We analyze human-specific KEGG pathways trying to understand the functional role of intrinsic disorder in proteins. Pathways provide a comprehensive picture of biological processes and allow better understanding of a protein's function within the specific context of its surroundings. Our study pinpoints a few specific pathways significantly enriched in disorder-containing proteins and identifies the role of these proteins within the framework of pathway relationships. Three major categories of relations are shown to be significantly enriched in disordered proteins: gene expression, protein binding and to a lesser degree, protein phosphorylation. Finally we find that relations involving protein activation and to some extent inhibition are characterized by low disorder content.
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http://dx.doi.org/10.1039/c1mb05274h | DOI Listing |
Nucleic Acids Res
January 2025
Department of Physics, 845 W Taylor St, University of Illinois Chicago, Chicago, IL 60607, USA.
Altered DNA dynamics at lesion sites are implicated in how DNA repair proteins sense damage within genomic DNA. Using laser temperature-jump (T-jump) spectroscopy combined with cytosine-analog Förster Resonance Energy Transfer (FRET) probes that sense local DNA conformations, we measured the intrinsic dynamics of DNA containing 3 base-pair mismatches recognized in vitro by Rad4 (yeast ortholog of XPC). Rad4/XPC recognizes diverse lesions from environmental mutagens and initiates nucleotide excision repair.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Department of Internal Medicine, Division of Gastroenterology and Hepatology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
Bone marrow transplantation (BMT) is mainly performed to restore an anti-tumor immune response, called the graft-versus-tumor (GVT) effect, against leukemia, myeloma and lymphoma. This GVT reactivity is driven by donor T cells, and it can also cause lethal graft-versus-host disease (GVHD). We previously demonstrated that the colonization of mice with helminths preserves the GVT response while suppressing GVHD.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Department of Anatomy, Cellular and Molecular Research Group, Faculty of Medicine, Masaryk University, Kamenice 3, CZ-625 00 Brno, Czech Republic.
CXCL12 and CXCR4 proteins and mRNAs were monitored in the dorsal root ganglia (DRGs) of lumbar (L4-L5) and cervical (C7-C8) spinal segments of naïve rats, rats subjected to sham operation, and those undergoing unilateral complete sciatic nerve transection (CSNT) on post-operation day 7 (POD7). Immunohistochemical, Western blot, and RT-PCR analyses revealed bilaterally increased levels of CXCR4 protein and mRNA in both lumbar and cervical DRG neurons after CSNT. Similarly, CXCL12 protein levels increased, and CXCL12 mRNA was upregulated primarily in lumbar DRGs ipsilateral to the nerve lesion.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
The prevalence of cardiovascular disease varies with sex, and the impact of intrinsic sex-based differences on vasculature is not well understood. Animal models can provide important insights into some aspects of human biology; however, not all discoveries in animal systems translate well to humans. To explore the impact of chromosomal sex on proteomic phenotypes, we used iPSC-derived vascular smooth muscle cells from healthy donors of both sexes to identify sex-based proteomic differences and their possible effects on cardiovascular pathophysiology.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Jiangxi Provincial Key Laboratory of Oil-Tea Camellia Resource Cultivation and Utilization, Jiangxi Academy of Forestry, Nanchang 330032, China.
Color variation in plant leaves has a significant impact on their photosynthesis and plant growth. yellow-leaf mutants are ideal materials for studying the mechanisms of pigment synthesis and photosynthesis, but their mechanism of leaf variation is not clear. We systematically elucidated the intrinsic causes of leaf yellowing in the new variety 'Diecui Liuji' in terms of changes in its cell structure, pigment content, and transcript levels.
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