Interlocked molecules exhibit structural isomerization that is different from that of molecules whose connectedness is solely through covalent bonds. A mechanical bond, or the interlocking of components, provides a rich conformational landscape. The ability of synthetic chemists to design directional motion between these mechanical conformers suggests mechanical bonds as building blocks in the design of synthetic molecular motors and machines. Here we examine the complexity of mechanical conformers of radial catenanes with n anisotropically repulsive rings (coined "keyrings") threaded onto a single central ring for n ≤ 10. For a given number of rings, n, the ratio of the key length to the main ring radius, λ, determines the mechanical conformer. We show that this system displays symmetrical in-plane conformers for short keys and co-conformers of lower symmetry where the keys lie out of the plane for longer keys.
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http://dx.doi.org/10.1021/acs.jpca.8b08646 | DOI Listing |
Cells
January 2025
Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 5 1-1-1 Higashi, Tsukuba 305-8565, Ibaraki, Japan.
Nestin is a type VI intermediate filament protein and a well-known neural stem cell marker. It is also expressed in high-grade cancer cells, forming copolymerized filaments with vimentin. We previously showed that nestin inhibits the binding of vimentin's tail domain to actin filaments (AFs) by steric hindrance through its large nestin tail domain (NTD), thereby increasing three-dimensional cytoskeleton network mobility, enhancing cell flexibility, and promoting cancer progression.
View Article and Find Full Text PDFRSC Adv
January 2025
College of Agriculture and Biological Science, Dali University Dali 671000 China
The conformational dynamics and activation mechanisms of KRAS proteins are of great importance for targeted cancer therapy. However, the detailed molecular mechanics of KRAS activation induced by GTP binding remains unclear. In this study, we systematically investigated how GTP/GDP exchange affects the thermodynamic and kinetic properties of KRAS and explored the activation mechanism using molecular dynamics (MD) simulations, Markov state models (MSMs), and neural relational inference (NRI) models.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States.
Ribonucleotide reductase (RNR) is essential for DNA synthesis and repair in all living organisms. The mechanism of RNR requires long-range radical transport through a proton-coupled electron transfer (PCET) pathway spanning two different protein subunits. Herein, the direct PCET reaction between the interfacial tyrosine residues, Y356 and Y731, is investigated with a vibronically nonadiabatic theory that treats the transferring proton and all electrons quantum mechanically.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Biological Sciences, Purdue University, West Lafayette, 47907, Indiana, USA.
RNA plays a crucial role not only in information transfer as messenger RNA during gene expression but also in various biological functions as non-coding RNAs. Understanding mechanical mechanisms of function needs tertiary structure information; however, experimental determination of three-dimensional RNA structures is costly and time-consuming, leading to a substantial gap between RNA sequence and structural data. To address this challenge, we developed NuFold, a novel computational approach that leverages state-of-the-art deep learning architecture to accurately predict RNA tertiary structures.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; Shanghai Aquatic Products Processing and Storage Engineering Technology Research Center, Shanghai 201306, China; National Experimental Teaching Demonstration Center for Food Science and Engineering (Shanghai Ocean University), Shanghai 201306, China. Electronic address:
Phenolic acid-chitosan derivatives have received extensive attention due to their greatly enhanced mechanical, antibacterial and antioxidant properties, especially in food preservation. The chitosan-gentianic acid (CS-g-GA) was prepared and its impact on myofibrillar proteins (MPs) in sea bass (Lateolabrax maculatus) during refrigerated storage was investigated in this study. Fish fillets were immersed in distilled water, CS, GA and CS-g-GA solutions, respectively, followed by an 18-day refrigerated storage.
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