1
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Adorinni S, Gentile S, Bellotto O, Kralj S, Parisi E, Cringoli MC, Deganutti C, Malloci G, Piccirilli F, Pengo P, Vaccari L, Geremia S, Vargiu AV, De Zorzi R, Marchesan S. Peptide Stereochemistry Effects from p Ka-Shift to Gold Nanoparticle Templating in a Supramolecular Hydrogel. ACS Nano 2024; 18:3011-3022. [PMID: 38235673 DOI: 10.1021/acsnano.3c08004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The divergent supramolecular behavior of a series of tripeptide stereoisomers was elucidated through spectroscopic, microscopic, crystallographic, and computational techniques. Only two epimers were able to effectively self-organize into amphipathic structures, leading to supramolecular hydrogels or crystals, respectively. Despite the similarity between the two peptides' turn conformations, stereoconfiguration led to different abilities to engage in intramolecular hydrogen bonding. Self-assembly further shifted the pKa value of the C-terminal side chain. As a result, across the pH range 4-6, only one epimer predominated sufficiently as a zwitterion to reach the critical molar fraction, allowing gelation. By contrast, the differing pKa values and higher dipole moment of the other epimer favored crystallization. The four stereoisomers were further tested for gold nanoparticle (AuNP) formation, with the supramolecular hydrogel being the key to control and stabilize AuNPs, yielding a nanocomposite that catalyzed the photodegradation of a dye. Importantly, the AuNP formation occurred without the use of reductants other than the peptide, and the redox chemistry was investigated by LC-MS, NMR, and infrared scattering-type near field optical microscopy (IR s-SNOM). This study provides important insights for the rational design of simple peptides as minimalistic and green building blocks for functional nanocomposites.
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Affiliation(s)
- Simone Adorinni
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Serena Gentile
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Ottavia Bellotto
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Slavko Kralj
- Materials Synthesis Department, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Evelina Parisi
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Maria C Cringoli
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Caterina Deganutti
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Giuliano Malloci
- Physics Department, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Federica Piccirilli
- Elettra Sincrotrone Trieste, 34149 Basovizza, Italy
- Area Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Paolo Pengo
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Lisa Vaccari
- Elettra Sincrotrone Trieste, 34149 Basovizza, Italy
| | - Silvano Geremia
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Attilio V Vargiu
- Physics Department, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Rita De Zorzi
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
| | - Silvia Marchesan
- Chemical Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy
- Unit of Trieste, INSTM, 34127 Trieste, Italy
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2
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Cacioppo M, De Zorzi R, Syrgiannis Z, Bellich B, Bertoncin P, Jou IA, Brady JW, Rizzo R, Cescutti P. Microscopy and modelling investigations on the morphology of the biofilm exopolysaccharide produced by Burkholderia multivorans strain C1576. Int J Biol Macromol 2023; 253:127294. [PMID: 37813217 PMCID: PMC10872726 DOI: 10.1016/j.ijbiomac.2023.127294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
Bacteria form very often biofilms where they embed in a self-synthesized matrix exhibiting a gel-like appearance. Matrices offer several advantages, including defence against external threats and the easiness of intercellular communication. In infections, biofilm formation enhances bacteria resistance against antimicrobials, causing serious clinical problems for patients' treatments. Biofilm matrices are composed of proteins, extracellular DNA, and polysaccharides, the latter being the major responsible for matrix architecture. The repeating unit of the biofilm polysaccharide synthesized by Burkholderia multivorans strain C1576 contains two mannoses and two sequentially linked rhamnoses, one of them 50 % methylated on C-3. Rhamnose, a 6-deoxysugar, has lower polarity than other common monosaccharides and its methylation further reduces polarity. This suggests a possible role of this polysaccharide in the biofilm matrix; in fact, computer modelling and atomic force microscopy studies evidenced intra- and inter-molecular non-polar interactions both within polysaccharides and with aliphatic molecules. In this paper, the polysaccharide three-dimensional morphology was investigated using atomic force microscopy in both solid and solution states. Independent evidence of the polymer conformation was obtained by transmission electron microscopy which confirmed the formation of globular compact structures. Finally, data from computer dynamic simulations were used to model the three-dimensional structure.
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Affiliation(s)
- Michele Cacioppo
- Department of Chemical and Pharmaceutical Sciences, INSTM UdR Trieste, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, INSTM UdR Trieste, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Zois Syrgiannis
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Barbara Bellich
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Paolo Bertoncin
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Ining A Jou
- Food Science Department, Cornell University, 101A Stocking Hall, Ithaca, NY 14853, USA
| | - John W Brady
- Food Science Department, Cornell University, 101A Stocking Hall, Ithaca, NY 14853, USA
| | - Roberto Rizzo
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Paola Cescutti
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy.
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3
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Parisi E, Adorinni S, Garcia AM, Kralj S, De Zorzi R, Marchesan S. Self-assembling tripeptide forming water-bound channels and hydrogels. J Pept Sci 2023; 29:e3524. [PMID: 37226306 DOI: 10.1002/psc.3524] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023]
Abstract
D-Ser(tBu)-L-Phe-L-Trp is described as a self-assembling tripeptide that yields nanofibrillar hydrogels at physiological conditions (phosphate buffer at pH 7.4). The peptide is characterized by several spectroscopic methods, such as circular dichroism and fluorescence, oscillatory rheometry, and transmission electron microscopy. Single-crystal X-ray diffraction reveals supramolecular packing into water-bound channels and allows the visualization of the intermolecular interactions holding together peptide stacks.
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Affiliation(s)
- Evelina Parisi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Simone Adorinni
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Ana M Garcia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Slavko Kralj
- Department for Materials Synthesis, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Silvia Marchesan
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
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4
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Shaheen A, Tariq A, Ismat F, Naveed H, De Zorzi R, Iqbal M, Storici P, Mirza O, Walz T, Rahman M. Identification of additional mechanistically important residues in the multidrug transporter styMdtM of Salmonella Typhi. J Biomol Struct Dyn 2023:1-10. [PMID: 37787617 DOI: 10.1080/07391102.2023.2263882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
Multidrug efflux is a well-established mechanism of drug resistance in bacterial pathogens like Salmonella Typhi. styMdtM (locus name; STY4874) is a multidrug efflux transporter of the major facilitator superfamily expressed in S. Typhi. Functional assays identified several residues important for its transport activity. Here, we used an AlphaFold model to identify additional residues for analysis by mutagenesis. Mutation of peripheral residue Cys185 had no effect on the structure or function of the transporter. However, substitution of channel-lining residues Tyr29 and Tyr231 completely abolished transport function. Finally, mutation of Gln294, which faces peripheral helices of the transporter, resulted in the loss of transport of some substrates. Crystallization studies yielded diffraction data for the wild-type protein at 4.5 Å resolution and allowed the unit cell parameters to be established as a = b = 64.3 Å, c = 245.4 Å, α = β = γ = 90°, in space group P4. Our studies represent a further stepping stone towards a mechanistic understanding of the clinically important multidrug transporter styMdtM.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aqsa Shaheen
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Pakistan
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Anam Tariq
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A, Trieste, Italy
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MA, USA
| | - Fouzia Ismat
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Hammad Naveed
- Department of Computer Science, National University of Computer & Emerging Sciences - FAST, Lahore, Pakistan
| | - Rita De Zorzi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Mazhar Iqbal
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Paola Storici
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A, Trieste, Italy
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, NY, USA
| | - Moazur Rahman
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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5
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Adorinni S, Goti G, Rizzo L, Grassi F, Kralj S, Matroodi F, Natali M, De Zorzi R, Marchesan S, Dell'Amico L. Self-assembly of benzophenone-diphenylalanine conjugate into a nanostructured photocatalyst. Chem Commun (Camb) 2023. [PMID: 37254947 DOI: 10.1039/d3cc01673k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The conjugation of photoactive benzophenone with diphenylalanine yielded a self-assembling photocatalyst that was probed in the E → Z photoisomerisation of stilbene derivatives.
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Affiliation(s)
- Simone Adorinni
- Chemical and Pharmaceutical Sciences Dept., University of Trieste, V. Giorgieri 1, Trieste 34127, Italy.
| | - Giulio Goti
- Chemical Sciences Dept., University of Padova, V. Marzolo 1, Padova 35131, Italy.
| | - Lorenzo Rizzo
- Chemical Sciences Dept., University of Padova, V. Marzolo 1, Padova 35131, Italy.
| | - Federica Grassi
- Chemical Sciences Dept., University of Padova, V. Marzolo 1, Padova 35131, Italy.
| | - Slavko Kralj
- Materials Synthesis Dept., Jožef Stefan Institute, Jamova 39, Ljubljana 1000, Slovenia
- Pharmaceutical Technology Dept., University of Ljubljana, Aškerčeva 7, Ljubljana 1000, Slovenia
| | - Fatima Matroodi
- Elettra Sincrotrone Trieste, Basovizza, Trieste 34149, Italy
| | - Mirco Natali
- Department of Chemical, Pharmaceutical, and Agricultural Sciences, University of Ferrara, V. Borsari 46, Ferrara 44121, Italy
| | - Rita De Zorzi
- Chemical and Pharmaceutical Sciences Dept., University of Trieste, V. Giorgieri 1, Trieste 34127, Italy.
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Dept., University of Trieste, V. Giorgieri 1, Trieste 34127, Italy.
| | - Luca Dell'Amico
- Chemical Sciences Dept., University of Padova, V. Marzolo 1, Padova 35131, Italy.
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6
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Paulikat M, Vitone D, Schackert FK, Schuth N, Barbanente A, Piccini G, Ippoliti E, Rossetti G, Clark AH, Nachtegaal M, Haumann M, Dau H, Carloni P, Geremia S, De Zorzi R, Quintanar L, Arnesano F. Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes. J Chem Inf Model 2023; 63:161-172. [PMID: 36468829 DOI: 10.1021/acs.jcim.2c01164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Chloroquine (CQ) is a first-choice drug against malaria and autoimmune diseases. It has been co-administered with zinc against SARS-CoV-2 and soon dismissed because of safety issues. The structural features of Zn-CQ complexes and the effect of CQ on zinc distribution in cells are poorly known. In this study, state-of-the-art computations combined with experiments were leveraged to solve the structural determinants of zinc-CQ interactions in solution and the solid state. NMR, ESI-MS, and X-ray absorption and diffraction methods were combined with ab initio molecular dynamics calculations to address the kinetic lability of this complex. Within the physiological pH range, CQ binds Zn2+ through the quinoline ring nitrogen, forming [Zn(CQH)Clx(H2O)3-x](3+)-x (x = 0, 1, 2, and 3) tetrahedral complexes. The Zn(CQH)Cl3 species is stable at neutral pH and at high chloride concentrations typical of the extracellular medium, but metal coordination is lost at a moderately low pH as in the lysosomal lumen. The pentacoordinate complex [Zn(CQH)(H2O)4]3+ may exist in the absence of chloride. This in vitro/in silico approach can be extended to other metal-targeting drugs and bioinorganic systems.
