Lucie Bednářová
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View article: Prebiotically Plausible Peptides can Self-assemble into β-rich Nanostructures
Prebiotically Plausible Peptides can Self-assemble into β-rich Nanostructures Open
Modern proteins are remarkable polymers built from a 20-amino-acid alphabet, shaped by billions of years of evolution. Yet in Earth’s prebiotic era, several amino acids – particularly the canonical basic residues lysine, arginine, and hist…
View article: Ancient amino acid sets enable stable protein folds
Ancient amino acid sets enable stable protein folds Open
Early proteins likely arose from a chemically limited set of amino acids available through prebiotic chemistry, raising a central question in molecular evolution: could such primitive compositions yield stable, functional folds? Using de n…
View article: Beyond Traditional SPAAC: Achieving Orthogonality and Rapid Kinetics with Fluoroalkyl Azides
Beyond Traditional SPAAC: Achieving Orthogonality and Rapid Kinetics with Fluoroalkyl Azides Open
Strain-promoted azide–alkyne cycloaddition (SPAAC) is a cornerstone of bioorthogonal chemistry, offering metal-free and biocompatible ligation for applications ranging from bioconjugation to live-cell imaging. However, its relatively slow …
View article: Milligram‐Scale Enzymatic Synthesis of Base‐Modified DNA through Primer Extension: Polymerase Synthesis and NMR Structures of DNA Containing Phenyl‐Substituted Nucleobases
Milligram‐Scale Enzymatic Synthesis of Base‐Modified DNA through Primer Extension: Polymerase Synthesis and NMR Structures of DNA Containing Phenyl‐Substituted Nucleobases Open
Milligram (≈200 nmol) scale enzymatic synthesis of base‐modified DNA is developed based on primer extension using easily accessible and cheap KOD (exo–) DNA polymerase with optimized protocol and streamlined isolation. The methodology is a…
View article: Discovery and isolation of novel capsaicinoids and their TRPV1-related activity
Discovery and isolation of novel capsaicinoids and their TRPV1-related activity Open
Chilis contain capsaicin and other structurally related molecules known as capsaicinoids. Capsaicin's target protein, the transient receptor potential cation channel subfamily V member 1 (TRPV1), has been linked to many post-activation eff…
View article: Zwitterionic DNA: enzymatic synthesis of hypermodified DNA bearing four different cationic substituents at all four nucleobases
Zwitterionic DNA: enzymatic synthesis of hypermodified DNA bearing four different cationic substituents at all four nucleobases Open
We designed and synthesized a set of four 2′-deoxyribonucleoside 5′-O-triphosphates (dNTPs) bearing cationic substituents (protonated amino, methylamino, dimethylamino and trimethylammonium groups) attached to position 5 of pyrimidines or …
View article: Oligomerization Function of the Native Exon 5 Sequence of Ameloblastin Fused with Calmodulin
Oligomerization Function of the Native Exon 5 Sequence of Ameloblastin Fused with Calmodulin Open
The evolution of proteins is primarily driven by the combinatorial assembly of a limited set of pre-existing modules known as protein domains. This modular architecture not only supports the diversity of natural proteins but also provides …
View article: Design of Zn‐Binding Peptide(s) from Protein Fragments
Design of Zn‐Binding Peptide(s) from Protein Fragments Open
We designed a minimalistic zinc(II)‐binding peptide featuring the Cys 2 His 2 zinc‐finger motif. To this aim, several tens of thousands of (His/Cys)‐X n ‐(His/Cys) protein fragments ( n =2–20) were first extracted from the 3D protein struc…
View article: From boom to bloom: synthesis of diazidodifluoromethane, its stability and applicability in the ‘click’ reaction
From boom to bloom: synthesis of diazidodifluoromethane, its stability and applicability in the ‘click’ reaction Open
Diazidodifluoromethane was prepared from dibromodifluoromethane, sodium azide and an alkanethiolate initiator.
View article: Rücktitelbild: Stereocontrolled Synthesis of Chiral Helicene‐Indenido <i>ansa</i>‐ and Half‐Sandwich Metal Complexes and Their Use in Catalysis (Angew. Chem. 1/2025)
Rücktitelbild: Stereocontrolled Synthesis of Chiral Helicene‐Indenido <i>ansa</i>‐ and Half‐Sandwich Metal Complexes and Their Use in Catalysis (Angew. Chem. 1/2025) Open
View article: Discovery and isolation of novel capsaicinoids and their TRPV1-related activity
Discovery and isolation of novel capsaicinoids and their TRPV1-related activity Open
Chilis contain capsaicin and other structurally related molecules known as capsaicinoids. Capsaicin’s target protein, the transient receptor potential cation channel subfamily V member 1 (TRPV1), has been linked to many post-activation eff…
View article: Stereocontrolled Synthesis of Chiral Helicene‐Indenido <i>ansa</i>‐ and Half‐Sandwich Metal Complexes and Their Use in Catalysis
Stereocontrolled Synthesis of Chiral Helicene‐Indenido <i>ansa</i>‐ and Half‐Sandwich Metal Complexes and Their Use in Catalysis Open
Despite recent tremendous progress in the synthesis of nonplanar chiral aromatics, and helicenes in particular, their conversion to half‐sandwich or sandwich transition metal complexes still lags behind, although they represent an attracti…
View article: Stereocontrolled Synthesis of Chiral Helicene‐Indenido <i>ansa</i>‐ and Half‐Sandwich Metal Complexes and Their Use in Catalysis
Stereocontrolled Synthesis of Chiral Helicene‐Indenido <i>ansa</i>‐ and Half‐Sandwich Metal Complexes and Their Use in Catalysis Open
Despite recent tremendous progress in the synthesis of nonplanar chiral aromatics, and helicenes in particular, their conversion to half‐sandwich or sandwich transition metal complexes still lags behind, although they represent an attracti…
