TIBOR KOZAR - Academia.edu (original) (raw)
Papers by TIBOR KOZAR
Biomedicines
The global outbreak of SARS-CoV-2/COVID-19 provided the stage to accumulate an enormous biomedica... more The global outbreak of SARS-CoV-2/COVID-19 provided the stage to accumulate an enormous biomedical data set and an opportunity as well as a challenge to test new concepts and strategies to combat the pandemic. New research and molecular medical protocols may be deployed in different scientific fields, e.g., glycobiology, nanopharmacology, or nanomedicine. We correlated clinical biomedical data derived from patients in intensive care units with structural biology and biophysical data from NMR and/or CAMM (computer-aided molecular modeling). Consequently, new diagnostic and therapeutic approaches against SARS-CoV-2 were evaluated. Specifically, we tested the suitability of incretin mimetics with one or two pH-sensitive amino acid residues as potential drugs to prevent or cure long-COVID symptoms. Blood pH values in correlation with temperature alterations in patient bodies were of clinical importance. The effects of biophysical parameters such as temperature and pH value variation in ...
HAL (Le Centre pour la Communication Scientifique Directe), Mar 15, 1998
Biopolymers, 1998
Conformations of the alpha-L-Rhap(1-2)-beta-D-Glc1-OMe and beta-D-Galp(1-3)-beta-D-Glc1-OMe disac... more Conformations of the alpha-L-Rhap(1-2)-beta-D-Glc1-OMe and beta-D-Galp(1-3)-beta-D-Glc1-OMe disaccharides and the branched title trisaccharide were examined in DMSO-d6 solution by 1H-nmr. The distance mapping procedure was based on rotating frame nuclear Overhauser effect (NOE) constraints involving C- and O-linked protons, and hydrogen-bond constraints manifested by the splitting of the OH nmr signals for partially deuteriated samples. An "isotopomer-selected NOE" method for the unequivocal identification of mutually hydrogen-bonded hydroxyl groups was suggested. The length of hydrogen bonds thus detected is considered the only one motionally nonaveraged nmr-derived constraint. Molecular mechanics and molecular dynamics methods were used to model the conformational properties of the studied oligosaccharides. Complex conformational search, relying on a regular phi, psi-grid based scanning of the conformational space of the selected glycosidic linkage, combined with simultaneous modeling of different allowed orientations of the pendant groups and the third, neighboring sugar residue, has been carried out. Energy minimizations were performed for each member of the phi, psi grid generated set of conformations. Conformational clustering has been done to group the minimized conformations into families with similar values of glycosidic torsion angles. Several stable syn and anti conformations were found for the 1-->2 and 1-->3 bonds in the studied disaccharides. Vicinal glycosylation affected strongly the occupancy of conformational states in both branches of the title trisaccharide. The preferred conformational family of the trisaccharide (with average phi, psi values of 38 degrees, 17 degrees for the 1-->2 and 48 degrees, 1 degree for the 1-->3 bond, respectively) was shown by nmr to be stabilized by intramolecular hydrogen bonding between the nonbonded Rha and Gal residues.
Colloids and Surfaces B: Biointerfaces, 2021
Amphiphilic compounds, both detergents and lipids, are important tools for in vitro analysis of w... more Amphiphilic compounds, both detergents and lipids, are important tools for in vitro analysis of water-soluble and integral membrane proteins. A key question is whether these two groups of amphiphilic molecules use the same pathway to affect structural and functional integrity of proteins. In the present study, we tested the effect of non-ionic detergent dodecyl maltoside (DDM), two phospholipids, 1,2-dimyristoyl-sn-glycero-3- phosphocholine (DMPC), 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), and the detergent-phospholipid mixtures on insulin amyloidogenesis in vitro. Amyloidogenesis of insulin is significantly affected by DDM in a time-and dose-dependent manner, but only slightly affected by either of phospholipids. Addition of DHPC or DMPC to detergent does not alter the inhibiting pattern, suggesting that DDM preferably binds to insulin. The molecular modeling revealed that DDM and the phospholipids occupy equivalent binding sites. DDM, due to the presence of maltose with several oxygen atoms (hydroxylic, glycosidic and ring) is involved in more hydrogen bonds than DHPC or DMPC. Hydrophobic interactions are important factors to stabilize both, DDM and phospholipids in their binding sites. Our results indicate that certain detergents (applying DDM as an example) and selected phospholipids are not always interchangeable in their use to investigate the effect of amphiphilic compounds on the behavior of amyloid-prone proteins.