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Affiliation(s)
- Mirko Paulikat
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52428Jülich, Germany
| | - Daniele Vitone
- Department of Chemistry, University of Bari "Aldo Moro", 70125Bari, Italy
| | - Florian K Schackert
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52428Jülich, Germany.,Department of Physics, RWTH Aachen University, 52062Aachen, Germany
| | - Nils Schuth
- Department of Chemistry, Center for Research and Advanced Studies (Cinvestav), 07360Mexico City, Mexico
| | | | | | - Emiliano Ippoliti
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52428Jülich, Germany
| | - Giulia Rossetti
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52428Jülich, Germany.,Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52428Jülich, Germany.,Department of Neurology, RWTH Aachen University, 52062Aachen, Germany
| | - Adam H Clark
- Paul Scherrer Institute, 5232Villigen, Switzerland
| | | | - Michael Haumann
- Department of Physics, Freie Universität Berlin, 14195Berlin, Germany
| | - Holger Dau
- Department of Physics, Freie Universität Berlin, 14195Berlin, Germany
| | - Paolo Carloni
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52428Jülich, Germany.,Department of Physics, RWTH Aachen University, 52062Aachen, Germany
| | - Silvano Geremia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127Trieste, Italy
| | - Liliana Quintanar
- Department of Chemistry, Center for Research and Advanced Studies (Cinvestav), 07360Mexico City, Mexico
| | - Fabio Arnesano
- Department of Chemistry, University of Bari "Aldo Moro", 70125Bari, Italy
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7
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Medagli B, Soler MA, De Zorzi R, Fortuna S. Antibody Affinity Maturation Using Computational Methods: From an Initial Hit to Small-Scale Expression of Optimized Binders. Methods Mol Biol 2023; 2552:333-359. [PMID: 36346602 DOI: 10.1007/978-1-0716-2609-2_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nanobodies (VHHs) are engineered fragments of the camelid single-chain immunoglobulins. The VHH domain contains the highly variable segments responsible for antigen recognition. VHHs can be easily produced as recombinant proteins. Their small size is a good advantage for in silico approaches. Computer methods represent a valuable strategy for the optimization and improvement of their binding affinity. They also allow for epitope selection offering the possibility to design new VHHs for regions of a target protein that are not naturally immunogenic. Here we present an in silico mutagenic protocol developed to improve the binding affinity of nanobodies together with the first step of their in vitro production. The method, already proven successful in improving the low Kd of a nanobody hit obtained by panning, can be employed for the ex novo design of antibody fragments against selected protein target epitopes.
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Affiliation(s)
- Barbara Medagli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy.
| | - Miguel A Soler
- CONCEPT Lab, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Mathematics, Computer Science and Physics, University of Udine, Udine, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy.
- CONCEPT Lab, Istituto Italiano di Tecnologia, Genova, Italy.
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8
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Scarel E, Bellotto O, Rozhin P, Kralj S, Tortora M, Vargiu AV, De Zorzi R, Rossi B, Marchesan S. Single-atom substitution enables supramolecular diversity from dipeptide building blocks. Soft Matter 2022; 18:2129-2136. [PMID: 35179536 DOI: 10.1039/d1sm01824h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dipeptides are popular building blocks for supramolecular gels that do not persist in the environment and may find various applications. In this work, we show that a simple substitution on the aromatic side-chain of phenylalanine with either fluorine or iodine enables supramolecular diversity upon self-assembly at neutral pH, leading to hydrogels or crystals. Each building block is characterized by 1H- and 13C-NMR spectroscopy, LC-MS, circular dichroism, and molecular models. The supramolecular behaviour is monitored with a variety of techniques, including circular dichroism, oscillatory rheology, transmission electron microscopy, attenuated total reflectance Fourier-transformed infrared spectroscopy, visible Raman spectroscopy, synchrotron-radiation single-crystal X-ray diffraction and UV Resonance Raman spectroscopy, allowing key differences to be pinpointed amongst the halogenated analogues.
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Affiliation(s)
- Erica Scarel
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Ottavia Bellotto
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Petr Rozhin
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Slavko Kralj
- Jožef Stefan Institute, Materials Synthesis Dept., Jamova 39, 1000 Ljubljana, Slovenia
- University of Ljubljana, Pharmaceutical Technology Dept., Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Mariagrazia Tortora
- Area Science Park, Padriciano 99, 34149 Trieste, Italy
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy.
| | - Attilio V Vargiu
- University of Cagliari, Physics Dept., 09042 Monserrato, Cagliari, Italy
| | - Rita De Zorzi
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy.
| | - Silvia Marchesan
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
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9
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Fagnen C, Bannwarth L, Oubella I, Zuniga D, Haouz A, Forest E, Scala R, Bendahhou S, De Zorzi R, Perahia D, Vénien-Bryan C. Integrative Study of the Structural and Dynamical Properties of a KirBac3.1 Mutant: Functional Implication of a Highly Conserved Tryptophan in the Transmembrane Domain. Int J Mol Sci 2021; 23:335. [PMID: 35008764 PMCID: PMC8745282 DOI: 10.3390/ijms23010335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 12/02/2022] Open
Abstract
ATP-sensitive potassium (K-ATP) channels are ubiquitously expressed on the plasma membrane of cells in several organs, including the heart, pancreas, and brain, and they govern a wide range of physiological processes. In pancreatic β-cells, K-ATP channels composed of Kir6.2 and SUR1 play a key role in coupling blood glucose and insulin secretion. A tryptophan residue located at the cytosolic end of the transmembrane helix is highly conserved in eukaryote and prokaryote Kir channels. Any mutation on this amino acid causes a gain of function and neonatal diabetes mellitus. In this study, we have investigated the effect of mutation on this highly conserved residue on a KirBac channel (prokaryotic homolog of mammalian Kir6.2). We provide the crystal structure of the mutant KirBac3.1 W46R (equivalent to W68R in Kir6.2) and its conformational flexibility properties using HDX-MS. In addition, the detailed dynamical view of the mutant during the gating was investigated using the in silico method. Finally, functional assays have been performed. A comparison of important structural determinants for the gating mechanism between the wild type KirBac and the mutant W46R suggests interesting structural and dynamical clues and a mechanism of action of the mutation that leads to the gain of function.
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Affiliation(s)
- Charline Fagnen
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, 4 Ave. des Sciences, 91190 Gif-sur-Yvette, France;
| | - Ludovic Bannwarth
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Iman Oubella
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Dania Zuniga
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Ahmed Haouz
- Institut Pasteur, C2RT-Plate-Forme de Cristallographie CNRS-UMR3528, 75724 Paris, France;
| | - Eric Forest
- CNRS, IBS, CEA, University Grenoble Alpes, 38044 Grenoble, France;
| | - Rosa Scala
- CNRS UMR7370, LP2M, Labex ICST, Faculté de Médecine, University Côte d’Azur, 06560 Nice, France; (R.S.); (S.B.)
| | - Saïd Bendahhou
- CNRS UMR7370, LP2M, Labex ICST, Faculté de Médecine, University Côte d’Azur, 06560 Nice, France; (R.S.); (S.B.)
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgeri 1, 34127 Trieste, Italy;
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, 4 Ave. des Sciences, 91190 Gif-sur-Yvette, France;
| | - Catherine Vénien-Bryan
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
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10
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Bellotto O, Kralj S, Melchionna M, Pengo P, Kisovec M, Podobnik M, De Zorzi R, Marchesan S. Self-Assembly of Unprotected Dipeptides into Hydrogels: Water-Channels Make the Difference. Chembiochem 2021; 23:e202100518. [PMID: 34784433 PMCID: PMC9299199 DOI: 10.1002/cbic.202100518] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/15/2021] [Indexed: 12/24/2022]
Abstract
Unprotected dipeptides are attractive building blocks for environmentally friendly hydrogel biomaterials by virtue of their low‐cost and ease of preparation. This work investigates the self‐assembling behaviour of the distinct stereoisomers of Ile‐Phe and Phe‐Ile in phosphate buffered saline (PBS) to form hydrogels, using transmission electron microscopy (TEM), attenuated total reflectance infrared spectroscopy (ATR‐IR), circular dichroism (CD), and oscillatory rheometry. Each peptide purity and identity was also confirmed by 1H‐ and 13C‐NMR spectroscopy and HPLC‐MS. Finally, single‐crystal XRD data allowed the key interactions responsible for the supramolecular packing into amphipathic layers or water‐channels to be revealed. The presence of the latter in the crystal structure is a distinctive feature of the only gelator of this work that self‐organizes into stable hydrogels, with fast kinetics and the highest elastic modulus amongst its structural isomers and stereoisomers.
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Affiliation(s)
- Ottavia Bellotto
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Slavko Kralj
- Materials Synthesis Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.,Department of Pharmaceutical Technology, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Michele Melchionna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy.,Unit of Trieste, INSTM, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Paolo Pengo
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Matic Kisovec
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Silvia Marchesan
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy.,Unit of Trieste, INSTM, Via L. Giorgieri 1, 34127, Trieste, Italy
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11
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Fagnen C, Bannwarth L, Zuniga D, Oubella I, De Zorzi R, Forest E, Scala R, Guilbault S, Bendahhou S, Perahia D, Vénien-Bryan C. Unexpected Gating Behaviour of an Engineered Potassium Channel Kir. Front Mol Biosci 2021; 8:691901. [PMID: 34179097 PMCID: PMC8222812 DOI: 10.3389/fmolb.2021.691901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/26/2021] [Indexed: 11/24/2022] Open
Abstract
In this study, we investigated the dynamics and functional characteristics of the KirBac3.1 S129R, a mutated bacterial potassium channel for which the inner pore-lining helix (TM2) was engineered so that the bundle crossing is trapped in an open conformation. The structure of this channel has been previously determined at high atomic resolution. We explored the dynamical characteristics of this open state channel using an in silico method MDeNM that combines molecular dynamics simulations and normal modes. We captured the global and local motions at the mutation level and compared these data with HDX-MS experiments. MDeNM provided also an estimation of the probability of the different opening states that are in agreement with our electrophysiological experiments. In the S129R mutant, the Arg129 mutation releases the two constriction points in the channel that existed in the wild type but interestingly creates another restriction point.
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Affiliation(s)
- Charline Fagnen
- UMR 7590, CNRS, Muséum National d'Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, Sorbonne Université, Paris, France.,Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
| | - Ludovic Bannwarth
- UMR 7590, CNRS, Muséum National d'Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, Sorbonne Université, Paris, France
| | - Dania Zuniga
- UMR 7590, CNRS, Muséum National d'Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, Sorbonne Université, Paris, France
| | - Iman Oubella
- UMR 7590, CNRS, Muséum National d'Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, Sorbonne Université, Paris, France
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Eric Forest
- IBS University Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Rosa Scala
- Faculté de Médecine, CNRS UMR7370, LP2M, Labex ICST, University Côte d'Azur, Nice, France
| | - Samuel Guilbault
- Faculté de Médecine, CNRS UMR7370, LP2M, Labex ICST, University Côte d'Azur, Nice, France
| | - Saïd Bendahhou
- Faculté de Médecine, CNRS UMR7370, LP2M, Labex ICST, University Côte d'Azur, Nice, France
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
| | - Catherine Vénien-Bryan
- UMR 7590, CNRS, Muséum National d'Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, Sorbonne Université, Paris, France
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12
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Shaheen A, Ismat F, Iqbal M, Haque A, Ul-Haq Z, Mirza O, De Zorzi R, Walz T, Rahman M. Characterization of the multidrug efflux transporter styMdtM from Salmonella enterica serovar Typhi. Proteins 2021; 89:1193-1204. [PMID: 33983672 DOI: 10.1002/prot.26141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/14/2021] [Accepted: 05/07/2021] [Indexed: 11/09/2022]
Abstract
Salmonellae are foodborne pathogens and the major cause of gastroenteritis in humans. Salmonellae express multidrug efflux transporters that play a key role in their drug resistance, which is becoming an increasing problem for therapeutic intervention. Despite their biomedical importance, the mechanisms underlying substrate transport by multidrug efflux transporters remain poorly understood. Here, we describe the first characterization of a multidrug transporter belonging to the major facilitator superfamily from the genus Salmonella. We show that several clinical Salmonella Typhi (S. Typhi) isolates constitutively express the styMdtM (STY4874) gene, which encodes a known multidrug-resistance (MDR) transporter. Guided by the structure of the Escherichia coli (E. coli) homolog, we studied two residues critical for substrate transport, Asp25 and Arg111. Mutation of Asp25 to glutamate did not affect the transport function of styMdtM, whereas mutation to alanine reduced its transport activity, suggesting that a negative charge at this position is critical for substrate translocation across the membrane. Substrate-affinity measurements by intrinsic fluorescence spectroscopy showed that the Asp25Ala mutant retained its capacity to bind substrate, albeit at a lower level. Mutation of Arg111 to alanine resulted in a decrease in secondary structure content of the transporter, and mutation to lysine completely destabilized the structure of the transporter. A homology model of styMdtM suggests that Arg111 is important for stabilizing the transmembrane domain by mediating necessary interactions between neighboring helices. Together, our studies provide new structural and mechanistic insights into the Salmonella MDR transporter styMdtM.
