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Pivovarenko VG, Klymchenko AS. Fluorescent Probes Based on Charge and Proton Transfer for Probing Biomolecular Environment. CHEM REC 2024; 24:e202300321. [PMID: 38158338 DOI: 10.1002/tcr.202300321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Fluorescent probes for sensing fundamental properties of biomolecular environment, such as polarity and hydration, help to study assembly of lipids into biomembranes, sensing interactions of biomolecules and imaging physiological state of the cells. Here, we summarize major efforts in the development of probes based on two photophysical mechanisms: (i) an excited-state intramolecular charge transfer (ICT), which is represented by fluorescent solvatochromic dyes that shift their emission band maximum as a function of environment polarity and hydration; (ii) excited-state intramolecular proton transfer (ESIPT), with particular focus on 5-membered cyclic systems, represented by 3-hydroxyflavones, because they exhibit dual emission sensitive to the environment. For both ICT and ESIPT dyes, the design of the probes and their biological applications are summarized. Thus, dyes bearing amphiphilic anchors target lipid membranes and report their lipid organization, while targeting ligands direct them to specific organelles for sensing their local environment. The labels, amino acid and nucleic acid analogues inserted into biomolecules enable monitoring their interactions with membranes, proteins and nucleic acids. While ICT probes are relatively simple and robust environment-sensitive probes, ESIPT probes feature high information content due their dual emission. They constitute a powerful toolbox for addressing multitude of biological questions.
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Affiliation(s)
- Vasyl G Pivovarenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, 01033, Kyiv, Ukraine
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, ITI SysChem, Université de Strasbourg, 67401, Illkirch, France
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2
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Caporale A, Adorinni S, Lamba D, Saviano M. Peptide-Protein Interactions: From Drug Design to Supramolecular Biomaterials. Molecules 2021; 26:1219. [PMID: 33668767 PMCID: PMC7956380 DOI: 10.3390/molecules26051219] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
The self-recognition and self-assembly of biomolecules are spontaneous processes that occur in Nature and allow the formation of ordered structures, at the nanoscale or even at the macroscale, under thermodynamic and kinetic equilibrium as a consequence of specific and local interactions. In particular, peptides and peptidomimetics play an elected role, as they may allow a rational approach to elucidate biological mechanisms to develop new drugs, biomaterials, catalysts, or semiconductors. The forces that rule self-recognition and self-assembly processes are weak interactions, such as hydrogen bonding, electrostatic attractions, and van der Waals forces, and they underlie the formation of the secondary structure (e.g., α-helix, β-sheet, polyproline II helix), which plays a key role in all biological processes. Here, we present recent and significant examples whereby design was successfully applied to attain the desired structural motifs toward function. These studies are important to understand the main interactions ruling the biological processes and the onset of many pathologies. The types of secondary structure adopted by peptides during self-assembly have a fundamental importance not only on the type of nano- or macro-structure formed but also on the properties of biomaterials, such as the types of interaction, encapsulation, non-covalent interaction, or covalent interaction, which are ultimately useful for applications in drug delivery.
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Affiliation(s)
- Andrea Caporale
- IC-CNR, c/o Area Science Park, S.S. 14 Km 163.5 Basovizza, 34149 Trieste, Italy;
| | - Simone Adorinni
- Dipartimento di Scienze Chimiche e Farmaceutiche di Università di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy;
| | - Doriano Lamba
- IC-CNR, c/o Area Science Park, S.S. 14 Km 163.5 Basovizza, 34149 Trieste, Italy;
- Istituto Nazionale Biostrutture e Biosistemi, Consorzio Interuniversitario, Viale delle Medaglie d’Oro 305, I-00136 Roma, Italy
| | - Michele Saviano
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche (IC-CNR), Via Giovanni Amendola 122/O, 70126 Bari, Italy
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3
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Lampel A, Ulijn RV, Tuttle T. Guiding principles for peptide nanotechnology through directed discovery. Chem Soc Rev 2018; 47:3737-3758. [PMID: 29748676 DOI: 10.1039/c8cs00177d] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.
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Affiliation(s)
- A Lampel
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), New York, NY, USA.