Marine Drugs
Osteoarthritis belongs to the most common joint diseases in humans and animals and shows increase... more Osteoarthritis belongs to the most common joint diseases in humans and animals and shows increased incidence in older patients. The bioactivities of collagen hydrolysates, sulfated glucosamine and a special fatty acid enriched dog-food were tested in a dog patient study of 52 dogs as potential therapeutic treatment options in early osteoarthritis. Biophysical, biochemical, cell biological and molecular modeling methods support that these well-defined substances may act as effective nutraceuticals. Importantly, the applied collagen hydrolysates as well as sulfated glucosamine residues from marine organisms were strongly supported by both an animal model and molecular modeling of intermolecular interactions. Molecular modeling of predicted interaction dynamics was evaluated for the receptor proteins MMP-3 and ADAMTS-5. These proteins play a prominent role in the maintenance of cartilage health as well as innate and adapted immunity. Nutraceutical data were generated in a veterinary cl...
Cells
Mitochondrial cytochrome c oxidase (CcO) is a multisubunit integral membrane complex consisting o... more Mitochondrial cytochrome c oxidase (CcO) is a multisubunit integral membrane complex consisting of 13 dissimilar subunits, as well as three to four tightly bound molecules of cardiolipin (CL). The monomeric unit of CcO is able to form a dimer and participate in the formation of supercomplexes in the inner mitochondrial membrane. The structural and functional integrity of the enzyme is crucially dependent on the full subunit complement and the presence of unperturbed bound CL. A direct consequence of subunit loss, CL removal, or its oxidative modification is the destabilization of the quaternary structure, loss of the activity, and the inability to dimerize. Thus, the intimate interplay between individual components of the complex is imperative for regulation of the CcO aggregation state. While it appears that the aggregation state of CcO might affect its conformational stability, the functional role of the aggregation remains unclear as both monomeric and dimeric forms of CcO seem t...
EPJ Web of Conferences
Detailed understanding of the interactions of novel metal-containing nanoparticles with biologica... more Detailed understanding of the interactions of novel metal-containing nanoparticles with biological membranes, macromolecules and other molecular targets of the living cell is crucial for the elucidation of the biological actions of such functionalized nanosystems. We present here the construction and modeling of thiolate-protected gold clusters and the prediction of their static and dynamic properties.
Photodiagnosis and Photodynamic Therapy
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Colloids and Surfaces B: Biointerfaces
Biochimica et Biophysica Acta (BBA) - Bioenergetics
AIP Conference Proceedings, 1995
Colloids and surfaces. B, Biointerfaces, 2017
Two nonionic detergents, Triton X-100 (TX-100) and n-dodecyl-β-d-maltoside (DDM) were tested for ... more Two nonionic detergents, Triton X-100 (TX-100) and n-dodecyl-β-d-maltoside (DDM) were tested for their ability to affect lysozyme amyloid aggregation. We have demonstrated that fibrillization of lysozyme is completely inhibited by low sub-micellar concentrations of both of these detergents. The apparent IC50 values were calculated to be 22μM and 26μM for TX-100 and DDM, respectively. The detergent/protein ratio is not the only parameter controlling inhibition. The precise timing of the detergent addition was found to be also crucial. It appears that the primary inhibitory activity of detergents resulted from inhibition of nuclei formation, in addition to inhibition of fibril polymerization at the early stage of protofibrils growth. The docking study revealed that Asn-59, Trp-63 and Ala-107, all present within the lysozyme amyloidogenic region, were involved in the interaction with both detergents. In addition, TX-100 also interacted with Gln-57 and Asp-103 within lysozyme. Moreover,...
Glycoconjugate J, 1998
Three-dimensional structures of the natural substrate unit for the enzyme N-acetylglucosamine-tra... more Three-dimensional structures of the natural substrate unit for the enzyme N-acetylglucosamine-transferase II, GlcNAc-Man 3-GlcNAc 2 , were investigated by molecular modelling methods. Molecular dynamics (MD) and molecular mechanics calculations on two hexasaccharides, namely GlcNAc-Man 3-GlcNAc 2-Asn and GlcNAc-Man 3-GlcNAc 2-OMe were performed by the Biosym/MSI software using the CVFF and CFF95 force fields in vacuum. The MD simulations were calculated for 3 ns at different simulation temperatures and for two values of dielectric constant, D ؍ 1 and D ؍ 4. From each 3 ns trajectory, 3050 structures have been optimized. The local minima obtained have been clustered into families exhibiting similar values of glycosidic torsional angles T, V , and W. The influence of the simulation conditions and force fields used on the conformational behaviour and structure of the title oligosaccharides is discussed.
