Publications by authors named "Béla Viskolcz"

63 Publications

The Analysis of Human Serum N-Glycosylation in Patients with Primary and Metastatic Brain Tumors.

Life (Basel) 2021 Jan 6;11(1). Epub 2021 Jan 6.

Institute of Chemistry, Faculty of Materials Science and Engineering, University of Miskolc, 3515 Miskolc, Hungary.

The identification of patients with different brain tumors is solely built on imaging diagnostics, indicating the need for novel methods to facilitate disease recognition. Glycosylation is a chemical modification of proteins, reportedly altered in several inflammatory and malignant diseases, providing a potential alternative route for disease detection. In this paper, we report the quantitative analysis of serum N-glycosylation of patients diagnosed with primary and metastatic brain tumors. PNGase-F-digested and procainamide-labeled serum glycans were purified by magnetic nanoparticles, followed by quantitative liquid chromatographic analysis. The glycan structures were identified by the combination of single quad mass spectrometric detection and exoglycosidase digestions. Linear discriminant analysis provided a clear separation of different disease groups and healthy controls based on their N-glycome pattern. Altered distribution of biantennary neutral, sialylated but nonfucosylated, and sialylated-fucosylated structures were found to be the most significant changes. Our results demonstrate that serum glycosylation monitoring could improve the detection of malignancy.
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http://dx.doi.org/10.3390/life11010029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7825111PMC
January 2021

A "keto-enol" plaque buster mechanism to diminish Alzheimer's β-Amyloid burden.

Biochem Biophys Res Commun 2020 10 20;532(1):82-87. Epub 2020 Aug 20.

Bioinformatics and Molecular Surgery Unit, Institute of Chemistry, Faculty of Materials Science and Engineering, University of Miskolc, Miskolc, Hungary.

Curcumin and related compounds have been validated to remove even well-developed human β-amyloid plaques from the brain of transgenic mice, in vivo. However, their molecular mechanism of the plaque buster activity is rather unknown. Computational chemistry was employed here to better understand the β-amyloid protein elimination. According to our docking studies, a tautomeric "keto-enol" flip-flop mechanism is proposed that may chop up β-amyloid plaques in Alzheimer's due to removing each hairpin-foldamers one by one from both ends of aggregated fibrils. According to the experimented models, other bi-stable "keto-enol" pharmacophores might be identified to break up amyloid plaques and enhance rapid clearance of toxic aggregates in Alzheimer's disease.
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http://dx.doi.org/10.1016/j.bbrc.2020.07.086DOI Listing
October 2020

Membrane Flash Index: Powerful and Perspicuous Help for Efficient Separation System Design.

ACS Omega 2020 Jun 17;5(25):15136-15145. Epub 2020 Jun 17.

Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3, HU 1111 Budapest , Hungary.

There are different factors and indices to characterize the performance of a pervaporation membrane, but none of them gives information about their capabilities in the area of liquid separation compared to the most convenient alternative, which is distillation. Membrane flash index (MFLI) can be considered the first and only one that shows if the membrane is more efficient or not than distillation and quantifies this feature too. Therefore, the MFLI helps select the best separation alternative in the case of process design. In this study, the evaluation and capabilities of membrane flash index are comprehensively investigated in the cases of six aqueous mixtures: methyl alcohol-water, ethyl alcohol-water, isobutyl alcohol-water, tetrahydrofuran-water, -butyl alcohol-water, and isopropanol-water. It must be concluded that the separation capacity of organophilic type membranes is remarkably lower than hydrophilic membranes in all cases of separation. The study of the MFLI is extended with the consideration of other binary interaction parameters like separation factor, permeation flux, selectivity, and pervaporation separation index (PSI) in order to find a descriptive relationship between them. For the same membrane material type, descriptive function can be determined between feed concentration and MFLI and PSI and separation factor, which can be used to calculate each other's value. On the basis of the indices and especially the MFLI, a significant help can be given to the process design engineer to select the right liquid separation alternative and, in the case of pervaporation, find the most appropriate membrane.
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http://dx.doi.org/10.1021/acsomega.0c01063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7331041PMC
June 2020

Beyond Chelation: EDTA Tightly Binds Taq DNA Polymerase, MutT and dUTPase and Directly Inhibits dNTPase Activity.

Biomolecules 2019 10 17;9(10). Epub 2019 Oct 17.

Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.

EDTA is commonly used as an efficient chelator of metal ion enzyme cofactors. It is highly soluble, optically inactive and does not interfere with most chemicals used in standard buffers making EDTA a common choice to generate metal-free conditions for biochemical and biophysical investigations. However, the controversy in the literature on metal-free enzyme activities achieved using EDTA or by other means called our attention to a putative effect of EDTA beyond chelation. Here, we show that EDTA competes for the nucleotide binding site of the nucleotide hydrolase dUTPase by developing an interaction network within the active site similar to that of the substrate. To achieve these findings, we applied kinetics and molecular docking techniques using two different dUTPases. Furthermore, we directly measured the binding of EDTA to dUTPases and to two other dNTPases, the Taq polymerase and MutT using isothermal titration calorimetry. EDTA binding proved to be exothermic and mainly enthalpy driven with a submicromolar dissociation constant considerably lower than that of the enzyme:substrate or the Mg:EDTA complexes. Control proteins, including an ATPase, did not interact with EDTA. Our findings indicate that EDTA may act as a selective inhibitor against dNTP hydrolyzing enzymes and urge the rethinking of the utilization of EDTA in enzymatic experiments.
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http://dx.doi.org/10.3390/biom9100621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6843921PMC
October 2019

Purification of Fluorescently Derivatized N-Glycans by Magnetic Iron Nanoparticles.

