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Wyniki wyszukiwania dla: PROTEIN-LIGAND%20INTERACTIONS
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Efficacious Alkaline Copper Corrosion Inhibition by a Mixed Ligand Copper(II) Complex of 2,2′-Bipyridine and Glycine: Electrochemical and Theoretical Studies
PublikacjaA mixed ligand copper(II) complex, namely, [Cu(BPy)(Gly)Cl]⋅2H2O (CuC) (BPy=2,2′-bipyridine and Gly=glycine), was synthesized and characterized. The synthesized CuC complex was tested as inhibitor to effectively mitigate the corrosion of copper in alkaline solutions using the linear sweep voltammetry (LSV) and linear polarization resistance (LPR) techniques. For the sake of comparison, such two D.C. electrochemical techniques were...
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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
PublikacjaWater 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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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublikacjaPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublikacjaSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublikacjaEfficient brain function requires as much as 20% of the total oxygen intake to support normal neuronal cell function. This level of oxygen usage, however, leads to the generation of free radicals, and thus can lead to oxidative stress and potentially to age-related cognitive decay and even neurodegenerative diseases. The regulation of this system requires a complex monitoring network to maintain proper oxygen homeostasis. Furthermore,...
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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublikacjaThe 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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Alternative and New Protein Sources
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Stabilizing agents and protein stability
PublikacjaBiałka są kluczowymi elementami żywych organizmów, jak również efektywnymi katalizatorami w biotechnologii i medycynie. Szybki rozwój wielu gałęzi biotechnologii wiąże się z coraz większym zapotrzebowaniem na produkty białkowe charakteryzujące się wysoką stabilnością. Jednym ze sposobów osiągnięcia większej stabilności białek jest wykorzystanie małych związków organicznych, tzw. osmolitów. Do tej grupy związków należą aminokwasy,...
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Colloidal aspects of protein digestion
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Ln2(SeO3)2(SO4)(H2O)2 (Ln=Sm, Dy, Yb): A Mixed‐Ligand Pathway to New Lanthanide(III) Multifunctional Materials Featuring Nonlinear Optical and Magnetic Anisotropy Properties
PublikacjaBottom-up assembly of optically nonlinear and magnetically anisotropic lanthanide materials involving precisely placed spin carriers and optimized metal-ligand coordination offers a potential route to developing electronic architectures for coherent radiation generation and spin-based technologies, but the chemical design historically has been extremely hard to achieve. To address this, we developed a worthwhile avenue for creating...
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Generation and Characterization of a DNA-GCN4 Oligonucleotide-Peptide Conjugate: The Impact DNA/Protein Interactions on the Sensitization of DNA
PublikacjaRadiotherapy, the most common therapy for the treatment of solid tumors, exerts its effects by inducing DNA damage. To fully understand the extent and nature of this damage, DNA models that mimic the in vivo situation should be utilized. In a cellular context, genomic DNA constantly interacts with proteins and these interactions could influence both the primary radical processes (triggered by ionizing radiation) and secondary reactions,...
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublikacjaNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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Assembly of Lipopolysaccharide in Escherichia coli Requires the Essential LapB Heat Shock Protein
PublikacjaHere, we describe two new heat shock proteins involved in the assembly of LPS in Escherichia coli, LapA and LapB (lipopolysaccharide assembly protein A and B). lapB mutants were identified based on an increased envelope stress response. Envelope stress responsive pathways control key steps in LPS biogenesis and respond to defects in the LPS assembly. Accordingly, the LPS content in ΔlapB or Δ(lapA lapB) mutants was elevated, with...
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A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library.
PublikacjaThe presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublikacjaTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Identification of evolutionary conserved DNA sequence and corresponding S21 ribosomal protein region for diagnostic purposes of all Borrelia spirochetes
PublikacjaIt is still under investigation, whether all Borrelia sp. causing Lyme borreliosis and other diseases are already identified and properly classified as human pathogens. For this reason, it is of great importance to develop a diagnostic ELISA test that detects all Borrelia sp. The aim of this study was to identify conserved DNA and protein regions present in all currently known Borrelia sp. In experimental studies 31 available Borrelia...
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Quality Control of Bacterial Extracellular Vesicles with Total Protein Content Assay, Nanoparticles Tracking Analysis, and Capillary Electrophoresis
PublikacjaExtracellular 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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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublikacjaLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Endocrine responses following exhaustive strength exercise with and without the use of protein and protein-carbohydrate supplements
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Synthesis and characterization of mononuclear Zn(II), Co(II) and Ni(II) complexes containing a sterically demanding silanethiolate ligand derived from tris(2,6-diisopropylphenoxy)silanethiol
PublikacjaFour heteroleptic complexes of zinc(II), cobalt(II) and nickel(II) containing a monodentate silanethiolate ligand derived from tris(2,6-diisopropylphenoxy)silanethiol (TDST), were prepared and characterized. The geometries of ligands in the complexes are typical: distorted tetrahedral in zinc and cobalt(II) complexes and square planar in nickel(II) compound. Magnetic studies performed for Ni(II) and Co(II) compounds confirm the...