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Affiliation(s)
- Aqsa Shaheen
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan.,Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Fouzia Ismat
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
| | - Mazhar Iqbal
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
| | - Abdul Haque
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan.,Akhuwat First University, Faisalabad, Punjab, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Sindh, Pakistan
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rita De Zorzi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.,Laboratory of Molecular Electron Microscopy, Rockefeller University, New York, New York, USA
| | - Moazur Rahman
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.,School of Biological Sciences, University of the Punjab, Lahore, Punjab, Pakistan
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13
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Garcia AM, Melchionna M, Bellotto O, Kralj S, Semeraro S, Parisi E, Iglesias D, D’Andrea P, De Zorzi R, Vargiu AV, Marchesan S. Nanoscale Assembly of Functional Peptides with Divergent Programming Elements. ACS Nano 2021; 15:3015-3025. [PMID: 33576622 PMCID: PMC8023796 DOI: 10.1021/acsnano.0c09386] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Self-assembling peptides are being applied both in the biomedical area and as building blocks in nanotechnology. Their applications are closely linked to their modes of self-assembly, which determine the functional nanostructures that they form. This work brings together two structural elements that direct nanoscale self-association in divergent directions: proline as a β-breaker and the β-structure-associated diphenylalanine motif, into a single tripeptide sequence. Amino acid chirality was found to resolve the tension inherent to these conflicting self-assembly instructions. Stereoconfiguration determined the ability of each of the eight possible Pro-Phe-Phe stereoisomers to self-associate into diverse nanostructures, including nanoparticles, nanotapes, or fibrils, which yielded hydrogels with gel-to-sol transition at a physiologically relevant temperature. Three single-crystal structures and all-atom molecular dynamics simulations elucidated the ability of each peptide to establish key interactions to form long-range assemblies (i,e., stacks leading to gelling fibrils), medium-range assemblies (i.e., stacks yielding nanotapes), or short-range assemblies (i.e., dimers or trimers that further associated into nanoparticles). Importantly, diphenylalanine is known to serve as a binding site for pathological amyloids, potentially allowing these heterochiral systems to influence the fibrillization of other biologically relevant peptides. To probe this hypothesis, all eight Pro-Phe-Phe stereoisomers were tested in vitro on the Alzheimer's disease-associated Aβ(1-42) peptide. Indeed, one nonfibril-forming stereoisomer effectively inhibited Aβ fibrillization through multivalent binding between diphenylalanine motifs. This work thus defined heterochirality as a useful feature to strategically develop future therapeutics to interfere with pathological processes, with the additional value of resistance to protease-mediated degradation and biocompatibility.
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Affiliation(s)
- Ana M. Garcia
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Michele Melchionna
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
- INSTM, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Ottavia Bellotto
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Slavko Kralj
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
- Materials
Synthesis Department, Jožef Stefan
Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Sabrina Semeraro
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Evelina Parisi
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Daniel Iglesias
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Paola D’Andrea
- Life
Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Rita De Zorzi
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Attilio V. Vargiu
- Physics
Department, University of Cagliari, S.P. 8, km. 0.700, 09042 Monserrato, Italy
| | - Silvia Marchesan
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
- INSTM, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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14
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Zuccaccia D, Pinalli R, De Zorzi R, Semeraro M, Credi A, Zuccaccia C, Macchioni A, Geremia S, Dalcanale E. Hierarchical self-assembly and controlled disassembly of a cavitand-based host–guest supramolecular polymer. Polym Chem 2021. [DOI: 10.1039/d0py01483d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two hierarchical aggregation modes of cavitand-based supramolecular polymers allow implementing orthogonal disassembly procedures: electrochemical reduction for linear chains and solvent-driven dissolution for bundles.
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Affiliation(s)
- Daniele Zuccaccia
- Dipartimento di Scienze Agroalimentari Ambientali e Animali
- Università di Udine
- 33100 Udine
- Italy
| | - Roberta Pinalli
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale and Unità INSTM
- UdR Parma
- Università di Parma
- 43124 Parma
| | - Rita De Zorzi
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università di Trieste
- 34127 Trieste
- Italy
| | - Monica Semeraro
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- 40136 Bologna
- Italy
| | - Alberto Credi
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- 40136 Bologna
- Italy
| | - Cristiano Zuccaccia
- Dipartimento Chimica
- Biologia e Biotecnologia and CIRCC
- Università di Perugia
- 06123 Perugia
- Italy
| | - Alceo Macchioni
- Dipartimento Chimica
- Biologia e Biotecnologia and CIRCC
- Università di Perugia
- 06123 Perugia
- Italy
| | - Silvano Geremia
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università di Trieste
- 34127 Trieste
- Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale and Unità INSTM
- UdR Parma
- Università di Parma
- 43124 Parma
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15
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Kralj S, Bellotto O, Parisi E, Garcia AM, Iglesias D, Semeraro S, Deganutti C, D’Andrea P, Vargiu AV, Geremia S, De Zorzi R, Marchesan S. Heterochirality and Halogenation Control Phe-Phe Hierarchical Assembly. ACS Nano 2020; 14:16951-16961. [PMID: 33175503 PMCID: PMC7872421 DOI: 10.1021/acsnano.0c06041] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/30/2020] [Indexed: 05/05/2023]
Abstract
Diphenylalanine is an amyloidogenic building block that can form a versatile array of supramolecular materials. Its shortcomings, however, include the uncontrolled hierarchical assembly into microtubes of heterogeneous size distribution and well-known cytotoxicity. This study rationalized heterochirality as a successful strategy to address both of these pitfalls and it provided an unprotected heterochiral dipeptide that self-organized into a homogeneous and optically clear hydrogel with excellent ability to sustain fibroblast cell proliferation and viability. Substitution of one l-amino acid with its d-enantiomer preserved the ability of the dipeptide to self-organize into nanotubes, as shown by single-crystal XRD analysis, whereby the pattern of electrostatic and hydrogen bonding interactions of the backbone was unaltered. The effect of heterochirality was manifested in subtle changes in the positioning of the aromatic side chains, which resulted in weaker intermolecular interactions between nanotubes. As a result, d-Phe-l-Phe self-organized into homogeneous nanofibrils with a diameter of 4 nm, corresponding to two layers of peptides around a water channel, and yielded a transparent hydrogel. In contrast with homochiral Phe-Phe stereoisomer, it formed stable hydrogels thermoreversibly. d-Phe-l-Phe displayed no amyloid toxicity in cell cultures with fibroblast cells proliferating in high numbers and viability on this biomaterial, marking it as a preferred substrate over tissue-culture plastic. Halogenation also enabled the tailoring of d-Phe-l-Phe self-organization. Fluorination allowed analogous supramolecular packing as confirmed by XRD, thus nanotube formation, and gave intermediate levels of bundling. In contrast, iodination was the most effective strategy to augment the stability of the resulting hydrogel, although at the expense of optical transparency and biocompatibility. Interestingly, iodine presence hindered the supramolecular packing into nanotubes, resulting instead into amphipathic layers of stacked peptides without the occurrence of halogen bonding. By unravelling fine details to control these materials at the meso- and macro-scale, this study significantly advanced our understanding of these systems.
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Affiliation(s)
- Slavko Kralj
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
- Materials
Synthesis Department, Jožef Stefan
Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Ottavia Bellotto
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Evelina Parisi
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Ana M. Garcia
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Daniel Iglesias
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Sabrina Semeraro
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Caterina Deganutti
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Paola D’Andrea
- Life
Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Attilio V. Vargiu
- Physics
Department, University of Cagliari, s.p. 8, km. 0.700, 09042 Monserrato, Italy
| | - Silvano Geremia
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Rita De Zorzi
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Silvia Marchesan
- Chemical
and Pharmaceutical Sciences Department, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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16
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Bellotto O, Kralj S, De Zorzi R, Geremia S, Marchesan S. Supramolecular hydrogels from unprotected dipeptides: a comparative study on stereoisomers and structural isomers. Soft Matter 2020; 16:10151-10157. [PMID: 32935720 DOI: 10.1039/d0sm01191f] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Amino acid stereoconfiguration has been shown to play a key role in the self-assembly of unprotected tripeptides into hydrogels under physiological conditions. Dramatic changes were noted for hydrophobic sequences based on the diphenylalanine motif from the formation of amorphous aggregates in the case of homochiral peptides to nanostructured and stable hydrogels in the case of heterochiral stereoisomers. Herein, we report that by further shortening the sequence to a dipeptide, the overall differences between isomers are less marked, with both homo- and hetero-chiral dipeptides forming gels, although with different stability over time. The soft materials are studied by a number of spectroscopic and microcopic techniques, and single-crystal X-ray diffraction to unveil the supramolecular interactions of these hydrogel building blocks.
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Affiliation(s)
- Ottavia Bellotto
- University of Trieste, Chem. Pharm. Sc. Dept., Via Giorgieri 1, 34127 Trieste, Italy.
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17
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Asaro F, Boga C, Zorzi RD, Geremia S, Gigli L, Nitti P, Semeraro S. ( R)-10-Hydroxystearic Acid: Crystals vs. Organogel. Int J Mol Sci 2020; 21:ijms21218124. [PMID: 33143206 PMCID: PMC7662707 DOI: 10.3390/ijms21218124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/03/2022] Open
Abstract
The chiral (R)-10-hydroxystearic acid ((R)-10-HSA) is a positional homologue of both (R)-12-HSA and (R)-9-HSA with the OH group in an intermediate position. While (R)-12-HSA is one of the best-known low-molecular-weight organogelators, (R)-9-HSA is not, but it forms crystals in several solvents. With the aim to gain information on the structural role of hydrogen-bonding interactions of the carbinol OH groups, we investigated the behavior of (R)-10-HSA in various solvents. This isomer displays an intermediate behavior between (R)-9 and (R)-12-HSA, producing a stable gel exclusively in paraffin oil, while it crystallizes in other organic solvents. Here, we report the X-ray structure of a single crystal of (R)-10-HSA as well as some structural information on its polymorphism, obtained through X-ray Powder Diffraction (XRPD) and Infrared Spectroscopy (IR). This case study provides new elements to elucidate the structural determinants of the microscopic architectures that lead to the formation of organogels of stearic acid derivatives.