Biophysical Journal, 2016
polymers confer distinct mechanical and biological properties to single bacteria and to mature bi... more polymers confer distinct mechanical and biological properties to single bacteria and to mature biofilms. When individual bacteria attach to a surface, intracellular levels of cyclic-di-GMP increase. Cyclic-di-GMP is required to change gene expression to initiate the transition to the biofilm state. What specific cues control cyclic-di-GMP production were previously unknown-we show that this is controlled by mechanical shear stress, which is primarily impacted by bacterial motility and the EPS coating on bacteria. This opens up the possibility of making a new class of anti-biofilm surface, by using a 2D fluid that cannot sustain a lateral shear stress and thereby preventing activation of the cyclic-di-GMP signal. P. aeruginosa biofilm infections in the cystic fibrosis (CF) lung often last for decades, ample time for the infecting strain(s) to evolve. Production of alginate is well-known to tend to increase during CF infections. More recently, it is becoming recognized that CF infections also evolve to increase PSL production. Alginate chemically protects biofilms, but also makes them softer and weaker. Here, we show that PSL stiffens and strengthens biofilms, and that increased PSL production in biofilms grown from CF clinical isolates completely rescues the mechanical weakening caused by alginate.
Glycoconjugate Journal, 1997
The determination of conformational preferences of oligosaccharides is best approached by describ... more The determination of conformational preferences of oligosaccharides is best approached by describing their preferred conformations on potential energy surfaces as a function of the glycosidic linkage phi, psi torsional angles. For proper molecular mechanics modelling the flexibility of the rotatable pendant groups must also be considered. The so called adiabatic maps partially mimic the flexibility within the 10 dimensional conformational space of the pendant groups of the given disaccharide. These molecular mechanics maps are considered to be the state-of-the art of the phi, psi potential energy surface of disaccharides recently calculated. The RAMM (RAndom Molecular Mechanics) method was shown to be able to calculate such profiles automatically. Additionally, based on the continuum solvent approach, RAMM allows the calculation of the effects of solvent on conformational energy profiles. Molecular dynamics simulations are also useful tools to study the influence of solvent on conformational behaviour of oligosaccharides. The capability of the RAMM calculational protocol to locate low-energy conformers on the multidimensional potential energy hypersurfaces of disaccharides is illustrated and compared with molecular dynamics simulations with and without inclusion of the solvent.
Biomedicines
The global outbreak of SARS-CoV-2/COVID-19 provided the stage to accumulate an enormous biomedica... more The global outbreak of SARS-CoV-2/COVID-19 provided the stage to accumulate an enormous biomedical data set and an opportunity as well as a challenge to test new concepts and strategies to combat the pandemic. New research and molecular medical protocols may be deployed in different scientific fields, e.g., glycobiology, nanopharmacology, or nanomedicine. We correlated clinical biomedical data derived from patients in intensive care units with structural biology and biophysical data from NMR and/or CAMM (computer-aided molecular modeling). Consequently, new diagnostic and therapeutic approaches against SARS-CoV-2 were evaluated. Specifically, we tested the suitability of incretin mimetics with one or two pH-sensitive amino acid residues as potential drugs to prevent or cure long-COVID symptoms. Blood pH values in correlation with temperature alterations in patient bodies were of clinical importance. The effects of biophysical parameters such as temperature and pH value variation in ...
HAL (Le Centre pour la Communication Scientifique Directe), Mar 15, 1998
Biopolymers, 1998
Conformations of the alpha-L-Rhap(1-2)-beta-D-Glc1-OMe and beta-D-Galp(1-3)-beta-D-Glc1-OMe disac... more Conformations of the alpha-L-Rhap(1-2)-beta-D-Glc1-OMe and beta-D-Galp(1-3)-beta-D-Glc1-OMe disaccharides and the branched title trisaccharide were examined in DMSO-d6 solution by 1H-nmr. The distance mapping procedure was based on rotating frame nuclear Overhauser effect (NOE) constraints involving C- and O-linked protons, and hydrogen-bond constraints manifested by the splitting of the OH nmr signals for partially deuteriated samples. An "isotopomer-selected NOE" method for the unequivocal identification of mutually hydrogen-bonded hydroxyl groups was suggested. The length of hydrogen bonds thus detected is considered the only one motionally nonaveraged nmr-derived constraint. Molecular mechanics and molecular dynamics methods were used to model the conformational properties of the studied oligosaccharides. Complex conformational search, relying on a regular phi, psi-grid based scanning of the conformational space of the selected glycosidic linkage, combined with simultaneous modeling of different allowed orientations of the pendant groups and the third, neighboring sugar residue, has been carried out. Energy minimizations were performed for each member of the phi, psi grid generated set of conformations. Conformational clustering has been done to group the minimized conformations into families with similar values of glycosidic torsion angles. Several stable syn and anti conformations were found for the 1-->2 and 1-->3 bonds in the studied disaccharides. Vicinal glycosylation affected strongly the occupancy of conformational states in both branches of the title trisaccharide. The preferred conformational family of the trisaccharide (with average phi, psi values of 38 degrees, 17 degrees for the 1-->2 and 48 degrees, 1 degree for the 1-->3 bond, respectively) was shown by nmr to be stabilized by intramolecular hydrogen bonding between the nonbonded Rha and Gal residues.
Colloids and Surfaces B: Biointerfaces, 2021
Amphiphilic compounds, both detergents and lipids, are important tools for in vitro analysis of w... more Amphiphilic compounds, both detergents and lipids, are important tools for in vitro analysis of water-soluble and integral membrane proteins. A key question is whether these two groups of amphiphilic molecules use the same pathway to affect structural and functional integrity of proteins. In the present study, we tested the effect of non-ionic detergent dodecyl maltoside (DDM), two phospholipids, 1,2-dimyristoyl-sn-glycero-3- phosphocholine (DMPC), 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), and the detergent-phospholipid mixtures on insulin amyloidogenesis in vitro. Amyloidogenesis of insulin is significantly affected by DDM in a time-and dose-dependent manner, but only slightly affected by either of phospholipids. Addition of DHPC or DMPC to detergent does not alter the inhibiting pattern, suggesting that DDM preferably binds to insulin. The molecular modeling revealed that DDM and the phospholipids occupy equivalent binding sites. DDM, due to the presence of maltose with several oxygen atoms (hydroxylic, glycosidic and ring) is involved in more hydrogen bonds than DHPC or DMPC. Hydrophobic interactions are important factors to stabilize both, DDM and phospholipids in their binding sites. Our results indicate that certain detergents (applying DDM as an example) and selected phospholipids are not always interchangeable in their use to investigate the effect of amphiphilic compounds on the behavior of amyloid-prone proteins.
Marine Drugs
Osteoarthritis belongs to the most common joint diseases in humans and animals and shows increase... more Osteoarthritis belongs to the most common joint diseases in humans and animals and shows increased incidence in older patients. The bioactivities of collagen hydrolysates, sulfated glucosamine and a special fatty acid enriched dog-food were tested in a dog patient study of 52 dogs as potential therapeutic treatment options in early osteoarthritis. Biophysical, biochemical, cell biological and molecular modeling methods support that these well-defined substances may act as effective nutraceuticals. Importantly, the applied collagen hydrolysates as well as sulfated glucosamine residues from marine organisms were strongly supported by both an animal model and molecular modeling of intermolecular interactions. Molecular modeling of predicted interaction dynamics was evaluated for the receptor proteins MMP-3 and ADAMTS-5. These proteins play a prominent role in the maintenance of cartilage health as well as innate and adapted immunity. Nutraceutical data were generated in a veterinary cl...
Cells
Mitochondrial cytochrome c oxidase (CcO) is a multisubunit integral membrane complex consisting o... more Mitochondrial cytochrome c oxidase (CcO) is a multisubunit integral membrane complex consisting of 13 dissimilar subunits, as well as three to four tightly bound molecules of cardiolipin (CL). The monomeric unit of CcO is able to form a dimer and participate in the formation of supercomplexes in the inner mitochondrial membrane. The structural and functional integrity of the enzyme is crucially dependent on the full subunit complement and the presence of unperturbed bound CL. A direct consequence of subunit loss, CL removal, or its oxidative modification is the destabilization of the quaternary structure, loss of the activity, and the inability to dimerize. Thus, the intimate interplay between individual components of the complex is imperative for regulation of the CcO aggregation state. While it appears that the aggregation state of CcO might affect its conformational stability, the functional role of the aggregation remains unclear as both monomeric and dimeric forms of CcO seem t...
EPJ Web of Conferences
Detailed understanding of the interactions of novel metal-containing nanoparticles with biologica... more Detailed understanding of the interactions of novel metal-containing nanoparticles with biological membranes, macromolecules and other molecular targets of the living cell is crucial for the elucidation of the biological actions of such functionalized nanosystems. We present here the construction and modeling of thiolate-protected gold clusters and the prediction of their static and dynamic properties.
