SUMMARY: Every protein family has a set of characteristic secondary structures. However, due to individual variations, a single structure is not enough to represent the whole family. OverProt can create a secondary structure consensus, showing the general fold of the family as well as its variation. Our server provides precomputed results for all CATH superfamilies and user-defined computations, visualized by an interactive viewer, which shows the secondary structure element type, length, frequency of occurrence, spatial variability and β-connectivity. AVAILABILITY AND IMPLEMENTATION: OverProt Server is freely available at https://overprot.ncbr.muni.cz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• konsensus MeSH
• počítače MeSH
• proteiny * chemie   MeSH
• sekundární struktura proteinů MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny * MeSH

SUMMARY: Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2D diagrams for all domains from the CATH and all proteins from PDB databases. These 2D diagrams are generated based on a whole protein family, and they also consider information about the 3D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2D diagrams, which provide an overview of a whole protein family's secondary structures. 2DProts is updated weekly and is integrated into CATH. AVAILABILITY AND IMPLEMENTATION: Freely accessible at https://2dprots.ncbr.muni.cz. The web interface was implemented in JavaScript. The database was implemented in Python. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• databáze faktografické MeSH
• proteiny * chemie   MeSH
• sekundární struktura proteinů MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny * MeSH

The ability to predict and design protein structures has led to numerous applications in medicine, diagnostics and sustainable chemical manufacture. In addition, the wealth of predicted protein structures has advanced our understanding of how life's molecules function and interact. Honouring the work that has fundamentally changed the way scientists research and engineer proteins, the Nobel Prize in Chemistry in 2024 was awarded to David Baker for computational protein design and jointly to Demis Hassabis and John Jumper, who developed AlphaFold for machine-learning-based protein structure prediction. Here, we highlight notable contributions to the development of these computational tools and their importance for the design of functional proteins that are applied in organic synthesis. Notably, both technologies have the potential to impact drug discovery as any therapeutic protein target can now be modelled, allowing the de novo design of peptide binders and the identification of small molecule ligands through in silico docking of large compound libraries. Looking ahead, we highlight future research directions in protein engineering, medicinal chemistry and material design that are enabled by this transformative shift in protein science.

• Klíčová slova
• AlphaFold, Computational protein design, Nobel prize, Protein engineering, Protein structure prediction,
• MeSH
• biokatalýza MeSH
• konformace proteinů MeSH
• proteinové inženýrství MeSH
• proteiny * chemie   metabolismus   MeSH
• strojové učení MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteiny * MeSH

Interactions between nucleic acids and proteins are some of the most important interactions in biology because they are the cornerstones for fundamental biological processes, such as replication, transcription, and recombination [...].

• Klíčová slova
• DNA base sequence, DNA structure, G-quadruplex, Z-DNA, cruciform, nucleic acid–protein interactions,
• MeSH
• DNA chemie   MeSH
• G-kvadruplexy * MeSH
• konformace nukleové kyseliny MeSH
• molekulární struktura MeSH
• nukleové kyseliny * MeSH
• proteiny metabolismus   MeSH
• Publikační typ
• úvodníky MeSH
• Názvy látek
• DNA MeSH
• nukleové kyseliny * MeSH
• proteiny MeSH

BACKGROUND: PsbO, the manganese-stabilising protein, is an indispensable extrinsic subunit of photosystem II. It plays a crucial role in the stabilisation of the water-splitting Mn4CaO5 cluster, which catalyses the oxidation of water to molecular oxygen by using light energy. PsbO was also demonstrated to have a weak GTPase activity that could be involved in regulation of D1 protein turnover. Our analysis of psbO sequences showed that many angiosperm species express two psbO paralogs, but the pairs of isoforms in one species were not orthologous to pairs of isoforms in distant species. RESULTS: Phylogenetic analysis of 91 psbO sequences from 49 land plant species revealed that psbO duplication occurred many times independently, generally at the roots of modern angiosperm families. In spite of this, the level of isoform divergence was similar in different species. Moreover, mapping of the differences on the protein tertiary structure showed that the isoforms in individual species differ from each other on similar positions, mostly on the luminally exposed end of the β-barrel structure. Comparison of these differences with the location of differences between PsbOs from diverse angiosperm families indicated various selection pressures in PsbO evolution and potential interaction surfaces on the PsbO structure. CONCLUSIONS: The analyses suggest that similar subfunctionalisation of PsbO isoforms occurred parallelly in various lineages. We speculate that the presence of two PsbO isoforms helps the plants to finely adjust the photosynthetic apparatus in response to variable conditions. This might be mediated by diverse GTPase activity, since the isoform differences predominate near the predicted GTP-binding site.