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4
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Burgers PP, Bruystens J, Burnley RJ, Nikolaev VO, Keshwani M, Wu J, Janssen BJC, Taylor SS, Heck AJR, Scholten A. Structure of smAKAP and its regulation by PKA-mediated phosphorylation. FEBS J 2016; 283:2132-48. [PMID: 27028580 DOI: 10.1111/febs.13726] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/04/2016] [Accepted: 03/29/2016] [Indexed: 12/27/2022]
Abstract
UNLABELLED The A-kinase anchoring protein (AKAP) smAKAP has three extraordinary features; it is very small, it is anchored directly to membranes by acyl motifs, and it interacts almost exclusively with the type I regulatory subunits (RI) of cAMP-dependent kinase (PKA). Here, we determined the crystal structure of smAKAP's A-kinase binding domain (smAKAP-AKB) in complex with the dimerization/docking (D/D) domain of RIα which reveals an extended hydrophobic interface with unique interaction pockets that drive smAKAP's high specificity for RI subunits. We also identify a conserved PKA phosphorylation site at Ser66 in the AKB domain which we predict would cause steric clashes and disrupt binding. This correlates with in vivo colocalization and fluorescence polarization studies, where Ser66 AKB phosphorylation ablates RI binding. Hydrogen/deuterium exchange studies confirm that the AKB helix is accessible and dynamic. Furthermore, full-length smAKAP as well as the unbound AKB is predicted to contain a break at the phosphorylation site, and circular dichroism measurements confirm that the AKB domain loses its helicity following phosphorylation. As the active site of PKA's catalytic subunit does not accommodate α-helices, we predict that the inherent flexibility of the AKB domain enables its phosphorylation by PKA. This represents a novel mechanism, whereby activation of anchored PKA can terminate its binding to smAKAP affecting the regulation of localized cAMP signaling events. DATABASE Structural data are available in the PDB under accession number 5HVZ.
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Affiliation(s)
- Pepijn P Burgers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Jessica Bruystens
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Rebecca J Burnley
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
| | | | - Malik Keshwani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Jian Wu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Bert J C Janssen
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA.,Department of Pharmacology, University of California San Diego, La Jolla, California, USA.,The Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, USA
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Arjen Scholten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
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5
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Sigg SJ, Postupalenko V, Duskey JT, Palivan CG, Meier W. Stimuli-Responsive Codelivery of Oligonucleotides and Drugs by Self-Assembled Peptide Nanoparticles. Biomacromolecules 2016; 17:935-45. [PMID: 26871486 DOI: 10.1021/acs.biomac.5b01614] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ever more emerging combined treatments exploiting synergistic effects of drug combinations demand smart, responsive codelivery carriers to reveal their full potential. In this study, a multifunctional stimuli-responsive amphiphilic peptide was designed and synthesized to self-assemble into nanoparticles capable of co-bearing and -releasing hydrophobic drugs and antisense oligonucleotides for combined therapies. The rational design was based on a hydrophobic l-tryptophan-d-leucine repeating unit derived from a truncated sequence of gramicidin A (gT), to entrap hydrophobic cargo, which is combined with a hydrophilic moiety of histidines to provide electrostatic affinity to nucleotides. Stimuli-responsiveness was implemented by linking the hydrophobic and hydrophilic sequence through an artificial amino acid bearing a disulfide functional group (H3SSgT). Stimuli-responsive peptides self-assembled in spherical nanoparticles in sizes (100-200 nm) generally considered as preferable for drug delivery applications. Responsive peptide nanoparticles revealed notable nucleotide condensing abilities while maintaining the ability to load hydrophobic cargo. The disulfide cleavage site introduced in the peptide sequence induced responsiveness to physiological concentrations of reducing agent, serving to release the incorporated molecules. Furthermore, the peptide nanoparticles, singly loaded or coloaded with boron-dipyrromethene (BODIPY) and/or antisense oligonucleotides, were efficiently taken up by cells. Such amphiphilic peptides that led to noncytotoxic, reduction-responsive nanoparticles capable of codelivering hydrophobic and nucleic acid payloads simultaneously provide potential toward combined treatment strategies to exploit synergistic effects.
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Affiliation(s)
- Severin J Sigg
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Viktoriia Postupalenko
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Jason T Duskey
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Wolfgang Meier
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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6
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Ruffoni A, Cavanna MV, Argentiere S, Locarno S, Pellegrino S, Gelmi ML, Clerici F. Aqueous self-assembly of short hydrophobic peptides containing norbornene amino acid into supramolecular structures with spherical shape. RSC Adv 2016. [DOI: 10.1039/c6ra17116h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The preparation and self-assembly of short hydrophobic peptides containing the non-coded norbornene amino acid is reported. The formation of a supramolecular assembly in water was assessed by TEM and DLS.
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Affiliation(s)
- Alessandro Ruffoni
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | | | | | - Silvia Locarno
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | - Sara Pellegrino
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | - Maria Luisa Gelmi
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | - Francesca Clerici
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
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7
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Rad-Malekshahi M, Lempsink L, Amidi M, Hennink WE, Mastrobattista E. Biomedical Applications of Self-Assembling Peptides. Bioconjug Chem 2015; 27:3-18. [DOI: 10.1021/acs.bioconjchem.5b00487] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mazda Rad-Malekshahi
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Ludwijn Lempsink
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Maryam Amidi
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Wim E. Hennink
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics,
Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 3584
CG Utrecht, The Netherlands
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8
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Rad-Malekshahi M, Visscher KM, Rodrigues JPGLM, de Vries R, Hennink WE, Baldus M, Bonvin AMJJ, Mastrobattista E, Weingarth M. The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail. J Am Chem Soc 2015; 137:7775-84. [DOI: 10.1021/jacs.5b02919] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mazda Rad-Malekshahi
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Koen M. Visscher
- NMR
Spectroscopy, Bijvoet Center for Biomolecular Research, Department
of Chemistry, Faculty of Science, Utrecht University, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - João P. G. L. M. Rodrigues
- NMR
Spectroscopy, Bijvoet Center for Biomolecular Research, Department
of Chemistry, Faculty of Science, Utrecht University, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Renko de Vries
- Laboratory
of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Wim E. Hennink
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Marc Baldus
- NMR
Spectroscopy, Bijvoet Center for Biomolecular Research, Department
of Chemistry, Faculty of Science, Utrecht University, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Alexandre M. J. J. Bonvin
- NMR
Spectroscopy, Bijvoet Center for Biomolecular Research, Department
of Chemistry, Faculty of Science, Utrecht University, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Markus Weingarth
- NMR
Spectroscopy, Bijvoet Center for Biomolecular Research, Department
of Chemistry, Faculty of Science, Utrecht University, Padualaan
8, 3584 CH Utrecht, The Netherlands
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9
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Wang JX, Cai TT, Li JL, Zhuo RX, Zhang XZ. Micro-size cell-like vesicles based on gemini-like amphiphilic peptide. RSC Adv 2014. [DOI: 10.1039/c4ra00986j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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10
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Guo T, Yang J, Zeng L, Wang H, Tong Q, Li X. Does there exist an intrinsic relationship between the flexibility and self-assembly of pepfactants? MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.817673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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11
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Pivovarenko VG, Zamotaiev OM, Shvadchak VV, Postupalenko VY, Klymchenko AS, Mély Y. Quantification of local hydration at the surface of biomolecules using dual-fluorescence labels. J Phys Chem A 2012; 116:3103-9. [PMID: 22394312 DOI: 10.1021/jp2101732] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
By using four labels of the 3-hydroxyflavone family displaying selective sensitivity to hydrogen bond (HB) donors and poor response to other polar molecules, we developed an approach for measuring local water concentration [H(2)O](L) (or partial volume of water: W(A) = [H(2)O](L)/55.6) in the label surrounding both in solvent mixtures and in biomolecules by the intensity ratio of two emissive forms of the label, N*/T*. Using a series of binary water/solvent mixtures with limited preferential solvation effects, a linear dependence of log(N*/T*) on the local concentration of HB donor was obtained and then used as a calibration curve for estimating the W(A) values in the surroundings of the probes conjugated to biomolecules. By this approach, we estimated the hydration of the labels in different peptides and their complexes with DNAs. We found that W(A) values for the label at the peptide N-terminus are lower (0.63-0.91) than for free labels and depend strongly on the nature of the N-terminal amino acid. When complexed with different DNAs, the estimated hydration of the labels conjugated to the labeled peptides was much lower (W(A) = 0-0.47) and depended on the DNA nature and linker-label structure. Thus, the elaborated method allows a site-specific evaluation of hydration at the surface of a biomolecule through the determination of the partial volume of water. We believe the developed procedure can be successfully applied for monitoring hydration at the surface of any biomolecule or nanostructure.
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Affiliation(s)
- Vasyl G Pivovarenko
- Organic Chemistry Chair, Chemistry Faculty, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine
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12
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Schuster TB, de Bruyn Ouboter D, Bruns N, Meier W. Exploiting dimerization of purely peptidic amphiphiles to form vesicles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:2158-2162. [PMID: 21626692 DOI: 10.1002/smll.201100701] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Indexed: 05/30/2023]
Affiliation(s)
- Thomas B Schuster
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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