Nanomaterials (Basel) 2019 Oct 17;9(10). Epub 2019 Oct 17.

Faculty of Materials Science and Engineering, Institute of Chemistry, University of Miskolc, 3515 Miskolc, Hungary.

A novel glycoanalytical approach was developed in this study for the purification of fluorescently derivatized N-glycans. Polyethylene glycol (PEG) modified iron-nanoparticles were synthetized by the combination of sonochemical treatment and combustion method. The prepared nanomaterials were applied for a systematic clean-up optimization to maximize purification efficiency of 2-AA labelled glycans. PEG 1000 modified iron-oxalate was found to be the most effective for the selective enrichment of serum N-glycans providing high reproducibility. Different acetonitrile percentages for binding and washing steps were also tested to ensure the same relative peak areas compared to the unpurified sample. The generated novel clean-up strategy provides a potential route to use in-house synthetized magnetic nanoparticles for glycan sample preparation.
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http://dx.doi.org/10.3390/nano9101480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6835309PMC
October 2019

Urethane Formation with an Excess of Isocyanate or Alcohol: Experimental and Ab Initio Study.

Polymers (Basel) 2019 Sep 22;11(10). Epub 2019 Sep 22.

Institute of Chemistry, University of Miskolc, Miskolc-Egyetemváros A/2, H-3515 Miskolc, Hungary.

A kinetic and mechanistic investigation of the alcoholysis of phenyl isocyanate using 1-propanol as the alcohol was undertaken. A molecular mechanism of urethane formation in both alcohol and isocyanate excess is explored using a combination of an accurate fourth generation Gaussian thermochemistry (G4MP2) with the Solvent Model Density (SMD) implicit solvent model. These mechanisms were analyzed from an energetic point of view. According to the newly proposed two-step mechanism for isocyanate excess, allophanate is an intermediate towards urethane formation via six-centered transition state (TS) with a reaction barrier of 62.6 kJ/mol in the THF model. In the next step, synchronous 1,3-H shift between the nitrogens of allophanate and the cleavage of the C-N bond resulted in the release of the isocyanate and the formation of a urethane bond via a low-lying TS with 49.0 kJ/mol energy relative to the reactants. Arrhenius activation energies of the stoichiometric, alcohol excess and the isocyanate excess reactions were experimentally determined by means of HPLC technique. The activation energies for both the alcohol (measured in our recent work) and the isocyanate excess reactions were lower compared to that of the stoichiometric ratio, in agreement with the theoretical calculations.
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http://dx.doi.org/10.3390/polym11101543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6835639PMC
September 2019

Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models.

J Phys Chem B 2019 09 10;123(37):7869-7884. Epub 2019 Sep 10.

Institute of Chemistry , University of Miskolc , Egyetemváros A/2 , H-3515 Miskolc , Hungary.

1,4-Dioxane is a cytotoxic B2-type human carcinogen, a serious water pollutant produced solely by industrial activity. The effect of 1,4-dioxane on phospholipid membrane models composed of dipalmitoyl-phosphatidylcholine (DPPC) and its branched isomer (isodipalmitoyl-phosphatidylcholine, IPPC) was investigated using MD simulations. Clear and polluted membranes were compared by membrane parameters such as area per lipid (APL), volume per lipid (VPL), compressibility modulus, membrane thickness, and orderliness of lipid tails. While neat systems significantly differ from each other, the presence of the pollutant has the same effect on both types of lipid membranes. High density of dioxane appears in the vicinity of ester groups, which pushes away lipid headgroups from each other, leading to an overall change in lipid structure: APL and VPL grows, while the orderliness of lipid tails, membrane thickness, and compressibility modulus decrease. Orientational preferences of water and dioxane molecules were also investigated and different membrane regions have been specified according to the stance of water molecules. Free-energy profile for 1,4-dioxane penetration mechanism into DPPC membranes was carried out using metadynamics for two different concentrations of the pollutant ( = 7.51 g/dm, = 75.10 g/dm), which showed that the higher the concentration is, the lower the free energy of penetration gets. Only a small free-energy barrier was found in the headgroup region and accumulation of dioxane is thermodynamically unfavored in the middle of the bilayer. The penetration mechanism has been described in detail based on the orientational preference of 1,4-dioxane molecules and the free-energy profiles.
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http://dx.doi.org/10.1021/acs.jpcb.9b04313DOI Listing
September 2019

Serum N-Glycosylation in Parkinson's Disease: A Novel Approach for Potential Alterations.

Molecules 2019 Jun 13;24(12). Epub 2019 Jun 13.

Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co., Dublin A94 X099, Ireland.

In this study, we present the application of a novel capillary electrophoresis (CE) method in combination with label-free quantitation and support vector machine-based feature selection (support vector machine-estimated recursive feature elimination or SVM-RFE) to identify potential glycan alterations in Parkinson's disease. Specific focus was placed on the use of neutral coated capillaries, by a dynamic capillary coating strategy, to ensure stable and repeatable separations without the need of non-mass spectrometry (MS) friendly additives within the separation electrolyte. The developed online dynamic coating strategy was applied to identify serum N-glycosylation by CE-MS/MS in combination with exoglycosidase sequencing. The annotated structures were quantified in 15 controls and 15 Parkinson's disease patients by label-free quantitation. Lower sialylation and increased fucosylation were found in Parkinson's disease patients on tri-antennary glycans with 2 and 3 terminal sialic acids. The set of potential glycan alterations was narrowed by a recursive feature elimination algorithm resulting in the efficient classification of male patients.
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http://dx.doi.org/10.3390/molecules24122220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6630595PMC
June 2019

Oxidatively-mediated in silico epimerization of a highly amyloidogenic segment in the human calcitonin hormone (hCT).

