The early decades of Cell witnessed key discoveries that coalesced into the field of chaperones, protein folding, and protein quality control.
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Exploring force-driven stochastic folding dynamics in mechano-responsive proteins and implications in phenotypic variation.
Nat Commun
January 2025
Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India.
Single-point mutations are pivotal in molecular zoology, shaping functions and influencing genetic diversity and evolution. Here we study three such genetic variants of a mechano-responsive protein, cadherin-23, that uphold the structural integrity of the protein, but showcase distinct genotypes and phenotypes. The variants exhibit subtle differences in transient intra-domain interactions, which in turn affect the anti-correlated motions among the constituent β-strands.
View Article and Find Full Text PDFExtracellular calreticulin regulates fibrogenic and immunogenic properties of hepatic stellate cells.
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Liver fibrosis is a persistent damage repair response triggered by various etiological factors, resulting in an excessive accumulation of extracellular matrix (ECM). Activated hepatic stellate cells (HpSCs) are the primary source of ECM proteins. Therefore, specifically targeting HpSCs has become a crucial approach for treating liver fibrosis.
View Article and Find Full Text PDFMapping conformational landscape in protein folding: Benchmarking dimensionality reduction and clustering techniques on the Trp-Cage mini-protein.
Biophys Chem
January 2025
Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India. Electronic address:
Quantitative characterization of protein conformational landscapes is a computationally challenging task due to their high dimensionality and inherent complexity. In this study, we systematically benchmark several widely used dimensionality reduction and clustering methods to analyze the conformational states of the Trp-Cage mini-protein, a model system with well-documented folding dynamics. Dimensionality reduction techniques, including Principal Component Analysis (PCA), Time-lagged Independent Component Analysis (TICA), and Variational Autoencoders (VAE), were employed to project the high-dimensional free energy landscape onto 2D spaces for visualization.
View Article and Find Full Text PDFMolecular Origami: Designing Functional Molecules of the Future.
Molecules
January 2025
Department of Chemistry and Materials Engineering, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita 564-8680, Osaka, Japan.
In the field of chemical biology, DNA origami has been actively researched. This technique, which involves folding DNA strands like origami to assemble them into desired shapes, has made it possible to create complex nanometer-sized structures, marking a major breakthrough in nanotechnology. On the other hand, controlling the folding mechanisms and folded structures of proteins or shorter peptides has been challenging.
View Article and Find Full Text PDFThe Use of Dansyl Chloride to Probe Protein Structure and Dynamics.
Int J Mol Sci
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Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
Dansyl labeling is a widely used approach for enhancing the detection of small molecules by UV spectroscopy and mass spectrometry. It has been successfully applied to identify and quantify a variety of biological and environmental specimens. Despite clear advantages, the dansylation reaction has found very few applications in the study of proteins.
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