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Affiliation(s)
- Fioretta Asaro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy; (S.G.); (P.N.); (S.S.)
- Correspondence: (F.A.); (R.D.Z.); Tel.: +39-040-5583951 (F.A.)
| | - Carla Boga
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy;
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy; (S.G.); (P.N.); (S.S.)
- Correspondence: (F.A.); (R.D.Z.); Tel.: +39-040-5583951 (F.A.)
| | - Silvano Geremia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy; (S.G.); (P.N.); (S.S.)
| | - Lara Gigli
- Elettra–Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, Basovizza, 34149 Trieste, Italy;
| | - Patrizia Nitti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy; (S.G.); (P.N.); (S.S.)
| | - Sabrina Semeraro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy; (S.G.); (P.N.); (S.S.)
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18
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Squarcina A, Santoro A, Hickey N, De Zorzi R, Carraro M, Geremia S, Bortolus M, Di Valentin M, Bonchio M. Neutralization of Reactive Oxygen Species at Dinuclear Cu(II)-Cores: Tuning the Antioxidant Manifold in Water by Ligand Design. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | | | - Neal Hickey
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | | | - Silvano Geremia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
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19
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Cringoli MC, Romano C, Parisi E, Waddington LJ, Melchionna M, Semeraro S, De Zorzi R, Grönholm M, Marchesan S. Bioadhesive supramolecular hydrogel from unprotected, short d,l-peptides with Phe-Phe and Leu-Asp-Val motifs. Chem Commun (Camb) 2020; 56:3015-3018. [PMID: 32048648 DOI: 10.1039/c9cc09947f] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The uncapped tripeptide DPhe-Phe-Leu acts as self-assembly template to yield supramolecular hydrogel biomaterials. As an example, self-assembling DPhe-Phe-Leu-Asp-Val contains the LDV bioadhesive motif for β1 integrin activation. Hydrogels made of the two peptides successfully mimic fibronectin of the extracellular matrix and lead to high cell viability, adhesion, and spreading.
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Affiliation(s)
- Maria Cristina Cringoli
- University of Trieste, Chemical and Pharmaceutical Sc. Dept., Via L. Giorgieri 1, 34127 Trieste, Italy.
| | - Chiara Romano
- University of Trieste, Chemical and Pharmaceutical Sc. Dept., Via L. Giorgieri 1, 34127 Trieste, Italy.
| | - Evelina Parisi
- University of Trieste, Chemical and Pharmaceutical Sc. Dept., Via L. Giorgieri 1, 34127 Trieste, Italy.
| | | | - Michele Melchionna
- University of Trieste, Chemical and Pharmaceutical Sc. Dept., Via L. Giorgieri 1, 34127 Trieste, Italy.
| | - Sabrina Semeraro
- University of Trieste, Chemical and Pharmaceutical Sc. Dept., Via L. Giorgieri 1, 34127 Trieste, Italy.
| | - Rita De Zorzi
- University of Trieste, Chemical and Pharmaceutical Sc. Dept., Via L. Giorgieri 1, 34127 Trieste, Italy.
| | - Mikaela Grönholm
- Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences and Drug Research Program, Faculty of Pharmacy, University of Helsinki, PB 56, 00014, Finland.
| | - Silvia Marchesan
- University of Trieste, Chemical and Pharmaceutical Sc. Dept., Via L. Giorgieri 1, 34127 Trieste, Italy.
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20
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Garcia AM, Lavendomme R, Kralj S, Kurbasic M, Bellotto O, Cringoli MC, Semeraro S, Bandiera A, De Zorzi R, Marchesan S. Self-Assembly of an Amino Acid Derivative into an Antimicrobial Hydrogel Biomaterial. Chemistry 2020; 26:1880-1886. [PMID: 31868256 DOI: 10.1002/chem.201905681] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Indexed: 02/06/2023]
Abstract
N-(4-Nitrobenzoyl)-Phe self-assembled into a transparent supramolecular hydrogel, which displayed high fibroblast and keratinocyte cell viability. The compound showed a mild antimicrobial activity against E. coli both as a hydrogel and in solution. Single-crystal XRD data revealed packing details, including protonation of the C-terminus due to an apparent pKa shift, as confirmed by pH titrations. MicroRaman analysis revealed almost identical features between the gel and crystal states, although more disorder in the former. The hydrogel is thermoreversible and disassembles within a range of temperatures that can be fine-tuned by experimental conditions, such as gelator concentration. At the minimum gelling concentration of 0.63 wt %, the hydrogel disassembles in a physiological temperature range of 39-42 °C, thus opening the way to its potential use as a biomaterial.
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Affiliation(s)
- Ana M Garcia
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Roy Lavendomme
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Slavko Kralj
- Materials Synthesis Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Marina Kurbasic
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Ottavia Bellotto
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Maria C Cringoli
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Sabrina Semeraro
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Antonella Bandiera
- Dipartimento di Scienze della Vita, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Rita De Zorzi
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Silvia Marchesan
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
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21
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Abstract
Minimalistic peptides composed of d- and l-amino acids are attractive building blocks for functional supramolecular materials, including catalysts. d-Amino acids have long been known to promote turn conformations in peptides, yet unexpected twists continue to emerge on their effects on self-assembly. The combination of single-crystal X-ray diffraction and full-atom molecular dynamics have finally unraveled fine details of how l-d-l-tripeptides visit different conformations in solution and establish key interactions in supramolecular structures.
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22
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Efthymiou S, Salpietro V, Malintan N, Poncelet M, Kriouile Y, Fortuna S, De Zorzi R, Payne K, Henderson LB, Cortese A, Maddirevula S, Alhashmi N, Wiethoff S, Ryten M, Botia JA, Provitera V, Schuelke M, Vandrovcova J, Walsh L, Torti E, Iodice V, Najafi M, Karimiani EG, Maroofian R, Siquier-Pernet K, Boddaert N, De Lonlay P, Cantagrel V, Aguennouz M, El Khorassani M, Schmidts M, Alkuraya FS, Edvardson S, Nolano M, Devaux J, Houlden H. Biallelic mutations in neurofascin cause neurodevelopmental impairment and peripheral demyelination. Brain 2019; 142:2948-2964. [PMID: 31501903 PMCID: PMC6763744 DOI: 10.1093/brain/awz248] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/19/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022] Open
Abstract
Axon pathfinding and synapse formation are essential processes for nervous system development and function. The assembly of myelinated fibres and nodes of Ranvier is mediated by a number of cell adhesion molecules of the immunoglobulin superfamily including neurofascin, encoded by the NFASC gene, and its alternative isoforms Nfasc186 and Nfasc140 (located in the axonal membrane at the node of Ranvier) and Nfasc155 (a glial component of the paranodal axoglial junction). We identified 10 individuals from six unrelated families, exhibiting a neurodevelopmental disorder characterized with a spectrum of central (intellectual disability, developmental delay, motor impairment, speech difficulties) and peripheral (early onset demyelinating neuropathy) neurological involvement, who were found by exome or genome sequencing to carry one frameshift and four different homozygous non-synonymous variants in NFASC. Expression studies using immunostaining-based techniques identified absent expression of the Nfasc155 isoform as a consequence of the frameshift variant and a significant reduction of expression was also observed in association with two non-synonymous variants affecting the fibronectin type III domain. Cell aggregation studies revealed a severely impaired Nfasc155-CNTN1/CASPR1 complex interaction as a result of the identified variants. Immunofluorescence staining of myelinated fibres from two affected individuals showed a severe loss of myelinated fibres and abnormalities in the paranodal junction morphology. Our results establish that recessive variants affecting the Nfasc155 isoform can affect the formation of paranodal axoglial junctions at the nodes of Ranvier. The genetic disease caused by biallelic NFASC variants includes neurodevelopmental impairment and a spectrum of central and peripheral demyelination as part of its core clinical phenotype. Our findings support possible overlapping molecular mechanisms of paranodal damage at peripheral nerves in both the immune-mediated and the genetic disease, but the observation of prominent central neurological involvement in NFASC biallelic variant carriers highlights the importance of this gene in human brain development and function.
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Affiliation(s)
- Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, UK
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, Queen Square, London, UK
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, UK
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, Queen Square, London, UK
| | - Nancy Malintan
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, Queen Square, London, UK
| | - Mallory Poncelet
- INSERM U1051, Institut de Neurosciences de Montpellier (INM), Université de Montpellier, Montpellier, France
| | - Yamna Kriouile
- Unit of Neuropediatrics and Neurometabolism, Pediatric Department 2, Rabat Children's Hospital, and Faculty of Medicine and Pharmacy of Rabat, University Mohammed V of Rabat, Morocco
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Katelyn Payne
- Riley Hospital for Children, Indianapolis, Indiana, IN, USA
| | | | - Andrea Cortese
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, UK
| | - Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Nadia Alhashmi
- Department of Genetics, College of Medicine, Sultan Qaboos University, Sultanate of Oman
| | - Sarah Wiethoff
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, UK
- Center for Neurology and Hertie Institute for Clinical Brain Research, Eberhard Karls-University, Tübingen, Germany
| | - Mina Ryten
- Department of Neurodegenerative Diseases, UCL Institute of Neurology, Queen Square, London, UK
| | - Juan A Botia
- Department of Neurodegenerative Diseases, UCL Institute of Neurology, Queen Square, London, UK
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, E, Spain
| | - Vincenzo Provitera
- Department of Neurology, Istituti Clinici Scientifici Maugeri IRCCS, Italy
| | - Markus Schuelke
- Department of Neuropediatrics, Charité Universitätsmedizin Berlin, Germany
| | - Jana Vandrovcova
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, UK
| | - Laurence Walsh
- Riley Hospital for Children, Indianapolis, Indiana, IN, USA
| | | | - Valeria Iodice
- Department of Brain Repair and Rehabilitation, Institute of Neurology, University College London, UK
- Autonomic Unit, National Hospital Neurology and Neurosurgery, UCL NHS Trust, London, UK
| | - Maryam Najafi
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands
| | - Ehsan Ghayoor Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, Cranmer Terrace, London, UK
| | - Reza Maroofian
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, Cranmer Terrace, London, UK
| | - Karine Siquier-Pernet
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Nathalie Boddaert
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatric Radiology, Necker Enfants Malades University Hospital, APHP, Paris, France
| | - Pascale De Lonlay
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
- Inserm, U1151, Institut Necker-Enfants Malades, Paris, France
| | - Vincent Cantagrel
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Mhammed Aguennouz
- Department of Clinical and Experimental Medicine, University of Messina, Sicily
| | - Mohamed El Khorassani
- Unit of Neuropediatrics and Neurometabolism, Pediatric Department 2, Rabat Children's Hospital, and Faculty of Medicine and Pharmacy of Rabat, University Mohammed V of Rabat, Morocco
| | - Miriam Schmidts
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands
- Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University, Faculty of Medicine, Mathildenstrasse 1, Freiburg, Germany
| | - Fowzan S Alkuraya
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Simon Edvardson
- Paediatric Neurology Unit, Hadassah Medical Center, Jerusalem, Israel
| | - Maria Nolano
- Department of Neurology, Istituti Clinici Scientifici Maugeri IRCCS, Italy
- Department of Neurosciences, Reproductive and Odontostomatological Sciences, University "Federico II" of Naples, Italy
| | - Jérôme Devaux
- INSERM U1051, Institut de Neurosciences de Montpellier (INM), Université de Montpellier, Montpellier, France
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, UK
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23
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Asaro F, Boga C, Demitri N, De Zorzi R, Drioli S, Gigli L, Micheletti G, Nitti P, Zangrando E. X-Ray Crystal Structures and Organogelator Properties of (R)-9-Hydroxystearic Acid. Molecules 2019; 24:molecules24152854. [PMID: 31390777 PMCID: PMC6695734 DOI: 10.3390/molecules24152854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/02/2019] [Accepted: 08/03/2019] [Indexed: 11/22/2022]
Abstract
(R)-9-hydroxystearic acid, (R)-9-HSA, is a chiral nonracemic hydroxyacid of natural origin possessing interesting properties as an antiproliferative agent against different cancer types. Considering its potential application for medical and pharmaceutical purposes, the structures and rheological properties of (R)-9-HSA were investigated. Oscillatory rheology measurements reveal that (R)-9-HSA gels only paraffin oil, with less efficiency and thermal stability than its positional isomer (R)-12-HSA. Conversely, (R)-9-HSA affords crystals from methanol, acetonitrile, and carbon tetrachloride. The single crystal structures obtained both at 293 K and 100 K show non-centrosymmetric twisted carboxylic acid dimers linked at the midchain OHs into long, unidirectional chains of hydrogen bonds, owing to head-tail ordering of the molecules. Synchrotron X-ray powder diffraction experiments, performed on the solids obtained from different solvents, show the occurrence of polymorphism in paraffin oil and through thermal treatment of the solid from methanol.
