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Stimulated by cyclodextrins high yield synthesis of azocrown analogues comprising pyrrole or imidazole residues
PublicationThe influence of cyclodextrins (CDs) on the formation of azocrown ethers comprising pyrrole, imidazole and substituted imidazole has been studied. Pyrrole, imidazole, 2-methyl-, 4-methyl- and 4-phenylimidazole were coupled with bisdiazonium salts derived from bis-1,5-(2-aminophenoxy)-3-oxapentane or bis-1,8-(2-aminophenoxy)-3,6-dioxaoctane to form macrocyclic compounds with two azo units. The syntheses were performed under standard...
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Lower rim substituted p-tert-butylcalix[4]arene; Part 14. Synthesis, structures and binding studies of calix[4]arene thioamides
PublicationA number of p-tert-butylcalix[4]arene thioamides were synthesized and characterized by 1H-NMR and elemental analysis. Compounds 1-5 are O-substituted derivatives with -CH2-C(=S)-N-X groups, where NX = morpholidyl, NEt2, NHC2H4Ph, NHCH2Ph and NHEt,respectively. The X-ray structures of the ligands 1, 3, 5 and of the complex 3Pb(ClO4)2, (compound 6), are presented and their slightly distorted cone conformation is established. The...
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Influence of temperature and interactions with ligands on dissociation of dsDNA and ligand-dsDNA complexes of various types of binding : an electrochemical study.
PublicationSeveral medicinally important compounds that bind to dsDNA strands via intercalation (C-1311, C-1305, EtBr), major groove binding (Hoechst 33258) and covalent binding (cis-Pt) were examined. The obtained results suggest that both the transfer of conformation B to C and the denaturation process, for the ligand-dsDNA complexes, except for covalently bound cis-Pt, took place at higher temperatures compared to the unbound helix. Furthermore,...
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A spectroscopic study of the cis/trans-isomers of penta-2,4-dienoic acid attached to gold nanoclusters
PublicationIn this theoretical work, we present a spectroscopic analysis of the cis/trans-isomers of a molecular switch, penta-2,4-dienoic acid, attached to gold clusters of different size (1, 2 and 20 gold atoms). We have simulated 4 different spectroscopic techniques: Infrared spectroscopy, normal Raman scattering, absorption spectra and resonance Raman scattering. We discuss how the position and the conformation of the molecule determine...
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Unassisted formation of hemiaminal ether from 4-aminopyridine and o-vanillin - experimental and theoretical study
PublicationThe reactions between o-vanillin and three isomeric aminopyridines lead to imines of diverse spatial conformation and reactivity. The direct products of these simple reactions carried out in methanol are either imine compounds formed in the reactions of 2- amino- and 3-aminopyridine with o-vanillin or the α-aminoether formed in the reaction of o-vanillin with 4-aminopyridine. The Schiff-type derivative of 4-aminopyridine and o-vanillin,...
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AMCA to TAMRA long range resonance energy transfer on a flexible peptide
PublicationFörster resonance energy transfer between 7-amino-4-methyl-3-coumarinylacetic acid, (AMCA, donor) and 5- carboxytetramethylrhodamine, (TAMRA, acceptor) bound to Lys(AMCA)-Gly-Pro-Arg-Ser-Leu-Ser-Gly-Lys (TAMRA)-NH2 peptide is demonstrated by various spectroscopic techniques in glycerol at room temperature. In particular, nonexponential character of fluorescence intensity decay evidences the distance distribution between the donor...
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<i>N,N,N</i>-Trimethyl-N-(methyl 5-deoxy-2,3-<i>O</i>-isopropylidene-β-D-ribofuranosid-5- yl)ammonium 4-methylbenzenesulfonate sesquihydrate.
PublicationThe structure of the title compound, [C12H24NO4][C7H7O3S]·1.5H2O, contains alternating layers parallel to (001) of hydrophobic and polar character, stabilized by C-H...O hydrogen bonding. The furan ring adopts an envelope conformation with the C(OMe) atom as the flap, and the dioxolane ring is twisted about one of the O-C(methine) bonds. A comparison to related compounds is presented. The tosylate-O atoms were disordered over two...
