We have shown by theoretical studies of alanine peptides that the C(α)D(α) stretch frequency could be particularly useful for determining peptide structure because of its sensitivity to the ϕ,ψ torsion angles at the C(α) atom. To demonstrate that this is a robust methodology worthy of experimental exploration, we have also shown that this mode is even more determinative of conformation in aqueous solution, mainly as a result of the development of differential C(α)--D(α)···O(water) interactions. As further assurance, we now determine the influence of the side chain on this band, showing for aliphatic, a polar, and an aromatic side chains that the dependence is minor and explaining why this is also expected for other side chains. These results should stimulate new experimental methodologies in the field of peptide structure determination.
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http://dx.doi.org/10.1002/bip.21523 | DOI Listing |
Cell Mol Biol (Noisy-le-grand)
January 2025
College of Life Sciences, Liaoning Normal University, Dalian 116000, Liaoning Province, China.
Liaoning cashmere goat is an outstanding breed in China primarily for cashmere production, with strict controls against genetic outflow. Melatonin(MT) is a key factor affecting cashmere growth, and preliminary transcriptome sequencing indicated that melatonin upregulates the expression of the PIP5K1A gene in skin fibroblasts. To predict the physicochemical properties of PIP5K1A in Liaoning cashmere goats, ascertain the tissue localization of PIP5K1A in their skin, and explore the role and mechanism of PIP5K1A in the proliferation of skin fibroblasts.
View Article and Find Full Text PDFBMC Bioinformatics
January 2025
College of Artificial Intelligence, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095, Jiangsu, China.
Antimicrobial peptides (AMPs) have been widely recognized as a promising solution to combat antimicrobial resistance of microorganisms due to the increasing abuse of antibiotics in medicine and agriculture around the globe. In this study, we propose UniAMP, a systematic prediction framework for discovering AMPs. We observe that feature vectors used in various existing studies constructed from peptide information, such as sequence, composition, and structure, can be augmented and even replaced by information inferred by deep learning models.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Plant Molecular Biology and Physiology, Albrecht-von-Haller Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077, Göttingen, Germany.
Class I glutaredoxins (GRXs) are nearly ubiquitous proteins that catalyse the glutathione (GSH)-dependent reduction of mainly glutathionylated substrates. In land plants, a third class of GRXs has evolved (class III). Class III GRXs regulate the activity of TGA transcription factors through yet unexplored mechanisms.
View Article and Find Full Text PDFJ Biol Chem
January 2025
Department of Bioengineering, School of Engineering, The University of Tokyo; Institute of Medical Science, The University of Tokyo; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Japan. Electronic address:
Post-translational modification of proteins is a crucial biological reaction that regulates protein functions by altering molecular properties. The specific detection of such modifications in proteins has made significant contributions to molecular biology research and holds potential for future drug development applications. In HIV research, for example, tyrosine sulfation at the N-terminus of C-C chemokine receptor type 5 (CCR5) is considered to significantly enhance HIV infection efficiency.
View Article and Find Full Text PDFClin Exp Med
January 2025
Department of Hematology-Oncology, Imam Hossein Educational Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
IL-27 is structurally an immune-enhancing and pleiotropic two-chain cytokine associated with IL-12 and IL-6 families. IL-27 contains two subunits, namely IL-27p28 and EBI3. A heterodimer receptor of IL-27, composed of IL27Rα (WSX1) and IL6ST (gp130) chains, mediates the IL-27 function following the activation of STAT1 and STAT3 signaling pathways.
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