Dusan Hesek - Academia.edu (original) (raw)
Papers by Dusan Hesek
ChemInform, Feb 21, 1989
www.cheminform.wiley-vch.de Quinoline derivatives R 0410 Convergent Synthesis of 1,1'-Biisoquinol... more www.cheminform.wiley-vch.de Quinoline derivatives R 0410 Convergent Synthesis of 1,1'-Biisoquinolines Tethered to Calamitic Subunits.-The synthesis of 1,1'-bisisoquinolines tethered with a variety of alkoxy substituents (calmitic units) is described. Key feature of the route is the final formation of the bisisoquinoline via a Gabriel-Colman reaction.-(KAPATSINA, E.; LORDON, M.;
한국미생물학회 학술대회논문집, May 1, 2012
ChemBioChem
Clostridioides difficile is a spore‐forming human pathogen responsible for significant morbidity ... more Clostridioides difficile is a spore‐forming human pathogen responsible for significant morbidity and mortality. Infections by this pathogen ensue dysbiosis of the intestinal tract, which leads to germination of the spores. The process of spore formation requires a transition for the cell‐wall peptidoglycan of the vegetative C. difficile to that of spores, which entails the formation of muramyl‐δ‐lactam. We describe a set of reactions for three recombinant C. difficile proteins, GerS, CwlD, and PdaA1, with the use of four synthetic peptidoglycan analogs. CwlD and PdaA1 excise the peptidoglycan stem peptide and the acetyl moiety of N‐acetyl muramate, respectively. The reaction of CwlD is accelerated in the presence of GerS. With the use of a suitable substrate, we document that PdaA1 catalyzes a novel zinc‐dependent transamidation/transpeptidation reaction, an unusual reaction that requires excision of the stem peptide as a pre‐requisite.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
The solvent extraction of uranium(VI) with a para-tertiary butyl 1,3-acid-diethyl amide substitut... more The solvent extraction of uranium(VI) with a para-tertiary butyl 1,3-acid-diethyl amide substituted calix[4]arene ligand in dichloromethane has been studied. UO 2 +2 was found to extract into the dichloromethane phase with a metal:ligand ratio of 1. X-ray crystallographic analysis of a single crystal indicated a dimeric species of 2 UO 2 +2 :2 ligands. The extraction mechanism is pH dependent due to the increased availability of deprotonated hydroxyl groups with increase in pH.
Computational and Structural Biotechnology Journal, 2021
Graphical abstract
Biochemistry, 2021
The soluble lytic transglycosylase Cj0843c from Campylobacter jejuni breaks down cell-wall peptid... more The soluble lytic transglycosylase Cj0843c from Campylobacter jejuni breaks down cell-wall peptidoglycan (PG). Its nonhydrolytic activity sustains cell-wall remodeling and repair. We report herein our structure-function studies probing the substrate preferences and recognition by this enzyme. Our studies show that Cj0843c exhibits both exolytic and endolytic activities and forms the N-acetyl-1,6-anhydromuramyl (anhMurNAc) peptidoglycan termini, the typical transformation catalyzed by lytic transglycosylase. Cj0843c shows a trend toward a preference for substrates with anhMurNAc ends and those with peptide stems. Mutagenesis revealed that the catalytic E390 is critical for activity. In addition, mutagenesis showed that R388 and K505, located in the positively charged pocket near E390, also serve important roles. Mutation of R326, on the opposite side of this positively charged pocket, enhanced activity. Our data point to different roles for positively charged residues in this pocket for productive binding of the predominantly negatively charged PG. We also show by X-ray crystallography and by molecular dynamics simulations that the active site of Cj0843c is still capable of binding GlcNAc containing di- and trisaccharides without MurNAc moieties, without peptide stems, and without the anhMurNAc ends.
ACS Pharmacology & Translational Science, 2020
Nature Communications, 2020
Assembly of the peptidoglycan is crucial in maintaining viability of bacteria and in defining bac... more Assembly of the peptidoglycan is crucial in maintaining viability of bacteria and in defining bacterial cell shapes, both of which are important for existence in the ecological niche that the organism occupies. Here, eight crystal structures for a member of the cell-shape-determining class of Campylobacter jejuni, the peptidoglycan peptidase 3 (Pgp3), are reported. Characterization of the turnover chemistry of Pgp3 reveals cell wall d,d-endopeptidase and d,d-carboxypeptidase activities. Catalysis is accompanied by large conformational changes upon peptidoglycan binding, whereby a loop regulates access to the active site. Furthermore, prior hydrolysis of the crosslinked peptide stem from the saccharide backbone of the peptidoglycan on one side is a pre-requisite for its recognition and turnover by Pgp3. These analyses reveal the noncanonical nature of the transformations at the core of the events that define the morphological shape for C. jejuni as an intestinal pathogen.