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Structural Control of Photoinduced Dynamics in 4H-Imidazole- Ruthenium Dyes
PublicationThe photoinduced dynamics of a series ofterpyridine 4H-imidazole-ruthenium complexes, which constitutea new family of panchromatic dyes, is investigated. Thedynamics involves two excited states localized within the 4Himidazolesphere. Upon MLCT excitation, an excited state ispopulated, which is localized on the central part of the 4Himidazoleligand caused by its nonplanar conformation. Thepopulation of the second excited state is...
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Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions
PublicationAlthough osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage...
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Photoelectron spectroscopy of a series of acetate and propionate esters
PublicationThe electronic state and photoionization spectroscopy of a series of acetate esters: methyl acetate, isopropyl acetate, butyl acetate and pentyl acetate as well as two propionates: methyl propionate and ethyl propionate, have been determined using vacuum-ultraviolet photoelectron spectroscopy. These experimental investigations are complemented by ab initio calculations. The measured first adiabatic and vertical ionization energies...
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Polycyclic aromatic hydrocarbons as test probes to investigate the retention behavior of 1,3-alternate calix[4]arene silica-bonded stationary phases
PublicationA series of polycyclic aromatic hydrocarbons (PAHs) of different size and shape has been used to characterize the chromatographic behavior of five calix[4]arene stationary phases in 1,3-alternate conformation synthesized in our laboratory. The selection of linear, fourring nonlinear, and five-ring PAHs gave data on selectivity changes across range of the calix[4]arene columns. Retention of the 12 aromatic solutes has been evaluated...
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A mobile loop order–disorder transition modulates the speed of chaperonin cycling
PublicationMolecular machines order and disorder polypeptides as they form and dissolve large intermolecular interfaces, but the biological significance of coupled ordering and binding has been established in few, if any, macromolecular systems. The ordering and binding of GroES co-chaperonin mobile loops accompany an ATP-dependent conformational change in the GroEL chaperonin that promotes client protein folding. Following ATP hydrolysis,...
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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublicationAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
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Oxolane Ammonium Salts (Muscarine-Like)—Synthesis and Microbiological Activity
PublicationCommercially available 2-deoxy-D-ribose was used to synthesize the appropriate oxolane derivative—(2R,3S)-2-(hydroxymethyl)oxolan-3-ol—by reduction and dehydration/cyclization in an acidic aqueous solution. Its monotosyl derivative, as a result of the quaternization reaction, allowed us to obtain eight new muscarine-type derivatives containing a quaternary nitrogen atom and a hydroxyl group linked to the oxolane ring. Their structure...
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Structure and Molecular Dynamics in Renewable Polyamides from Dideoxy-Diamino Isohexide
PublicationThe chemical structure, the conformation, andthe flexibility of the polymer chain fragments present in thepolyamides synthesized from 2,5-diamino-2,5-dideoxy-1,4;3,6-dianhydrosorbitol, 1,4-diaminobutane, and either sebacic orbrassylic acid have been studied by liquid-state 2D NMRspectroscopy viz. correlation spectra (COSY) and heteronuclearmultiple-bond correlation spectra (gHMBC), by 13Ccross-polarization/magic-angle spinning...
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Physical crosslinking of hyaluronic acid in the presence of phospholipids in an aqueous nano-environment
PublicationHyaluronic acid and phospholipids are two components in the synovial joint cavity that contribute to joint lubrication synergistically. Molecular dynamics simulations were performed and hydrogen bonds in hyaluronic acid were analyzed to identify specific sites that are responsible for its physical cross-linking. Two molecular masses of hyaluronic acid, 10 kDa and 160 kDa, were considered. We use molecular dynamics simulations and...
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Rubrene Thin Films with Viably Enhanced Charge Transport Fabricated by Cryo-Matrix-Assisted Laser Evaporation
PublicationAmong organic semiconductors, rubrene (RB; C42H28) is of rapidly growing interest for the development of organic and hybrid electronics due to exceptionally long spin diffusion length and carrier mobility up to 20 cm2V−1s−1 in single crystals. However, the fabrication of RB thin films resembling properties of the bulk remains challenging, mainly because of the RB molecule’s twisted conformation. This hinders the formation of orthorhombic...
