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Search results for: PROTEINS, DATA-ASSISTED MODELING, CONFORMATIONAL ENSEMBLES, NUCLEAR MAGNETIC RESONANCE, SMALL-ANGLE X-RAY SCATTERING, CHEMICAL CROSS-LINKING COUPLED WITH MASS SPECTROSCOPY, MOLECULAR DYNAMICS, COARSE GRAINING
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Recent Developments in Data-Assisted Modeling of Flexible Proteins
PublicationMany proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublicationA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
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Local structural and chemical ordering of nanosized Pt(3±δ)Co probed by multiple-scattering x-ray absorption spectroscopy
PublicationThis work reports a detailed investigation of the local structure and chemical disorder of a Pt(3±δ)Co thin film and Pt(3±δ)Co nanoparticles. We have used a combination of techniques including x-ray absorption spectroscopy (XAS), x-ray diffraction (XRD), and high-resolution transmission electron microscopy (TEM). The important effect of chemical ordering on pair and three-atom configurations has been studied using computer simulations...
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Enzymatic and Chemical Cross-Linking of Bacterial Cellulose/Fish Collagen Composites—A Comparative Study
PublicationThis article compares the properties of bacterial cellulose/fish collagen composites (BC/Col) after enzymatic and chemical cross-linking. In our methodology, two transglutaminases are used for enzymatic cross-linking—one recommended for the meat and the other proposed for the fish industry—and pre-oxidated BC (oxBC) is used for chemical cross-linking. The structure of the obtained composites is characterized by scanning electron...
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Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
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Study of the Layer-Type BST Thin Film with X-ray Diffraction and X-ray Photoelectron Spectroscopy
PublicationIn the present paper, results of X-ray photoelectron studies of electroceramic thin films of barium strontium titanate, Ba1xSrxTiO3 (BST), composition deposited on stainless-steel substrates are presented. The thin films were prepared by the sol-gel method. A spin-coating deposition of BST layers with different chemical compositions was utilized so the layer-type structure of (0-2) connectivity was formed. After the deposition,...
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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Strategies for optimizing the phase correction algorithms in Nuclear Magnetic Resonance spectroscopy
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X-ray Photoelectron Spectroscopy of Carboxylic Acids as Corrosion Inhibitors of Aluminium Alloys
PublicationThe datasets, titled X-ray Photoelectron Spectroscopy studies of citric acid adsorption on aluminium alloy 5754 in alkaline media and X-ray Photoelectron Spectroscopy studies of various carboxylic acids adsorption on aluminium alloys in alkaline media, contain XPS studies of the corrosion inhibitory action of selected dicarboxylic acids towards commercially available aluminium alloy 5754 in alkaline media at pH=11. These datasets...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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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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Nuclear Magnetic Resonance Metabolomics Reveals Qualitative and Quantitative Differences in the Composition of Human Breast Milk and Milk Formulas
PublicationCommercial formula milk (FM) constitutes the best alternative to fulfill the nutritional requirements of infants when breastfeeding is precluded. Here, we present the comparative study of polar metabolite composition of human breast milk (HBM) and seven different brands of FM by nuclear magnetic resonance spectroscopy. The results of the multivariate data analysis exposed qualitative and quantitative differences between HBM and...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Analysis and characterization of coordination compounds by resonance Raman spectroscopy
PublicationResonance Raman spectroscopy has become a powerful tool to study excited-state geometries, excited-state charge distributions and photoinduced reaction dynamics in coordination compounds. Due to their rich photophysical properties coordination compounds are utilized for a variety of applications ranging from DNA sensing to photocatalysis. This review features recent applications of various resonance Raman scattering techniques...
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.
PublicationAmphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selectivederivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed...
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Small-Angle Neutron Scattering Study of the Structure of Mixed Micellar Solutions Based on Heptaethylene Glycol Monotetradecyl Ether and Cesium Dodecyl Sulfate
PublicationThe micellization in mixed aqueous systems based on a nonionic surfactant, heptaethylene glycol monotetradecyl ether (C14E7), and an anionic surfactant, cesium dodecyl sulfate, has been investigated by small-angle neutron scattering. Preliminary data on the behavior of the C14E7 aqueous solutions (with three concentrations, 0.17, 0.5, and 1%) mixed with a small amount of anionic surfactant, cesium dodecyl sulfate, are reported.
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Unsaturated, biobased polyesters and their cross-linking via radical copolymerization
PublicationBiobased, unsaturated polyesters derived from isosorbide, maleic anhydride and succinic acid were synthesized and characterized. The presence of maleic anhydride units in the structure of the polyesters allowed converting them into cured coatings by radical copolymerization with cross-linking agents such as 2-hydroxyethyl methacrylate, N-vinyl-2-pyrrolidinone, acrylic acid or methacrylamide. The investigated polyesters were obtained...
