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Silk fibroin (SF) hydrogels possess excellent biocompatibility and biomimetic properties of the extracellular matrix. Among them, the mild chemical crosslinked SF hydrogels show great application potential in the fields of 3D cell culture and tissue repairing and thus have attracted widespread attention. However, the mobility of hydrophobic chain segments of SF molecules in these chemical crosslinked hydrogels can easily cause the molecules to undergo a self-assembly process from random coil to -sheet conformation due to its lower energy state, thus inducing an inevitable conformational transition process. This process further leads to dynamic changes of important material features, such as the hydrogel pore size and mechanical properties, which can probably bring some non-negligible and unknown impacts on cell behaviors and their biomedical applications. In this study, a typical mild crosslinking system composed of horseradish peroxidase and hydrogen peroxide was chosen to prepare SF hydrogels. A feasible protein conformational transition rate controlling strategy based on hydrogel crosslinking density regulation was also proposed. Our results demonstrate that the lower the hydrogel crosslinking density, the faster the conformational transition rate. Subsequently, SF hydrogels with different conformational transition rates were successfully constructed to investigate the impact of the protein conformational transition rate accompanied with initial crosslinking density on the proliferation and chondrogenic differentiation of encapsulated stem cells. Results comprehensively illustrated that the conformational transition process could effectively regulate cell behavior. The hydrogel with an appropriate conformational transition rate obviously promoted the proliferation and chondrogenesis of encapsulated stem cells, while too fast or too slow transition processes slowed down these cell activities. These findings are hopefully to provide valuable guidance for the development and efficient usage of SF hydrogels in the fields of 3D cell culture and tissue engineering.
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http://dx.doi.org/10.1093/rb/rbaf019 | DOI Listing |
J Phys Chem B
September 2025
Department of Chemistry, IIT Jodhpur, Jodhpur, Rajasthan 342037, India.
The dynamics of the aggregated light-harvesting complex (LHCII) associated with its antenna pigments can be crucial for a transition between light-harvesting and dissipative states, which is pivotal for nonphotochemical quenching (NPQ). To this end, aggregation of pigment-binding LHCII monomers and PsbS-associated trimers in neutral and low lumenal pH respectively, has been investigated when embedded in the plant thylakoid membranes, using coarse-grained molecular dynamics simulations. Both pigment-binding LHCII monomers and PsbS-associated trimers dynamically form and break dimers and higher-order aggregates in thylakoids within the simulation time.
View Article and Find Full Text PDFJ Inorg Biochem
September 2025
Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States. Electronic address:
Omega loop C (residues 40-57) of cytochrome c (Cytc) is a common location for naturally-occurring variants of human Cytc that cause thrombocytopenia 4 (THC4). These variants are characterized by significant increases in the intrinsic peroxidase activity of Cytc, which appears to be linked to increased dynamics in Ω-loop D (residues 71-85). The mutations in Ω-loop C enhance the dynamics of Ω-loop D by decreasing the acid dissociation constant of the trigger group (pK) of the alkaline conformational transition.
View Article and Find Full Text PDFChem Asian J
September 2025
School of Chemistry and Chemical Engineering, Hainan University, Haikou, 570228, China.
Molecules that exhibit excited-state intramolecular proton transfer (ESIPT) have demonstrated great promise in fluorescent probes. The electronic effect of substituents has an important influence on the ESIPT process. In this study, we investigated the effects of substituents on the ESIPT mechanism and the photophysical behavior of single-benzene fluorophore (SBF) derivatives with computational chemistry methods.
View Article and Find Full Text PDFACS Appl Mater Interfaces
September 2025
Department of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea.
Cyclic peptides (CPs) are versatile building blocks whose conformational constraints foster ordered supramolecular architectures with potential in biomedicine, nanoelectronics, and catalysis. Herein, we report the development of biomimetic antifreeze materials by conjugating CPs bearing ice-binding residues to 4-arm polyethylene glycol (PEG) via click chemistry. The concentration-dependent self-assembly of these CP-PEG conjugates induces programmable morphological transitions, forming nanotube networks above the critical aggregation concentration (CAC) and two-dimensional nanosheet networks near the CAC.
View Article and Find Full Text PDFJ Chem Inf Model
September 2025
College of Agriculture and Biological Science, Dali University, Dali 671000, China.
The E76K mutation in protein tyrosine phosphatase (PTP) SHP2 is a recurrent driver of developmental disorders and cancers, yet the mechanism by which this single-site substitution promotes persistent activation remains elusive. Here, we combine path-based conformational sampling, unbiased molecular dynamics (MD) simulations, Markov state models (MSMs), and neural relational inference (NRI) to elucidate how E76K reshapes the activation landscape and regulatory architecture of SHP2. Using a minimum-action trajectory derived from experimentally determined closed and open structures, we generated representative transition intermediates to guide the unbiased MD simulations.
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