Despite possessing marked structural similarities, the chemokines macrophage inflammatory protein-1alpha (MIP-1alpha; CCL3) and RANTES (CCL5) display differential activity in hematopoietic progenitor-cell-inhibitory assays, with MIP-1alpha being active and RANTES inactive in this context. We have sought to identify the key structural determinants of this property of MIP-1alpha. This has involved constructing MIP-1alpha/RANTES chimeras by swapping structural domains between the 2 proteins. Results indicate that, in contrast to other chemokine functions, neither the N nor the C termini are key determinants of inhibitory activity. The motif that appears to be most important for this activity lies between the second and fourth cysteines of MIP-1alpha and further domain swap analysis has narrowed this down to the 3 10 helical turn preceding the first beta-strand in MIP-1alpha. More detailed analysis has highlighted the role played by a specific dipeptide motif in the proliferation-inhibitory activity of chemokines. The involvement of the 3 10 helical-turn motif in chemokine function is unprecedented and this study therefore identifies a novel, functionally essential motif within chemokines. In addition, this study further attests to the alternative mechanisms of action used by MIP-1alpha in inhibition of hematopoietic progenitor-cell proliferation and regulation of leukocyte migration.
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http://dx.doi.org/10.1182/blood-2005-08-3112 | DOI Listing |
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January 2025
Leicester Institute for Pharmaceutical Innovation, Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester, LE1 9BH, UK.
Guiding molecular assembly of peptides into rationally engineered nanostructures remains a major hurdle against the development of functional peptide-based nanomaterials. Various non-covalent interactions come into play to drive the formation and stabilization of these assemblies, of which electrostatic interactions are key. Here, the atomistic mechanisms by which electrostatic interactions contribute toward controlling self-assembly and lateral association of ultrashort β-sheet forming peptides are deciphered.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Knowledge City, SAS Nagar, Mohali 140306, Punjab, India.
GntR/FadR family featuring an N-terminal winged helix-turn-helix DNA-binding domain and a C-terminal α-helical effector-binding and oligomerization domain constitutes one of the largest families of transcriptional regulators. Several GntR/FadR regulators govern the metabolism of sugar acids, carbon sources implicated in bacterial-host interactions. Although effectors are known for a few sugar acid regulators, the unavailability of relevant structures has left their allosteric mechanism unexplored.
View Article and Find Full Text PDFBinding of transcription factors (TFs) at gene regulatory elements controls cellular epigenetic state and gene expression. Current genome-wide chromatin profiling approaches have inherently limited resolution, complicating assessment of TF occupancy and co-occupancy, especially at individual alleles. In this work, we introduce Accessible Chromatin by Cytosine Editing Site Sequencing with ATAC-seq (ACCESS-ATAC), which harnesses a double-stranded DNA cytosine deaminase (Ddd) enzyme to stencil TF binding locations within accessible chromatin regions.
View Article and Find Full Text PDFBioinformatics
December 2024
Independent Scientist, Reading, MA 01867, United States.
Motivation: Beta turns are the most common type of secondary structure in proteins after alpha helices and beta sheets and play many key structural and functional roles. Turn backbone (BB) geometry has been classified at multiple levels of precision, but the current picture of side chain (SC) structure and interaction in turns is incomplete, because the distribution of SC conformations associated with each sequence motif has commonly been represented only by a static image of a single, typical structure for each turn BB geometry, and only motifs which specify a single amino acid (e.g.
View Article and Find Full Text PDFbioRxiv
December 2024
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306.
CrgA is a key transmembrane (TM) protein in the cell division process of (), the pathogen responsible for tuberculosis. While many of the divisome proteins have been identified, their structures and interactions remain largely unknown. Previous studies of CrgA using oriented-sample solid-state NMR have defined the tilt and rotation of the TM helices, but the cytoplasmic and periplasmic domains and even the oligomeric state were uncharacterized.
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