View article: Unveiling the DHX15–G-patch interplay in retroviral RNA packaging
Unveiling the DHX15–G-patch interplay in retroviral RNA packaging Open
We explored how a simple retrovirus, Mason-Pfizer monkey virus (M-PMV) to facilitate its replication process, utilizes DHX15, a cellular RNA helicase, typically engaged in RNA processing. Through advanced genetic engineering techniques, we…
View article: Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides
Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides Open
Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbo…
View article: HIV-1 Infection Reduces NAD Capping of Host Cell snRNA and snoRNA
HIV-1 Infection Reduces NAD Capping of Host Cell snRNA and snoRNA Open
Nicotinamide adenine dinucleotide (NAD) is a critical component of the cellular metabolism and also serves as an alternative 5' cap on various RNAs. However, the function of the NAD RNA cap is still under investigation. We studied NAD capp…
View article: Solid-state vibrational circular dichroism for pharmaceutical applications: polymorphs and cocrystal of sofosbuvir
Solid-state vibrational circular dichroism for pharmaceutical applications: polymorphs and cocrystal of sofosbuvir Open
X-ray diffraction is a commonly used technique in the pharmaceutical industry for the determination of the atomic and molecular structure of crystals. However, it is costly, sometimes time-consuming, and it requires a considerable degree o…
View article: Unveiling the DHX15 - G-patch Interplay in Retroviral RNA Packaging
Unveiling the DHX15 - G-patch Interplay in Retroviral RNA Packaging Open
We explored how a simple retrovirus, Mason-Pfizer monkey virus (M-PMV) to facilitate its replication process, utilizes DHX15, a cellular RNA helicase, typically engaged in RNA processing. Through advanced genetic engineering techniques, we…
View article: Stereoselective Reduction of Steroidal 4-Ene-3-ketones in the Presence of Biomass-Derived Ionic Liquids Leading to Biologically Important 5β-Steroids
Stereoselective Reduction of Steroidal 4-Ene-3-ketones in the Presence of Biomass-Derived Ionic Liquids Leading to Biologically Important 5β-Steroids Open
The stereoselective reduction of the steroidal 4-ene-3-ketone moiety (enone) affords the 5β-steroid backbone that is a key structural element of biologically important neuroactive steroids. Neurosteroids have been currently studied as nove…
View article: Chiroptical Spectroscopy Complemented by Quantum Chemical Calculations Accurately Predicts the Absolute Configuration of P-Chirogenic Compounds
Chiroptical Spectroscopy Complemented by Quantum Chemical Calculations Accurately Predicts the Absolute Configuration of P-Chirogenic Compounds Open
View article: Undescribed and Known Phenolic Acid Derivatives with Significant Antioxidant Activity from the Scorzonera Parviflora Jacq. Roots
Undescribed and Known Phenolic Acid Derivatives with Significant Antioxidant Activity from the Scorzonera Parviflora Jacq. Roots Open
View article: Undescribed and Known Phenolic Acid Derivatives with Significant Antioxidant Activity from the Scorzonera Parviflora Jacq. Roots
Undescribed and Known Phenolic Acid Derivatives with Significant Antioxidant Activity from the Scorzonera Parviflora Jacq. Roots Open
View article: Parent Porphyrin (Porphine) and its Complexes with 3d Metals
Parent Porphyrin (Porphine) and its Complexes with 3d Metals Open
We report an improved synthesis of porphine from d-tartaric acid, its conversion to complexes with Mg(II), V(IV), Mn(III), Fe(III), Co(II), Ni(II), Cu(II) and Zn(II), their IR, UV-vis, NMR, XPS, and mass spectra, and single crystal X-ray d…
View article: What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments
What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments Open
We investigate short peptides and their propensity to form specific secondary structures. We show that the propensity might start to appear in sequences as short as several (3-11) amino acids.
View article: Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases
Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases Open
We designed and synthesized a set of four 2′-deoxyribonucleoside 5′-O-triphosphates (dNTPs) derived from 5-substituted pyrimidines and 7-substituted 7-deazapurines bearing anionic substituents (carboxylate, sulfonate, phosphonate, and phos…
View article: Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors
Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors Open
A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition st…
View article: Superanionic DNA. Enzymatic Synthesis of Hypermodified DNA Bearing Four Different Anionic Substituents at all Four Nucleobases
Superanionic DNA. Enzymatic Synthesis of Hypermodified DNA Bearing Four Different Anionic Substituents at all Four Nucleobases Open
Additional supporting simulation data for "Superanionic DNA. Enzymatic Synthesis of Hypermodified DNA Bearing Four Different Anionic Substituents at all Four Nucleobases". Includes starting coordinates, topologies, and trajectories, as wel…
View article: Superanionic DNA. Enzymatic Synthesis of Hypermodified DNA Bearing Four Different Anionic Substituents at all Four Nucleobases
Superanionic DNA. Enzymatic Synthesis of Hypermodified DNA Bearing Four Different Anionic Substituents at all Four Nucleobases Open
Additional supporting simulation data for "Superanionic DNA. Enzymatic Synthesis of Hypermodified DNA Bearing Four Different Anionic Substituents at all Four Nucleobases". Includes starting coordinates, topologies, and trajectories, as wel…
View article: CCDC 2195107: Experimental Crystal Structure Determination
CCDC 2195107: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …
View article: CCDC 2195102: Experimental Crystal Structure Determination
CCDC 2195102: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …