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Search results for: PROTEIN/NUCLEIC ACID INTERACTIONS
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Amino Acid Based Antimicrobial Agents – Synthesis and Properties
PublicationStructures of several dozen of known antibacterial, antifungal or antiprotozoal agents are based on the amino acid scaffold. In most of them, the amino acid skeleton is of a crucial importance for their antimicrobial activity, since very often they are structural analogs of amino acid intermediates of different microbial biosynthetic pathways. Particularly, some aminophosphonate or aminoboronate analogs of protein amino acids are...
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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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In silico epitope prediction of Borrelia burgdorferi sensu lato antigens for the detection of specific antibodies
PublicationDespite many years of research, serodiagnosis of Lyme disease still faces many obstacles. Difficulties arise mainly due to the low degree of amino acid sequence conservation of the most immunogenic antigens among B. burgdorferi s.l. genospecies, as well as differences in protein production depending on the environment in which the spirochete is located. Mapping B-cell epitopes located on antigens allows for a better understanding...
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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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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublicationIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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Isolation and some properties of collagen from the backbone of Baltic cod(Gadus morhua)
PublicationOssein from Baltic cod backbone was obtained after extraction of non-collagenous protein with 0.1 M NaOH solution and demineralization with 1.0 M HCl solution. The extractions were performed at 4 C for24, 48 and 72 h using a solid/solution ratio from 1:4 to 1:8 (w/v). After 48 h of extraction in 0.5 M acetic acid only about 25% of collagen was dissolved. After 48 h of extraction at optimal concentration of pepsin(4 mg/g ossein)...
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Solvation phenomena in ternary system tetramethylurea-methylacetamide-water: Insights from volumetric, compressibility and FTIR analysis
PublicationThe properties of the ternary systems N,N,N’,N’-tetramethylurea - N-methylacetamide - water were investigated using Fourier-transform infrared spectroscopy (FTIR), volumetric and compression measurements. Densities and sound velocities were determined in order to obtain the apparent molar volumes (VΦ) and apparent molar isentropic compressions (ΚS,Φ). These values were then extrapolated to infinite dilution. Additionally, interaction parameters...
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Amyloid fibril formation in the presence of water structure-affecting solutes
PublicationThe impact of the differently hydrated non-electrolytes (protein structure destabilizers) on the fibrillation of hen egg white lysozyme (HEWL) was investigated. Two isomeric urea derivatives i.e. butylurea (BU) and N,N,N′,N′-tetramethylurea (TMU) were chosen as a tested compounds. The obtained results show that butylurea exerts greater impact on HEWL and its fibrillation than tetramethylurea. Both substances decrease the time of...
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Supramolecular Synthesis Based on a Combination of Se···N Secondary Bonding Interactions with Hydrogen and Halogen Bonds
PublicationExamination of the solid state structures of 2,1,3-benzoselenadiazole complexes with hydrogen or halogen bond donors has demonstrated that the 2,1,3-benzoselenadiazole molecules preferably form centrosymmetric dimers with use of [Se–N]2 supramolecular synthon, whereas the two remaining nitrogen atoms not involved in the [Se–N]2 supramolecular interactions can act as acceptors of hydrogen or halogen bonds. Cocrystallization of selenadiazoles...
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Novel primosomal protein B from Clostridium pastuerianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Novel primosomal protein B from Clostridium pasteurianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Taurine as a water structure breaker and protein stabilizer
PublicationThe enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between...
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Cloning, expression, and biochemical characterization of a coldactive GDSL-esterase of a Pseudomonas sp. S9 isolated from Spitsbergen island soil
PublicationAn estS9 gene, encoding an esterase of the psychrotolerant bacterium Pseudomonas sp. S9 was cloned and sequenced. The deduced sequence revealed a protein of 636 amino acid residues with a molecular mass of 69 kDa.Further amino acid sequence analysis revealed that the EstS9 enzyme contained a G-D-S-L motif centered at a catalytic serine, an N-terminal catalytic domain and a C-terminal autotransporter domain. Two recombinant E. coli...
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Conserved motifs of MutL proteins
PublicationtThe MutL protein is best known for its function in DNA mismatch repair (MMR). However, there isevidence to suggest that MutL is not only the linker connecting the functions of MutS and MutH in MMR,but that it also participates in other repair systems, such as Very Short Patch (VSP), Base Excision (BER)and Nucleotide Excision Repair (NER). This study set out to identify the most highly conserved aminoacid sequence motifs in MutL...
