Insights in structural biology can be gained by analyzing protein architectures and characterizing their structural similarities. Current computational approaches enable a comparison of a variety of structural and physicochemical properties in protein space. Here we describe the automated detection of rotational symmetries within a representative set of nearly 10,000 nonhomologous protein structures. To find structural symmetries in proteins initially, equivalent pairs of secondary structure elements (SSE), i.e., alpha-helices and beta-strands, are assigned. Thereby, we also allow SSE pairs to be assigned in reverse sequential order. The results highlight that the generation of symmetric, i.e., repetitive, protein structures is one of nature's major strategies to explore the universe of possible protein folds. This way structurally separated 'islands' of protein folds with a significant amount of symmetry were identified. The complete results of the present study are available at http://agknapp.chemie.fu-berlin.de/gplus, where symmetry analysis of new protein structures can also be performed.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/ci900185z | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
GDFold2: A fast and parallelizable protein folding environment with freely defined objective functions.
Protein Sci
February 2025
MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.
An important step of mainstream protein structure prediction is to model the 3D protein structure based on the predicted 2D inter-residue geometric information. This folding step has been integrated into a unified neural network to allow end-to-end training in state-of-the-art methods like AlphaFold2, but is separately implemented using the Rosetta folding environment in some traditional methods like trRosetta. Despite the inferiority in prediction accuracy, the conventional approach allows for the sampling of various protein conformations compatible with the predicted geometric constraints, partially capturing the dynamic information.
View Article and Find Full Text PDFViscoelasticity of a single poly-protein probed step-by-step during its mechanical unfolding and refolding under the force-clamp conditions.
RSC Adv
January 2025
Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-089 Warsaw Poland
One of still outstanding issues in protein folding is to be able to directly observe structural changes occurring along the folding pathway. Herein, we report on changes of the viscoelastic properties for a single protein molecule measured along its mechanically-induced unfolding and refolding trajectories. We use a model system, the I27 poly-protein, and investigate its conformational changes force-clamp AFM (FC-AFM) spectroscopy.
View Article and Find Full Text PDFChaperones as Potential Pharmacological Targets for Treating Protein Aggregation Illness.
Curr Protein Pept Sci
January 2025
Department of Pharmacy, Panipat Institute of Engineering and Technology, India.
The three-dimensional structure of proteins, achieved through the folding of the nascent polypeptide chain in vivo, is largely facilitated by molecular chaperones, which are crucial for determining protein functionality. In addition to aiding in the folding process, chaperones target misfolded proteins for degradation, acting as a quality control system within the cell. Defective protein folding has been implicated in a wide range of clinical conditions, including neurodegenerative and metabolic disorders.
View Article and Find Full Text PDFLarge and Stable Nanopores Formed by Complement Component 9 for Characterizing Single Folded Proteins.
ACS Nano
January 2025
Adolphe Merkle Institute, University of Fribourg, Fribourg 1700, Switzerland.
Biological nanopores offer a promising approach for single-molecule analysis of nucleic acids, peptides, and proteins. The work presented here introduces a biological nanopore formed by the self-assembly of complement component 9 (C9). This exceptionally large and cylindrical protein pore is composed of 20 ± 4 monomers of C9 resulting in a diameter of 10 ± 4 nm and an effective pore length of 13 nm.
View Article and Find Full Text PDFIs Ockham's razor losing its edge? New perspectives on the principle of model parsimony.
Proc Natl Acad Sci U S A
February 2025
Department of Computer Science, University of Manchester, Manchester M13 9PL, United Kingdom.
The preference for simple explanations, known as the parsimony principle, has long guided the development of scientific theories, hypotheses, and models. Yet recent years have seen a number of successes in employing highly complex models for scientific inquiry (e.g.
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!