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Effect of Nanohydroxyapatite on Silk Fibroin–Chitosan Interactions—Molecular Dynamics Study
PublicationFibroin–chitosan composites, especially those containing nanohydroxyapatite, show potential for bone tissue regeneration. The physicochemical properties of these biocomposites depend on the compatibility between their components. In this study, the intermolecular interactions of fibroin and chitosan were analyzed using a molecular dynamics approach. Two types of systems were investigated: one containing acetic acid and the other...
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Molecular and structural characteristics of cod gelatin films modifiedwith EDC and TGase
PublicationCod gelatin films before and after cross-linking of gelatin with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) or transglutaminase (TGase) have been characterized by FT-IR spectroscopy and DSC analysis. For comparison, a film prepared from unmodified pig gelatin has been also analysed. The difference spectra showed that cod gelatin during the film formation involved first of all water-to-amide hydrogen bonds, and the film...
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3,3'-Dibenzoyl-1,1'-dibenzyl-1,1'-(ethane-1,2-diyl)dithiourea
PublicationIn the title compound, C32H30N4O2S2, the carbonyl and thiocarbonyl groups are found in a rare synclinal conformation, with an S-C···C-O pseudo-torsion angle of 62.6(2)°. The molecule has Ci = S2 point-group symmetry with a crystallographic center of inversion located in the middle of the ethylene bridge. One of the symmetry-independent phenyl...
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Interactions of telomeric proteins with nucleic acids: sequence recognition on intact and oxidatively damaged telomeres
PublicationTelomeres are complex nucleoprotein assemblies that play a vital role in the maintenance of functional ends of linear chromosomes. Telomeric DNA, composed of tandem repeats of the 5'-TTAGGG-3' motif, solves the so-called end replication problem: as chromosomes shorten with each cell division, no information is lost, and the telomere can be re-extended. In the cell, many protein factors regulate telomere length, nuclear positioning...
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Chiral and achiral crystals, charge-assisted hydrogen-bond patterns and self-organization of selected solid diaminium thiosulfates
PublicationAbstract A series of diaminium thiosulfates, derivatives of diamines: NH2CH2CH(CH3)NH2 (1) and NH2(CH2)nNH2, n = 3-6 (2-5 respectively)and thiosulfuric acid were prepared and their structures determined by crystal X-ray diffraction analysis. Compounds 1, 2 and 4 turned out to be hydrates. The crystal structure of 1,2-proylenediaminium thiosulfate is chiral and exhibits spontaneous resolution. Crystals for both enantiomers...
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(R,R)-1-Acetyl-1'-(2,4,6-trinitrophenyl)-2,2'-bipyrrolidine
Publication(R,R)-1-Acetyl-1'-(2,4,6-trinitrophenyl)-2,2'-bipyrrolidine has been synthesized and its rentgenostructure has been determined. The structure of the title molecule, C16H19N5O7, is mainly determined by the steric effect of a bulky 2,4,6-trinitrophenyl group attached to the N atom of a pyrrolidine ring. Both pyrrolidine rings adopt an envelope conformation, with one of the methylene C atoms as the flap in each case, and the N-C-C-N...
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Poly-L-Lysine-functionalized fluorescent diamond particles: pH triggered fluorescence enhancement via surface charge modulation
PublicationRecently, the interest in applying fluorescent diamond particles (FDPs) containing nitrogen-vacancy (NV) centers for enhancing the mechanical and chemical properties of some materials, biological imaging, and sensing has been expanding rapidly. The unique properties of NV centers such as intensive, time-stable fluorescence, and an electron spin, which exhibits long coherence time and may be manipulated using external stimuli, such...
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Thermodynamic, Anticoagulant, and Antiproliferative Properties of Thrombin Binding Aptamer Containing Novel UNA Derivative
PublicationThrombin is a serine protease that plays a crucial role in hemostasis, fibrinolysis, cell proliferation, and migration. Thrombin binding aptamer (TBA) is able to inhibit the activity of thrombin molecule via binding to its exosite I. This 15-nt DNA oligonucleotide forms an intramolecular, antiparallel G-quadruplex structure with a chair-like conformation. In this paper, we report on our investigations on the influence of certain...
