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Ligand-Modified Boron-Doped Diamond Surface: DFT Insights into the Electronic Properties of Biofunctionalization
PublicationWith the increasing power of computation systems, theoretical calculations provide a means for quick determination of material properties, laying out a research plan, and lowering material development costs. One of the most common is Density Functional Theory (DFT), which allows us to simulate the structure of chemical molecules or crystals and their interaction. In developing a new generation of biosensors, understanding the nature...
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublicationThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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A New Expression System Based on Psychrotolerant Debaryomyces macquariensis Yeast and Its Application to the Production of Cold-Active β-D-Galactosidase from Paracoccus sp. 32d
PublicationYeasts provide attractive host/vector systems for heterologous gene expression. The currently used yeast-based expression platforms include mesophilic and thermotolerant species. A eukaryotic expression system working at low temperatures could be particularly useful for the production of thermolabile proteins and proteins that tend to form insoluble aggregates. For this purpose, an expression system based on an Antarctic psychrotolerant...
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[NCh-bio] Advances in Biotechnology: Protein Folding and Assembly
e-Learning Courses{mlang pl} Dyscyplina: nauki chemiczne Zajęcia obowiązkowe dla doktorantów I i II roku z obszaru biotechnologii Prowadzący: dr hab. Gracjana Klein-Raina, prof. PG Liczba godzin: 15 Forma zajęć: wykład {mlang} {mlang en} Discipline: chemical sciences Obligatory course for 1st and 2nd-year PhD students from biotechnology area Academic teachers: dr hab. Gracjana Klein-Raina, prof. PG Total hours of training: 15 teaching...
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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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Boron-doped carbon nanowalls for fast and direct detection of cytochrome C and ricin by matrix-free laser desorption/ionization mass spectrometry
PublicationDetecting proteins via surface assisted laser desorption/ionization mass spectrometry (SALDI-MS) method is still highly challenging, and only few examples of nanomaterials have been demonstrated to perform such detection so far. In this study, carbon nanowalls (CNWs), vertically aligned graphene sheet-based materials, presenting specific morphology, dimensions, and boron doping levels have shown improved performances for both qualitative...
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Expression of a GDSL esterase from Pseudomonas sp. S9 in Pichiapastoris
PublicationCold active lipolytic enzymes are promising to replace the conventional enzymes processes of biotechnological industries. One of the most important feature of the cold-active lipases and esterases is that they offer economic benefits through energy saving. In general, they exhibit high activity at low temperatures and low thermostability at moderate temperatures. Lipolytic enzyme EstS9 was isolated from Pseudomonas sp. S9. A multiple...
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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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Gracjana Klein-Raina dr hab.
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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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Impact of high-pressure processing on the bioactive compounds of milk - A comprehensive review
PublicationHigh-pressure processing (HPP) is a promising alternative to thermal pasteurization. Recent studies highlighted the effectivity of HPP (400–600 MPa and exposure times of 1–5 min) in reducing pathogenic microflora for up to 5 logs. Analysis of modern scientific sources has shown that pressure affects the main components of milk including fat globules, lactose, casein micelles. The behavior of whey proteins under HPP is very important...
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Identification of antigen Ag43 in uropathogenic Escherichia coli Dr+ strains and defining its role in the pathogenesis of urinary tract infections
PublicationUrinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are among the most common bacterial infectious diseases in the developed world. The urovirulence of UPEC is mainly associated with the surface-exposed fimbrial adhesins and adhesins of the autotransporter (AT) family. The best studied of theses proteins is antigen 43 (Ag43) mediating cell aggregation, adhesion and biofilm development as the causes of...
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Monitoring of lysozyme thermal denaturation by volumetric measurements and nanoDSF technique in the presence of N-butylurea
PublicationThe results of thermal studies of denaturation of hen egg white lysozyme (HEWL) in water and an aqueous solution of N-butylurea (BU) are presented. High-precision densimetric measurements were used to characterize and analyze the changes of the specific volume, v, during temperature elevation. The temperature of the midpoint of protein denaturation was also determined by nanoDSF technique (differential scanning fluorimetry). The...
