The conformational diffusion coefficient for intrachain motions in biopolymers, D, sets the timescale for structural dynamics. Recently, force spectroscopy has been applied to determine D both for unfolded proteins and for the folding transitions in proteins and nucleic acids. However, interpretation of the results remains unsettled. We investigated how instrumental effects arising from the force probes used in the measurement can affect the value of D recovered via force spectroscopy. We compared estimates of D for the folding of DNA hairpins found from measurements of rates and energy landscapes made using optical tweezers with estimates obtained from the same single-molecule trajectories via the transition path time. The apparent D obtained from the rates was much lower than the result found from the same data using transition time analysis, reflecting the effects of the mechanical properties of the force probe. Deconvolution of the finite compliance effects on the measurement allowed the intrinsic value to be recovered. These results were supported by Brownian dynamics simulations of the effects of force-probe compliance and bead size.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190644 | PMC |
| http://dx.doi.org/10.1016/j.bpj.2014.08.007 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Quantitative Prediction of Protein-Polyelectrolyte Binding Thermodynamics: Adsorption of Heparin-Analog Polysulfates to the SARS-CoV-2 Spike Protein RBD.
JACS Au
January 2025
Department of Physics, Freie Universität Berlin, Arnimallee 14, Berlin 14195, Germany.
Interactions of polyelectrolytes (PEs) with proteins play a crucial role in numerous biological processes, such as the internalization of virus particles into host cells. Although docking, machine learning methods, and molecular dynamics (MD) simulations are utilized to estimate binding poses and binding free energies of small-molecule drugs to proteins, quantitative prediction of the binding thermodynamics of PE-based drugs presents a significant obstacle in computer-aided drug design. This is due to the sluggish dynamics of PEs caused by their size and strong charge-charge correlations.
View Article and Find Full Text PDFAl doped silica glass: investigation of structural response and defect interactions based on crystalline models.
Phys Chem Chem Phys
January 2025
The Quartz Corp, Hellandsveien 14, 8270, Drag, Norway.
High purity quartz glass is an important material in high-tech industries like semiconductors and photovoltaics due to, among other properties, its good mechanical performance at high temperatures. Small amounts of Al in silica glass (in the range between 20 ppm and 100 ppm) have previously been shown to increase the viscosity of the SiO glass. The underlying mechanism for this increase is, however, not well understood.
View Article and Find Full Text PDFThe combined antimicrobial activity of α-lactalbumin and thymol against Escherichia coli and Staphylococcus aureus.
Food Chem
January 2025
College of Food Science and Engineering, Jilin University, Changchun 130062, China. Electronic address:
Thymol showed good antimicrobial activity, however, the poor aqueous solubility limits it to apply in food industry. α-Lactalbumin can be used to delivery hydrophobic molecules, then enhancing their biological activities. The study investigates the potential of α-lactalbumin to expand the application range of thymol, further to evaluate the antimicrobial activity of the α-lactalbumin-thymol complexation.
View Article and Find Full Text PDFQuantum chemical studies of carbon-based graphene-like nanostructures: from benzene to coronene.
J Mol Model
January 2025
Department of Chemistry, Federal Institute of Education, Science and Technology of Espírito Santo, Av. Min. Salgado Filho, Vila Velha, 29106-010, Espírito Santo, Brazil.
Context: This study presents quantum chemical analysis of 14 distinct carbon-based nanostructures (CBN), ranging from simple molecules, like benzene, to more complex structures, such as coronene, which serves as an exemplary graphene-like model. The investigation focuses on elucidating the relationships between molecular orbital (MO) energies, the energy band gaps, electron occupation numbers (eON), electronic conduction, and the compound topologies, seeking to find the one that approaches most of a graphene-like structure for in silico studies. Through detailed examination of molecular properties including chemical hardness and chemical potential, we demonstrate that the electronic exchange between orbitals is directly influenced by the structural topology of the carbon-based nanostructures, as the electron occupation numbers and the molecular orbital energies.
View Article and Find Full Text PDFThickness Dependence in Phase Formation and Properties of TaSe Layers Grown on GaP(111).
ACS Appl Mater Interfaces
January 2025
Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, Junia-ISEN, UMR 8520-IEMN, F-59000 Lille, France.
The effect of growth temperature and subsequent annealing on the epitaxy of both single- and few-layer TaSe on Se-terminated GaP(111) substrates is investigated. The selective growth of the 1T and 1H phases is shown up to 1 ML according to X-ray and ultraviolet photoelectron spectroscopies. The 1H monolayer, favored at low temperatures, exhibits a very homogeneous coverage after annealing, while the 1T ML, grown at high temperatures, is characterized by a better in-plane orientation.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!