ACS Chemical Biology, 2019
Cloning of the bglX (PA1726) gene and purification of BglX wild-type and D286N variant S1 Generat... more Cloning of the bglX (PA1726) gene and purification of BglX wild-type and D286N variant S1 Generation of a bglX::Tn strain harboring a BglX-producing plasmid (bglX::Tn/pBglX) S1
Nature Communications, 2019
SPOR domains are widely present in bacterial proteins that recognize cell-wall peptidoglycan stra... more SPOR domains are widely present in bacterial proteins that recognize cell-wall peptidoglycan strands stripped of the peptide stems. This type of peptidoglycan is enriched in the septal ring as a product of catalysis by cell-wall amidases that participate in the separation of daughter cells during cell division. Here, we document binding of synthetic denuded glycan ligands to the SPOR domain of the lytic transglycosylase RlpA from Pseudomonas aeruginosa (SPOR-RlpA) by mass spectrometry and structural analyses, and demonstrate that indeed the presence of peptide stems in the peptidoglycan abrogates binding. The crystal structures of the SPOR domain, in the apo state and in complex with different synthetic glycan ligands, provide insights into the molecular basis for recognition and delineate a conserved pattern in other SPOR domains. The biological and structural observations presented here are followed up by molecular-dynamics simulations and by exploration of the effect on binding o...
Wound Repair and Regeneration, 2019
Diabetic foot ulcers are characterized by hypoxia. For many patients, hyperbaric oxygen (HBO) the... more Diabetic foot ulcers are characterized by hypoxia. For many patients, hyperbaric oxygen (HBO) therapy is the last recourse for saving the limb from amputation, for which the molecular basis is not understood. We previously identified the active form of matrix metalloproteinase‐9 (MMP‐9) as responsible for diabetic foot ulcer's recalcitrance to healing. Transcription of mmp‐9 to the inactive zymogen is upregulated during hypoxia. Activation of the zymogen is promoted by proteases and reactive oxygen species (ROS). We hypothesized that the dynamics of these two events might lead to a lowering of active MMP‐9 levels in the wounded tissue. We employed the full‐thickness excisional db/db mouse model to study wound healing, and treated the mice to 3.0 atm of molecular oxygen for 90 minutes, 5 days per week for 10 days in an HBO research chamber. Treatment with HBO accelerated diabetic wound healing compared to untreated mice, with more completed and extended reepithelialization. We im...
ChemInform, Feb 21, 1989
www.cheminform.wiley-vch.de Quinoline derivatives R 0410 Convergent Synthesis of 1,1'-Biisoquinol... more www.cheminform.wiley-vch.de Quinoline derivatives R 0410 Convergent Synthesis of 1,1'-Biisoquinolines Tethered to Calamitic Subunits.-The synthesis of 1,1'-bisisoquinolines tethered with a variety of alkoxy substituents (calmitic units) is described. Key feature of the route is the final formation of the bisisoquinoline via a Gabriel-Colman reaction.-(KAPATSINA, E.; LORDON, M.;
한국미생물학회 학술대회논문집, May 1, 2012
ChemBioChem
Clostridioides difficile is a spore‐forming human pathogen responsible for significant morbidity ... more Clostridioides difficile is a spore‐forming human pathogen responsible for significant morbidity and mortality. Infections by this pathogen ensue dysbiosis of the intestinal tract, which leads to germination of the spores. The process of spore formation requires a transition for the cell‐wall peptidoglycan of the vegetative C. difficile to that of spores, which entails the formation of muramyl‐δ‐lactam. We describe a set of reactions for three recombinant C. difficile proteins, GerS, CwlD, and PdaA1, with the use of four synthetic peptidoglycan analogs. CwlD and PdaA1 excise the peptidoglycan stem peptide and the acetyl moiety of N‐acetyl muramate, respectively. The reaction of CwlD is accelerated in the presence of GerS. With the use of a suitable substrate, we document that PdaA1 catalyzes a novel zinc‐dependent transamidation/transpeptidation reaction, an unusual reaction that requires excision of the stem peptide as a pre‐requisite.
An entry from the Cambridge Structural Database, the world's repository for small molecule cr... more An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
The solvent extraction of uranium(VI) with a para-tertiary butyl 1,3-acid-diethyl amide substitut... more The solvent extraction of uranium(VI) with a para-tertiary butyl 1,3-acid-diethyl amide substituted calix[4]arene ligand in dichloromethane has been studied. UO 2 +2 was found to extract into the dichloromethane phase with a metal:ligand ratio of 1. X-ray crystallographic analysis of a single crystal indicated a dimeric species of 2 UO 2 +2 :2 ligands. The extraction mechanism is pH dependent due to the increased availability of deprotonated hydroxyl groups with increase in pH.
