A5021053274- Protein Structure and Dynamics
- Enzyme Structure and Function
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Protein purification and stability
- Block Copolymer Self-Assembly
- Polymer Surface Interaction Studies
- Biofuel production and bioconversion
- CRISPR and Genetic Engineering
- Protein Interaction Studies and Fluorescence Analysis
- Liquid Crystal Research Advancements
- Earthquake Detection and Analysis
- Drug Transport and Resistance Mechanisms
- Advanced biosensing and bioanalysis techniques
- Glycosylation and Glycoproteins Research
- Cell Image Analysis Techniques
- Bacterial Genetics and Biotechnology
- Supramolecular Self-Assembly in Materials
- ATP Synthase and ATPases Research
- Optical Systems and Laser Technology
- Advanced Polymer Synthesis and Characterization
- RNA Interference and Gene Delivery
- Material Dynamics and Properties
- Autism Spectrum Disorder Research
European Molecular Biology Laboratory
2020-2025
Centre for Structural Systems Biology
2024-2025
European Molecular Biology Laboratory
2018-2022
SIB Swiss Institute of Bioinformatics
2022
Deutsches Elektronen-Synchrotron DESY
2022
Krasnoyarsk State Medical University
2021
Kurchatov Institute
2016-2020
Lomonosov Moscow State University
2017
The
Abstract Small‐angle scattering (SAS) of X‐rays and neutrons is a fundamental tool to study the nanostructural properties, in particular, biological macromolecules solution. In structural biology, SAS recently transformed from specialization into general technique leading dramatic increase number publications reporting models. The growing amount data recorded published has led an urgent need for global repository that includes both primary response this, small‐angle bank (SASBDB) was...
Temperature-induced oligomerization of albumin before and after protein melting was studied using SAXS interpreted in terms interaction potential.
We describe the updated size-exclusion chromatography small angle X-ray scattering (SEC-SAXS) set-up used at P12 bioSAXS beam line of European Molecular Biology Laboratory (EMBL) PETRAIII synchrotron, DESY Hamburg (Germany). The addition size exclusion (SEC) directly on-line to SAXS capillary has become a well-established approach reduce effects sample heterogeneity on measurements. additional use multi-angle laser light (MALLS), UV absorption spectroscopy, refractive index (RI), and...
AlphaPulldown2 streamlines protein structural modeling by automating workflows, improving code adaptability, and optimizing data management for large-scale applications. It introduces an automated Snakemake pipeline, compressed storage, support additional backends like UniFold AlphaLink2, a range of other improvements. These upgrades make versatile platform predicting both binary interactions complex multi-unit assemblies. is freely available at https://github.com/KosinskiLab/AlphaPulldown....
While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, gap between number known protein sequences and experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational modeling approaches. powerful on own, most methods have strengths weaknesses. Therefore, it benefits researchers examine models various model providers perform comparative analysis...
Members of the SH3- and ankyrin repeat (SHANK) protein family are considered as master scaffolds postsynaptic density glutamatergic synapses. Several missense mutations within canonical SHANK3 isoform have been proposed causative for development autism spectrum disorders (ASDs). However, there is a surprising paucity data linking mutation-induced changes in structure dynamics to occurrence ASD-related synaptic phenotypes. In this proof-of-principle study, we focus on two ASD-associated point...
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity.Aptamer affinity entirely depends on its tertiary structure charge distribution.Therefore, length optimization essential for increasing aptamer specificity affinity.Here, we present general procedure finding the most populated atomistic structures aptamers.Based existed LC-18 lung adenocarcinoma, new truncated (LC-18t)...
Small-angle X-ray scattering (SAXS) experiments are widely used for the characterization of biological macromolecules in solution. SAXS patterns contain information on size and shape dissolved particles nanometer resolution. Here we propose a method primary data analysis based application artificial neural networks (NNs). Trained synthetic data, feedforward NNs able to reliably predict molecular weight maximum intraparticle distance (Dmax) directly from experimental data. The is applicable...
Membrane proteins (MPs) are the target of numerous structural and functional studies in biological medical/pharmaceutical sciences. Strategies for high-throughput analysis MPs their perturbations driven by ligands having potential therapeutic applications uncommon, often requiring scaled up crystallization, electron microscopy, nuclear magnetic resonance (NMR) efforts. Small-angle X-ray scattering (SAXS) provides a rapid means to study low resolution structures conformational changes native...
The application of small angle X-ray scattering (SAXS) to the structural characterization transmembrane proteins (MPs) in detergent solutions has become a routine procedure at synchrotron BioSAXS beamlines around world. SAXS provides overall parameters and low resolution shapes solubilized MPs, but is also meaningfully employed hybrid modeling procedures that combine data with information provided by high-resolution techniques (eg. macromolecular crystallography, nuclear magnetic resonance...
Abstract Multiblock copolymers with charged blocks are complex systems that show great potential for enhancing the structural control of block copolymers. A pentablock terpolymer PMMA‐ b ‐PDMAEMA‐ ‐P2VP‐ ‐PMMA is investigated. It contains two types midblocks, which weak cationic polyelectrolytes, namely poly(2‐(dimethylamino)ethyl methacrylate) (PDMAEMA) and poly(2‐vinylpyridine) (P2VP). Furthermore, these end‐capped short hydrophobic poly(methyl (PMMA) in dilute aqueous solution thin films....
The structures of a molecular brush in good solvent are investigated using synchrotron small-angle X-ray scattering wide range concentrations. under study, PiPOx239-g-PnPrOx14, features relatively long poly(2-isopropenyl-2-oxazoline) (PiPOx) backbone and short poly(2-n-propyl-2-oxazoline) (PnPrOx) side chains. As solvent, ethanol is used. By model fitting, the overall size persistence length as well interaction strength determined. At this, interplay between form structure factor taken into...
Replacing water with dimethyl sulfoxide (DMSO) completely reshapes the free-energy landscapes of solvated proteins. In DMSO, a powerful hydrogen-bond (HB) acceptor, formation HBs between backbone NH groups and solvent is favored over involving protein's carbonyl groups. This entails profound structural disruption globular proteins proteinaceous aggregates (e.g., amyloid fibrils) upon transfer to DMSO. Here, we investigate an unusual DMSO-induced conformational transition β2-amyloid fibrils...
Intrinsic protein flexibility is of overwhelming relevance for intermolecular recognition and adaptability highly dynamic ensemble complexes, the phenomenon essential understanding numerous biological processes. These conformational ensembles—encounter complexes—lack a unique organization, which prevents determination well-defined high resolution structures. This case complexes involving oncoprotein SET/template-activating factor-Iβ (SET/TAF-Iβ), histone chaperone whose functions...
X-ray diffraction and high-resolution adiabatic calorimetry have been used to study the polymorphic behaviour of 75OBC liquid crystal. On heating from room temperature, crystal phase (Cr-I) melts directly smectic A (Sm-A) then isotropic phase. cooling undergoes successive transitions Sm-A, hexatic B (Hex-B), crystalline (Cr-II) phases, next another – Cr-III. The latter two phases were shown relax slowly Cr-I phase, which is stable at low temperatures. data indicate that Cr-II possesses...
Abstract AlphaPulldown2 streamlines protein structural modeling by automating workflows, improving code adaptability, and optimizing data management for large-scale applications. It introduces an automated Snakemake pipeline, compressed storage, support additional backends like UniFold AlphaLink2, a range of other improvements. These upgrades make versatile platform predicting both binary interactions complex multi-unit assemblies. Availability is freely available at...
Abstract Members of the SH3- and ankyrin-rich repeat (SHANK) protein family are considered as master scaffolds post-synaptic density glutamatergic synapses. Several missense mutations within canonical SHANK3 isoform have been proposed causative for development autism spectrum disorders (ASDs). However, there is a surprising paucity data linking mutation-induced changes in structure dynamics to occurrence ASD-related synaptic phenotypes. In this work, we focus on two ASD-associated point...
Abstract The application of small angle X-ray scattering (SAXS) to the structural characterization transmembrane proteins (MPs) in detergent solutions has become a routine procedure at most synchrotron BioSAXS beamlines around world. SAXS provides overall parameters and low resolution shapes solubilized MPs, but is also meaningfully employed hybrid modeling procedures that combine data with information provided by high-resolution techniques ( eg. macromolecular crystallography, nuclear...
Small angle X-ray scattering (SAXS) is a powerful technique for analyzing dilute solutions of proteins, nucleic acids and other macromolecules in solution under wide range conditions.The primary SAXS data analysis steps include estimation the overall particle parameters (the radius gyration Rg, maximum intraparticle distance Dmax, molecular weight MW) computation pair distribution function p(r).The latter represents histogram distances between pairs points particle, weighted by product their...
Abstract While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, gap between number known protein sequences and experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational modelling approaches. powerful on own, most methods have strengths weaknesses. Therefore, it benefits researchers examine models various model providers perform comparative...