Describing the whole story of protein folding is currently the main enigmatic problem in molecular bioinformatics study. Protein folding mechanisms have been intensively investigated with experimental as well as simulation techniques. Since a protein folds into its specific 3D structure from a unique amino acid sequence, it is interesting to extract as much information as possible from the amino acid sequence of a protein. Analyses based on inter-residue average distance statistics and a coarse-grained Gō-model simulation were conducted on Ig and FN3 domains of a titin protein to decode the folding mechanisms from their sequence data and native structure data, respectively. The central region of all domains was predicted to be an initial folding unit, that is, stable in an early state of folding. This common feature coincides well with the experimental results and underscores the significance of the β-sandwich proteins' common structure, namely, the key strands for folding and the Greek-key motif, which is located in the central region. We confirmed that our sequence-based techniques were able to predict the initial folding event just next to the denatured state and that a 3D-based Gō-model simulation can be used to investigate the whole process of protein folding.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1002/prot.25862 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
The novel use of the CFTR corrector C17 in muscular dystrophy: Pharmacological profile and in vivo efficacy.
Biochem Pharmacol
January 2025
Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy,. Electronic address:
Sarcoglycanopathies are rare forms of severe muscular dystrophies currently without a therapy. Mutations in sarcoglycan (SG) genes cause the reduction or absence of the SG-complex, a tetramer located in the sarcolemma that plays a protective role during muscle contraction. Missense mutations in SGCA, which cause α-sarcoglycanopathy, otherwise known as LGMD2D/R3, lead to folding defective forms of α-SG that are discarded by the cell quality control.
View Article and Find Full Text PDFCalreticulin-From the Endoplasmic Reticulum to the Plasma Membrane-Adventures of a Wandering Protein.
Cancers (Basel)
January 2025
Department of Pathology, Dalhousie University, Halifax, NS B3H 1X5, Canada.
Calreticulin (CRT) is a 46 kDa highly conserved protein initially identified as calregulin, a prominent Ca-binding protein of the endoplasmic reticulum (ER). Subsequent studies have established that CRT functions in the ER's protein folding response and Ca homeostatic mechanisms. An ER retention signal on the carboxyl terminus of CRT suggested that CRT was restricted to the ER.
View Article and Find Full Text PDFDesign and Aerodynamic Analysis of a Flapping Mechanism for Foldable Biomimetic Aircraft.
Biomimetics (Basel)
January 2025
Automotive Parts Research Institute, Hunan University of Technology, Hengyang 421002, China.
This study investigates the unsteady aerodynamic mechanisms underlying the efficient flight of birds and proposes a biomimetic flapping-wing aircraft design utilizing a double-crank double-rocker mechanism. Building upon a detailed analysis of avian flight dynamics, a two-stage foldable flapping mechanism was developed, integrating an optimized double-crank double-rocker structure with a secondary linkage system. This design enables synchronized wing flapping and spanwise folding, significantly enhancing aerodynamic efficiency and dynamic performance.
View Article and Find Full Text PDFCaledonian reactivation and reworking of Timanian thrust systems and implications for latest Mesoproterozoic to mid-Paleozoic tectonics and magmatism in northern Baltica.
Open Res Eur
October 2024
Brønnøy Kalk, Velfjord, Nordland, 8960, Norway.
Background: The Trollfjorden-Komagelva Fault Zone is the southernmost thrust fault of the Timanian Orogen and extends for thousands of kilometers from northwestern Russia to northern Norway. Though there is little about its location onshore northeastern Norway, where it is mapped as a major fault system dominantly comprised of NNE-dipping thrust faults, its continuation to the west below Caledonian nappes and offshore post-Caledonian sedimentary basins remains a matter of debate.
Methods: The present study provides a more definitive answer about the continuation of Trollfjorden-Komagelva Fault Zone west of the Varanger Peninsula by using seismic reflection, bathymetric, topographic, and magnetic data onshore Finnmark and offshore on the Finnmark Platform.
Engineering hydrogen bonding at tyrosine-201 in the orange carotenoid protein using halogenated analogues.
Photosynth Res
January 2025
Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
The Orange Carotenoid Protein (OCP) is a unique water-soluble photoactive protein that plays a critical role in regulating the balance between light harvesting and photoprotective responses in cyanobacteria. The challenge in understanding OCP´s photoactivation mechanism stems from the heterogeneity of the initial configurations of its embedded ketocarotenoid, which in the dark-adapted state can form up to two hydrogen bonds to critical amino acids in the protein's C-terminal domain, and the extremely low quantum yield of primary photoproduct formation. While a series of experiments involving point mutations within these contacts helped us to identify these challenges, they did not resolve them.
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!