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Identification, cloning, expression, and characterizationof a highly thermostable single-stranded-DNA-binding protein (SSB) from Deinococcus murrayi
PublikacjaZidentyfikowano i scharakteryzowano białko SSB-podobne, pochodzące z Deinococcus murrayi (DmuSSB). Otrzymany w reakcji PCR fragment zawierający kompletny gen ssb sklonowano w systemie ekspresyjnym Escherichia coli. Gen składa się z 826 nt, kodujących 276 reszt aminokwasowych z wyliczoną teoretycznie masą cząsteczkową monomeru równą 30,14 kDa. DmuSSB zawiera dwie domeny wiążące jednoniciowe DNA OBna monomer I funkcjonuje jako homodimer....
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A cryptic ribosome binding site, false signals in reporter systems and avoidance of protein translation chaos
PublikacjaThe expression of reporter gene may be induced by activation of cryptic signalling sequences, as we found while constructing the mutS-lacZ fusion gene. We cloned the Escherichia coli lacZ gene encoding beta-galactosidase into a plasmid vector carrying the Thermus thermophilus mutS gene. The clones expected to produce beta-galactosidase as the C-terminal fusion were selected for the complementation of beta-galactosidase activity...
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Role of Lentivirus-Mediated Overexpression of Programmed Death-Ligand 1 on Corneal Allograft Survival
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The Analysis of Hyperfine Shifts of Mono-Ligand High-Spin Cobalt(II) Pyrazolylborate Complexes
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Thermostability and photophysical properties of mixed-ligand carboxylate/benzimidazole Zn(II)-coordination polymers
PublikacjaThe reaction between Zn(NO3)2*6H2O or Zn(CH3COO)2*2H2O and isophthalic acid (1,3-H2bdc) in the presence of benzimidazole (Hbzim) in dimethylformamide (DMF)/ethanol (EtOH)/H2O solvent mixture at room temperature yielded two structurally different coordination polymers: [Zn2(1,3-bdc)2(Hbzim)2] (1) and [Zn2(1,3-bdc)(bzim)2] (2). (1) is a 2D-layered framework with a molecule of benzimidazole coordinated to the Zn center, whereas (2)...
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A Proliferation-Inducing Ligand and B-Cell Activating Factor Are Upregulated in Patients with Essential Thrombocythemia
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Effect of carbazole and pyrrolidine functionalization of phenanthroline ligand on ground- and excited-state properties of rhenium(I) complexes. Interplay between 3MLCT and 3IL/3ILCT
PublikacjaNew rhenium(I) tricarbonyl complexes based on the phenanthroline ligand were designed and synthesized to investigate the role of carbazole (cbz) and pyrrolidine (pyrr) substituents in determining thermal, electrochemical and optoelectronic properties. Both pyrr and cbz are electron-releasing substituents, but they differ in the steric hindrance and electron delocalization ability. The impact of pyrr and cbz on ground- and excited-state...
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Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis
PublikacjaSingle-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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Occlusion phenomenon of redox probe by protein as a way of voltammetric detection of non-electroactive C-reactive protein
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Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans—Expression and characterization
PublikacjaDNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the...
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t-SNE Highlights Phylogenetic and Temporal Patterns of SARS-CoV-2 Spike and Nucleocapsid Protein Evolution
PublikacjaWe propose applying t-distributed stochastic neighbor embedding to protein sequences of SARS-CoV-2 to construct, visualize and study the evolutionary space of the coronavirus. The basic idea is to explore the COVID-19 evolution space by using modern manifold learning techniques applied to evolutionary distances between variants. Evolutionary distances have been calculated based on the structures of the nucleocapsid and spike proteins.
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PROTEIN ENGINEERING DESIGN & SELECTION
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World Research Journal of Peptide and Protein
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Advances in Protein Chemistry and Structural Biology
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Current Topics in Peptide and Protein Research
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International Journal of Peptide and Protein Research
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AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS
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Reactions of (Ph)tBuP-P(SiMe3)Li·3THF with [(PNP)TiCl2] and [MeNacNacTiCl2·THF]. Synthesis of first PNP titanium(IV) complex with phosphanylphosphinidene ligand [(PNP)Ti(Cl){η2-P-P(Ph)tBu}]
PublikacjaLithium derivative of diphosphane (Ph)tBuP-P(SiMe3)Li (1) was isolated for the first time and investigated in reactions with β-diketiminate (MeNacnac− = [Ar]NC(Me)CHC(Me)N[Ar]; Ar = 2,6-iPr2C6H3) and PNP-pincer (PNP = N[2-PiPr2-4-methylphenyl]2) Ti(III) complexes. The β-diketiminate titanium(III) complex containing phosphanylphosphido ligand [MeNacNacTi(Cl){η2-P(SiMe3)-P(Ph)tBu}] (2) was prepared in reaction of [MeNacNacTiCl2·THF]...