Comput Biol Chem 2019 Jun 8;80:259-269. Epub 2019 Apr 8.

Institue of Chemistry, Faculty of Materials Science and Engineering, University of Miskolc, H-3515 Miskolc, Hungary; Ferenc Rákóczi II. Transcarpathian Hungarian Institute, Beregszász, Transcarpathia, 90200, Ukraine.

In order to study the effects of peptide exposure to oxidative attack, we chose a model reaction in which the hydroxyl radical discretely abstracts a hydrogen atom from the α-carbon of each residue of a highly amyloidogenic region in the human calcitonin hormone, hCT. Based on a combined Molecular Mechanics / Quantum Mechanics approach, the extended and folded L- and D-configuration and radical intermediate hCT peptides were optimized to obtain their compactness, secondary structure and relative thermodynamic data. The results suggest that the epimerization of residues is generally an exergonic process that can explain the cumulative nature of molecular aging. Moreover, the configurational inversion induced conformational changes can cause protein dysfunction. The epimerization of the central residue to the D-configuration induced a hairpin structure in hCT, concomitant with a possible oligomerization of human calcitonin into Aβ(1-42)-like amyloid fibrils present in patients suffering from Alzheimer's disease.
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http://dx.doi.org/10.1016/j.compbiolchem.2019.04.005DOI Listing
June 2019

An Ab Initio Investigation of the 4,4'-Methlylene Diphenyl Diamine (4,4'-MDA) Formation from the Reaction of Aniline with Formaldehyde.

Polymers (Basel) 2019 Mar 1;11(3). Epub 2019 Mar 1.

Institute of Chemistry, University of Miskolc, Miskolc-Egyetemváros A/2, H-3515 Miskolc, Hungary.

The most commonly applied industrial synthesis of 4,4'-methylene diphenyl diamine (4,4'-MDA), an important polyurethane intermediate, is the reaction of aniline and formaldehyde. Molecular understanding of the 4,4'-MDA formation can provide strategy to prevent from side reactions. In this work, a molecular mechanism consisted of eight consecutive, elementary reaction steps from anilines and formaldehyde to the formation of 4,4'-MDA in acidic media is proposed using accurate G3MP2B3 composite quantum chemical method. Then G3MP2B3-SMD results in aqueous and aniline solutions were compared to the gas phase mechanism. Based on the gas phase calculations standard enthalpy of formation, entropy and heat capacity values were evaluated using G3MP2B3 results for intermediates The proposed mechanism was critically evaluated and important side reactions are considered: the competition of formation of protonated p-aminobenzylaniline (PABAH⁺), protonated aminal (AMH⁺) and o-aminobenzylaniline (OABAH⁺). Competing reactions of the 4,4'-MDA formation is also thermodynamically analyzed such as the formation of 2,4-MDAH⁺, 3,4-MDAH⁺. AMH⁺ can be formed through loose transition state, but it becomes kinetic dead-end, while formation of significant amount of 2,4-MDA is plausible through low-lying transition state. The acid strength of the key intermediates such as N-methylenebenzeneanilium, PABAH⁺, 4-methylidenecyclohexa-2,5-diene-1-iminium, and AMH⁺ was estimated by relative p calculation.
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http://dx.doi.org/10.3390/polym11030398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6473863PMC
March 2019

Formation Mechanism of Benzo(a)pyrene: One of the Most Carcinogenic Polycyclic Aromatic Hydrocarbons (PAH).

Molecules 2019 Mar 15;24(6). Epub 2019 Mar 15.

Institute of Chemistry, University of Miskolc, Miskolc-Egyetemváros, H-3515 Miskolc, Hungary.

The formation of polycyclic aromatic hydrocarbons (PAHs) is a strong global concern due to their harmful effects. To help the reduction of their emissions, a crucial understanding of their formation and a deep exploration of their growth mechanism is required. In the present work, the formation of benzo(a)pyrene was investigated computationally employing chrysene and benz(a)anthracene as starting materials. It was assumed a type of methyl addition/cyclization (MAC) was the valid growth mechanism in this case. Consequently, the reactions implied addition reactions, ring closures, hydrogen abstractions and intramolecular hydrogen shifts. These steps of the mechanism were computed to explore benzo(a)pyene formation. The corresponding energies of the chemical species were determined via hybrid density funcional theory (DFT), B3LYP/6-31+G(d,p) and M06-2X/6-311++G(d,p). Results showed that the two reaction routes had very similar trends energetically, the difference between the energy levels of the corresponding molecules was just 6.13 kJ/mol on average. The most stable structure was obtained in the benzo(a)anthracene pathway.
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http://dx.doi.org/10.3390/molecules24061040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6470522PMC
March 2019

Synthesis Optimization and Characterization of Nitrogen-Doped Bamboo-Shaped Carbon Nanotubes.

J Nanosci Nanotechnol 2019 Jan;19(1):429-435

Institute of Chemistry, University of Miskolc, Miskolc-Egyetemváros, 3515, Hungary.