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Stabilization of N-, N,N-, N,N'-Methylated and Unsubstituted Simple Amidine Salts by Multifurcated Hydrogen Bonds
PublicationIn the light of the usefulness of amidines in medicinal chem., this paper considers the effects on biol. properties and chem. reactivities of org. mols. affected by intramol. interactions. The study of chem. shifts has been an important source of information on the electronic structure of amidine salts and their ability to form non-covalent bonds with nucleic acids. The NMR and IR results demonstrate that hydrogen bonds are...
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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Enhancing colloidal stability of nanodiamond via surface modification with dendritic molecules for optical sensing in physiological environments
PublicationPre-treatment of diamond surface in low-temperature plasma for oxygenation and in acids for carboxylation was hypothesized to promote the branching density of the hyperbranched glycidol polymer. This was expected to increase the homogeneity of the branching level and suppress interactions with proteins. As a result, composite nanodiamonds with reduced hydrodynamic diameters that are maintained in physiological environments were...
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Enhanced susceptibility of SARS-CoV-2 spike RBD protein assay targeted by cellular receptors ACE2 and CD147: Multivariate data analysis of multisine impedimetric response
PublicationSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the cells through the binding of spike protein to the host cell surface-expressing angiotensin-converting enzyme 2 (ACE2) or by endocytosis mediated by extracellular matrix metalloproteinase inducer (CD147). We present extended statistical studies of the multisine dynamic electrochemical impedance spectroscopy (DEIS) revealing interactions between Spike RBD and...
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublicationInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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4-[(tert-Butyldimethylsilyl)oxy]-6-methoxy-7-methyl-5-(oxiran-2-ylmethyl)-2-benzofuran-3(1H)-one
PublicationThe title compound, C19H28O5Si, was obtained in the reaction of 1,3-dihydro-4-[(tert-butyldimethylsilyl)oxy]-6-methoxy-7-methyl-3-oxo-5-(prop-2-enyl)isobenzofuran with meta-chloroperbenzoic acid. This reaction is one of the stages of the total synthesis of mycophenolic acid, which we attempted to modify. The title compound forms crystals with only weak intermolecular interactions. The strongest stacking interaction is found between...
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Characterization of Bioactivity of Selective Molecules in Fruit Wines by FTIR and NMR Spectroscopies, Fluorescence and Docking Calculations
PublicationFourier transform infrared (FTIR) and proton nuclear magnetic resonance (1H NMR) spectroscopies were applied to characterize and compare the chemical shifts in the polyphenols’ regions of some fruit wines. The obtained results showed that FTIR spectra (1800–900 cm−1) and 1H NMR (δ 6.5–9.3 ppm) of different fruit wines can be used as main indices of the year of vintage and quality of fruit wines. In addition to the classical determination...
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The mechanical properties and bactericidal degradation effectiveness of tannic acid-based thin films for wound care
PublicationThe surface area is the most important aspect when considering the interactions between a material and the surrounding environment. Chitosan (CTS) and tannic acid (TA) were previously successfully tested by us to obtain thin films to serve as wound dressings or food packaging materials. However, surface properties as well as the antimicrobial activity of the material were not considered. They are important if the material is likely...
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Evidence of mutations conferring resistance to clarithromycin in wastewater and activated sludge
PublicationThe occurrence of clarithromycin in wastewater samples and of the activated sludge bacteria possibly resistant to this pharmaceutical was the object of the study. Samples of wastewater or activated sludge were taken from a municipal wastewater treatment plant in summer and winter and characterised regarding their clarithromycin concentrations and the presence of nucleic acid fragments (Cla-sequences) known to be responsible for...
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublicationFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublicationWater molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel...
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Quality Control of Bacterial Extracellular Vesicles with Total Protein Content Assay, Nanoparticles Tracking Analysis, and Capillary Electrophoresis
PublicationExtracellular vesicles (EVs) were isolated from Pectobacterium zantedeschiae culturing media using direct ultracentrifugation (UC), iodixanol cushion ultracentrifugation (ICUC), and iodixanol density gradient ultracentrifugation (IDGUC) techniques. The isolates were characterized with total protein content assay (bicinchoninic acid assay, BCA), nanoparticles tracking analysis (NTA), and capillary electrophoresis (CE). A satisfactory...
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Problem of aggregation in dye-DNA interaction, calorimetry studies
PublicationNucleic acids are the biological target for many antimicrobial, antitumor and antiviral drugs. Ligand-DNA interactions can be classified into two major categories: 1. covalent binding, which can provide to intermolecular adducts, 2. physico-chemical interactions, which can be divided into intercalation (e.g. adriamycin) or groove binding (e.g. dystamycin). There are several methods to investigate interactions between drug and DNA....