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Interatomic potential suitable for the modeling of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe test the potentials available for elemental carbon, with the scope to choose the potential suitable for the modeling of penta-graphene, the latest two dimensional carbon allotrope. By using molecular statics and molecular dynamics simulations we show that there is only one potential e namely the Tersoff-type potential proposed by Erhart and Albe in 2005 e which is able to correctly describe all the important features of penta-graphene....
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TIME-OF-FLIGHT DIFFERENTIAL ELECTRON SCATTERING FROM MOLECULAR TARGETS: BENCHMARK CROSS SECTIONS
PublicationWe report time-of-flight differential cross section (DCS) measurements for the electron impact excitation transition in H2. In this work, agreement between available theory and experiment is excellent overall, and marks a transition in electron molecule scattering where differential scattering of excitation is found to be in such precise agreement. We also prove that the newly built apparatus can be used for accurate measurement...
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Enhancement of the Magnetic Coupling in Exfoliated CrCl 3 Crystals Observed by Low‐Temperature Magnetic Force Microscopy and X‐ray Magnetic Circular Dichroism
PublicationMagnetic crystals formed by 2D layers interacting by weak van der Waals forces are currently a hot research topic. When these crystals are thinned to nanometric size, they can manifest strikingly different magnetic behavior compared to the bulk form. This can be the result of, for example, quantum electronic confinement effects, the presence of defects, or pinning of the crystallographic structure in metastable phases induced by...
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X-Ray Diffraction, Mössbauer Spectroscopy and Magnetoelectric Effect Studies of Multiferroic Bi5Ti3FeO15 Ceramics
PublicationBi5Ti3FeO15 ceramics belongs to multiferroic class of materials. In this work it was prepared by solid-state sintering method and investigated by X-ray diffraction, Mössbauer spectroscopy, and magnetoelectric effect measurements. As it was proved by X-ray diffraction studies the single-phase Bi5Ti3FeO15 compound was obtained. The Mössbauer investigations revealed paramagnetic character of the compound at room temperature as well...
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Time-of-flight electron scattering from molecular hydrogen: Benchmark cross sections for excitation of the X1Σ+g→b3Σ+u transition
PublicationThe electron impact X1Σ+g to b3Σ+u transition in molecular hydrogen is one of the most important dissociation pathways to forming atomic hydrogen atoms, and is of great importance in modeling astrophysical and industrial plasmas where molecular hydrogen is a substantial constituent. Recently it has been found that the convergent close-coupling (CCC) cross sections of Zammit et al. [Phys. Rev. A 95, 022708 (2017)] are up to a factor...
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Common methods for the chiral determination of amphetamine and related compounds II: Capillary electrophoresis and nuclear magnetic resonance
PublicationAmphetamine group and related ring-substituted substances are generally synthetic compounds, belonging to one of the most heavily abused drug groups in recent years. Some compounds in this class also originate from plants. Analysis of the enantiomers of AM-type compounds and metabolites is extremely important for a number of scientific disciplines. From studies of biological activity or mechanisms through determination of precursor...
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublicationOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Kinetics of cross-linking processes of fast-curing polyurethane system
PublicationThis work focuses on the application of thermal analysis and kinetics investigations to analyze chemical processes during cross-linking of the complex fast-curing polyurethane system. Non-isothermal Differential Scanning Calorimetry (DSC) measurements were performed for both stoichiometric mixtures of polyol and isocyanate component and for mixture with large isocyanate excess. Isoconversional methods were used to calculate initial...
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Application of vibrational spectroscopy, thermal analyses and X-Ray diffraction in the rapid evaluation of the stability in solid-state of ranitidine, famotidine and cimetidine
PublicationThis paper reports the study on applicability of Fourier transform infrared (FTIR), near-infrared (NIR) and Raman spectroscopy, differential scanning calorimetry (DSC) and X-ray diffraction (XRD) for the estimation of the chemical stability and photostability of histamine H2-receptor antagonist substances. Ranitidine hydrochloride (RAN), famotidine (FAM) and cimetidine (CIM) were tested and differences in sensitivity were measured...
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Nuclear magnetic shielding constants of Dirac one-electron atoms in some low-lying discrete energy eigenstates
PublicationWe present tabulated data for the nuclear magnetic shielding constants (σ) of the Dirac one-electron atoms with a pointlike, motionless and spinless nucleus of charge Ze. Utilizing the exact general analytical formula for σ derived by us (Stefańska, 2016) valid for an arbitrary discrete energy eigenstate, we have computed the numerical values of the magnetic shielding factors for the ground state and for the first and the second...
