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Castro VIB, Gao Y, Brito A, Chen J, Reis RL, Pashkuleva I, Pires RA. Cooling rate uncovers epimer-dependent supramolecular organization of carbohydrate amphiphiles. J Mater Chem B 2024; 12:6996-7000. [PMID: 38949321 DOI: 10.1039/d4tb00728j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
We show distinct CH-π interactions and assembly pathways for the amphiphile N-(fluorenylmethoxycarbonyl)-galactosamine and its epimer N-(fluorenylmethoxycarbonyl)-glucosamine. These differences result in the formation of supramolecular nanofibrous systems with opposite chirality. Our results showcase the importance of the carbohydrates structural diversity for their specific biointeractions and the opportunity that their ample interactome offers for synthesis of versatile and tunable supramolecular (bio) materials.
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Affiliation(s)
- Vânia I B Castro
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Yuting Gao
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Department of Chemical Engineering, School of Environmental and Chemical Engineering, Shanghai University, Shangda Road 99, Shanghai 200444, P. R. China
| | - Alexandra Brito
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Jie Chen
- Department of Chemical Engineering, School of Environmental and Chemical Engineering, Shanghai University, Shangda Road 99, Shanghai 200444, P. R. China
| | - Rui L Reis
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Iva Pashkuleva
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ricardo A Pires
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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2
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Blachnio M, Zienkiewicz-Strzalka M, Derylo-Marczewska A, Nosach LV, Voronin EF. Chitosan-Silica Composites for Adsorption Application in the Treatment of Water and Wastewater from Anionic Dyes. Int J Mol Sci 2023; 24:11818. [PMID: 37511577 PMCID: PMC10380244 DOI: 10.3390/ijms241411818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
A series of new types of composites (biopolymer-silica materials) are proposed as selective and effective adsorbents. A new procedure for the synthesis of chitosan-nanosilica composites (ChNS) and chitosan-silica gel composites (ChSG) using geometrical modification of silica and mechanosorption of chitosan is applied. The highest adsorption efficiency was achieved at pH = 2, hence the desirability of modifications aimed at stabilizing chitosan in such conditions. The amount of chitosan in the synthesis grew to 1.8 times the adsorption capacity for the nanosilica-supported materials and 1.6 times for the silica gel-based composites. The adsorption kinetics of anionic dyes (acid red AR88) was faster for ChNS than for ChSG, which results from a silica-type effect. The various structural, textural, and physicochemical aspects of the chitosan-silica adsorbents were analyzed via small-angle X-ray scattering, scanning electron microscopy, low-temperature gas (nitrogen) adsorption, and potentiometric titration, as well as their adsorption effectiveness towards selected dyes. This indicates the synergistic effect of the presence of dye-binding groups of the chitosan component, and the developed interfacial surface of the silica component in composites.
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Affiliation(s)
- Magdalena Blachnio
- Faculty of Chemistry, Maria Curie-Sklodowska University, M. Curie-Sklodowska Sq. 3, 20-031 Lublin, Poland
| | | | - Anna Derylo-Marczewska
- Faculty of Chemistry, Maria Curie-Sklodowska University, M. Curie-Sklodowska Sq. 3, 20-031 Lublin, Poland
| | - Liudmyla V Nosach
- Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, 17 General Naumov Str., 03164 Kyiv, Ukraine
| | - Eugeny F Voronin
- Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, 17 General Naumov Str., 03164 Kyiv, Ukraine
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3
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Liu C, Pfister B, Osman R, Ritter M, Heutinck A, Sharma M, Eicke S, Fischer-Stettler M, Seung D, Bompard C, Abt MR, Zeeman SC. LIKE EARLY STARVATION 1 and EARLY STARVATION 1 promote and stabilize amylopectin phase transition in starch biosynthesis. SCIENCE ADVANCES 2023; 9:eadg7448. [PMID: 37235646 DOI: 10.1126/sciadv.adg7448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Starch, the most abundant carbohydrate reserve in plants, primarily consists of the branched glucan amylopectin, which forms semi-crystalline granules. Phase transition from a soluble to an insoluble form depends on amylopectin architecture, requiring a compatible distribution of glucan chain lengths and a branch-point distribution. Here, we show that two starch-bound proteins, LIKE EARLY STARVATION 1 (LESV) and EARLY STARVATION 1 (ESV1), which have unusual carbohydrate-binding surfaces, promote the phase transition of amylopectin-like glucans, both in a heterologous yeast system expressing the starch biosynthetic machinery and in Arabidopsis plants. We propose a model wherein LESV serves as a nucleating role, with its carbohydrate-binding surfaces helping align glucan double helices to promote their phase transition into semi-crystalline lamellae, which are then stabilized by ESV1. Because both proteins are widely conserved, we suggest that protein-facilitated glucan crystallization may be a general and previously unrecognized feature of starch biosynthesis.