• MeSH
• aminokyseliny metabolismus   MeSH
• druhová specificita MeSH
• fotosystém II (proteinový komplex) chemie   metabolismus   MeSH
• fylogeneze * MeSH
• Magnoliopsida genetika   metabolismus   MeSH
• molekulární modely MeSH
• otevřené čtecí rámce genetika   MeSH
• protein - isoformy chemie   metabolismus   MeSH
• rostlinné geny MeSH
• sekundární struktura proteinů MeSH
• sekvence aminokyselin MeSH
• substituce aminokyselin MeSH
• terciární struktura proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• aminokyseliny MeSH
• fotosystém II (proteinový komplex) MeSH
• photosystem II manganese-stabilizing protein MeSH Prohlížeč
• protein - isoformy MeSH

Autophagy is a catabolic process that was described to play a critical role in advanced stages of cancer, wherein it maintains tumor cell homeostasis and growth by supplying nutrients. Autophagy is also described to support alternative cellular trafficking pathways, providing a non-canonical autophagy-dependent inflammatory cytokine secretion mechanism. Therefore, autophagy inhibitors have high potential in the treatment of cancer and acute inflammation. In our study, we identified compound 1 as an inhibitor of the ATG12-ATG3 protein-protein interaction. We focused on the systematic modification of the original hit 1, a casein kinase 2 (CK2) inhibitor, to find potent disruptors of ATG12-ATG3 protein-protein interaction. A systematic modification of the hit structure led us to a wide plethora of compounds that maintain its ATG12-ATG3 inhibitory activity, which could act as a viable starting point to design new compounds with diverse therapeutic applications.

• Klíčová slova
• Autophagy, Autophagy inhibition, Protein–protein interaction, Small molecule,
• MeSH
• autofagie účinky léků   MeSH
• kaseinkinasa II antagonisté a inhibitory   metabolismus   MeSH
• knihovny malých molekul * chemie   farmakologie   chemická syntéza   MeSH
• lidé MeSH
• molekulární struktura MeSH
• proteiny spojené s autofagií * metabolismus   antagonisté a inhibitory   MeSH
• vazba proteinů MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kaseinkinasa II MeSH
• knihovny malých molekul * MeSH
• proteiny spojené s autofagií * MeSH

Interaction with the DNA minor groove is a significant contributor to specific sequence recognition in selected families of DNA-binding proteins. Based on a statistical analysis of 3D structures of protein-DNA complexes, we propose that distortion of the DNA minor groove resulting from interactions with hydrophobic amino acid residues is a universal element of protein-DNA recognition. We provide evidence to support this by associating each DNA minor groove-binding amino acid residue with the local dimensions of the DNA double helix using a novel algorithm. The widened DNA minor grooves are associated with high GC content. However, some AT-rich sequences contacted by hydrophobic amino acids (e.g., phenylalanine) display extreme values of minor groove width as well. For a number of hydrophobic amino acids, distinct secondary structure preferences could be identified for residues interacting with the widened DNA minor groove. These results hold even after discarding the most populous families of minor groove-binding proteins.