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Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations
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Cross-linking of epoxy-oligomeric mixtures in the presence of modified phenol-formaldehyde resins
PublicationCross-linking of epoxy oligomeric mixtures consisting of industrial epoxy resin ED-20, oligoetheracrylate TGM-3, peroxide derivative of epoxy resin ED-24 and phenol-formaldehyde oligomer with unsaturated methacrylate fragments or peroxide groups was studied in the presence of polyethylenepolyamine at room temperature and heated to 383, 403 or 423 K for 15, 30, 45, 60 and 75 minute. The influence of mixture composition, temperature...
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Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
PublicationCoarse-grained approaches, in which groups of atoms are represented by single interaction sites, are very important in biological and materials sciences because they enable us to cover the size- and time-scales by several orders of magnitude larger than those available all-atom simulations, while largely keeping the details of the systems studied. The coarse-grained approaches differ by the scheme of reduction and by the origin...
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Molecular dynamics simulations of the growth of poly (chloro-para-xylylene) films.
PublicationParylene C, poly(chloro-para-xylylene) is the most widely used member of the parylene family due to its excellent chemical and physical properties. In this work we analyzed the formation of the parylene C film using molecular mechanics and molecular dynamics methods. A five unit chain is necessary to create a stable hydrophobic cluster and to adhere to a covered surface. Two scenarios were deemed to take place. The obtained results...
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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
PublicationWe report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms...
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SEI Growth and Depth Profiling on ZFO Electrodes by Soft X-Ray Absorption Spectroscopy
PublicationZnFe2O4 (ZFO) Li-ion batteries (LIBs) represent a reliable, affordable, and safe energy storage technology for use in portable application. However, current LIB active materials (graphite, lithium/transition metal spinel or layered oxides, olivine structures) can store only limited energy since they rely on insertion storage based on solid-state host-guest interactions. Moreover, performances and durability of the cells are strongly...
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Comparative X-ray diffraction and Mössbauer spectroscopy studies of BiFeO3 ceramics prepared by conventional solid-state reaction and mechanical activation
PublicationThe aim of this work was to prepare BiFeO3 by modified solid-state sintering and mechanical activation processes and to investigate the structure and hyperfine interactions of the material. X-ray diffraction and Mössbauer spectroscopy were applied as complementary methods. In the case of sintering, BiFeO3 phase was obtained from the mixture of precursors with 3 and 5 % excess of Bi2O3 during heating at 1023 K. Small amounts of...
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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Modeling of the M X-ray line structures for tungsten and L X-ray line structures for molybdenum
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Normalized Partial Scattering Cross Section for Performance Evaluation of Low-Observability Scattering Structures
PublicationThe development of diffusion metasurfaces created new opportunities to elevate the stealthiness of combat aircraft. Despite the potential significance of metasurfaces, their rigorous design methodologies are still lacking, especially in the context of meticulous control over the scattering of electromagnetic (EM) waves through geometry parameter tuning. Another practical issue is insufficiency of the existing performance metrics,...
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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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Role of methylation in electron scattering on X(CH3)4 (X = C, Si, Ge) molecules
PublicationTotal cross sections (TCS) for low-energy electron scattering from X(CH3)4 (where X = C, Si, Ge) molecules have been measured using linear transmission method. Present results and those obtained previously for XH4 molecules were used to determine how methylation of the target is reflected in TCS energy dependence.
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First-order magnetic transition in single-crystalline CaFe2As2 detected by 75As nuclear magnetic resonance
PublicationPrzedstawione są wyniki badań jądrowego rezonansu magnetycznego na 75As dla kryształów CaFe2As2. Wyniki wskazują, że strukturalne i magnetyczne przejścia w CaFe2As2 są silnie skorelowane i są pierwszego rodzaju.
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The POCOBIO Database for Computed Scattering Cross-Sections for Positron Collisions with Biomolecular Systems
PublicationThe design of a database for positron interactions with biomolecular systems is outlined. The database contains only scattering cross sections, which are derived from theory. The data model is defined in a very flexible way, which facilitates the usage of weakly bound clusters of molecules and molecular systems with many tautomeric forms.
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A Novel Ru(II) Polypyridine Black Dye Investigated by Resonance Raman Spectroscopy and TDDFT Calculations
PublicationThe optical properties of a new(bipyridine)2Ru(4H-imidazole) complex presenting a remarkablebroad absorption in the visible range are investigated. Thestrong overlap of the absorption with the solar radiationspectrum renders the studied complex promising as a blackabsorber and hence as a starting structure for applications inthe field of dye-sensitized solar cells. The correlations betweenstructural and electronic features for...
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Confined lead nanogranules investigated by X-ray absorption spectroscopy
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