Photodiagnosis and Photodynamic Therapy
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Colloids and Surfaces B: Biointerfaces
Biochimica et Biophysica Acta (BBA) - Bioenergetics
AIP Conference Proceedings, 1995
Colloids and surfaces. B, Biointerfaces, 2017
Two nonionic detergents, Triton X-100 (TX-100) and n-dodecyl-β-d-maltoside (DDM) were tested for ... more Two nonionic detergents, Triton X-100 (TX-100) and n-dodecyl-β-d-maltoside (DDM) were tested for their ability to affect lysozyme amyloid aggregation. We have demonstrated that fibrillization of lysozyme is completely inhibited by low sub-micellar concentrations of both of these detergents. The apparent IC50 values were calculated to be 22μM and 26μM for TX-100 and DDM, respectively. The detergent/protein ratio is not the only parameter controlling inhibition. The precise timing of the detergent addition was found to be also crucial. It appears that the primary inhibitory activity of detergents resulted from inhibition of nuclei formation, in addition to inhibition of fibril polymerization at the early stage of protofibrils growth. The docking study revealed that Asn-59, Trp-63 and Ala-107, all present within the lysozyme amyloidogenic region, were involved in the interaction with both detergents. In addition, TX-100 also interacted with Gln-57 and Asp-103 within lysozyme. Moreover,...
Glycoconjugate J, 1998
Three-dimensional structures of the natural substrate unit for the enzyme N-acetylglucosamine-tra... more Three-dimensional structures of the natural substrate unit for the enzyme N-acetylglucosamine-transferase II, GlcNAc-Man 3-GlcNAc 2 , were investigated by molecular modelling methods. Molecular dynamics (MD) and molecular mechanics calculations on two hexasaccharides, namely GlcNAc-Man 3-GlcNAc 2-Asn and GlcNAc-Man 3-GlcNAc 2-OMe were performed by the Biosym/MSI software using the CVFF and CFF95 force fields in vacuum. The MD simulations were calculated for 3 ns at different simulation temperatures and for two values of dielectric constant, D ؍ 1 and D ؍ 4. From each 3 ns trajectory, 3050 structures have been optimized. The local minima obtained have been clustered into families exhibiting similar values of glycosidic torsional angles T, V , and W. The influence of the simulation conditions and force fields used on the conformational behaviour and structure of the title oligosaccharides is discussed.
Biophysical Journal, 2016
polymers confer distinct mechanical and biological properties to single bacteria and to mature bi... more polymers confer distinct mechanical and biological properties to single bacteria and to mature biofilms. When individual bacteria attach to a surface, intracellular levels of cyclic-di-GMP increase. Cyclic-di-GMP is required to change gene expression to initiate the transition to the biofilm state. What specific cues control cyclic-di-GMP production were previously unknown-we show that this is controlled by mechanical shear stress, which is primarily impacted by bacterial motility and the EPS coating on bacteria. This opens up the possibility of making a new class of anti-biofilm surface, by using a 2D fluid that cannot sustain a lateral shear stress and thereby preventing activation of the cyclic-di-GMP signal. P. aeruginosa biofilm infections in the cystic fibrosis (CF) lung often last for decades, ample time for the infecting strain(s) to evolve. Production of alginate is well-known to tend to increase during CF infections. More recently, it is becoming recognized that CF infections also evolve to increase PSL production. Alginate chemically protects biofilms, but also makes them softer and weaker. Here, we show that PSL stiffens and strengthens biofilms, and that increased PSL production in biofilms grown from CF clinical isolates completely rescues the mechanical weakening caused by alginate.
Glycoconjugate Journal, 1997
The determination of conformational preferences of oligosaccharides is best approached by describ... more The determination of conformational preferences of oligosaccharides is best approached by describing their preferred conformations on potential energy surfaces as a function of the glycosidic linkage phi, psi torsional angles. For proper molecular mechanics modelling the flexibility of the rotatable pendant groups must also be considered. The so called adiabatic maps partially mimic the flexibility within the 10 dimensional conformational space of the pendant groups of the given disaccharide. These molecular mechanics maps are considered to be the state-of-the art of the phi, psi potential energy surface of disaccharides recently calculated. The RAMM (RAndom Molecular Mechanics) method was shown to be able to calculate such profiles automatically. Additionally, based on the continuum solvent approach, RAMM allows the calculation of the effects of solvent on conformational energy profiles. Molecular dynamics simulations are also useful tools to study the influence of solvent on conformational behaviour of oligosaccharides. The capability of the RAMM calculational protocol to locate low-energy conformers on the multidimensional potential energy hypersurfaces of disaccharides is illustrated and compared with molecular dynamics simulations with and without inclusion of the solvent.