Nitrogen-doped bamboo-shaped carbon nanotubes (N-BCNT) were synthesized from butylamine using the catalytic chemical vapor deposition (CCVD) process. The carbon source was nitrogen content organic molecules, namely butylamine. Reaction conditions such as temperature, amount of carbon source and catalyst were optimized to produce high quality N-BCNT samples. The nitrogen content was measured by CHNS element analysis, while the butylamine conversion was calculated based on the weight of deposited carbon materials. The bamboo structure of the nanotubes was examined by high resolution transmission electron microscopy (HRTEM). Two different types of nitrogen incorporation forms, the pyridinic and the graphitic, were identified in the samples by X-ray photoelectron spectroscopy (XPS). The lattice defects were measured by Raman spectroscopy. The proportion of defect sites influenced by the nitrogen content which can be controlled by the synthesis temperature. The optimal conditions were identified for the economical synthesis of N-BCNTs with high nitrogen content for various applications.
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http://dx.doi.org/10.1166/jnn.2019.15776DOI Listing
January 2019

Development and Application of Carbon-Layer-Stabilized, Nitrogen-Doped, Bamboo-Like Carbon Nanotube Catalysts in CO Hydrogenation.

ChemistryOpen 2018 Oct 5;7(10):789-796. Epub 2018 Oct 5.

Institute of Chemistry University of Miskolc 3515 Miskolc Egyetemváros Hungary.

Nitrogen-doped, bamboo-like carbon nanotubes (BCNTs) were synthesized from butylamine by catalytic chemical vapor deposition (CCVD method). The nanotubes were oxidized by HSO/HNO treatment and used to prepare calcium alginate gelled BCNT spheres. These beads were first carbonized and then Pd, Rh and Ni nanoparticles were anchored on the surface of the spheres. These systems were then applied as catalysts in CO hydrogenation. The BCNT support was examined by Raman spectroscopy, dynamic light scattering (DLS) and X-ray photoelectron spectroscopy (XPS). The prepared catalysts were characterized by HRTEM and SEM. The oxidation pretreatment of BCNTs was successful, with the electrokinetic potential of the water-based dispersion of BCNTs measuring -59.9 mV, meaning the nanotube dispersion is stable. Pyridinic and graphitic types of incorporated nitrogen centers were identified in the structure of the nanotubes, according to the XPS measurements. The Pd-containing BCNT sphere catalyst was the most efficient in the catalytic studies. The highest conversion was reached on the Pd catalyst at 723 K, as well as at 873 K. The difference in the formation rate of CO was much less at 873 K between the Pd and Rh compared to the 723 K values. Accordingly, the application of Pd-containing BCNT/carbon-supported catalyst favored the generation of CO. However, the Ni-BCNT/carbon catalyst leads to the formation of CH as the major product.
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http://dx.doi.org/10.1002/open.201800162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173370PMC
October 2018

High efficiency two-photon uncaging coupled by the correction of spontaneous hydrolysis.

Org Biomol Chem 2018 03;16(11):1958-1970

Two-Photon Measurement Technology Research Group, The Faculty of Information Technology, Pázmány Péter Catholic University, Práter str 50, H-1083 Budapest, Hungary.

Two-photon (TP) uncaging of neurotransmitter molecules is the method of choice to mimic and study the subtleties of neuronal communication either in the intact brain or in slice preparations. However, the currently available caged materials are just at the limit of their usability and have several drawbacks. The local and focal nature of their use may for example be jeopardized by a high spontaneous hydrolysis rate of the commercially available compounds with increased photochemical release rate. Here, using quantum chemical modelling we show the mechanisms of hydrolysis and two-photon activation, and synthesized more effective caged compounds. Furthermore, we have developed a new enzymatic elimination method removing neurotransmitters inadvertently escaping from their compound during experiment. This method, usable both in one and two-photon experiments, allows for the use of materials with an increased rate of photochemical release. The efficiency of the new compound and the enzymatic method and of the new compound are demonstrated in neurophysiological experiments.
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http://dx.doi.org/10.1039/c8ob00025eDOI Listing
March 2018

Molecular Surgery Concept from Bench to Bedside: A Focus on TRPV1+ Pain-Sensing Neurons.

Front Physiol 2017 2;8:378. Epub 2017 Jun 2.

Institute of Chemistry, Faculty of Materials Science and Engineering, University of MiskolcMiskolc, Hungary.

"Molecular neurosurgery" is emerging as a new medical concept, and is the combination of two partners: (i) a molecular neurosurgery agent, and (ii) the cognate receptor whose activation results in the selective elimination of a specific subset of neurons in which this receptor is endogenously expressed. In general, a molecular surgery agent is a selective and potent ligand, and the target is a specific cell type whose elimination is desired through the molecular surgery procedure. These target cells have the highest innate sensitivity to the molecular surgery agent usually due to the highest receptor density being in their plasma membrane. The interaction between the ligand and its receptor evokes an overactivity of the receptor. If the receptor is a ligand-activated non-selective cation channel, the overactivity of receptor leads to excess Ca and Na influx into the cell and finally cell death. One of the best known examples of such an interaction is the effect of ultrapotent vanilloids on TRPV1-expressing pain-sensing neurons. One intrathecal resiniferatoxin (RTX) dose allows for the receptor-mediated removal of TRPV1+ neurons from the peripheral nervous system. The TRPV1 receptor-mediated ion influx induces necrotic processes, but only in pain-sensing neurons, and usually within an hour. Besides that, target-specific apoptotic processes are also induced. Thus, as a nano-surgery scalpel, RTX removes the neurons responsible for generating pain and inflammation from the peripheral nervous system providing an option in clinical management for the treatment of morphine-insensitive pain conditions. In the future, the molecular surgery concept can also be exploited in cancer research for selectively targeting the specific tumor cell.
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http://dx.doi.org/10.3389/fphys.2017.00378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5455100PMC
June 2017

Protein Stability and Unfolding Following Glycine Radical Formation.

Molecules 2017 Apr 19;22(4). Epub 2017 Apr 19.

Institute of Complex Systems: Structural Biochemistry (ICS-6) Forschungszentrum Jülich, 52425 Jülich, Germany.

Glycine (Gly) residues are particularly susceptible to hydrogen abstraction; which results in the formation of the capto-dative stabilized C-centered Gly radical (GLR) on the protein backbone. We examined the effect of GLR formation on the structure of the Trp cage; tryptophan zipper; and the villin headpiece; three fast-folding and stable miniproteins; using all-atom (OPLS-AA) molecular dynamics simulations. Radicalization changes the conformation of the GLR residue and affects both neighboring residues but did not affect the stability of the Trp zipper. The stability of helices away from the radical center in villin were also affected by radicalization; and GLR in place of Gly15 caused the Trp cage to unfold within 1 µs. These results provide new evidence on the destabilizing effects of protein oxidation by reactive oxygen species.
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http://dx.doi.org/10.3390/molecules22040655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6154654PMC
April 2017

A Hidden Active Site in the Potential Drug Target Mycobacterium tuberculosis dUTPase Is Accessible through Small Amplitude Protein Conformational Changes.

J Biol Chem 2016 Dec 4;291(51):26320-26331. Epub 2016 Nov 4.

From the Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary H1117,

dUTPases catalyze the hydrolysis of dUTP into dUMP and pyrophosphate to maintain the proper nucleotide pool for DNA metabolism. Recent evidence suggests that dUTPases may also represent a selective drug target in mycobacteria because of the crucial role of these enzymes in maintaining DNA integrity. Nucleotide-hydrolyzing enzymes typically harbor a buried ligand-binding pocket at interdomain or intersubunit clefts, facilitating proper solvent shielding for the catalyzed reaction. The mechanism by which substrate binds this hidden pocket and product is released in dUTPases is unresolved because of conflicting crystallographic and spectroscopic data. We sought to resolve this conflict by using a combination of random acceleration molecular dynamics (RAMD) methodology and structural and biochemical methods to study the dUTPase from Mycobacterium tuberculosis In particular, the RAMD approach used in this study provided invaluable insights into the nucleotide dissociation process that reconciles all previous experimental observations. Specifically, our data suggest that nucleotide binding takes place as a small stretch of amino acids transiently slides away and partially uncovers the active site. The in silico data further revealed a new dUTPase conformation on the pathway to a relatively open active site. To probe this model, we developed the Trp reporter and collected crystallographic, spectroscopic, and kinetic data that confirmed the interaction of Trp with the active site shielding C-terminal arm, suggesting that the RAMD method is effective. In summary, our computational simulations and spectroscopic results support the idea that small loop movements in dUTPase allow the shuttlingof the nucleotides between the binding pocket and the solvent.
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http://dx.doi.org/10.1074/jbc.M116.734012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159494PMC
December 2016

Radical Formation Initiates Solvent-Dependent Unfolding and β-sheet Formation in a Model Helical Peptide.

J Phys Chem B 2016 06 26;120(22):4878-89. Epub 2016 May 26.

Institute of Chemistry, Faculty of Material Science, University of Miskolc , Egyetemváros 1, H-3529 Miskolc, Hungary.

We examined the effects of Cα-centered radical formation on the stability of a model helical peptide, N-Ac-KK(AL)10KK-NH2. Three, 100 ns molecular dynamics simulations using the OPLS-AA force field were carried out on each α-helical peptide in six distinct binary TIP4P water/2,2,2-trifluoroethanol (TFE) mixtures. The α-helicity was at a maximum in 20% TFE, which was inversely proportional to the number of H-bonds between water molecules and the peptide backbone. The radial distribution of TFE around the peptide backbone was highest in 20% TFE, which enhanced helix stability. The Cα-centered radical initiated the formation of a turn within 5 ns, which was a smaller kink at high TFE concentrations, and a loop at lower TFE concentrations. The highest helicity of the peptide radical was measured in 100% TFE. The formation of hydrogen bonds between the peptide backbone and water destabilized the helix, whereas the clustering of TFE molecules around the radical center stabilized the helix. Following radical termination, the once helical structure converted to a β-sheet rich state in 100% water only, and this transition did not occur in the nonradical control peptide. This study gives evidence on how the formation of peptide radicals can initiate α-helical to β-sheet transitions under oxidative stress conditions.
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http://dx.doi.org/10.1021/acs.jpcb.6b00174DOI Listing
June 2016

Glutathione as a prebiotic answer to α-peptide based life.

J Phys Chem B 2015 Mar 3;119(10):3940-7. Epub 2015 Mar 3.

Department of Chemical Informatics, Faculty of Education, University of Szeged , Boldogasszony sgt. 6, Szeged, Hungary -6725.