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Affiliation(s)
- Fioretta Asaro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy.
| | - Carla Boga
- Department of Industrial Chemistry "Toso Montanari", University of Bologna, viale del Risorgimento 4, 40136 Bologna, Italy
| | - Nicola Demitri
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, Basovizza, 34149 Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
| | - Sara Drioli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
| | - Lara Gigli
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, Basovizza, 34149 Trieste, Italy
| | - Gabriele Micheletti
- Department of Industrial Chemistry "Toso Montanari", University of Bologna, viale del Risorgimento 4, 40136 Bologna, Italy
| | - Patrizia Nitti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy.
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
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24
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Salpietro V, Dixon CL, Guo H, Bello OD, Vandrovcova J, Efthymiou S, Maroofian R, Heimer G, Burglen L, Valence S, Torti E, Hacke M, Rankin J, Tariq H, Colin E, Procaccio V, Striano P, Mankad K, Lieb A, Chen S, Pisani L, Bettencourt C, Männikkö R, Manole A, Brusco A, Grosso E, Ferrero GB, Armstrong-Moron J, Gueden S, Bar-Yosef O, Tzadok M, Monaghan KG, Santiago-Sim T, Person RE, Cho MT, Willaert R, Yoo Y, Chae JH, Quan Y, Wu H, Wang T, Bernier RA, Xia K, Blesson A, Jain M, Motazacker MM, Jaeger B, Schneider AL, Boysen K, Muir AM, Myers CT, Gavrilova RH, Gunderson L, Schultz-Rogers L, Klee EW, Dyment D, Osmond M, Parellada M, Llorente C, Gonzalez-Peñas J, Carracedo A, Van Haeringen A, Ruivenkamp C, Nava C, Heron D, Nardello R, Iacomino M, Minetti C, Skabar A, Fabretto A, Raspall-Chaure M, Chez M, Tsai A, Fassi E, Shinawi M, Constantino JN, De Zorzi R, Fortuna S, Kok F, Keren B, Bonneau D, Choi M, Benzeev B, Zara F, Mefford HC, Scheffer IE, Clayton-Smith J, Macaya A, Rothman JE, Eichler EE, Kullmann DM, Houlden H. AMPA receptor GluA2 subunit defects are a cause of neurodevelopmental disorders. Nat Commun 2019; 10:3094. [PMID: 31300657 PMCID: PMC6626132 DOI: 10.1038/s41467-019-10910-w] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 05/22/2019] [Indexed: 01/22/2023] Open
Abstract
AMPA receptors (AMPARs) are tetrameric ligand-gated channels made up of combinations of GluA1-4 subunits encoded by GRIA1-4 genes. GluA2 has an especially important role because, following post-transcriptional editing at the Q607 site, it renders heteromultimeric AMPARs Ca2+-impermeable, with a linear relationship between current and trans-membrane voltage. Here, we report heterozygous de novo GRIA2 mutations in 28 unrelated patients with intellectual disability (ID) and neurodevelopmental abnormalities including autism spectrum disorder (ASD), Rett syndrome-like features, and seizures or developmental epileptic encephalopathy (DEE). In functional expression studies, mutations lead to a decrease in agonist-evoked current mediated by mutant subunits compared to wild-type channels. When GluA2 subunits are co-expressed with GluA1, most GRIA2 mutations cause a decreased current amplitude and some also affect voltage rectification. Our results show that de-novo variants in GRIA2 can cause neurodevelopmental disorders, complementing evidence that other genetic causes of ID, ASD and DEE also disrupt glutamatergic synaptic transmission.
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Affiliation(s)
- Vincenzo Salpietro
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto "Giannina Gaslini", 16147, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
| | - Christine L Dixon
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Hui Guo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, 98195, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410083, Hunan, China
| | - Oscar D Bello
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Gali Heimer
- Pediatric Neurology Unit, Safra Children's Hospital, Sheba Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 526121, Ramat Gan, Israel
| | - Lydie Burglen
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Département de Génétique et Embryologie Médicale, APHP, Hôpital Trousseau, 75012, Paris, France
| | - Stephanie Valence
- Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Service de Neurologie Pédiatrique, APHP, Hôpital Trousseau, 75012, Paris, France
| | | | - Moritz Hacke
- Biochemistry Center, Heidelberg University, D-69120, Heidelberg, Germany
| | - Julia Rankin
- Royal Devon and Exeter NHS Foundation Trust, Exeter, EX1 2ED, UK
| | - Huma Tariq
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Estelle Colin
- Department of Biochemistry and Genetics, University Hospital, 49933, Angers, France
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, 49100, Angers, France
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, University Hospital, 49933, Angers, France
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, 49100, Angers, France
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto "Giannina Gaslini", 16147, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
| | - Kshitij Mankad
- Great Ormond Street Hospital for Children, London, WC1N 3JH, UK
| | - Andreas Lieb
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Sharon Chen
- Division of Medical Genetics, Northwell Health/Hofstra University SOM, New York, 11020, USA
| | - Laura Pisani
- Division of Medical Genetics, Northwell Health/Hofstra University SOM, New York, 11020, USA
| | - Conceicao Bettencourt
- Department of Clinical and Movement Neurosciences and Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, WC1N 1PJ, UK
| | - Roope Männikkö
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Andreea Manole
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Alfredo Brusco
- Department of Medical Sciences, Medical Genetics Unit, University of Torino, 10126, Torino, Italy
| | - Enrico Grosso
- Department of Medical Sciences, Medical Genetics Unit, University of Torino, 10126, Torino, Italy
| | | | - Judith Armstrong-Moron
- Unit of Medical and Molecular Genetics, University Hospital Sant Joan de Deu Barcelona, 08950, Barcelona, Spain
| | - Sophie Gueden
- Unit of Neuropediatrics, University Hospital, Angers Cedex, 49933, France
| | - Omer Bar-Yosef
- Pediatric Neurology Unit, Safra Children's Hospital, Sheba Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 526121, Ramat Gan, Israel
| | - Michal Tzadok
- Pediatric Neurology Unit, Safra Children's Hospital, Sheba Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 526121, Ramat Gan, Israel
| | | | | | | | | | | | - Yongjin Yoo
- Department of Biomedical Sciences, Seoul National University, Seoul, 03080, South Korea
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University, Seoul, 03080, South Korea
| | - Yingting Quan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410083, Hunan, China
| | - Huidan Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410083, Hunan, China
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, 98195, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410083, Hunan, China
| | - Raphael A Bernier
- Department of Psychiatry, University of Washington, Seattle, WA, 98195, USA
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410083, Hunan, China
| | - Alyssa Blesson
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, Maryland, 21211, USA
| | - Mahim Jain
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, Maryland, 21211, USA
| | - Mohammad M Motazacker
- Department of Clinical Genetics, University of Amsterdam, Meibergdreef 9, 1105, Amsterdam, Netherlands
| | - Bregje Jaeger
- Department of Pediatric Neurology, Amsterdam UMC, 1105, Amsterdam, Netherlands
| | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, 3084, Australia
| | - Katja Boysen
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, 3084, Australia
| | - Alison M Muir
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Candace T Myers
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | | | - Lauren Gunderson
- Department of Clinical Genomics, Mayo Clinic, Rochester, 55902, MN, USA
| | | | - Eric W Klee
- Department of Clinical Genomics, Mayo Clinic, Rochester, 55902, MN, USA
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, Canada
- Department of Human Genetics, McGill University Health Centre, Montréal, QC, H4A 3J1, Canada
- Genome Québec Innovation Center, Montréal, QC, H3A 0G1, Canada
| | - Mara Parellada
- Child and Adolescent Psychiatry Department, Hospital General Universitario Gregorio Marañón, School of Medicine, Universidad Complutense, IiSGM, CIBERSAM, 28007, Madrid, Spain
| | - Cloe Llorente
- Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Maranon, Universidad Complutense, CIBERSAM, 28007, Madrid, Spain
| | - Javier Gonzalez-Peñas
- Hospital Gregorio Maranon, IiSGM, School of Medicine, Calle Dr Esquerdo, 46, 28007, Madrid, Spain
| | - Angel Carracedo
- Grupo de Medicina Xenómica, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica- IDIS- Servicio Galego de Saúde (SERGAS), 15706, 15782, Santiago de Compostela, Spain
| | - Arie Van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA, Leiden, Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA, Leiden, Netherlands
| | - Caroline Nava
- Department of Genetics, Assistance Publique - Hôpitaux de Paris, University Hôpital Pitié-Salpêtrière, 75013, Paris, France
| | - Delphine Heron
- Department of Genetics, Assistance Publique - Hôpitaux de Paris, University Hôpital Pitié-Salpêtrière, 75013, Paris, France
| | - Rosaria Nardello
- Department of Health Promotion,Mother and Child Care, Internal Medicine and Medical Specialities "G. D'Alessandro", University of Palermo, 90133, Palermo, Italy
| | - Michele Iacomino
- Laboratory of Neurogenetics and Neuroscience, IRCCS Istituto "Giannina Gaslini", 16147, Genova, Italy
| | - Carlo Minetti
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto "Giannina Gaslini", 16147, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
| | - Aldo Skabar
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", University of Trieste, 34134, Trieste, Italy
| | - Antonella Fabretto
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", University of Trieste, 34134, Trieste, Italy
| | - Miquel Raspall-Chaure
- Department of Pediatric Neurology, University Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Michael Chez
- Neuroscience Medical Group, 1625 Stockton Boulevard, Suite 104, Sacramento, CA, 95816, USA
| | - Anne Tsai
- Department of Genetics and Inherited Metabolic diseases, Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - Emily Fassi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Marwan Shinawi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John N Constantino
- William Greenleaf Eliot Division of Child & Adolescent Psychiatry, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34134, Trieste, Italy
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34134, Trieste, Italy
| | - Fernando Kok
- Neurogenetics Unit, Department of Neurology, University of Sao Paulo, Sao Paulo, 01308-000, Brazil
- Mendelics Genomic Analysis, Sao Paulo, SP, 04013-000, Brazil
| | - Boris Keren
- Department of Genetics, Assistance Publique - Hôpitaux de Paris, University Hôpital Pitié-Salpêtrière, 75013, Paris, France
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, University Hospital, 49933, Angers, France
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, 49100, Angers, France
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University, Seoul, 03080, South Korea
| | - Bruria Benzeev
- Pediatric Neurology Unit, Safra Children's Hospital, Sheba Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 526121, Ramat Gan, Israel
| | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, IRCCS Istituto "Giannina Gaslini", 16147, Genova, Italy
| | - Heather C Mefford
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, 3084, Australia
| | - Jill Clayton-Smith
- Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Lancashire, M13 9WL, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, M13 9WL, UK
| | - Alfons Macaya
- Department of Pediatric Neurology, University Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - James E Rothman
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Dimitri M Kullmann
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK.
