Density functional theory calculations were performed on a series of difluorinated-thienylfuran oligomers containing up to six repeat units. For any given oligomer, a building unit was chosen to be either in the transoid or in the cisoid conformation. The oligomers are found to be more stable in the all-cisoid conformation as a result of intramolecular F...H hydrogen bonding interactions, as well as stacking pi-pi interactions for the larger oligomers. The relative stability increases markedly with the size of the oligomers, allowing for the adoption of well-defined folding helical patterns for systems with at least five repeat units. Conveniently designed isodesmic reactions show that folding of the oligomers is a thermodynamically favorable process.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1039/b916415d | DOI Listing |
Int J Biol Macromol
January 2025
School of Physical Science and Technology, Ningbo University, Ningbo 315211, China; Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States. Electronic address:
Human calcitonin (hCT) is a peptide hormone that regulates calcium homeostasis, but its abnormal aggregation can disrupt physiological functions and increase the risk of medullary thyroid carcinoma. To elucidate the mechanisms underlying hCT aggregation, we investigated the self-assembly dynamics of hCT segments (hCT, hCT, and hCT) and the folding and dimerization of full-length hCT through microsecond atomistic discrete molecular dynamics (DMD) simulations. Our results revealed that hCT and hCT predominantly existed as isolated monomers with transient small-sized oligomers, indicating weak aggregation tendencies.
View Article and Find Full Text PDFAcc Chem Res
January 2025
Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States.
ConspectusProtein higher-order structure (HOS) is key to biological function because the mechanisms of protein machinery are encoded in protein three-dimensional structures. Mass spectrometry (MS)-based protein footprinting is advancing protein structure characterization by mapping solvent-accessible regions of proteins and changes in H-bonding, thereby providing higher order structural information. Footprinting provides insights into protein dynamics, conformational changes, and interactions, and when conducted in a differential way, can readily reveal those regions that undergo conformational change in response to perturbations such as ligand binding, mutation, thermal stress, or aggregation.
View Article and Find Full Text PDFJ Biomol Struct Dyn
December 2024
Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, India.
CapG, an enzyme expressed by , catalyzes an epimerization reaction to synthesize -acetyl-L-fucosamine, a constituent of capsule involved in pathogenesis. This protein has two domains, exists as the homohexamers in the solution, and usually produces products at hundred-nanomolar concentrations. To determine the folding-unfolding mechanism and the oligomeric form of CapG, particularly at low concentrations, we have investigated a recombinant CapG (rCapG) using different probes.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
December 2024
Department of Cell Biology, Harvard Medical School, Boston MA 02115.
A hallmark of neurodegenerative diseases (NDs) is the progressive loss of proteostasis, leading to the accumulation of misfolded proteins or protein aggregates, with subsequent cytotoxicity. To combat this toxicity, cells have evolved degradation pathways (ubiquitin-proteasome system and autophagy) that detect and degrade misfolded proteins. However, studying the underlying cellular pathways and mechanisms has remained a challenge, as formation of many types of protein aggregates is asynchronous, with individual cells displaying distinct kinetics, thereby hindering rigorous time-course studies.
View Article and Find Full Text PDFInt J Mol Sci
November 2024
Laboratory of Pathoneurochemistry, Department of Neurochemistry, Mossakowski Medical Research Institute, 02-106 Warsaw, Poland.
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!