| 1. |
- Lensink, Marc F., et al.
(författare)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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Ingår i: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Tidskriftsartikel (refereegranskat)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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| 2. |
- Raja, Erna, et al.
(författare)
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The protein kinase LKB1 negatively regulates bone morphogenetic protein receptor signaling
- 2016
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Ingår i: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 7:2, s. 1120-1143
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Tidskriftsartikel (refereegranskat)abstract
- The protein kinase LKB1 regulates cell metabolism and growth and is implicated in intestinal and lung cancer. Bone morphogenetic protein (BMP) signaling regulates cell differentiation during development and tissue homeostasis. We demonstrate that LKB1 physically interacts with BMP type I receptors and requires Smad7 to promote downregulation of the receptor. Accordingly, LKB1 suppresses BMP-induced osteoblast differentiation and affects BMP signaling in Drosophila wing longitudinal vein morphogenesis. LKB1 protein expression and Smad1 phosphorylation analysis in a cohort of non-small cell lung cancer patients demonstrated a negative correlation predominantly in a subset enriched in adenocarcinomas. Lung cancer patient data analysis indicated strong correlation between LKB1 loss-of-function mutations and high BMP2 expression, and these two events further correlated with expression of a gene subset functionally linked to apoptosis and migration. This new mechanism of BMP receptor regulation by LKB1 has ramifications in physiological organogenesis and disease.
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| 3. |
- Węgrzyn, Michał H., et al.
(författare)
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Tree height as the main factor causing disappearance of the terricolous lichens in the lichen Scots pine forests
- 2021
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 771
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Tidskriftsartikel (refereegranskat)abstract
- © 2021 Elsevier B.V. The lichen Scots pine forests habitats are undergoing rapid disappearance across Europe. Due to the semi-natural character of this habitat and an increase of the nitrification as a result of air pollution, determination of factors responsible for the decrease in lichen field layer cover requires a comprehensive approach. Our study aimed to investigate environmental factors necessary for the determination of active protection measures in order to maintain this vulnerable habitat. Specifically, we aimed to investigate: 1) the environmental factors influencing lichen cover in the lichen Scots pine forests of Bory Tucholskie National Park; 2) the differences in habitat variables between sites with lichen-rich and bryophyte-rich field layers. In our study, we used vegetation and microhabitat properties data collected over three years of surveys, as well as ALS LiDAR data. Our results indicated that lichen and bryophyte cover, tree height, tree cover, thickness of organic matter layer, soil temperature and soil water content differed between lichen-rich and bryophyte-rich sites. We found a significant negative relationship between lichen cover recorded within the field layer and tree height. The lichen-rich field layer developed better in areas with lower tree height and thinner layer of organic matter, which created a favorable habitat conditions for lichen development. Our research revealed the previously unknown impact of tree height for the development of lichen field layer. These findings can be used to plan the active conservation measures of lichen Scots pine forests.
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| 4. |
- Zieba, Agata, et al.
(författare)
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The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling
- 2015
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Ingår i: Omics. - : MARY ANN LIEBERT, INC. - 1536-2310 .- 1557-8100. ; 19:11, s. 659-668
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Tidskriftsartikel (refereegranskat)abstract
- The human uterus includes the complex endometrial mucosa, the endometrium that undergoes dynamic, hormone-dependent alterations throughout the life of fertile females. Here we have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to analyze gene expression patterns in the normal endometrium. Human endometrial tissues from five women were used for deep sequencing (RNA-Seq). The mRNA and protein expression data from the endometrium were compared to 31 (RNA) and 44 (protein) other normal tissue types, to identify genes with elevated expression in the endometrium and to localize the expression of corresponding proteins at a cellular resolution. Based on the expression levels of transcripts, we could classify all putative human protein coding genes into categories defined by expression patterns and found altogether 101 genes that showed an elevated pattern of expression in the endometrium, with only four genes showing more than five-fold higher expression levels in the endometrium compared to other tissues. In conclusion, our analysis based on transcriptomics and antibody-based protein profiling reports here comprehensive lists of genes with elevated expression levels in the endometrium, providing important starting points for a better molecular understanding of human reproductive biology and disease.
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