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK.
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25
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Kurbasic M, Semeraro S, Garcia AM, Kralj S, Parisi E, Deganutti C, De Zorzi R, Marchesan S. Microwave-Assisted Cyclization of Unprotected Dipeptides in Water to 2,5-Piperazinediones and Self-Assembly Study of Products and Reagents. SYNTHESIS-STUTTGART 2019. [DOI: 10.1055/s-0037-1612376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Dipeptides and their cyclized 2,5-piperazinedione (or diketopiperazine, DKP) derivatives are attractive building blocks for supramolecular hydrogels. The Phe-Phe, (p-nitro)-Phe-Phe, and Phe-Val dipeptides and their corresponding DKPs are studied for self-assembly in water. The DKPs were obtained in high yields by microwave-assisted cyclization of the dipeptides in water, demonstrating that use of their methyl ester derivatives as reported in the literature is not necessary for successful cyclization. Single-crystal XRD structures are reported for two DKPs as well as stable hydrogels at neutral pH.
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Affiliation(s)
- Marina Kurbasic
- Chemical & Pharmaceutical Sciences Dept., University of Trieste
| | | | - Ana M. Garcia
- Chemical & Pharmaceutical Sciences Dept., University of Trieste
| | - Slavko Kralj
- Chemical & Pharmaceutical Sciences Dept., University of Trieste
- Materials Synthesis Department, Jožef Stefan Institute
| | - Evelina Parisi
- Chemical & Pharmaceutical Sciences Dept., University of Trieste
| | | | - Rita De Zorzi
- Chemical & Pharmaceutical Sciences Dept., University of Trieste
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26
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Garcia AM, Iglesias D, Parisi E, Styan KE, Waddington LJ, Deganutti C, De Zorzi R, Grassi M, Melchionna M, Vargiu AV, Marchesan S. Chirality Effects on Peptide Self-Assembly Unraveled from Molecules to Materials. Chem 2018. [DOI: 10.1016/j.chempr.2018.05.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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27
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Tagliapietra M, Squarcina A, Hickey N, De Zorzi R, Geremia S, Sartorel A, Bonchio M. Hydrogen Evolution by Fe III Molecular Electrocatalysts Interconverting between Mono and Di-Nuclear Structures in Aqueous Phase. ChemSusChem 2017; 10:4430-4435. [PMID: 29096041 DOI: 10.1002/cssc.201701612] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/07/2017] [Indexed: 06/07/2023]
Abstract
A new FeL/Fe2 L2 manifold, with HL=2-({[di(2-pyridyl)methyl](methyl)amino}methyl)phenol, was prepared in gram scale (>50 % yield) and characterized in solution and solid state. The monomer/dimer interconversion is controlled in aqueous phase, upon varying the pH conditions. The electrocatalytic hydrogen evolution reaction (HER) occurs through the FeL monomer with added trifluoroacetic acid (TFA) and through the Fe2 L2 μ-oxo dimer in acetate buffer (pH 4.9), with an overpotential of about 1 V and faradaic yield up to 75 %. The resulting icat /ip values in the range 15-28 are among the highest reported for Fe-based electrocatalysts (icat is the catalytic current, whereas ip is the current of an Fe-based redox event).
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Affiliation(s)
- Mirko Tagliapietra
- Department of Chemical Sciences, ITM-CNR University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Andrea Squarcina
- Department of Chemical Sciences, ITM-CNR University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Neal Hickey
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy
| | - Silvano Geremia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy
| | - Andrea Sartorel
- Department of Chemical Sciences, ITM-CNR University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Marcella Bonchio
- Department of Chemical Sciences, ITM-CNR University of Padova, Via Marzolo 1, 35131, Padova, Italy
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28
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Saboe PO, Rapisarda C, Kaptan S, Hsiao YS, Summers SR, De Zorzi R, Dukovski D, Yu J, de Groot BL, Kumar M, Walz T. Role of Pore-Lining Residues in Defining the Rate of Water Conduction by Aquaporin-0. Biophys J 2017; 112:953-965. [PMID: 28297654 DOI: 10.1016/j.bpj.2017.01.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/22/2016] [Accepted: 01/26/2017] [Indexed: 11/19/2022] Open
Abstract
Compared to other aquaporins (AQPs), lens-specific AQP0 is a poor water channel, and its permeability was reported to be pH-dependent. To date, most water conduction studies on AQP0 were performed on protein expressed in Xenopus oocytes, and the results may therefore also reflect effects introduced by the oocytes themselves. Experiments with purified AQP0 reconstituted into liposomes are challenging because the water permeability of AQP0 is only slightly higher than that of pure lipid bilayers. By reconstituting high amounts of AQP0 and using high concentrations of cholesterol to reduce the permeability of the lipid bilayer, we improved the signal-to-noise ratio of water permeability measurements on AQP0 proteoliposomes. Our measurements show that mutation of two pore-lining tyrosine residues, Tyr-23 and Tyr-149 in sheep AQP0, to the corresponding residues in the high-permeability water channel AQP1 have additive effects and together increase the water permeability of AQP0 40-fold to a level comparable to that of AQP1. Molecular dynamics simulations qualitatively support these experimental findings and suggest that mutation of Tyr-23 changes the pore profile at the gate formed by residue Arg-187.
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Affiliation(s)
- Patrick O Saboe
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Chiara Rapisarda
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Shreyas Kaptan
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Yu-Shan Hsiao
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Samantha R Summers
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Rita De Zorzi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Danijela Dukovski
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Jiaheng Yu
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Manish Kumar
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania.
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts.
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29
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Cecot G, Marmier M, Geremia S, De Zorzi R, Vologzhanina AV, Pattison P, Solari E, Fadaei Tirani F, Scopelliti R, Severin K. The Intricate Structural Chemistry of M II2nL n-Type Assemblies. J Am Chem Soc 2017; 139:8371-8381. [PMID: 28603972 DOI: 10.1021/jacs.7b04861] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The reaction of cis-blocked, square-planar MII complexes with tetratopic N-donor ligands is known to give metallasupramolecular assemblies of the formula M2nLn. These assemblies typically adopt barrel-like structures, with the ligands paneling the sides of the barrels. However, alternative structures are possible, as demonstrated by the recent discovery of a Pt8L4 cage with unusual gyrobifastigium-like geometry. To date, the factors that govern the assembly of MII2nLn complexes are not well understood. Herein, we provide a geometric analysis of M2nLn complexes, and we discuss how size and geometry of the ligand is expected to influence the self-assembly process. The theoretical analysis is complemented by experimental studies using different cis-blocked PtII complexes and metalloligands with four divergent pyridyl groups. Mononuclear metalloligands gave mainly assemblies of type Pt8L4, which adopt barrel- or gyrobifastigium-like structures. Larger assemblies can also form, as evidenced by the crystallographic characterization of a Pt10L5 complex and a Pt16L8 complex. The former adopts a pentagonal barrel structure, whereas the latter displays a barrel structure with a distorted square orthobicupola geometry. The Pt16L8 complex has a molecular weight of more than 23 kDa and a diameter of 4.5 nm, making it the largest, structurally characterized M2nLn complex described to date. A dinuclear metalloligand was employed for the targeted synthesis of pentagonal Pt10L5 barrels, which are formed in nearly quantitative yields.
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Affiliation(s)
| | | | - Silvano Geremia
- Centro di Eccellenza in Biocristallografia, Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste , 34127 Trieste, Italy
| | - Rita De Zorzi
- Centro di Eccellenza in Biocristallografia, Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste , 34127 Trieste, Italy
| | - Anna V Vologzhanina
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences , 119991 Moscow, Russia
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30
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Bellich B, Di Fonzo S, Tavagnacco L, Paolantoni M, Masciovecchio C, Bertolotti F, Giannini G, De Zorzi R, Geremia S, Maiocchi A, Uggeri F, Masciocchi N, Cesàro A. Myelography Iodinated Contrast Media. 2. Conformational Versatility of Iopamidol in the Solid State. Mol Pharm 2017; 14:468-477. [PMID: 28059514 DOI: 10.1021/acs.molpharmaceut.6b00902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The phenomenon of polymorphism is of great relevance in pharmaceutics, since different polymorphs have different physicochemical properties, e.g., solubility, hence, bioavailability. Coupling diffractometric and spectroscopic experiments with thermodynamic analysis and computational work opens to a methodological approach which provides information on both structure and dynamics in the solid as well as in solution. The present work reports on the conformational changes in crystalline iopamidol, which is characterized by atropisomerism, a phenomenon that influences both the solution properties and the distinct crystal phases. The conformation of iopamidol is discussed for three different crystal phases. In the anhydrous and monohydrate crystal forms, iopamidol molecules display a syn conformation of the long branches stemming out from the triiodobenzene ring, while in the pentahydrate phase the anti conformation is found. IR and Raman spectroscopic studies carried out on the three crystal forms, jointly with quantum chemical computations, revealed that the markedly different spectral features can be specifically attributed to the different molecular conformations. Our results on the conformational versatility of iopamidol in different crystalline phases, linking structural and spectroscopic evidence for the solution state and the solid forms, provide a definite protocol for grasping the signals that can be taken as conformational markers. This is the first step for understanding the crystallization mechanism occurring in supersaturated solution of iopamidol molecules.
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Affiliation(s)
- Barbara Bellich
- Laboratory of Physical and Macromolecular Chemistry, Department of Chemical and Pharmaceutical Sciences, University of Trieste , via Giorgieri 1, I-34127 Trieste, Italy
| | - Silvia Di Fonzo
- Elettra Sincrotrone Trieste , Area Science Park, I-34149 Trieste, Italy
| | - Letizia Tavagnacco
- Laboratory of Physical and Macromolecular Chemistry, Department of Chemical and Pharmaceutical Sciences, University of Trieste , via Giorgieri 1, I-34127 Trieste, Italy
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnologies, University of Perugia , via Elce di Sotto 8, I-06123 Perugia, Italy
| | | | - Federica Bertolotti
- Department of Science and High Technology, To.Sca.Lab and INSTM, University of Insubria , via Valleggio 11, I-22100 Como, Italy
| | - Giovanna Giannini
- Laboratory of Physical and Macromolecular Chemistry, Department of Chemical and Pharmaceutical Sciences, University of Trieste , via Giorgieri 1, I-34127 Trieste, Italy
| | - Rita De Zorzi
- Laboratory of Physical and Macromolecular Chemistry, Department of Chemical and Pharmaceutical Sciences, University of Trieste , via Giorgieri 1, I-34127 Trieste, Italy
| | - Silvano Geremia
- Laboratory of Physical and Macromolecular Chemistry, Department of Chemical and Pharmaceutical Sciences, University of Trieste , via Giorgieri 1, I-34127 Trieste, Italy
| | - Alessandro Maiocchi
- Centro Ricerche Bracco, Bracco Imaging SpA , via Ribes 5, I-10010 Colleretto Giacosa, Turin, Italy
| | - Fulvio Uggeri
- Centro Ricerche Bracco, Bracco Imaging SpA , via Ribes 5, I-10010 Colleretto Giacosa, Turin, Italy
| | - Norberto Masciocchi
- Department of Science and High Technology, To.Sca.Lab and INSTM, University of Insubria , via Valleggio 11, I-22100 Como, Italy
| | - Attilio Cesàro
- Laboratory of Physical and Macromolecular Chemistry, Department of Chemical and Pharmaceutical Sciences, University of Trieste , via Giorgieri 1, I-34127 Trieste, Italy.,Elettra Sincrotrone Trieste , Area Science Park, I-34149 Trieste, Italy
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31
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D’Urso A, Brancatelli G, Hickey N, Farnetti E, De Zorzi R, Bonaccorso C, Purrello R, Geremia S. Interactions of a water-soluble calix[4]arene with spermine: solution and solid-state characterisation. Supramol Chem 2016. [DOI: 10.1080/10610278.2015.1125900] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Alessandro D’Urso
- Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy
| | - Giovanna Brancatelli
- Dipartimento di Scienze Chimiche e Farmaceutiche, Centro di Eccellenza di Biocristallografia, Università di Trieste, Trieste, Italy
| | - Neal Hickey
- Dipartimento di Scienze Chimiche e Farmaceutiche, Centro di Eccellenza di Biocristallografia, Università di Trieste, Trieste, Italy
| | - Erica Farnetti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Centro di Eccellenza di Biocristallografia, Università di Trieste, Trieste, Italy
| | - Rita De Zorzi
- Dipartimento di Scienze Chimiche e Farmaceutiche, Centro di Eccellenza di Biocristallografia, Università di Trieste, Trieste, Italy
| | | | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy
| | - Silvano Geremia
- Dipartimento di Scienze Chimiche e Farmaceutiche, Centro di Eccellenza di Biocristallografia, Università di Trieste, Trieste, Italy
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32
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Cecot G, Alameddine B, Prior S, Zorzi RD, Geremia S, Scopelliti R, Fadaei FT, Solari E, Severin K. Large heterometallic coordination cages with gyrobifastigium-like geometry. Chem Commun (Camb) 2016; 52:11243-11246. [DOI: 10.1039/c6cc06066h] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Large coordination cages with unusual gyrobifastigium-like geometry were obtained by combining cis-blocked PtII or PdII complexes with clathrochelate-based metalloligands.
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Affiliation(s)
- Giacomo Cecot
- Institut des Sciences et Ingénierie Chimiques
- École Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
| | - Bassam Alameddine
- Department of Mathematics and Natural Sciences
- Gulf University of Science & Technology (GUST)
- Kuwait
| | - Stéphanie Prior
- Institut des Sciences et Ingénierie Chimiques
- École Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
| | - Rita De Zorzi
- Centro di Eccellenza in Biocristallografia
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università di Trieste
- Trieste
- Italy
| | - Silvano Geremia
- Centro di Eccellenza in Biocristallografia
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università di Trieste
- Trieste
- Italy
| | - Rosario Scopelliti
- Institut des Sciences et Ingénierie Chimiques
- École Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
| | - Farzaneh T. Fadaei
- Institut des Sciences et Ingénierie Chimiques
- École Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
| | - Euro Solari
- Institut des Sciences et Ingénierie Chimiques
- École Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
| | - Kay Severin
- Institut des Sciences et Ingénierie Chimiques
- École Polytechnique Fédérale de Lausanne (EPFL)
- 1015 Lausanne
- Switzerland
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33
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De Zorzi R, Mi W, Liao M, Walz T. Single-particle electron microscopy in the study of membrane protein structure. Microscopy (Oxf) 2015; 65:81-96. [PMID: 26470917 DOI: 10.1093/jmicro/dfv058] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/20/2015] [Indexed: 01/13/2023] Open
Abstract
Single-particle electron microscopy (EM) provides the great advantage that protein structure can be studied without the need to grow crystals. However, due to technical limitations, this approach played only a minor role in the study of membrane protein structure. This situation has recently changed dramatically with the introduction of direct electron detection device cameras, which allow images of unprecedented quality to be recorded, also making software algorithms, such as three-dimensional classification and structure refinement, much more powerful. The enhanced potential of single-particle EM was impressively demonstrated by delivering the first long-sought atomic model of a member of the biomedically important transient receptor potential channel family. Structures of several more membrane proteins followed in short order. This review recounts the history of single-particle EM in the study of membrane proteins, describes the technical advances that now allow this approach to generate atomic models of membrane proteins and provides a brief overview of some of the membrane protein structures that have been studied by single-particle EM to date.
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Affiliation(s)
- Rita De Zorzi
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA Howard Hughes Medical Institute, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Wei Mi
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA Howard Hughes Medical Institute, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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34
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De March M, Brancatelli G, Demitri N, De Zorzi R, Hickey N, Geremia S. A general exit strategy of monoheme cytochromes c and c2 in electron transfer complexes? IUBMB Life 2015; 67:694-700. [PMID: 26311433 DOI: 10.1002/iub.1410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/28/2015] [Indexed: 11/06/2022]
Abstract
Using our previously reported maps of the electrostatic surface of horse heart ferri- and ferro-cyt c, comparisons were made between the complementary electrostatic surfaces of three cyt c peroxidase-cyt c complexes and the photosynthetic reaction center-cyt c complex, considering both iron oxidation states. The results obtained were consistent with a sliding mechanism for the electron shuttle on the surface of the protein complexes, promoted by the change in iron oxidation state. This mechanism was found to be in agreement with theoretical and NMR studies reported in the literature. Importantly, the analysis also provided a rationale for recognition of nonproductive associations. As we have previously reported the same conclusion on examination of redox partners of cyt c in the mitochondrial respiratory pathway, our hypothesis is that the proposed mechanism could represent a general exit strategy of monoheme cyts c and c2 in electron transfer complexes.
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Affiliation(s)
- Matteo De March
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Giovanna Brancatelli
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Nicola Demitri
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Neal Hickey
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
| | - Silvano Geremia
- Department of Chemical and Pharmaceutical Sciences, Centre of Excellence in Biocrystallography, University of Trieste, Trieste, Italy
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35
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Shaheen A, Ismat F, Iqbal M, Haque A, De Zorzi R, Mirza O, Walz T, Rahman M. Characterization of putative multidrug resistance transporters of the major facilitator-superfamily expressed in Salmonella Typhi. J Infect Chemother 2015; 21:357-62. [PMID: 25724589 DOI: 10.1016/j.jiac.2015.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/03/2014] [Accepted: 01/02/2015] [Indexed: 01/11/2023]
Abstract
Multidrug resistance mediated by efflux pumps is a well-known phenomenon in infectious bacteria. Although much work has been carried out to characterize multidrug efflux pumps in Gram-negative and Gram-positive bacteria, such information is still lacking for many deadly pathogens. The aim of this study was to gain insight into the substrate specificity of previously uncharacterized transporters of Salmonella Typhi to identify their role in the development of multidrug resistance. S. Typhi genes encoding putative members of the major facilitator superfamily were cloned and expressed in the drug-hypersensitive Escherichia coli strain KAM42, and tested for transport of 25 antibacterial compounds, including representative antibiotics of various classes, antiseptics, dyes and detergents. Of the 15 tested putative transporters, STY0901, STY2458 and STY4874 exhibited a drug-resistance phenotype. Among these, STY4874 conferred resistance to at least ten of the tested antimicrobials: ciprofloxacin, norfloxacin, levofloxacin, kanamycin, streptomycin, gentamycin, nalidixic acid, chloramphenicol, ethidium bromide, and acriflavine, including fluoroquinolone antibiotics, which were drugs of choice to treat S. Typhi infections. Cell-based functional studies using ethidium bromide and acriflavine showed that STY4874 functions as a H(+)-dependent exporter. These results suggest that STY4874 may be an important drug target, which can now be tested by studying the susceptibility of a STY4874-deficient S. Typhi strain to antimicrobials.
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Affiliation(s)
- Aqsa Shaheen
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Fouzia Ismat
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Mazhar Iqbal
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Abdul Haque
- The University of Faisalabad, Faisalabad, Pakistan
| | - Rita De Zorzi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Moazur Rahman
- Drug Discovery and Structural Biology Group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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36
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Dürr KL, Chen L, Stein RA, De Zorzi R, Folea IM, Walz T, Mchaourab HS, Gouaux E. Structure and dynamics of AMPA receptor GluA2 in resting, pre-open, and desensitized states. Cell 2014; 158:778-792. [PMID: 25109876 DOI: 10.1016/j.cell.2014.07.023] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 10/24/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) mediate the majority of fast excitatory signaling in the nervous system. Despite the profound importance of iGluRs to neurotransmission, little is known about the structures and dynamics of intact receptors in distinct functional states. Here, we elucidate the structures of the intact GluA2 AMPA receptor in an apo resting/closed state, in an activated/pre-open state bound with partial agonists and a positive allosteric modulator, and in a desensitized/closed state in complex with fluorowilliardiine. To probe the conformational properties of these states, we carried out double electron-electron resonance experiments on cysteine mutants and cryoelectron microscopy studies. We show how agonist binding modulates the conformation of the ligand-binding domain "layer" of the intact receptors and how, upon desensitization, the receptor undergoes large conformational rearrangements of the amino-terminal and ligand-binding domains. We define mechanistic principles by which to understand antagonism, activation, and desensitization in AMPA iGluRs.
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Affiliation(s)
- Katharina L Dürr
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Lei Chen
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Rita De Zorzi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - I Mihaela Folea
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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De March M, Demitri N, De Zorzi R, Casini A, Gabbiani C, Guerri A, Messori L, Geremia S. Nitrate as a probe of cytochrome c surface: Crystallographic identification of crucial “hot spots” for protein–protein recognition. J Inorg Biochem 2014; 135:58-67. [DOI: 10.1016/j.jinorgbio.2014.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 02/23/2014] [Accepted: 02/27/2014] [Indexed: 11/30/2022]
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38
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De Zorzi R, Brancatelli G, Melegari M, Pinalli R, Dalcanale E, Geremia S. Selectivity assessment in host–guest complexes from single-crystal X-ray diffraction data: the cavitand–alcohol case. CrystEngComm 2014. [DOI: 10.1039/c4ce01813c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solid-state selectivity of a cavitand receptor towards short alkyl chain alcohols was evaluated by analysis of X-ray diffraction data of isomorphous single crystals grown in competition binding experiments.