The energetics of peptide bond formation is an important factor not only in the design of chemical peptide synthesis, but it also has a role in protein biosynthesis. In this work, quantum chemical calculations at 10 different levels of theory including G3MP2B3 were performed on the energetics of glutathione formation. The strength of the peptide bond is found to be closely related to the acid strength of the to-be N-terminal and the basicity of the to-be C-terminal amino acid. It is shown that the formation of the first peptide activates the amino acid for the next condensation step, manifested in bacterial protein synthesis where the first step is the formation of an N-formylmethionine dipeptide. The possible role of glutathione in prebiotic molecular evolution is also analyzed. The implications of the thermodynamics of peptide bond formation in prebiotic peptide formation as well as in the preference of α- instead of β- or γ-amino acids are discussed. An empirical correction is proposed for the compensation of the error due to the incapability of continuum solvation models in describing the change of the first solvation shell when a peptide bond is formed from two zwitterions accompanied by the disappearance of one ion pair.
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http://dx.doi.org/10.1021/jp511582mDOI Listing
March 2015

The effect of hydroxyl moieties and their oxosubstitution on bile acid association studied in floating monolayers.

ScientificWorldJournal 2014 25;2014:152972. Epub 2014 Dec 25.

Department of Physical Chemistry and Materials Science, University of Szeged, Aradi Vt. 1, Szeged 6720, Hungary.

Bile salt aggregates are promising candidates for drug delivery vehicles due to their unique fat-solubilizing ability. However, the toxicity of bile salts increases with improving fat-solubilizing capability and so an optimal combination of efficient solubilization and low toxicity is necessary. To improve hydrophilicity (and decrease toxicity), we substituted hydroxyl groups of several natural bile acid (BA) molecules for oxogroups and studied their intrinsic molecular association behavior. Here we present the comparative Langmuir trough study of the two-dimensional (2D) association behavior of eight natural BAs and four oxoderivatives (traditionally called keto-derivatives) floated on an aqueous subphase. The series of BAs and derivatives showed systematic changes in the shape of the compression isotherms. Two types of association could be distinguished: the first transition was assigned to the formation of dimers through H-bonding and the second to the hydrophobic aggregation of BA dimers. Hydrophobic association of BA molecules in the films is linked to the ability of forming H-bonded dimers. Both H-bond formation and hydrophobic association weakened with increasing number of hydroxyl groups, decreasing distance between hydroxyl groups, and increasing oxosubstitution. The results also show that the Langmuir trough method is extremely useful in selecting appropriate BA molecules to design drug delivery systems.
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http://dx.doi.org/10.1155/2014/152972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317589PMC
October 2015

Mixed micelles of sodium cholate and sodium dodecylsulphate 1:1 binary mixture at different temperatures--experimental and theoretical investigations.

PLoS One 2014 8;9(7):e102114. Epub 2014 Jul 8.

Department of Chemical Informatics, Faculty of Education, University of Szeged, Szeged, Hungary.

Micellisation process for sodium dodecyl sulphate and sodium cholate in 1∶1 molar ratio was investigated in a combined approach, including several experimental methods and coarse grained molecular dynamics simulation. The critical micelle concentration (cmc) of mixed micelle was determined by spectrofluorimetric and surface tension measurements in the temperature range of 0-50°C and the values obtained agreed with each other within the statistical error of the measurements. In range of 0-25°C the cmc values obtained are temperature independent while cmc values were increased at higher temperature, which can be explained by the intensive motion of the monomers due to increased temperature. The evidence of existing synergistic effect among different constituent units of the micelle is indicated clearly by the interaction parameter (β1,2) calculated from cmc values according to Rubingh. As the results of the conductivity measurements showed the negative surface charges of the SDS-NaCA micelle are not neutralized by counterions. Applying a 10 µs long coarse-grained molecular dynamics simulation for system including 30-30 SDS and CA (with appropriate number of Na+ cations and water molecules) we obtained semi-quantitative agreement with the experimental results. Spontaneous aggregation of the surfactant molecules was obtained and the key steps of the micelle formation are identified: First a stable SDS core was formed and thereafter due to the entering CA molecules the size of the micelle increased and the SDS content decreased. In addition the size distribution and composition as well as the shape and structure of micelles are also discussed.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102114PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4087020PMC
October 2015

Molecular ageing: free radical initiated epimerization of thymopentin--a case study.

J Chem Phys 2014 May;140(20):205102

Department of Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725 Szeged, Hungary.

The epimerization of amino acid residues increases with age in living organisms. In the present study, the structural consequences and thermodynamic functions of the epimerization of thymopentin (TP-5), the active site of the thymic hormone thymopoietin, were studied using molecular dynamics and density functional theory methods. The results show that free radical-initiated D-amino acid formation is energetically favoured (-130 kJmol(-1)) for each residue and induces significant changes to the peptide structure. In comparison to the wild-type (each residue in the L-configuration), the radius of gyration of the D-Asp(3) epimer of the peptide decreased by 0.5 Å, and disrupted the intramolecular hydrogen bonding of the native peptide. Beyond establishing important structural, energetic and thermodynamic benchmarks and reference data for the structure of TP-5, these results disseminate the understanding of molecular ageing, the epimerization of amino acid residues.
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http://dx.doi.org/10.1063/1.4871684DOI Listing
May 2014

Global optimization of cholic acid aggregates.

J Chem Phys 2014 Apr;140(14):144302

Department of Chemical Informatics, Faculty of Education, University of Szeged, Boldogasszony sgt. 6, H-6725, Szeged, Hungary.

