase Engineering Database was used to classify CALA in the frame of the already established classification system. This involved the comparison of CALA to similar structures as well as sequence-based comparisons against the content of the LED.</p> <p>Results</p> <p>The new release 3.0 (December 2009) of the Lipase Engineering Database contains 24783 sequence entries for 18585 proteins as well as 656 experimentally determined protein structures, including the structure of CALA. In comparison to the previous release <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> with 4322 protein and 167 structure entries this update represents a significant increase in data volume. By comparing CALA to representative structures from all superfamilies, a structure from the deacetylase superfamily was found to be most similar to the structure of CALA. While the α/β hydrolase fold is conserved in both proteins, the major difference is found in the cap region. Sequence alignments between both proteins show a sequence similarity of only 15%. A multisequence alignment of both protein families was used to create hidden Markov models for the cap region of CALA and showed that the cap region of CALA is unique among all other proteins of the α/β hydrolase fold. By specifically comparing the substrate binding pocket of CALA to other binding pockets of α/β hydrolases, the binding pocket of <it>Candida rugosa </it>lipase was identified as being highly similar. This similarity also applied to the lid of <it>Candida rugosa </it>lipase in comparison to the potential lid of CALA.</p> <p>Conclusion</p> <p>The LED serves as a valuable tool for the systematic analysis of single proteins or protein families. The updated release 3.0 was used for the evaluation of α/β hydrolases. The HTML version of the database with new features is available at <url>http://www.led.uni-stuttgart.de</url> and provides sequences, structures and a set of analysis tools including phylogenetic trees and HMM profiles</p

Polarimetry with Disordered Photonic Structures

Post-print (lokagerð höfundar)In conventional Stokes polarimetry, where the polarimetric information is obtained from a series of intensity measurements, stable and accurate measurements typically require the optical elements to be carefully designed. Here, we propose a paradigm shift where deep neural network assisted polarimeters based on disordered photonic structures perform high quality polarimetric measurements while completely removing the need for specially designed polarization analyzers, demonstrating how disordered photonic structures fabricated without the use of any nanolithography techniques can enable accurate analysis of optical signals. We implement this concept with disorder- engineered nano-scatterers that allow for analyzing varying degrees of disorder and cellophane film that demonstrate the cost-saving potential of the concept. We demonstrate polarimetric performances, calibrated using deep neural networks, that are comparable to commercial polarimeters, does not require prior knowledge of the input wavelength and show a high degree of mechanical stability.This work was supported in part by the Icelandic Research Fund under Grant 187043-0611 and in part by the Air Force O ce for Scienti c Research under MURI Grant FA9550-14-1-0389. The authors thank J.P. Balthasar Mueller, Einar B. Magnusson and Noah Rubin for valuable help and advice. The processing of gold metasurfaces was performed at the nanofabrication facility at the University of Iceland.Peer Reviewe

STITCH: interaction networks of chemicals and proteins

The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely dispersed across numerous databases and the literature. To facilitate access to this data, STITCH (‘search tool for interactions of chemicals') integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. Our database contains interaction information for over 68 000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. STITCH is available at http://stitch.embl.d

Smittebeskyttende adfærd under anden bølge af covid-19 pandemien i Danmark

Et afgørende fokus under covid-19-pandemien har været på at motivere omfattende adfærdsændringer i befolkningen. I denne artikel undersøger vi, hvilke psykologiske faktorer der var mest afgørende for danskernes adfærd under anden bølge af pandemien. Baseret på en spørgeskemaundersøgelse, der er repræsentativ for den voksne danske befolkning, viser vi, at folk, der (1) oplever coronavirusset som en personlig trussel, (2) oplever, at en ændret adfærd gør en forskel (”responseffektivitet”), (3) oplever, at en ændret adfærd ikke har høje omkostninger (”responsomkostninger”), samt (4) har høj institutionel tillid, er mere tilbøjelige til at agere i overensstemmelse med de smittebeskyttende adfærdsråd. Samtidig viser vi, at faktorerne (2)-(4) neutraliserer sammenhængen mellem trusselsfølelsen og den smittebeskyttende adfærd. Dermed anviser vi en potentiel vej til at fremme adfærdsændringer under en krise, der går udenom den frygt

STITCH 3: zooming in on protein-chemical interactions

To facilitate the study of interactions between proteins and chemicals, we have created STITCH, an aggregated database of interactions connecting over 300 000 chemicals and 2.6 million proteins from 1133 organisms. Compared to the previous version, the number of chemicals with interactions and the number of high-confidence interactions both increase 4-fold. The database can be accessed interactively through a web interface, displaying interactions in an integrated network view. It is also available for computational studies through downloadable files and an API. As an extension in the current version, we offer the option to switch between two levels of detail, namely whether stereoisomers of a given compound are shown as a merged entity or as separate entities. Separate display of stereoisomers is necessary, for example, for carbohydrates and chiral drugs. Combining the isomers increases the coverage, as interaction databases and publications found through text mining will often refer to compounds without specifying the stereoisomer. The database is accessible at http://stitch.embl.d

Maternal Recreational Exercise during Pregnancy in relation to Children's BMI at 7 Years of Age

Exposures during fetal life may have long-term health consequences including risk of childhood overweight. We investigated the associations between maternal recreational exercise during early and late pregnancy and the children's body mass index (BMI) and risk of overweight at 7 years. Data on 40,280 mother-child pairs from the Danish National Birth Cohort was used. Self-reported information about exercise was obtained from telephone interviews around gestational weeks 16 and 30. Children's weight and height were reported in a 7-year follow-up and used to calculate BMI and overweight status. Data was analyzed using multiple linear and logistic regression models. Recreational exercise across pregnancy was inversely related to children's BMI and risk of overweight, but all associations were mainly explained by smoking habits, socioeconomic status, and maternal pre-pregnancy BMI. Additionally, we did not find exercise intensity or changes in exercise habits in pregnancy related to the children's BMI or risk of overweight

The Path to God is Through the Heart: Metaphoric Self-location as a Predictor of Religiosity

Metaphors linking the heart to warm intuition and the head to cold rationality may capture important differences between people because some locate the self in the heart and others locate the self in the head. Five studies (total N = 2575) link these individual differences to religious beliefs. Study 1 found that religious beliefs were stronger among heart-locators than head-locators. Studies 2 and 3 replicated this relationship in more diverse samples. Studies 4 and 5 focused on questions of mediation. Heart-locators believed in God to a greater extent partly because of empathy-related processes (Study 4) and partly because they tended to think in less analytic terms (Study 5). These studies extend our knowledge of how metaphors interact with personality processes