Unknown proteins or hypothetical proteins exist but have not been characterized or linked to known genes. Domains of unknown function are experimentally identified proteins with no known functional or structural domain. In this paper, the investigation and characterization of the likely functional aspects of a hypothetical protein, YP_001317347.1, from Staphylococcus aureus was performed using various computational methods and tools. Based on the analysis, the protein has a YbbR domain and is expected to bind ribosomal subunits. The analysis reported here helps in understanding the importance of YbbR domains and will aid in the development of novel antibacterial agents.
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http://dx.doi.org/10.1016/j.jiph.2015.03.007 | DOI Listing |
Mol Cell Proteomics
January 2025
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany. Electronic address:
Mass spectrometry-based proteomics has revolutionized bacterial identification and elucidated many molecular mechanisms underlying bacterial growth, community formation, and drug resistance. However, most research has been focused on a few model bacteria, overlooking bacterial diversity. In this study, we present the most extensive bacterial proteomic resource to date, covering 303 species, 119 genera, and five phyla with over 636,000 unique expressed proteins, confirming the existence of over 38,700 hypothetical proteins.
View Article and Find Full Text PDFAnal Chem
January 2025
Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States.
The nuclear pore complex (NPC) is the proteinous nanopore that solely regulates molecular transport between the nucleus and cytoplasm of a eukaryotic cell. Hypothetically, the NPC utilizes the hydrophobic barriers based on the repeats of phenylalanine-glycine (FG) units to selectively and efficiently transport macromolecules. Herein, we quantitatively assess the hydrophobicity of transport barriers confined in the nanopore by applying scanning electrochemical microscopy (SECM).
View Article and Find Full Text PDFSmall Methods
January 2025
Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, 510080, China.
Accurately defining cell boundaries for spatial transcriptomics is technically challenging. The current major approaches are nuclear staining or mathematical inference, which either exclude the cytoplasm or determine a hypothetical boundary. Here, a new method is introduced for defining cell boundaries: labeling cell membranes using genetically coded fluorescent proteins, which allows precise indexing of sequencing spots and transcripts within cells on sections.
View Article and Find Full Text PDFAndrology
January 2025
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.
The neuroendocrine system that comprises the glycoprotein hormones (GpHs) and their receptors is essential for reproduction and metabolism. Each GpH hormone is an αβ heterodimer of cystine-knot proteins and its cognate receptor is a G-protein coupled receptor (GPCR) distinguished by a large leucine-rich-repeat (LRR) extracellular domain that binds the hormone and a class A GPCR transmembrane domain that signals through an associating heterotrimeric G protein. Hence, the receptors are called LRR-containing GPCRs-LGRs.
View Article and Find Full Text PDFBiochemistry (Mosc)
December 2024
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
Nuclear export protein (NEP) of the influenza A virus, being one of the key components of the virus life cycle, is a promising model for studying characteristics of formation of amyloids by viral proteins. Using atomic force microscopy, comparative study of aggregation properties of the recombinant NEP variants, including the protein of natural structure, as well as modified variants with N- and C-terminal affinity His-tags, was carried out. All protein variants under physiological conditions are capable of forming aggregates of various morphologies: micelle-like nanoparticles, flexible protofibrils, rigid amyloid fibrils, etc.
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