A5049578097- RNA and protein synthesis mechanisms
- Advanced biosensing and bioanalysis techniques
- Protein Structure and Dynamics
- Lipid Membrane Structure and Behavior
- Bacteriophages and microbial interactions
- Supramolecular Self-Assembly in Materials
- Bioinformatics and Genomic Networks
- Glycosylation and Glycoproteins Research
- Chemical Synthesis and Analysis
- Advanced Fluorescence Microscopy Techniques
- CRISPR and Genetic Engineering
- Spectroscopy Techniques in Biomedical and Chemical Research
- Spectroscopy and Quantum Chemical Studies
- DNA and Biological Computing
- Bacterial Genetics and Biotechnology
- Advanced Proteomics Techniques and Applications
- Scientific Computing and Data Management
- SARS-CoV-2 and COVID-19 Research
- Enzyme Structure and Function
- Electron Spin Resonance Studies
- Monoclonal and Polyclonal Antibodies Research
- RNA Interference and Gene Delivery
- Erythrocyte Function and Pathophysiology
- Fungal and yeast genetics research
- Cellular transport and secretion
National Institute of Chemistry
2016-2025
EN-FIST Centre of Excellence (Slovenia)
2024-2025
University of Washington
2021-2024
Jožef Stefan Institute
2009-2014
New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the disease 2019 (COVID-19) pandemic. Here, we used a cell-free expression workflow rapidly screen optimize constructs containing multiple computationally designed miniprotein inhibitors SARS-CoV-2. We found broadest efficacy was achieved with homotrimeric version 75-residue angiotensin-converting enzyme (ACE2) mimic AHB2 (TRI2-2) geometrically match trimeric spike architecture....
Abstract The regulation of protein function by external or internal signals is one the key features living organisms. ability to directly control a selected would represent valuable tool for regulating biological processes. Here, we present generally applicable proteins called INSRTR, based on inserting peptide into loop target that retains its function. We demonstrate versatility and robustness coiled-coil-mediated regulation, which enables designs either inactivation activation functions,...
The coiled-coil dimer is a widespread protein structural motif and, due to its designability, represents an attractive building block for assembling modular nanostructures. specificity of pairing mainly based on hydrophobic and electrostatic interactions between residues at positions a, d, e, g the heptad repeat. Binding affinity, other hand, can also be affected by surface that face away from dimerization interface. Here we show how design local helical propensity interacting peptides used...
Protein-protein interactions (PPIs) regulate many cellular processes and engineered PPIs have cell gene therapy applications. Here, we introduce massively parallel PPI measurement by sequencing (MP3-seq), an easy-to-use highly scalable yeast two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs barcode enrichment can be read to provide a direct measure of interaction strength. We show that MP3-seq is quantitative scales over 100,000...
Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how applications can be created a reproducible manner when simple design goals for reproducibility met. We describe implementation test server framework 40 benchmarks, covering numerous Rosetta...
Abstract Protein-protein interactions (PPIs) are crucial for biological functions and have applications ranging from drug design to synthetic cell circuits. Coiled-coils been used as a model study the sequence determinants of specificity. However, building well-behaved sets orthogonal pairs coiled-coils remains challenging due inaccurate predictions orthogonality difficulties in testing at scale. To address this, we develop next-generation bacterial two-hybrid (NGB2H) method, which allows...
Toll-like receptor 5 (TLR5) is a of the innate immune system that recognizes flagellin from certain bacterial species and triggers an inflammatory response. The Salmonella dublin in complex with zebrafish TLR5 has been crystallized previously. In present study, we extrapolate structure this using structure-guided mutagenesis to determine recognition modes human mouse receptors demonstrate species-specific differences recognition. general, mode can be said more robust comparison receptor....
Fluorescence microspectroscopy (FMS) with environmentally sensitive dyes provides information about local molecular surroundings at microscopic spatial resolution. Until recently, only probes exhibiting large spectral shifts due to changes have been used. For filter-based experimental systems, where signal different wavelengths is acquired sequentially, photostability has required in addition. Herein, we systematically analyzed our fitting models and bleaching correction algorithms which...
Abstract Natural proteins are characterised by a complex folding pathway defined uniquely for each fold. Designed coiled-coil protein origami (CCPO) cages distinct from natural compact proteins, since their fold is prescribed discrete long-range interactions between orthogonal pairwise-interacting (CC) modules within single polypeptide chain. Here, we demonstrate that CCPO in stepwise sequential pathway. Molecular dynamics simulations and stopped-flow Förster resonance energy transfer (FRET)...
Lack of better understanding nanoparticles targeted delivery into cancer cells calls for advanced optical microscopy methodologies.Here we present a development fluorescence microspectroscopy (spectral imaging) based on white light spinning disk confocal microscope with emission wavelength selection by liquid crystal tunable filter.Spectral contrasting images was used to localize polymer and cell membranes labeled fluorophores that have substantially overlapping spectra.In addition, enabled...
Escape variants of SARS-CoV-2 are threatening to prolong the COVID-19 pandemic. To address this challenge, we developed multivalent protein-based minibinders as potential prophylactic and therapeutic agents. Homotrimers single fusions three distinct were designed geometrically match spike (S) trimer architecture optimized by cell-free expression found exhibit virtually no measurable dissociation upon binding. Cryo-electron microscopy (cryoEM) showed that these trivalent engage all receptor...
Multicomponent self-assembled supramolecular nanovesicles based on an amphiphilic derivative of β-cyclodextrin and phosphatidylcholine liposomes (PC-liposomes) functionalized with four structurally different adamantyl guanidines were prepared characterized. Incorporation efficiency the examined as well size surface charge was determined. Changes in confirmed that guanidinium groups exposed surface. ITC 1H NMR spectroscopy complemented by molecular dynamics (MD) simulations used to elucidate...
Modular protein engineering is a powerful approach for fabricating high-molecular-weight assemblies and biomaterials with nanoscale precision. Herein, we address the challenge of designing an extended filamentous architecture inspired by central rod domain human dystrophin, which protects sarcolemma during muscle contraction consists spectrin repeats composed three-helical bundles. A module three tandem was used as rigid building block self-assembling via coiled-coil (CC) dimer-forming...
Lack of better understanding nanoparticles targeted delivery into cancer cells calls for advanced optical microscopy methodologies. Here we present a development fluorescence microspectroscopy (spectral imaging) based on white light spinning disk confocal microscope with emission wavelength selection by liquid crystal tunable filter. Spectral contrasting images was used to localize polymer and cell membranes labeled fluorophores that have substantially overlapping spectra. In addition,...
All atom molecular dynamics (MD) models provide valuable insight into the of biophysical systems, but are limited in size or length by high computational demands. The latter can be reduced simulating long term diffusive (also known as Langevin Brownian motion) most interesting and important user-defined parts studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory therefore extended to millisecond lengths colvars subspace at a very small...
Polypeptides and polynucleotides are programmable natural polymers whose linear sequence can be easily designed synthesized by the cellular transcription/translation machinery. Nature primarily uses proteins as molecular machines nucleic acids medium for manipulation of heritable information. A protein's tertiary structure function is defined multiple cooperative weak long-range interactions that have been optimized through evolution. DNA nanotechnology orthogonal pairwise interacting...
Protein-protein interactions (PPIs) regulate many cellular processes, and engineered PPIs have cell gene therapy applications. Here we introduce massively parallel protein-protein interaction measurement by sequencing (MP3-seq), an easy-to-use highly scalable yeast-two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs, barcode enrichment can be read to provide a direct measure of strength. We show that MP3-seq is quantitative scales over...