Transporters from bacteria to humans contain inverted repeat domains thought to arise evolutionarily from the fusion of smaller membrane protein genes. Association between these domains forms the functional unit that enables transporters to adopt distinct conformations necessary for function. The small multidrug resistance (SMR) family provides an ideal system to explore the role of mutations in altering conformational preference since transporters from this family consist of antiparallel dimers that resemble the inverted repeats present in larger transporters. Here, we show using NMR spectroscopy how a single conservative mutation introduced into an SMR dimer is sufficient to change the resting conformation and function in bacteria. These results underscore the dynamic energy landscape for transporters and demonstrate how conservative mutations can influence structure and function.
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http://dx.doi.org/10.7554/eLife.48909 | DOI Listing |
G3 (Bethesda)
January 2025
Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.
Haplotyped-resolved phased assemblies aim to capture the full allelic diversity in heterozygous and polyploid species to enable accurate genetic analyses. However, building non-collapsed references still presents a challenge. Here, we used long-range interaction Hi-C reads (high-throughput chromatin conformation capture) and HiFi PacBio reads to assemble the genome of the apomictic cultivar Basilisks from Urochloa decumbens (2n = 4x = 36), an outcrossed tetraploid Paniceae grass widely cropped to feed livestock in the tropics.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Department of Chemistry, New York University, New York, NY 10003.
Frameshifting is an essential mechanism employed by many viruses including coronaviruses to produce viral proteins from a compact RNA genome. It is facilitated by specific RNA folds in the frameshift element (FSE), which has emerged as an important therapeutic target. For SARS-CoV-2, a specific 3-stem pseudoknot has been identified to stimulate frameshifting.
View Article and Find Full Text PDFJ Phys Chem A
January 2025
Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista 7, Santiago 8420524, Chile.
Covalent-organic frameworks (COFs) are useful architectures for two- (2D) and three-dimensional (3D) active materials. Recently, the characterization of the nonplanar benzo[5,6][1,4]dithiino[2,3-]thianthrene-6,13-dicarbonitrile (bTEpCN), as a prototypical section of 2D COFs, enables further understanding of the properties on such extended networks. Upon adsorption on the Au(111) surface, planarization of bTEpCN is achieved.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637.
Many proteins form paralogous multimers-molecular complexes in which evolutionarily related proteins are arranged into specific quaternary structures. Little is known about the mechanisms by which they acquired their stoichiometry (the number of total subunits in the complex) and heterospecificity (the preference of subunits for their paralogs rather than other copies of the same protein). Here, we use ancestral protein reconstruction and biochemical experiments to study historical increases in stoichiometry and specificity during the evolution of vertebrate hemoglobin (Hb), an αβ heterotetramer that evolved from a homodimeric ancestor after a gene duplication.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
Transcription factors guide tissue development by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. In turn, DNA and chromatin modifications direct the genomic binding of transcription factors. However, how transcription factors navigate chromatin features to selectively bind a small subset of all the possible genomic target loci remains poorly understood.
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