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Pre-treatment of bio fraction waste prior to fermentation processes
PublicationCurrent efforts are taken to increase resource efficiency, close material loops, and improve sustainable waste and by-products management. Thus, networking agro-food by-products and converting them into valuable products completely exhausting the potential of the raw material becomes significant. Model lignocellulosic and starch based biomass were subjected to pre-treatment with the application of acidic compounds, i.e. sulphuric...
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Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface
PublicationAlbumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions...
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Antioxidant Interactions between Major Phenolic Compounds Found in 'Ataulfo' Mango Pulp: Chlorogenic, Gallic, Protocatechuic and Vanillic Acids
PublicationPhenolic compounds are known to have antioxidant capacity; however, there is little information about molecular interactions between particular phenolics found in fruits at different developmental stages. Therefore, the total antioxidant capacity of the phenolic compounds of a fruit may not correspond to the sum of individual antioxidant capacity given by antioxidants from that tissue. In this study, individual antioxidant capacity...
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Interfacial water controls the process of adsorption of hyperactive antifreeze proteins onto the ice surface
PublicationA mechanism of interactions between the ice-binding surface of a hyperactive antifreeze protein molecule and the ice surface is proposed, involving the influence of water present between the two surfaces on the behavior of the approaching molecule. It is demonstrated that the interfacial water, even before its full solidification, can act as a factor that pushes away or pulls nearer the protein molecule to ensure its proper positioning....
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublicationHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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Toxoplasma gondii Recombinant antigen AMA1: Diagnostic Utility of Protein Fragments for the Detection of IgG and IgM Antibodies
PublicationToxoplasma gondii is an important zoonotic protozoan that infects a wide variety of vertebrates as intermediate hosts. For this reason, the diagnosis of this disease is very important and requires continuous improvement. One possibility is to use recombinant antigens in serological tests. Apical membrane antigen 1 (AMA1), a protein located in specific secretory organelles (micronemes) of T. gondii, is very interesting in regard...
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Interactions in aqueous solutions of K-peptide and DMSO – spectroscopic and calorimetric studies
PublicationIntroduction K-peptide (GILQINSRW) – short 9 amino acid fragment of the hen egg white lysozyme has the ability to form amyloid structures. Dimethyl sulfoxide (DMSO) is an osmolyte which can alter this ability. Our goal was to get an insight into the mechanism of Kpeptide-DMSO interactions in aqueous solutions. Such a knowledge can be helpful to understand processes leading to various neurodegenerative diseases. Methods ATR-FTIR...
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Bodybuilders and high-level meat consumers’ behavior towards rabbit, beef, chicken, turkey, and lamb meat: A comparative review
PublicationIn bodybuilders’ diets, protein plays a crucial role in supporting muscle growth and repairing damaged muscle tissue. These individuals meet their protein needs by combining dietary sources with supplements. Animal-based proteins are often preferred over plant-based proteins because they are believed to better support muscle protein synthesis. This review explores the meat consumption patterns of bodybuilders and high-level meat...
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis
PublicationSingle-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism such as DNAreplication, repair, and recombination, and is essential for cell survival. This study reports on the ssb-likegene cloning, gene expression and characterization of a single-stranded DNA-binding protein of Pseudoal-teromonas haloplanktis (PhaSSB) and is the first report of such a protein from psychrophilic microorganism.PhaSSB possesses...
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The hydration properties of protein stabilizer, trimethylamine-N-oxide in aqueous solutions of N-methylacetamide – The volumetric and compressibility studies between 288.15 and 308.15 K
PublicationApparent molar volumes and apparent molar isentropic compressions of the protein stabilizer, trimethylamine-N-oxide (TMAO) were determined from the densities and speed of sound measured at T = (288.15, 298.15 and 308.15) K in aqueous solutions of N-methylacetamide (NMA) at four different concentrations (2, 4, 6 and 8 mol/kg). The concentration dependencies of the calculated quantities extrapolated to the infinite dilution lead...
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Texture or Linker? Competitive Patterning of Receptor Assembly toward Ultra-Sensitive Impedimetric Detection of Viral Species at Gold-Nanotextured Titanium Surfaces
PublicationIn this work, we study the electrodes with a periodic matrix of gold particles pattered by titanium dimples and modified by 3-mercaptopropionic acid (MPA) followed by CD147 receptor grafting for specific impedimetric detection of SARS-CoV-2 viral spike proteins. The synergistic DFT and MM/MD modeling revealed that MPA adsorption geometries on the Au–Ti surface have preferential and stronger binding patterns through the carboxyl...
