"How do proteins fold?" Researchers have been studying different aspects of this question for more than 50 years. The most conceptual aspect of the problem is how protein can find the global free energy minimum in a biologically reasonable time, without exhaustive enumeration of all possible conformations, the so-called "Levinthal's paradox." Less conceptual but still critical are aspects about factors defining folding times of particular proteins and about perspectives of machine learning for their prediction. We will discuss in this review the key ideas and discoveries leading to the current understanding of folding kinetics, including the solution of Levinthal's paradox, as well as the current state of the art in the prediction of protein folding times.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7072185 | PMC |
| http://dx.doi.org/10.3390/biom10020250 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Engineering thermostable fluorescent DNA aptamer for the isothermal amplification of nucleic acids.
Biosens Bioelectron
January 2025
Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China. Electronic address:
Isothermal amplification-based nucleic acid detection technologies have become rapid and efficient tools for molecular diagnostics. Sequence-specific monitoring methods are crucial for isothermal amplification, as they help identify the occurrence of extended primer dimers, which can lead to false positive results. Fluorescent aptamers are promising tools for real-time monitoring of isothermal amplification but are inherently limited by thermostability.
View Article and Find Full Text PDFMapping conformational landscape in protein folding: Benchmarking dimensionality reduction and clustering techniques on the Trp-Cage mini-protein.
Biophys Chem
January 2025
Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India. Electronic address:
Quantitative characterization of protein conformational landscapes is a computationally challenging task due to their high dimensionality and inherent complexity. In this study, we systematically benchmark several widely used dimensionality reduction and clustering methods to analyze the conformational states of the Trp-Cage mini-protein, a model system with well-documented folding dynamics. Dimensionality reduction techniques, including Principal Component Analysis (PCA), Time-lagged Independent Component Analysis (TICA), and Variational Autoencoders (VAE), were employed to project the high-dimensional free energy landscape onto 2D spaces for visualization.
View Article and Find Full Text PDFFormulation Design of Orally Disintegrating Film Using Two Cellulose Derivatives as a Blend Polymer.
Pharmaceutics
January 2025
Laboratory of Advanced Pharmaceutical Process Engineering, Gifu Pharmaceutical University, 5-6-1 Mitahora-Higashi, Gifu 502-8585, Japan.
: Orally disintegrating film (ODF) is prepared using water-soluble polymers as film-forming agents. To improve mechanical and disintegration properties, some polymers need to be blended with others. This study aimed to investigate the utility of hydroxypropyl cellulose (HPC) and hydroxypropyl methyl cellulose (HPMC) as blend film-forming components for ODFs.
View Article and Find Full Text PDFExploring the Potential Effectiveness of Oil and Its Nano-Emulsion on (Lepidoptera: Nolidae).
Insects
January 2025
Plant Protection Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt.
(Lepidoptera: Nolidae) is a major pest of cotton and other crops in Egypt, and the widespread use of insecticides has led to resistance. This study evaluates, for the first time, the bioactivity of (Malpighiales: Euphorbiaceae) oil and its nano-emulsion (CTNE) against 25 newly hatched larvae of Boisd. We assessed their biological effects across different developmental stages and performed histological and ultrastructural examinations.
View Article and Find Full Text PDFGiant pit craters on the modern seafloor above magma-induced hydrothermal vent complexes of Scotia Sea, offshore Antarctica.
Sci Rep
January 2025
Department of Geology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland.
Massive injection of C depleted carbon to the ocean and atmosphere coincided with major environmental upheaval multiple times in the geological record. For several events, the source of carbon has been attributed to explosive venting of gas produced when magmatic sills intruded organic-rich sediment. The concept mostly derives from studies of a few ancient sedimentary basins with numerous hydrothermal vent complexes (HTVCs) where craters appear to have formed across large areas of the seafloor at the same time, but good examples remain rare in strata younger than the Early Eocene.
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!