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Cyanogenic Compounds and Estrogen Disruptors
PublicationBalanced diet consists largely of plants containing cyanogenic compounds in the form of the more common cyanogenic glycosides and sometimes lipids. Maize, wheat, rye, apples, barley, oats, sugar cane and yet many other plants consumed by humans contain cyanogenic compounds. However the risk of poisoning is negligible as it is very easy to remove the toxic HCN by grinding and drying in air or soaking in water and an additional...
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In vitro antioxidative and binding properties of phenolics in traditional, citrus and exotic fruits
PublicationMany polyphenols bind proteins, therefore our research was focused on the potential of protein binding to polyphenols of investigated fruits and their health-related effects. The contents of polyphenols and related antioxidant activities of traditional, citrus and exotic fruits were compared. The presence of polyphenols (flavonoids and phenolic acids) in the investigated samples and their interaction with human serum albumin (HSA)...
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Low-power microwave-induced fabrication of functionalised few-layer black phosphorus electrodes: A novel route towards Haemophilus Influenzae pathogen biosensing devices
PublicationIn this paper, various passivation schemes were applied at few-layer black phosphorus (FLBP) to achieve covalent functionalisation with 4-azidobenzoic acid, improving its electrochemical response intended for analytical and biosensing applications. The thermal and microwave assisted modification procedures in toluene and dime-thylformamide resulted in high reversibility of reactions on functionalised FLBP using a ferricyanide/ferrocya-nide...
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Cloning, Expression and Purification of Wild-Type Trehalose Synthase from Deinococcus geothermalis
PublicationThe aim of this study was isolation and cloning of trehalose synthase gene derived from extremophilic microorganism to the expression vectors in the Tabor-Studier system and its expression in Rosetta(DE3)pLysS Escherichia coli cells. The second phase of the study consisted of proteins purification using an initial denaturation of host proteins and salting-out proteins by ammonium sulfate.
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Ahmer Bin Hafeez
PeopleI have experience in Microbiology & Computational Biology, particularly bioinformatics, homology modeling, phylogenetics, structural biology, and drug discovery. 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 methods for the identification of novel targets and to...
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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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c-Myc inhibition and p21 modulation contribute to unsymmetrical bisacridines-induced apoptosis and senescence in pancreatic cancer cells
PublicationBackground Pancreatic cancer (PC) is one of the most aggressive cancers and is the seventh leading cause of cancer-related death worldwide. PC is characterized by rapid progression and resistance to conventional treatments. Mutations in KRAS, CDKN2A, TP53, SMAD4/DPC4, and MYC are major genetic alterations associated with poor treatment outcomes in patients with PC. Therefore, optimizing PC therapy is a tremendous challenge. Unsymmetrical...
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AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase
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Molecular simulation study of cooperativity in hydrophobic association
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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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Toxoplasma godnii recombinant chimeric antigens - IgM and IgG ELISAs - mouse serum samples
Open Research DataThis study presents an evaluation of tetravalent recombinant chimeric proteins containing fragments of the Toxoplasma gondii antigens, SAG2, SAG1, GRA1, GRA2, MIC1, MAG1, ROP1 and AMA1, as potential replacements of a the soluble, whole-cell tachyzoite lysate (TLA) used in serological assays. Recombinant chimeric proteins (SAG1-MIC1-MAG1-GRA2, SAG2-GRA1-ROP1-GRA2,...
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Toxoplasma gondii recombinant chimeric antigens - IgG and IgM ELISAs - human serum samples
Open Research DataThis study presents an evaluation of tetravalent recombinant chimeric proteins containing fragments of the Toxoplasma gondii antigens, SAG1, SAG2, GRA1, GRA2, MIC1, MAG1, ROP1 and AMA1, as potential replacements of a the soluble, whole-cell tachyzoite lysate (TLA) used in serological assays. Recombinant chimeric proteins (SAG1-MIC1-MAG1-GRA2, SAG2-GRA1-ROP1-GRA2,...