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Scarabaeidae as human food – A comprehensive review
PublicationRising global population and sustainable protein demand have sparked interest in unique food sources. Entomophagy, or insect consumption, presents a solution and Scarab beetles, part of the Scarabaeidae family, offer a novel food option. The comprehensive review underscores their potential as human food, with strong nutrition, low environmental impact, and the ability to ease strain on conventional agriculture. Nutritional analysis...
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Which casein in sodium caseinate is most resistant to in vitro digestion? Effect of emulsification and enzymatic structuring
PublicationWe investigated the resistance of individual constituent casein epitopes (αS1-, αS2-, β- and κ-CN) in food-grademilk protein sodium caseinate (NaCN) to simulated human gastro-duodenal digestion. The influence of NaCNadsorption to the surface of oil-in-water emulsion droplets and the effect of crosslinking of the protein withenzyme transglutaminase (TG) on the proteolysis were studied by indirect ELISA. TG crosslinking renderedfragments...
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublicationHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...
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Natural fish oil improves the differentiation and maturation of oligodendrocyte precursor cells to oligodendrocytes in vitro after interaction with the blood–brain barrier
PublicationThe blood–brain barrier (BBB) tightly controls the microenvironment of the central nervous system (CNS) to allow neurons to function properly. Additionally, emerging studies point to the beneficial effect of natural oils affecting a wide variety of physiological and pathological processes in the human body. In this study, using an in vitro model of the BBB, we tested the influence of natural fish oil mixture (FOM) vs. borage oil...
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Effect of choline chloride based natural deep eutectic solvents on aqueous solubility and thermodynamic properties of acetaminophen
PublicationIn this work, natural deep eutectic solvents (NADESs) containing choline chloride as hydrogen bond acceptor and 1,2-propanediol, malic acid and tartaric acid as hydrogen bond donors have been synthesized and applied to enhance the aqueous solubility of model sparingly water-soluble drug – acetaminophen. The results indicate that the greatest impact on the solubility of acetaminophen have deep eutectic solvents based on 1,2-propanediol...
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Influence of the ionic strength on the amyloid fibrillogenesis of hen egg white lysozyme
PublicationThe study investigates the role of the electrostatic interactions in the fibrillation of the hen egg white lysozyme (HEWL). In order to achieve this aim the influence of the cations Na+, Mg2+ and Al3+ on the amyloid fibril formation and amorphous aggregation was tested. The amyloids are formed in the solution without added salt but the Thioflavin T fluorescence gives the false-negative result. In these conditions, the HEWL fibrils...
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Multicopy Suppressor Analysis of Strains Lacking Cytoplasmic Peptidyl-Prolyl cis/trans Isomerases Identifies Three New PPIase Activities in Escherichia coli That Includes the DksA Transcription Factor
PublicationConsistent with a role in catalyzing rate-limiting step of protein folding, removal of genes encoding cytoplasmic protein folding catalysts belonging to the family of peptidyl-prolyl cis/trans isomerases (PPIs) in Escherichia coli confers conditional lethality. To address the molecular basis of the essentiality of PPIs, a multicopy suppressor approach revealed that overexpression of genes encoding chaperones (DnaK/J and GroL/S),...
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Interplay of hydrogen bonding and aryl-perfluoroaryl interactions in construction of supramolecular aggregates
PublicationThe stacking between aryl and perfluoroaryl units is an important class of the aromatic – aromatic interactions that has attracted rapidly growing interest in recent years. Continuing interest of our group in this subject it had been prepared three new complexes of pentafluorobenzoic acid with benzyl alcohol, 4-methylbenzyl alcohol and 4-tert-butylbenzyl alcohol and in the next step investigated their self-assembly modes by...
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Why Are Left-Handed G-Quadruplexes Scarce?
PublicationG-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear....
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Properties of water in the region between a tubulin dimer and a single motor head of kinesin
PublicationA kinesin is a molecular motor that can perform movement on a microtubule track in a stepping-like manner. This motion is connected with processes of association and dissociation of kinesin and tubulin. Water is an important participant in these kinds of molecular interactions. This is why we have decided to investigate the dynamical and structural properties of water in the region between the kinesin catalytic domain and the tubulin...