We investigate the dynamics of colloidal crystallization in a 32-particle system at a fixed value of interparticle depletion attraction that produces coexisting fluid and solid phases. Free energy landscapes (FELs) and diffusivity landscapes (DLs) are obtained as coefficients of 1D Smoluchowski equations using as order parameters either the radius of gyration or the average crystallinity. FELs and DLs are estimated by fitting the Smoluchowski equations to Brownian dynamics (BD) simulations using either linear fits to locally initiated trajectories or global fits to unbiased trajectories using Bayesian inference. The resulting FELs are compared to Monte Carlo Umbrella Sampling results. The accuracy of the FELs and DLs for modeling colloidal crystallization dynamics is evaluated by comparing mean first-passage times from BD simulations with analytical predictions using the FEL and DL models. While the 1D models accurately capture dynamics near the free energy minimum fluid and crystal configurations, predictions near the transition region are not quantitatively accurate. A preliminary investigation of ensemble averaged 2D order parameter trajectories suggests that 2D models are required to capture crystallization dynamics in the transition region.
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Int J Biol Macromol
December 2024
Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan. Electronic address:
The formation of the pyroglutamate variant of amyloid beta (pGlu-Aβ), which is extremely hydrophobic, rapidly aggregating, and highly neurotoxic, is mediated by the action of secretory glutaminyl cyclase (sQC). The pGlu-Aβ often acts as a seed for the aggregation of the full length Aβ and contributes to the overall load of Aβ plaques in Alzheimer's disease (AD). Therefore, inhibiting sQC is a potential approach to limit the formation of pGlu-Aβ and to modify the progression of AD.
View Article and Find Full Text PDFSpectrochim Acta A Mol Biomol Spectrosc
December 2024
Department of Chemistry, University of Hull, Hull HU6 7RX, UK. Electronic address:
Circular dichroism mapping (CDM) method was introduced by utilizing the highly collimated light beam of synchrotron radiation (SR) available at Diamond Light Source B23 beamline for scanning the thin films of the N phase. We apply SR-CDM to two achiral dimeric materials exhibiting the N phase: symmetric DTC5C9 and dissymmetric DTC5C9CB. The SR-CDM measurements directly capture the chiral information in the local N domains, providing the ultimate complement to the theoretical predictions of the helical structures: the spontaneous symmetry breaking in N phase is ambidextrous.
View Article and Find Full Text PDFColloids Surf B Biointerfaces
December 2024
Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:
Significant progress has been achieved with diversity of short peptide supramolecular assemblies. However, their programmable phase modulation by single stimulus remains a great challenge. Herein, we demonstrate a dipeptide supramolecular system undergoes sequentially coupled phase transitions upon hydrogen bonding association and dissociation triggered by a single fatty acid.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Department of Biochemistry, Brandeis University, Waltham, MA 02454.
Reversible protein phosphorylation directs essential cellular processes including cell division, cell growth, cell death, inflammation, and differentiation. Because protein phosphorylation drives diverse diseases, kinases and phosphatases have been targets for drug discovery, with some achieving remarkable clinical success. Most protein kinases are activated by phosphorylation of their activation loops, which shifts the conformational equilibrium of the kinase toward the active state.
View Article and Find Full Text PDFSubcell Biochem
December 2024
Structure and Cell Biology of Viruses Lab, CIC bioGUNE - Basque Research and Technology Alliance, Derio, Spain.
A virus particle must work as a strongroom to protect its genome, but at the same time it must undergo dramatic conformational changes to infect the cell in order to replicate and assemble progeny. Thus, viruses are miniaturized wonders whose structural complexity requires investigation by a combination of different techniques that can tackle both static and dynamic processes. In this chapter, we will illustrate how major structural techniques such as X-ray crystallography and electron microscopy can be combined with other techniques to determine the structure of complex viruses.
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