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Affiliation(s)
- Rita De Zorzi
- Centro di Eccellenza in Biocristallografia
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- 34127 Trieste, Italy
| | - Giovanna Brancatelli
- Centro di Eccellenza in Biocristallografia
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- 34127 Trieste, Italy
| | - Monica Melegari
- Dipartimento di Chimica
- Università degli Studi di Parma and INSTM Udr Parma
- 43124 Parma, Italy
| | - Roberta Pinalli
- Dipartimento di Chimica
- Università degli Studi di Parma and INSTM Udr Parma
- 43124 Parma, Italy
| | - Enrico Dalcanale
- Dipartimento di Chimica
- Università degli Studi di Parma and INSTM Udr Parma
- 43124 Parma, Italy
| | - Silvano Geremia
- Centro di Eccellenza in Biocristallografia
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- 34127 Trieste, Italy
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Zubcevic L, Bavro VN, Muniz JRC, Schmidt MR, Wang S, De Zorzi R, Venien-Bryan C, Sansom MSP, Nichols CG, Tucker SJ. Control of KirBac3.1 potassium channel gating at the interface between cytoplasmic domains. J Biol Chem 2013; 289:143-51. [PMID: 24257749 PMCID: PMC3879539 DOI: 10.1074/jbc.m113.501833] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
KirBac channels are prokaryotic homologs of mammalian inwardly rectifying potassium (Kir) channels, and recent structures of KirBac3.1 have provided important insights into the structural basis of gating in Kir channels. In this study, we demonstrate that KirBac3.1 channel activity is strongly pH-dependent, and we used x-ray crystallography to determine the structural changes that arise from an activatory mutation (S205L) located in the cytoplasmic domain (CTD). This mutation stabilizes a novel energetically favorable open conformation in which changes at the intersubunit interface in the CTD also alter the electrostatic potential of the inner cytoplasmic cavity. These results provide a structural explanation for the activatory effect of this mutation and provide a greater insight into the role of the CTD in Kir channel gating.
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Affiliation(s)
- Lejla Zubcevic
- From the Biological Physics Group, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, United Kingdom
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Bavro VN, De Zorzi R, Schmidt MR, Muniz JR, Zubcevic L, Sansom MS, Venien-Bryan C, Tucker SJ. Crystal Structure of a Prokaryotic Kir Channel in an Open Conformation. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.2928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Busi M, Cantadori B, Boccini F, De Zorzi R, Geremia S, Dalcanale E. Molecular Recognition with Ditopic Cavitand Re Complexes. European J Org Chem 2011. [DOI: 10.1002/ejoc.201001668] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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De Zorzi R, Guidolin N, Randaccio L, Geremia S. A bifunctionalized porous material containing discrete assemblies of copper-porphyrins and calixarenes metallated by ion diffusion. CrystEngComm 2010. [DOI: 10.1039/c0ce00440e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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De Zorzi R, Guidolin N, Randaccio L, Purrello R, Geremia S. Nanoporous crystals of calixarene/porphyrin supramolecular complex functionalized by diffusion and coordination of metal ions. J Am Chem Soc 2009; 131:2487-9. [PMID: 19187023 DOI: 10.1021/ja808850d] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A highly nanoporous material has been obtained by self-assembly of calixarene and porphyrin building blocks. This supramolecular zeolite-like structure was successively functionalized by diffusion and coordination of metal ions to form a new bifunctionalized nanoporous material containing a porphyrinic pigment together with a metal center.
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Affiliation(s)
- Rita De Zorzi
- Centro di Eccellenza in Biocristallografia, Dipartimento di Scienze Chimiche, Università di Trieste, Viale Giorgeri 1, 34127 Trieste, Italy
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Sooambar C, Troiani V, Bruno C, Marcaccio M, Paolucci F, Listorti A, Belbakra A, Armaroli N, Magistrato A, De Zorzi R, Geremia S, Bonifazi D. Synthesis, photophysical, electrochemical, and electrochemiluminescent properties of 5,15-bis(9-anthracenyl)porphyrin derivatives. Org Biomol Chem 2009; 7:2402-13. [PMID: 19462051 DOI: 10.1039/b820210a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Novel 5,15-bis(9-anthracenyl)porphyrin derivatives (, ) were synthesized by stepwise Suzuki-type coupling reactions using anthracenyl-boronates bearing various electronically active moieties. Absorption spectra of these porphyrin conjugates reveal some degree of delocalisation with the directly linked chromophores, particularly in the case of anthracenyl-porphyrin bearing dimethylanilino moieties at the two extremities. Fluorescence and 77 K phosphorescence properties indicate that the excitation energy is invariably funnelled to the lowest singlet and triplet states of the porphyrin chromophore. The latter levels have been probed also by transient absorption spectroscopy, showing the typical triplet features detected in meso-substituted porphyrins. Extensive electrochemical studies have been performed to unravel the electronic properties of the newly synthesized porphyrins. Low-temperature cyclic voltammetry investigations showed that the anthracenyl-porphyrins are capable of undergoing as many as four electron transfer processes. In particular, by means of UV-Vis-NIR spectroelectrochemical measurements, a NIR-centred intramolecular photoinduced intervalence charge transfer (IV-CT) from a neutral N,N-dimethylanilino moiety to the N,N-dimethylanilino radical cation has been observed for the doubly-oxidised porphyrin (2+). The molecules also showed unexpected electrogenerated chemiluminescence properties, which revealed to be largely controlled by the electronic characteristics of the peripheral anthracenyl substituents. The structural and the electronic properties of these complexes have been also characterised by DFT calculations, as well as by X-ray crystallographic analyses.
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Affiliation(s)
- Chloè Sooambar
- Università degli Studi di Trieste, Dipartimento di Scienze Farmaceutiche and INSTM UdR Trieste, Trieste, Italy
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Zeitouny J, Aurisicchio C, Bonifazi D, De Zorzi R, Geremia S, Bonini M, Palma CA, Samorì P, Listorti A, Belbakra A, Armaroli N. Photoinduced structural modifications in multicomponent architectures containing azobenzene moieties as photoswitchable cores. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b905287a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Sartorel A, Carraro M, Scorrano G, De Zorzi R, Geremia S, McDaniel ND, Bernhard S, Bonchio M. Polyoxometalate embedding of a tetraruthenium(IV)-oxo-core by template-directed metalation of [gamma-SiW10O36]8-: a totally inorganic oxygen-evolving catalyst. J Am Chem Soc 2008; 130:5006-7. [PMID: 18345628 DOI: 10.1021/ja077837f] [Citation(s) in RCA: 459] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solid state and solution evidence confirms the embedding of an adamantane-like, Ru4O6 fragment by the divacant, gamma-decatungstosilicate ligand. The resulting complex catalyzes water oxidation to oxygen with TON up to 500 and TOF > 450 h-1.
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Affiliation(s)
- Andrea Sartorel
- ITM-CNR and Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy.
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Campagnolo M, Campa C, Zorzi RD, Wuerges J, Geremia S. X-ray studies on ternary complexes of maltodextrin phosphorylase. Arch Biochem Biophys 2007; 471:11-9. [PMID: 18164678 DOI: 10.1016/j.abb.2007.11.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 11/14/2007] [Accepted: 11/18/2007] [Indexed: 10/22/2022]
Abstract
We report crystal structures of ternary complexes of maltodextrin phosphorylase with natural oligosaccharide and phosphate mimicking anions: nitrate, sulphate and vanadate. Electron density maps obtained from crystals grown in presence of Al(NO3)3 show a nitrate ion instead of the expected AlF4- in the catalytic site. The trigonal NO3- is coplanar with the Arg569 guanidinium group and mimics three of the four oxygen atoms of phosphate. The ternary complex with sulphate shows a partial occupancy of the anionic site. The low affinity of the sulphate ion, observed when the alpha-glucosyl substrate is present in the catalytic channel, is ascribed to restricted space for the anion. Even lower occupancy is observed for the larger vanadate anion. The Malp/G5/VO43- structure shows the partial occupancy of the oligosaccharide and the dislocation of the 380's loop. This has been attributed to the formation of oligosaccharide vanadate derivatives (confirmed by capillary electrophoresis) that reduces their effective concentration. The difficulty to trap a ternary complex mimicking the ground state has been correlated to the apparent lower affinity that natural substrates show regarding the intermediates of the enzymatic reaction.
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Affiliation(s)
- Mara Campagnolo
- CEB-Centre of Excellence in Biocrystallography, Department of Chemical Sciences, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
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48
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Pattarozzi M, Zonta C, Broxterman QB, Kaptein B, De Zorzi R, Randaccio L, Scrimin P, Licini G. Stereoselective iodocyclization of (S)-allylalanine derivatives: gamma-lactone vs cyclic carbamate formation. Org Lett 2007; 9:2365-8. [PMID: 17503837 DOI: 10.1021/ol070764k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient procedure for highly chemo- and stereoselective cyclization of (S)-allylalanine derivatives is reported (diastereomeric ratios up to 96:4) where the reaction course can be completely controlled by switching from gamma-lactones to cyclic carbamates simply with the proper choice of the amino acid protecting groups. Both processes are stereoconvergent and afford the (S,S)-products in high yields, short reaction times, and mild reaction conditions.
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Affiliation(s)
- Mariella Pattarozzi
- Dipartimento di Scienze Chimiche and ITM-CNR, Università di Padova, via Marzolo 1, I-35131 Padova, Italy
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49
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De Zorzi R, Dubessy B, Mulatier JC, Geremia S, Randaccio L, Dutasta JP. Structure of a 4:1:4 Supramolecular Assembly of Neutral TiiiiPO Cavitands and Tetrakis(N-methylpyridinium)porphyrin Iodide. J Org Chem 2007; 72:4528-31. [PMID: 17500565 DOI: 10.1021/jo070109q] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four tetraphosphorylated TiiiiPO cavitands 1 encapsulate the pyridinium heads of a tetrakis(N-methylpyridinium)porphyrin iodide to form a 4:1:4 (host)4/guest4+/4I- complex. The single-crystal X-ray diffraction analysis shows the arrangement of the four cavities bound to the CH3N+ groups of the porphyrin moiety and the four iodide anions nested between the phenethyl substituents of the hosts. 1H NMR investigations show that the structure is preserved in chloroform solution and underscore the effect of the counteranions.
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Affiliation(s)
- Rita De Zorzi
- Centro di Eccellenza in Biocristallografia, Dipartimento di Scienze Chimiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy
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50
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Gulino FG, Lauceri R, Frish L, Evan-Salem T, Cohen Y, De Zorzi R, Geremia S, Di Costanzo L, Randaccio L, Sciotto D, Purrello R. Noncovalent synthesis in aqueous solution and spectroscopic characterization of multi-porphyrin complexes. Chemistry 2006; 12:2722-9. [PMID: 16416494 DOI: 10.1002/chem.200500825] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The interactions of the tetracationic meso-tetrakis(N-methyl-4-pyridyl)porphyrin (H(2)TMPyP) and its metallo derivatives (MTMPyP) (where M=copper(II), zinc(II), and gold(III) with the octa-anionic form (at neutral pH) of 5,11,17,23-tetrasulfonato-25,26,27,28-tetrakis(hydroxycarbonylmethoxy)calix[4]arene (C(4)TsTc) lead to a series of complex species whose stoichiometry and porphyrin sequence can be easily tuned. Crystallographic, spectroscopic, and diffusion NMR studies converge towards a common picture in which a central 1:4 porphyrin/calixarene unit serves as a template for the formation of more complex species. These species arise by successive, stepwise addition of single porphyrin molecules above and below the plane of the 1:4 central core to ultimately give a 7:4 complex. Noticeably, the stoichiometry of the various complex species corresponds to the actual concentration ratio of porphyrins and calixarenes in solution allowing the stoichiometry of these species to be easily tuned. This behavior and the remarkable stability of these species allow homo-porphyrin and hetero-(metallo)porphyrin species to be formed with control of not only the stoichiometry but also the sequence of the porphyrin array. The flexibility and ease of this approach permit, in principle, the design and synthesis of porphyrin arrays for predetermined purposes. For example, we have shown that it is very easy to design and obtain mixed porphyrin species in which a foreseen photoinduced electron-transfer is indeed observed.
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Affiliation(s)
- Fabio G Gulino
- Dipartimento di Scienze Chimiche, Università di Catania, Viale A. Doria 6, 95125 Catania, Italy
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