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Suppressors of lapC mutation identify new regulators of LpxC, which mediates the first committed step in lipopolysaccharide biosynthesis
PublicationGram-negative bacteria, such as Escherichia coli, are characterized by an asymmetric outer membrane (OM) with lipopolysaccharide (LPS) located in the outer leaflet and phospholipids facing the inner leaflet. E. coli recruits LPS assembly proteins LapB, LapC and LapD in concert with FtsH protease to ensure a balanced biosynthesis of LPS and phospholipids. We recently reported that bacteria either lacking the periplasmic domain of...
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Application of human bile salts for in vitro digestion models
PublicationIn this study, experimental in vitro models simulating the environment of the human gastrointestinal tract were used to assess the impact of physiological surfactants, such as bile salts, on the kinetics of digestion. Bile salts are biosurfactants synthesised in the liver and secreted together with bile into the small intestine. There are many reports on the role of bile salts in lipolysis, but the knowledge of their influence...
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Aravind Ayyolath
PeopleI am interested in the biology of bacterial stress response and its growth under stress conditions. Our lab focuses on two aspects; protein folding and lipopolysaccharide biosynthesis and we address them with Escherichia coli models. Our recent studies have provided more evidence regarding several genes involved in the survival of bacteria under stress. I am also interested in disease biology and also in identifying proper therapeutic...
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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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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Two-step mechanism of J-domain action in driving Hsp70 function
PublicationJ-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s...
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Identification of Substrates of Cytoplasmic Peptidyl-Prolyl Cis/Trans Isomerases and Their Collective Essentiality in Escherichia Coli
PublicationProtein folding often requires molecular chaperones and folding catalysts, such as peptidyl-prolyl cis/trans isomerases (PPIs). The Escherichia coli cytoplasm contains six well-known PPIs, although a requirement of their PPIase activity, the identity of their substrates and relative enzymatic contribution is unknown. Thus, strains lacking all periplasmic and one of the cytoplasmic PPIs were constructed. Measurement of their PPIase...
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The effect of high pressure and subzero temperature on gelation of washed cod and salmon meat
PublicationThe objective of the present work is to examine the infl uence of pressure up to 193 MPa at subzero temperature (without freezing of water) on myofi brillar proteins of salmon and cod meat and on the properties of gels obtained from washed mince of these fi sh. The solubility of proteins from myofi brils of cod and salmon meat suspended in 100 mM KCl solution increased aft er treating the samples with pressure above 60 MPa. The...
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Overproduction of CaStr2p native and His-tag versions.
Open Research DataEnzyme of fungal L-methionine biosynthetic pathway: cystathionine-γ-synthase (CaStr2p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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Overproduction of homoserine O-acetyltransferase (CaMet2p) native and His-tag versions.
Open Research DataEnzyme of fungal L-methionine biosynthetic pathway: homoserine O-acetyltransferase (Met2p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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Overproduction of CaMet15p native and His-tag versions.
Open Research DataEnzyme of fungal L-methionine biosynthetic pathway: O-acetylhomoserine sulfhydrylase (Met15p) could be exploited as molecular target for antifungal chemotherapy. The goal of the study was to obtain conditions optimal for protein production with the use of prokaryotic cells. The constructed expression plasmids, designed in three different versions: encoding...
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Induction of immune responses in sheep by vaccination with liposome-entrapped DNA complexes encoding Toxoplasma gondii MIC3 gene
PublicationToxoplasma gondii is a parasite that has been extensively studied due to its medical and veterinary importance in terminating pregnancies. Consequently, a satisfactory vaccine is required to control itsadverse effects on pregnant animals. The microneme protein, MIC3, is a major adhesion protein that binds to the surface of host cells and parasites, and is therefore a potential vaccine against T. gondii.The viability of MIC3 as...