Computational and Structural Biotechnology Journal, 2021
Graphical abstract
Biochemistry, 2021
The soluble lytic transglycosylase Cj0843c from Campylobacter jejuni breaks down cell-wall peptid... more The soluble lytic transglycosylase Cj0843c from Campylobacter jejuni breaks down cell-wall peptidoglycan (PG). Its nonhydrolytic activity sustains cell-wall remodeling and repair. We report herein our structure-function studies probing the substrate preferences and recognition by this enzyme. Our studies show that Cj0843c exhibits both exolytic and endolytic activities and forms the N-acetyl-1,6-anhydromuramyl (anhMurNAc) peptidoglycan termini, the typical transformation catalyzed by lytic transglycosylase. Cj0843c shows a trend toward a preference for substrates with anhMurNAc ends and those with peptide stems. Mutagenesis revealed that the catalytic E390 is critical for activity. In addition, mutagenesis showed that R388 and K505, located in the positively charged pocket near E390, also serve important roles. Mutation of R326, on the opposite side of this positively charged pocket, enhanced activity. Our data point to different roles for positively charged residues in this pocket for productive binding of the predominantly negatively charged PG. We also show by X-ray crystallography and by molecular dynamics simulations that the active site of Cj0843c is still capable of binding GlcNAc containing di- and trisaccharides without MurNAc moieties, without peptide stems, and without the anhMurNAc ends.
ACS Pharmacology & Translational Science, 2020
Nature Communications, 2020
Assembly of the peptidoglycan is crucial in maintaining viability of bacteria and in defining bac... more Assembly of the peptidoglycan is crucial in maintaining viability of bacteria and in defining bacterial cell shapes, both of which are important for existence in the ecological niche that the organism occupies. Here, eight crystal structures for a member of the cell-shape-determining class of Campylobacter jejuni, the peptidoglycan peptidase 3 (Pgp3), are reported. Characterization of the turnover chemistry of Pgp3 reveals cell wall d,d-endopeptidase and d,d-carboxypeptidase activities. Catalysis is accompanied by large conformational changes upon peptidoglycan binding, whereby a loop regulates access to the active site. Furthermore, prior hydrolysis of the crosslinked peptide stem from the saccharide backbone of the peptidoglycan on one side is a pre-requisite for its recognition and turnover by Pgp3. These analyses reveal the noncanonical nature of the transformations at the core of the events that define the morphological shape for C. jejuni as an intestinal pathogen.
ACS Chemical Biology, 2019
Cloning of the bglX (PA1726) gene and purification of BglX wild-type and D286N variant S1 Generat... more Cloning of the bglX (PA1726) gene and purification of BglX wild-type and D286N variant S1 Generation of a bglX::Tn strain harboring a BglX-producing plasmid (bglX::Tn/pBglX) S1
Nature Communications, 2019
SPOR domains are widely present in bacterial proteins that recognize cell-wall peptidoglycan stra... more SPOR domains are widely present in bacterial proteins that recognize cell-wall peptidoglycan strands stripped of the peptide stems. This type of peptidoglycan is enriched in the septal ring as a product of catalysis by cell-wall amidases that participate in the separation of daughter cells during cell division. Here, we document binding of synthetic denuded glycan ligands to the SPOR domain of the lytic transglycosylase RlpA from Pseudomonas aeruginosa (SPOR-RlpA) by mass spectrometry and structural analyses, and demonstrate that indeed the presence of peptide stems in the peptidoglycan abrogates binding. The crystal structures of the SPOR domain, in the apo state and in complex with different synthetic glycan ligands, provide insights into the molecular basis for recognition and delineate a conserved pattern in other SPOR domains. The biological and structural observations presented here are followed up by molecular-dynamics simulations and by exploration of the effect on binding o...
Wound Repair and Regeneration, 2019
Diabetic foot ulcers are characterized by hypoxia. For many patients, hyperbaric oxygen (HBO) the... more Diabetic foot ulcers are characterized by hypoxia. For many patients, hyperbaric oxygen (HBO) therapy is the last recourse for saving the limb from amputation, for which the molecular basis is not understood. We previously identified the active form of matrix metalloproteinase‐9 (MMP‐9) as responsible for diabetic foot ulcer's recalcitrance to healing. Transcription of mmp‐9 to the inactive zymogen is upregulated during hypoxia. Activation of the zymogen is promoted by proteases and reactive oxygen species (ROS). We hypothesized that the dynamics of these two events might lead to a lowering of active MMP‐9 levels in the wounded tissue. We employed the full‐thickness excisional db/db mouse model to study wound healing, and treated the mice to 3.0 atm of molecular oxygen for 90 minutes, 5 days per week for 10 days in an HBO research chamber. Treatment with HBO accelerated diabetic wound healing compared to untreated mice, with more completed and extended reepithelialization. We im...