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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PTD4 Peptide Increases Neural Viability in an In Vitro Model of Acute Ischemic Stroke
PublicationIschemic stroke is a disturbance in cerebral blood flow caused by brain tissue ischemia and hypoxia. We optimized a multifactorial in vitro model of acute ischemic stroke using rat primary neural cultures. This model was exploited to investigate the pro-viable activity of cell-penetrating peptides: arginine-rich Tat(49–57)-NH2 (R49KKRRQRRR57-amide) and its less basic analogue, PTD4 (Y47ARAAARQARA57-amide). Our model included glucose...
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Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1-ATPase
PublicationF1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned...
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A Series of Novel 3D Coordination Polymers Based on the Quinoline-2,4-dicarboxylate Building Block and Lanthanide(III) Ions—Temperature Dependence Investigations
PublicationA series of novel 3D coordination polymers [Ln2(Qdca)3(H2O)x]yH2O (x = 3 or 4, y = 0–4) assembled from selected lanthanide ions (Ln(III) = Nd, Eu, Tb, and Er) and a non-explored quinoline- 2,4-dicarboxylate building block (Qdca2 = C11H5NO4 2) were prepared under hydrothermal conditions at temperatures of 100, 120, and 150 C. Generally, an increase in synthesis temperature resulted in structural transformations and the formation...
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Establishing the allosteric mechanism in CRISPR‐Cas9
PublicationAllostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR‐Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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An Investigation of Polyamides Based on Isoidide-2,5-dimethyleneamine as a Green Rigid Building Block with Enhanced Reactivity
PublicationNovel, semicrystalline polyamides and copolyamides were synthesized from a new carbohydrate-based diamine, namely isoidide-2,5-dimethyleneamine (IIDMA). In combination with 1,6-hexamethylene diamine (1,6-HDA) as well as the biobased sebacic acid (SA) or brassylic acid (BrA), the desired copolyamides were obtained via melt polymerization of the nylon salts followed by a solid-state polycondensation (SSPC) process. Depending on the...
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Enzymatic cross-linking of β-lactoglobulin in solution and at air–water interface: Structural constraints
PublicationEffective and controlled use of cross-linking enzymes in structure engineering of food systems depends on characterization of the favorable conditions for enzyme-substrate complex and the limiting factors for the desired modification. In this respect, we analyzed the susceptibility of bovine β-lactoglobulin (BLG) to enzymatic cross-linking by Trichoderma reesei tyrosinase (TrTyr) and transglutaminase (TG). Changes in BLG molecular...
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The carbohydrate glycosylphosphatidylinositol anchor chain under mechanical stress
PublicationCarbohydrates have quite complicated micro heterogenic structure which may undergo different structural transitions. Due to their extreme flexibility it is very difficult to investigate such structural changes experimentally. In these studies we want to predict what structural and conformational changes are possible in the carbohydrate
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Synthetic, Structural, and Spectroscopic Characterization of a Novel Family of High-Spin Iron(II) [(β-Diketiminate)(phosphanylphosphido)] Complexes
PublicationThis work describes a series of iron(II) phosphanylphosphido complexes. These compounds were obtained by reacting lithiated diphosphanes R2PP(SiMe3)Li (R = t-Bu, i-Pr) with an iron(II) β-diketiminate complex, [LFe(μ2-Cl)2Li(DME)2] (1), where DME = 1,2-dimethoxyethane and L = Dippnacnac (β-diketiminate). While the reaction of 1 with t-Bu2PP(SiMe3)Li yields [LFe(η1-Me3SiPPt- Bu2)] (2), that of 1 with equimolar amounts of i-Pr2PP(SiMe3)Li,...
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Absolute configurations of C34 and C35 of antibiotic niphimycin A
PublicationThe relative configurations of four stereogenic centers of the C33-C42 fragment of niphimycin A were assigned as 2S*, 3R*, 4S* and 6S*, based upon 1H NMR analysis with double-quantum filtered COSY and nuclear Overhauser spectroscopy experiments. These data were then correlated with absolute configurations at C36 and C38 of niphimycin A, which were declared previously as 36S and 38S [3]. This allowed for the assignment of the absolute...