A5017465726- Lipid Membrane Structure and Behavior
- Spectroscopy Techniques in Biomedical and Chemical Research
- Protein Structure and Dynamics
- Metabolomics and Mass Spectrometry Studies
- Spectroscopy and Quantum Chemical Studies
- Electrohydrodynamics and Fluid Dynamics
- Advanced biosensing and bioanalysis techniques
- Antimicrobial Peptides and Activities
- Machine Learning in Bioinformatics
- Bacterial Genetics and Biotechnology
- Various Chemistry Research Topics
- Mass Spectrometry Techniques and Applications
- Radiation Therapy and Dosimetry
- Lipid metabolism and biosynthesis
- Photoreceptor and optogenetics research
- Microbial Metabolic Engineering and Bioproduction
- Glycosylation and Glycoproteins Research
- DNA and Biological Computing
- Nuclear Physics and Applications
- Amino Acid Enzymes and Metabolism
- thermodynamics and calorimetric analyses
- Spectroscopy and Chemometric Analyses
- Advancements in Photolithography Techniques
- Enzyme Catalysis and Immobilization
- Advanced Fluorescence Microscopy Techniques
University of Groningen
2019-2024
Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry
2016-2021
Institut de Biologie Physico-Chimique
2020
Czech Academy of Sciences
2018
International Olive Council
2016-2017
Charles University
2016
Abstract Cell membranes provide a selective semi-permeable barrier to the passive transport of molecules. This property differs greatly between organisms. While cytoplasmic membrane bacterial cells is highly permeable for weak acids and glycerol, yeasts can maintain large concentration gradients. Here we show that such differences arise from physical state plasma membrane. By combining stopped-flow kinetic measurements with molecular dynamics simulations, performed systematic analysis...
Binding affinities and stoichiometries of Na+ Ca2+ ions to phospholipid bilayers are paramount significance in the properties functionality cellular membranes. Current estimates binding cations are, however, inconsistent due limitations available experimental computational methods. In this work, we improve description details a 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer by implicitly including electronic polarization as mean field correction, known continuum correction (ECC)....
The molecular electrometer – reorientation of lipid head due to bound charge allows direct quantitative vetting simulations against noninvasive NMR experiments; most simulation models overestimated lipid–cation affinities.
In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations biomolecules. While effects are highly pronounced molecules with an opposite total charge, they also non-negligible interactions overall neutral molecules. For instance, neglecting these in important biomolecules like amino acids phospholipids structure proteins membranes having a large impact on interpreting experimental data as well...
Phosphatidylserine (PS) is a negatively charged lipid type commonly found in eukaryotic membranes, where it interacts with proteins via nonspecific electrostatic interactions as well specific binding. Moreover, the presence of calcium ions, PS lipids can induce membrane fusion and phase separation. Molecular details these phenomena remain poorly understood, partly because accurate models to interpret experimental data have not been available. Here we gather set previously published NMR C–H...
Abstract Antimicrobial resistance is one of the leading concerns in medical care. Here we study mechanism action an antimicrobial cationic tripeptide, AMC-109, by combining high speed-atomic force microscopy, molecular dynamics, fluorescence assays, and lipidomic analysis. We show that AMC-109 activity on negatively charged membranes derived from Staphylococcus aureus consists two crucial steps. First, self-assembles into stable aggregates consisting a hydrophobic core surface, with...
Lipid membranes are central to cellular life. Complementing experiments, computational modeling has been essential in unraveling complex lipid-biomolecule interactions, crucial both academia and industry. The Martini model, a coarse-grained force field for efficient molecular dynamics simulations, is widely used study membrane phenomena but faced limitations, particularly capturing realistic lipid phase behavior. Here, we present refined 3 models with mapping scheme that distinguishes tails...
Phosphatidylserine (PS) lipids are important signaling molecules and the most common negatively charged in eukaryotic membranes. The can be often regulated by calcium, but its interactions with PS headgroups not fully understood. Classical molecular dynamics (MD) simulations potentially give detailed description of lipid-ion interactions, results strongly depend on used force field. Here, we apply electronic continuum correction (ECC) to Amber Lipid17 parameters...
Interest in lipid interactions with proteins and other biomolecules is emerging not only fundamental biochemistry but also the field of nanobiotechnology where lipids are commonly used, for example, carriers mRNA vaccines. The outward-facing components cellular membranes nanoparticles, headgroups, regulate membrane approaching substances, such as proteins, drugs, RNA, or viruses. Because headgroup conformational ensembles have been experimentally determined physiologically relevant...
Two approaches for modeling of the transmembrane potential, as present in all eukaryotic cells, are examined detail and compared with each other. One approach uses an externally applied electric field, whereas other maintains imbalance ions on two sides a membrane. We demonstrate that both methods provide converged results concerning structural parameters membrane which practically indistinguishable from other, at least monovalent ions. Effects field detailed molecular structure phospholipid...
All-atomistic (AA) and coarse-grain (CG) simulations have been successfully applied to investigate a broad range of biomolecular processes. However, the accessible time length scales AA simulation are limited specific molecular details CG simplified. Here, we propose virtual site (VS) based hybrid scheme that can concurrently couple resolutions in single membrane simulation, mitigating shortcomings either representation. With some adjustments make force fields compatible, demonstrate lipid...
Force-field parameters of the first row transition metals together with a few additional common elements such as those from second (Rh, Ru) and third (Hg, Pt) rows in ligated forms were determined based on density functional theory calculations. Bonding characteristics by averaging metal–ligand force constants optimal geometries several chosen complexes each metal most oxidation numbers structural arrangements. Parameters Lennard-Jones potential supermolecular model. Our molecular mechanical...
Abstract Microbial synthesis of nutraceutically and pharmaceutically interesting plant polyphenols represents a more environmentally friendly alternative to chemical or extraction. However, most are cytotoxic for microorganisms as they believed negatively affect cell integrity transport processes. To increase the production performance engineered factories, strategies have be developed mitigate these detrimental effects. Here, we examine accumulation stilbenoid resveratrol in membrane wall...
The CorA family of proteins plays a housekeeping role in the homeostasis divalent metal ions many bacteria and archaea as well mitochondria eukaryotes, rendering it an important target to study mechanisms transport regulation across different life domains. Despite numerous studies, mechanistic details channel gating are still not entirely understood. Here, we use all-atom coarse-grained molecular dynamics simulations combined with vitro experiments investigate influence cations on function...
Abstract Fluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well obtaining quantitative information on orientation of fluorescent molecules associated with cellular features. Such can provide insights into protein structure, aid development genetically encoded probes, and allow determinations lipid membrane properties. However, quantitating interpreting biological systems has been laborious unreliable. Here we present a set open...
Abstract Cell membranes provide a selective semi-permeable barrier to the passive transport of molecules. This property differs greatly between organisms. While cytoplasmic membrane bacterial cells is highly permeable for weak acids and glycerol, yeasts can maintain large concentration gradients. Here we show that such differences arise from physical state plasma membrane. By combining stopped-flow kinetic measurements with molecular dynamics simulations, performed systematic analysis...
During industrial processes, yeasts are exposed to harsh conditions, which eventually lead adaptation of the strains. In laboratory, it is possible use experimental evolution link evolutionary biology response these pressures for improvement a specific yeast strain. this work, we aimed study wine in stress conditions high ethanol concentrations present stopped fermentations and secondary processes champagne production. We used commercial Saccharomyces cerevisiae × S. uvarum hybrid assessed...