Hsp70 chaperones use ATP to remodel native protein oligomers and stable aggregates by entropic pulling

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Proteins are the molecular machines of life, driving essential biological processes such as enzymatic catalysis, cellular signaling, and immune responses. The ability to design entirely new proteins with desired structures and functions has immense implica ...

The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses molecular dynamics sim ...

Rhodamines have been continuously optimized in brightness, biocompatibility, and color to fulfill the demands of modern bioimaging. However, the problem of phototoxicity caused by the excited fluorophore under long-term illumination has been largely neglec ...

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

Engineering protein biosensors that sensitively respond to specific biomolecules by triggering precise cellular responses is a major goal of diagnostics and synthetic cell biology. Previous biosensor designs have largely relied on binding structurally well ...

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approa ...

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

Detailed understanding of the mechanism by which Hsp70 chaperones protect cells against protein aggregation is hampered by the lack of a comprehensive characterization of the aggregates, which are typically heterogeneous. Here we designed a reporter chaper ...

The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...

Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families ...

Increasing the protein production capacity of the PURE cell-free transcription-translation (TX-TL) system will be key to implementing complex synthetic biological circuits, and to establishing a fully self-regenerating system as a basis for the development ...

Organohalide respiration (OHR) is a bacterial anaerobic process that use halogenated compounds, e.g. tetrachloroethene (PCE), as terminal electron acceptors. D. restrictus strain PER-K23, an obligate OHR bacterium (OHRB), and D. hafniense strain TCE1, a ba ...

Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses and direct improvement efforts. The latest efforts focused on better describing disordered proteins while retaining proper description of ...

The rnlAB toxin-antitoxin operon from Escherichia co/ifunctions as an anti-phage defense system. RnlA was identified as a member of the HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding domain) superfamily of ribonucleases. The activity of the tox ...

Predicting interactions between proteins and other biomolecules solely based on structure remains a challenge in biology. A high-level representation of protein structure, the molecular surface, displays patterns of chemical and geometric features that fin ...

The present relates to a method for generating variants of a protein based on a native protein regulated by allosteric pathway, the method comprising:- i) providing 3D structures of the native protein;- ii) identifying at least one pair of coupled alloster ...

Gene delivery using vector or viral-based methods is often limited by technical and safety barriers. A promising alternative that circumvents these shortcomings is the direct delivery of proteins into cells. Here we introduce a non-viral, ligand-mediated p ...

BackgroundLarge-scale datasets of protein structures and sequences are becoming ubiquitous in many domains of biological research. Experimental approaches and computational modelling methods are generating biological data at an unprecedented rate. The deta ...

The present relates to a method for generating variants of a protein based on a native protein regulated by allosteric pathway, the method comprising: - i) providing 3D structures of the native protein; - ii) identifying at least one pair of coupled allost ...

Hsp70 chaperones use ATP to remodel native protein oligomers and stable aggregates by entropic pulling

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Computational design of complex protein folds and soluble analogs of membrane proteins

The effect of hydration and dynamics on the mass density of single proteins

Gentle Rhodamines for Live-Cell Fluorescence Microscopy

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis

Generative power of a protein language model trained on multiple sequence alignments

Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins

De novo designed proteins: a study in engineering novel folds and functions

A fluorescent multi-domain protein reveals the unfolding mechanism of Hsp70

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Improved Cell-Free Transcription-Translation Reactions in Microfluidic Chemostats Augmented with Hydrogel Membranes for Continuous Small Molecule Dialysis

Characterization of the electron-accepting part of the organohalide respiration chain of Dehalobacter and Desulfitobacterium

Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization

Alternative dimerization is required for activity and inhibition of the HEPN ribonuclease RnlA

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

Method for generating variants of a protein

A ligand-based system for receptor-specific delivery of proteins

rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics

Method for generating variants of a protein