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Understanding the interactions between protein stabilizers and the peptide bond through the analysis of the volumetric and compressibility properties for the model systems
PublikacjaThis work confirms our earlier supposition, that volumetric and acoustic parameters for simple model proposed by us are directly related to stabilizing/destabilizing effect of osmolytes on proteins structure. The apparent molar volumes, V and the apparent molar isentropic compressions, KS,, of glycine and N,N,N –trimethylglycine (betaine) were determined from densities and speed of sound measurements in aqueous solution of N-methylacetamide...
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Unwinding Au+···Au+ Bonded Filaments in Ligand-Supported Gold(I) Polymer under Pressure
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An investigation on the chemistry of the R2P=P ligand: reactions of a phosphanylphosphinidene complex of tungsten(VI) with electrophilic reagents
PublikacjaThe nucleophilic properties of the title compound [(2,6-i-Pr2C6H3N)2(Cl)W(η2-t-Bu2PvP)]Li·3DME (1) were investigated in reactions with selected electrophilic reagents such as MeI, M(CO)5THF (M = Cr, Mo, W), AlCl3, and GaCl3. Methylation of 1 by MeI yields phosphanylphosphido complexes [(2,6-i-Pr2C6H3N)2W(X)(1,2-η-t-Bu2PvP–CH3)] (X = Cl, I) (2-Cl/2-I) with the formation of a new P–C bond. Moreover, 1 reacts with electrophilic compounds...
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Gold(III) complexes with chloride and cyanopyridines: Facilitated hydrolysis of nitrile ligand to amide and antibacterial activity
PublikacjaA range of novel simple gold(III) compounds has been synthesized in their monocrystalline form, including two previously unknown chloro-complexes of Au3+ with 2-cyanopyridine or 3-cyanopyridine, respectively. Our investigations have revealed the intricate nature of the reaction between 2-cyanopyridine and tetrachloroauric acid, yielding at least three distinct products. The main product, obtained in high yield, is a salt featuring...
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Ahmer Bin Hafeez
OsobyI have experience in Computational Biology, particularly bioinformatics, homology modeling, phylogenetics, structural biology, and drug discovery. Furthermore, I have hands-on experience with Bioinformatics software. Currently, my interest lies in translatable omics studies and drug discovery against novel protein targets involved in cancer and infectious diseases and Host-Pathogen PPIs. My aim involves the use of computational...
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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
PublikacjaFat 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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Highly selective impedimetric determination of Haemophilus influenzae protein D using maze-like boron-doped carbon nanowall electrodes
PublikacjaThis study reports a novel impedimetric immunosensor for protein D detection in purified and bacterial (Haemophilus influenzae, Hi) samples. The detection was based on antigen recognition by anti-protein D antibodies (apD) immobilised at the maze-like boron-doped carbon nanowall electrodes (B:CNW). The B:CNW electrodes were synthesised, and their surface was characterised by scanning electron microscopy (SEM) and X-ray photoelectron...
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Reactivity study of a β-diketiminate titanium(III) complex with a phosphanylphosphido ligand towards chlorophosphanes. A new method of synthesis of β-diketiminate titanium(IV) complexes with versatile phosphanylphosphinidenes
PublikacjaThe reactivity of ab-diketiminate titanium(III) complex with a phosphanylphosphido ligand, [MeNacNacTi(Cl){g2-P(SiMe3)-PtBu2}] (1)(MeNacNac= [Ar]NC(Me)CHC(Me)N[Ar]; Ar = 2,6-iPr2Ph), was investigatedtowards selected chlorophosphanes, such astBu2PCl,iPr2PCl, Cy2PCl, (Cy)tBuPCl, (Me)tBuPCl, (Ph)tBuPCl, Ph2PCl, (iPr2N)tBuPCl and (Et2N)2PCl. The reactions withtBu2PCl and Ph2PCl lead mainly to theearlier described complex [MeNacNacTi(Cl){g2-P-PtBu2}]...
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Apple pectin complexes with whey protein isolate
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Some applications of thermophiles and their enzymes for protein processing
PublikacjaPrzedstawiono charakterystykę, właściwości oraz możliwości zastosowań enzymów proteolitycznych wytwarzanych przez termofile. Zaletą tych biokatalizatorów jest między innymi duża odporność na działanie rozpuszczalników organicznych, detergentów i innych czynników denaturujących białka oraz mała wrażliwość na zmiany pH. Dokonano też przeglądu czynników powodujących dużą stabilność proteaz z termofili.
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ANALYSIS OF THE p53 PROTEIN GENE EXPRESSION MODEL
PublikacjaWe study the asymptotic behaviour of the solutions of the p53-Mdm2 model proposed by Monk (2003). The p53 gene is crucial for cellular inhibition of the angiogenesis process, while Mdm2 is a negative regulator of the p53 tumor-suppressor. We investigate the stability of the positive steady state and perform some numerical experiments.