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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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Pilicides effectively hinder chaperone-usher interactions in all Gram-negative bacteria
PublicationThe chaperone-usher pathway of adhesive structures biogenesis is highly conserved in all Gram-negative bacteria. Pili are polymers of thousands protein subunits that possess conserved immunoglobuline-like structure denoted by lack of the seventh G strand. The effect of this structural defect is a hydrophobic acceptor cleft. The folding of protein subunits is strictly dependent on the action of specific periplasmic chaperone protein...
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MutS3: a MutS homologue of unknown biological function
PublicationThe homologues of MutS proteins are widespread among both Prokaryotes and Eukaryotes. MutS designated as MutS1 is a part of MMR (mismatch repair) system which is responsible for removal of mispaired bases and small insertion/deletion loops in DNA. Initially, the only MutS homologues known were those engaged in mismatch repair and these were later designated as MutS1. Subsequently, the MutS2 homologue was distinguished. MutS2 does...
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Determination of long-chain aldehydes using a novel quartz crystal microbalance sensor based on a biomimetic peptide
PublicationThere is an increasingly popular trend aimed at improvement of fundamental metrological parameters of sensors via implementation of materials mimicking biological olfactory systems. This study presents investigation on usefulness of the peptide mimicking HarmOBP7 region as a receptor element of the piezoelectric sensor for selective analysis of long-chain aldehydes. Identification of odorant binding proteins creates new possibilities...
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Bioactivities of Phenolic Compounds from Kiwifruit and Persimmon
PublicationFruit used in the common human diet in general, and kiwifruit and persimmon particularly, displays health properties in the prevention of heart disease. This study describes a combination of bioactivity, multivariate data analyses and fluorescence measurements for the differentiating of kiwifruit and persimmon, their quenching and antioxidant properties. The metabolic differences are shown, as well in the results of bioactivities...
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Regulated assembly of lipopolysaccharide and sensing of its alterations in Escherichia coli
PublicationThis thesis describes mechanism of the regulation of the transcription of the rpoE gene encoding an essential RNA polymerase subunit in Escherichia coli. The RpoE regulates extracytoplasmic stress response regulon and is required to initiate transcription of genes, whose products are involvedin the folding of periplasmic proteins and synthesis and transport of outer membrane components. The transcriptional regulation of the rpoE...
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Antimicrobial Activity of Selected Antimicrobial Peptides Against Planktonic Culture and Biofilm of Acinetobacter baumannii
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Anticandidal Activity of Omiganan and Its Retro Analog Alone and in Combination with Fluconazole
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Alanine Scanning Studies of the Antimicrobial Peptide Aurein 1.2
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Probiotic potential of Bacillus Isolates from Polish Bee Pollen and Bee Bread
PublicationThe main goal of this study was the evaluation of the probiotic potential of 10 Bacillus spp. strains isolated from 5 bee bread and 3 bee pollen samples. The antagonistic interaction with Staphylococcus aureus and Escherichia coli was a primary criterion for the preliminary selection of the isolates. Three out of ten strains—PY2.3 (isolated from pollen), BP20.15 and BB10.1 (both isolated from bee bread)—were found to be possible...
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Attenuation of Hyperglycemia in Diabetic Rats Assisted by Immobilized Probiotic in Sodium Alginate
PublicationDiabetes mellitus type 2 (DM2) is the most common chronic disease worldwide, characterized mainly by increased glucose concentration in the blood and affecting several organs’ functionality. The daily consumption of probiotic bacteria can help control diabetes and reduce the damage caused. Cell immobilization techniques are a powerful tool that provides physical cell protection to such probiotic bacteria against gastrointestinal...
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Fusion of DNA-binding domain of Pyrococcus furiosus ligase with TaqStoffel DNA polymerase as a useful tool in PCR with difficult targets
PublicationThe DNA coding sequence of TaqStoffel polymer- ase was fused with the DNA-binding domain of Pyrococcus furiosus ligase. The resulting novel recombinant gene was cloned and expressed in E. coli. The recombinant enzyme was purified and its enzymatic features were studied. The fusion protein (PfuDBDlig-TaqS) was found to have enhanced processivity as a result of the conversion of the Taq DNA polymerase from a relatively low processive...
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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...