One of the smallest proteins with end-to-end β-sheet is the designed 36-residue protein DS119. We recently suggested that the rate-limiting step in the folding of the βαβ protein is the formation of the central helix that then provides a scaffold for the parallel β-sheet formed by the two chain ends. In the present report we investigate whether and how this folding mechanism depends on the energy function, and compare the efficiency of molecular dynamics and Monte Carlo implementations of multicanonical sampling. While we find the native structure with similar frequency as in our previous simulations, we observe that the folding mechanism differs for both force fields.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1063/1.4865127 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Molecular Insights into the Control Mechanism of the Solid-Liquid Interface Interaction on Shale Oil Occurrence: Grand Canonical Monte Carlo and Molecular Dynamics Simulations Investigation.
Langmuir
January 2025
Hubei Key Laboratory of Oil and Gas Exploration and Development Theory and Technology (China University of Geosciences), Wuhan 430074, China.
The strong solid-liquid interaction leads to the complicated occurrence characteristics of shale oil. However, the solid-liquid interface interaction and its controls of the occurrence state of shale oil are poorly understood on the molecular scale. In this work, the adsorption behavior and occurrence state of shale oil in pores of organic/inorganic matter under reservoir conditions were investigated by using grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations.
View Article and Find Full Text PDFReducing Structural Nonidentifiabilities in Upstream Bioprocess Models Using Profile-Likelihood.
Biotechnol Bioeng
January 2025
Boehringer Ingelheim Pharma GmbH & Co.KG, Biopharmaceuticals Germany, Biberach an der Riß, Germany.
Process models are increasingly used to support upstream process development in the biopharmaceutical industry for process optimization, scale-up and to reduce experimental effort. Parametric unstructured models based on biological mechanisms are highly promising, since they do not require large amounts of data. The critical part in the application is the certainty of the parameter estimates, since uncertainty of the parameter estimates propagates to model predictions and can increase the risk associated with those predictions.
View Article and Find Full Text PDFProbabilistic assessment of the cumulative risk from dietary heavy metal exposure in Chongqing, China using a hazard-driven approach.
Sci Rep
January 2025
School of Public Health, Chongqing Medical University, Chongqing, China.
Cumulative risk assessment is significant for evaluating the combined exposure to multiple substances, but its widespread acceptance and application have been limited due to the complexity of clarifying and assessing actual exposure. In this study, we conducted a cumulative risk assessment based on hazard-driven criteria to evaluate the co-exposure to elemental contaminants in the diet of the population in Chongqing Municipality. The cumulative risk was calculated and evaluated using Monte Carlo modeling and the modified Reference Point Index (mRPI) method.
View Article and Find Full Text PDFBiosorption of rhodamine B and sunset yellow dyes on cross-linked chitosan-alginate biocomposite beads: Experimental and theoretical studies.
Int J Biol Macromol
January 2025
Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Ibn Zohr University, Agadir 80000, Morocco. Electronic address:
This research explores the biosorption of Rhodamine B (Rd-B) and Sunset Yellow (SY) dyes using cross-linked chitosan-alginate (Ch-A) biocomposite beads, combining experimental investigations with theoretical studies to elucidate the biosorption mechanisms. The biocomposite beads were synthesized through an eco-friendly cross-linking method, and their structural properties were characterized using various characterization techniques. Complementary theoretical studies using Monte Carlo (MC) simulations and molecular dynamics (MD) calculations provided insights into the molecular interactions between the dyes and the biocomposite beads.
View Article and Find Full Text PDFMulti-layer shielding optimization of a high activity Am-Be mixed field irradiation facility.
Appl Radiat Isot
January 2025
Experimental Nuclear Physics Department, Nuclear Research Centre, Egyptian Atomic Energy Authority, Egypt; Cyclotron Facility, Egyptian Atomic Energy Authority, Egypt.
Neutron and gamma-ray shielding design for a 30Ci (1.11TBq) Am-Be irradiation facility is studied using MCNP5 Monte Carlo simulation code. The study focuses on the optimization of the shielding layers of the previously planned neutron irradiation facility.
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!