In spite of recent investigations into the potential pharmaceutical importance of bile acids as drug carriers, the structure of bile acid aggregates is largely unknown. Here, we used global optimization techniques to find the lowest energy configurations for clusters composed between 2 and 10 cholate molecules, and evaluated the relative stabilities of the global minima. We found that the energetically most preferred geometries for small aggregates are in fact reverse micellar arrangements, and the classical micellar behaviour (efficient burial of hydrophobic parts) is achieved only in systems containing more than five cholate units. Hydrogen bonding plays a very important part in keeping together the monomers, and among the size range considered, the most stable structure was found to be the decamer, having 17 hydrogen bonds. Molecular dynamics simulations showed that the decamer has the lowest dissociation propensity among the studied aggregation numbers.
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http://dx.doi.org/10.1063/1.4869832DOI Listing
April 2014

Absorption spectrum and absolute absorption cross sections of CH3O2 radicals and CH3I molecules in the wavelength range 7473-7497 cm(-1).

J Phys Chem A 2013 Dec 19;117(48):12802-11. Epub 2013 Nov 19.

PysicoChimie des Processus de Combustion et de l'Atmosphère PC2A, CNRS - University Lille 1, Cité Scientifique , Bât. C11, 59655 Villeneuve d'Ascq, France.

The absorption spectrum of CH3O2 radicals and CH3I molecules has been measured in the range 7473-7497 cm(-1). CH3O2 radicals have been generated by 248 nm laser photolysis of CH3I in the presence of O2, and the relative absorption has been measured by time-resolved continuous-wave cavity ring-down spectroscopy (cw-CRDS). Calibration of the relative absorption spectrum has been carried out on three distinct wavelengths by carefully measuring CH3O2 decays under different experimental conditions and extracting the initial radical concentration (and with this the absolute absorption cross sections) by using the well-known rate constant for the CH3O2 self-reaction. The following, pressure-independent absorption cross sections were determined: 3.41 × 10(-20), 3.40 × 10(-20), and 2.11 × 10(-20) cm(2) at 7748.18, 7489.16, and 7493.33 cm(-1). These values are 2-3 times higher than previous determinations ( Pushkarsky, M. B.; Zalyubovsky, S. J.; Miller, T. A. J. Chem. Phys. 2000, 112 (24), 10695 - 10698 and Atkinson, D. B.; Spillman, J. L. J. Phys. Chem. A 2002, 106 (38), 8891 - 8902). The absorption spectrum of the stable precursor CH3I has also been determined and three characteristic sharp absorption lines with absorption cross sections up to 2 × 10(-21) cm(2) have been observed in this wavelength range.
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http://dx.doi.org/10.1021/jp408686sDOI Listing
December 2013

Glutathione--hydroxyl radical interaction: a theoretical study on radical recognition process.

PLoS One 2013 9;8(9):e73652. Epub 2013 Sep 9.

Department of Chemical Informatics, Faculty of Education, University of Szeged, Szeged, Hungary.

Non-reactive, comparative (2 × 1.2 μs) molecular dynamics simulations were carried out to characterize the interactions between glutathione (GSH, host molecule) and hydroxyl radical (OH(•), guest molecule). From this analysis, two distinct steps were identified in the recognition process of hydroxyl radical by glutathione: catching and steering, based on the interactions between the host-guest molecules. Over 78% of all interactions are related to the catching mechanism via complex formation between anionic carboxyl groups and the OH radical, hence both terminal residues of GSH serve as recognition sites. The glycine residue has an additional role in the recognition of OH radical, namely the steering. The flexibility of the Gly residue enables the formation of further interactions of other parts of glutathione (e.g. thiol, α- and β-carbons) with the lone electron pair of the hydroxyl radical. Moreover, quantum chemical calculations were carried out on selected GSH/OH(•) complexes and on appropriate GSH conformers to describe the energy profile of the recognition process. The relative enthalpy and the free energy changes of the radical recognition of the strongest complexes varied from -42.4 to -27.8 kJ/mol and from -21.3 to 9.8 kJ/mol, respectively. These complexes, containing two or more intermolecular interactions, would be the starting configurations for the hydrogen atom migration to quench the hydroxyl radical via different reaction channels.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073652PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767814PMC
July 2014

Atropisomerism of the Asn α radicals revealed by Ramachandran surface topology.

J Phys Chem B 2013 Oct 3;117(41):12402-9. Epub 2013 Oct 3.

Department of Chemical Informatics, Faculty of Education, University of Szeged , 6726 Szeged, Hungary.

C radicals are typically trigonal planar and thus achiral, regardless of whether they originate from a chiral or an achiral C-atom (e.g., C-H + (•)OH → C• + H2O). Oxidative stress could initiate radical formation in proteins when, for example, the H-atom is abstracted from the Cα-carbon of an amino acid residue. Electronic structure calculations show that such a radical remains achiral when formed from the achiral Gly, or the chiral but small Ala residues. However, when longer side-chain containing proteogenic amino acid residues are studied (e.g., Asn), they provide radicals of axis chirality, which in turn leads to atropisomerism observed for the first time for peptides. The two enantiomeric extended backbone structures, •βL and •βD, interconvert via a pair of enantiotopic reaction paths, monitored on a 4D Ramachandran surface, with two distinct transition states of very different Gibbs-free energies: 37.4 and 67.7 kJ/mol, respectively. This discovery requires the reassessment of our understanding on radical formation and their conformational and stereochemical behavior. Furthermore, the atropisomerism of proteogenic amino acid residues should affect our understanding on radicals in biological systems and, thus, reframes the role of the D-residues as markers of molecular aging.
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http://dx.doi.org/10.1021/jp4070906DOI Listing
October 2013

Penicillin's catalytic mechanism revealed by inelastic neutrons and quantum chemical theory.

Phys Chem Chem Phys 2013 Dec 12;15(47):20447-20455. Epub 2013 Jun 12.

Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.

Penicillin, travels through bodily fluids, targeting and acylatively inactivating enzymes responsible for cell-wall synthesis in gram-positive bacteria. Somehow, it avoids metabolic degradation remaining inactive en route. To resolve this ability to switch from a non-active, to a highly reactive form, we investigated the dynamic structure-activity relationship of penicillin by inelastic neutron spectroscopy, reaction kinetics, NMR and multi-scale theoretical modelling (QM/MM and post-HF ab initio). Results show that by a self-activating physiological pH-dependent two-step proton-mediated process, penicillin changes geometry to activate its irreversibly reactive acylation, facilitated by systemic intramolecular energy management and cooperative vibrations. This dynamic mechanism is confirmed by the first ever reported characterisation of an antibiotic by neutrons, achieved on the TOSCA instrument (ISIS facility, RAL, UK).
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http://dx.doi.org/10.1039/c3cp50868dDOI Listing
December 2013

Homology Modeling and Validation of the Human M1 Muscarinic Acetylcholine Receptor.

Mol Inform 2012 Sep 7;31(9):635-8. Epub 2012 Sep 7.

University of Szeged, Department of Chemical Informatics, Szeged, Boldogasszony sgt 6, H-6725, Hungary tel: +36-62-454-720, fax: +36-62-545-720.

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http://dx.doi.org/10.1002/minf.201200062DOI Listing
September 2012

The Effect of Newly Developed OPLS-AA Alanyl Radical Parameters on Peptide Secondary Structure.

J Chem Theory Comput 2012 Aug 6;8(8):2569-80. Epub 2012 Jul 6.

Department of Chemical Informatics, Faculty of Education, University of Szeged , Boldogasszony sgt. 6, H-6725 Szeged, Hungary.

Recent studies using ab initio calculations have shown that Cα-centered radical formation by H-abstraction from the backbone of peptide residues has dramatic effects on peptide structure and have suggested that this reaction may contribute to the protein misfolding observed in Alzheimer's and Parkinson's diseases. To enable the effects of Cα-centered radicals to be studied in longer peptides and proteins over longer time intervals, force-field parameters for the Cα-centered Ala radical were developed for use with the OPLS force field by minimizing the sum of squares deviation between the quantum chemical and OPLS-AA energy hypersurfaces. These parameters were used to determine the effect of the Cα-centered Ala radical on the structure of a hepta-alanyl peptide in molecular dynamics (MD) simulations. A negligible sum-of-squares energy deviation was observed in the stretching parameters, and the newly developed OPLS-AA torsional parameters showed a good agreement with the LMP2/cc-pVTZ(-f) hypersurface. The parametrization also demonstrated that derived force-field bond length and bond angle parameters can deviate from the quantum chemical equilibrium values, and that the improper torsional parameters should be developed explicitly with respect to the coupled torsional parameters. The MD simulations showed planar conformations of the Cα-containing residue (Alr) are preferred and these conformations increase the formation of γ-, α-, and π-turn structures depending on the position in the turn occupied by the Alr residue. Higher-ordered structures are destabilized by Alr except when this residue occupies position "i + 1" of the 310-helix. These results offer new insight into the protein-misfolding mechanisms initiated by H-abstraction from the Cα of peptide and protein residues.
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http://dx.doi.org/10.1021/ct300059fDOI Listing
August 2012

Conformation-dependent ˙OH/H2O2 hydrogen abstraction reaction cycles of Gly and Ala residues: a comparative theoretical study.

J Phys Chem B 2012 Jan 10;116(3):1143-54. Epub 2012 Jan 10.

Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6.

To determine if (•)OH can initiate the unfolding of an amino acid residue, the elementary reaction coordinates of H abstraction by (•)OH different conformations (β(L), γ(L), γ(D), α(L), and α(D)) of Gly and Ala dimethyl amides were computed using first-principles quantum computations. The MPWKCIS1K/6-311++G(3df,2p)//BHandHLYP/6-311+G(d,p) level of theory was selected after different combinations of functionals and basis sets were compared. The structures of Gly and Ala in the elementary reaction steps were compared to the conformers of the Gly, Gly(•), Ala, and Ala(•) structures in the absence of (•)OH/H(2)O, which were identified by optimizing the minima of the respective potential energy surfaces. A dramatic change in conformation is observed in the Gly and Ala conformers after conversion to Gly(•) and Ala(•), respectively, and this change can be monitored along the minimal energy pathway. The β(L) conformer of Gly (-0.3 kJ mol(-1)) and Ala (-1.6 kJ mol(-1)) form the lowest-lying transition states in the reaction with (•)OH, whereas the side chain of Ala strongly destabilizes the α conformers compared to the γ conformers, which could cause the lower reactivity shown in Ala. This effect shown in Ala could affect the abstraction of hydrogen from Ala and the other chiral amino acid residues in the helices. The energy of subsequent hydrogen abstraction reactions between Ala(•) and Gly(•) and H(2)O(2) remains approximately 90 kJ mol(-1) below the entrance level of the (•)OH reaction, indicating that the (•)OH radical can initiate an α to β transition in an amino acid residue if a molecule such as H(2)O(2) can provide the hydrogen atom necessary to re-form Gly and Ala. This work delineates the mechanism of the rapid (•)OH-initiated unfolding of peptides and proteins which has been proposed in Alzheimer's and other peptide misfolding diseases involving amyloidogenic peptides.
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http://dx.doi.org/10.1021/jp2089559DOI Listing
January 2012