• Klíčová slova
• DNA shape, hydrophobic, indirect readout, minor groove, protein–DNA interaction, specific recognition,
• MeSH
• algoritmy MeSH
• aminokyselinové motivy MeSH
• aminokyseliny chemie   MeSH
• Arabidopsis metabolismus   MeSH
• DNA vazebné proteiny metabolismus   MeSH
• DNA chemie   MeSH
• fenylalanin chemie   MeSH
• hydrofobní a hydrofilní interakce * MeSH
• konformace nukleové kyseliny MeSH
• kyselina glutamová chemie   MeSH
• lidé MeSH
• proteiny chemie   MeSH
• Saccharomyces cerevisiae metabolismus   MeSH
• sekundární struktura proteinů MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• aminokyseliny MeSH
• DNA vazebné proteiny MeSH
• DNA MeSH
• fenylalanin MeSH
• kyselina glutamová MeSH
• proteiny MeSH

In this paper, we present a novel algorithm for measuring protein similarity based on their 3-D structure (protein tertiary structure). The algorithm used a suffix tree for discovering common parts of main chains of all proteins appearing in the current research collaboratory for structural bioinformatics protein data bank (PDB). By identifying these common parts, we build a vector model and use some classical information retrieval (IR) algorithms based on the vector model to measure the similarity between proteins--all to all protein similarity. For the calculation of protein similarity, we use term frequency × inverse document frequency ( tf × idf ) term weighing schema and cosine similarity measure. The goal of this paper is to introduce new protein similarity metric based on suffix trees and IR methods. Whole current PDB database was used to demonstrate very good time complexity of the algorithm as well as high precision. We have chosen the structural classification of proteins (SCOP) database for verification of the precision of our algorithm because it is maintained primarily by humans. The next success of this paper would be the ability to determine SCOP categories of proteins not included in the latest version of the SCOP database (v. 1.75) with nearly 100% precision.

• MeSH
• algoritmy * MeSH
• data mining metody   MeSH
• databáze proteinů MeSH
• lidé MeSH
• proteiny chemie   MeSH
• reprodukovatelnost výsledků MeSH
• strukturní homologie proteinů * MeSH
• terciární struktura proteinů * MeSH
• umělá inteligence MeSH
• výpočetní biologie metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• proteiny MeSH

Structure determination of RNA-protein complexes is essential for our understanding of the multiple layers of RNA-mediated posttranscriptional regulation of gene expression. Over the past 20years, NMR spectroscopy became a key tool for structural studies of RNA-protein interactions. Here, we review the progress being made in NMR structure determination of large ribonucleoprotein assemblies. We discuss approaches for the design of RNA-protein complexes for NMR structural studies, established and emerging isotope and segmental labeling schemes suitable for large RNPs and how to gain distance restraints from NOEs, PREs and EPR and orientational information from RDCs and SAXS/SANS in such systems. The new combination of NMR measurements with MD simulations and its potential will also be discussed. Application and combination of these various methods for structure determination of large RNPs will be illustrated with three large RNA-protein complexes (>40kDa) and other interesting complexes determined in the past six and a half years.

• Klíčová slova
• Biomolecular NMR, Integrated structural biology, Isotope labeling, NMR assignments, NMR structure determination, RNA-protein complex, RNA-protein interaction,
• MeSH
• izotopové značení metody   MeSH
• izotopy chemie   MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• molekulární modely MeSH
• nukleární magnetická rezonance biomolekulární metody   MeSH
• proteiny chemie   MeSH
• ribonukleoproteiny chemie   MeSH
• RNA chemie   MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• izotopy MeSH
• proteiny MeSH
• ribonukleoproteiny MeSH
• RNA MeSH

A systematic method for the analysis of the hydration structure of proteins is demonstrated on the case study of lysozyme. The method utilises multiple structural data of the same protein deposited in the protein data bank. Clusters of high water occupancy are localised and characterised in terms of their interaction with protein. It is shown that they constitute a network of interconnected hydrogen bonds anchored to the protein molecule. The high occupancy of the clusters does not directly correlate with water-protein interaction energy as was originally hypothesised. The highly occupied clusters rather correspond to the nodes of the hydration network that have the maximum number of hydrogen bonds including both the protein atoms and the surrounding water clusters.

• Klíčová slova
• X-ray crystallography, cluster algorithm, interaction enthalpy, protein hydration structure, water,
• MeSH
• bakteriofág T4 chemie   enzymologie   MeSH
• databáze proteinů MeSH
• molekulární modely MeSH
• muramidasa chemie   MeSH
• termodynamika MeSH
• virové proteiny chemie   MeSH
• voda chemie   MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• muramidasa MeSH
• virové proteiny MeSH
• voda MeSH