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Affiliation(s)
- Chun Liu
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Barbara Pfister
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Rayan Osman
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Maximilian Ritter
- Institute for Building Materials, ETH Zurich, Stefano-Franscini-Platz 3, 8093 Zurich, Switzerland
| | - Arvid Heutinck
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Mayank Sharma
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Simona Eicke
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | | | - David Seung
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Coralie Bompard
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Melanie R Abt
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
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4
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Bobbili KB, Sivaji N, Priya B, Suguna K, Surolia A. Structure and interactions of the phloem lectin (phloem protein 2) Cus17 from Cucumis sativus. Structure 2023; 31:464-479.e5. [PMID: 36882058 DOI: 10.1016/j.str.2023.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/28/2022] [Accepted: 02/08/2023] [Indexed: 03/08/2023]
Abstract
Phloem protein 2 (PP2) contributes crucially to phloem-based defense in plants by binding to carbohydrates displayed by pathogens. However, its three-dimensional structure and the sugar binding site remained unexplored. Here, we report the crystal structure of the dimeric PP2 Cus17 from Cucumis sativus in its apo form and complexed with nitrobenzene, N-acetyllactosamine, and chitotriose. Each protomer of Cus17 consists of two antiparallel four-stranded twisted β sheets, a β hairpin, and three short helices forming a β sandwich architectural fold. This structural fold has not been previously observed in other plant lectin families. Structure analysis of the lectin-carbohydrate complexes reveals an extended carbohydrate binding site in Cus17, composed mostly of aromatic amino acids. Our studies suggest a highly conserved tertiary structure and a versatile binding site capable of recognizing motifs common to diverse glycans on plant pathogens/pests, which makes the PP2 family suited for phloem-based plant defense.
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Affiliation(s)
- Kishore Babu Bobbili
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Nukathoti Sivaji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Badma Priya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Kaza Suguna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
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5
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Hernández-Lima J, Ramírez-Gualito K, Quiroz-García B, Silva-Portillo AL, Carrillo-Nava E, Cortés-Guzmán F. How solvent determines the molecular reactive conformation and the selectivity: Solvation spheres and energy. Front Chem 2022; 10:1012769. [PMID: 36247683 PMCID: PMC9557062 DOI: 10.3389/fchem.2022.1012769] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
In solution, the solvent determines the molecular conformation and the chemical reaction viability and selectivity. When solvent-solute and solvent-solvent interactions present similar strengths, explicit salvation is the best way to describe a system. The problem to solve is how big the explicit shell should be. In this paper, we want to answer one of the fundamental questions in the implementation of explicit solvation, exactly how many solvent molecules should be added and where they should be placed. Here we determine the first solvent sphere around a molecule and describe how it controls the conformation and selectivity of a selected reaction. NMR experiments were carried out to identify the number of solvent molecules around the solute that constitutes the first solvent sphere, and the interaction between this solvent sphere and the solute was detected using DFT and QTAIM calculations. A new approach to the solvation energy is presented. Finally, we established the role of solvent molecules in the conformation of the solute and in the transition states that produce the two possible products of the reaction.
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Affiliation(s)
| | - Karla Ramírez-Gualito
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Ciudad de Mexico, México
| | | | | | | | - Fernando Cortés-Guzmán
- Instituto de Química, Unversidad Nacional Autónoma de México, Coyoacan, Mexico
- *Correspondence: Fernando Cortés-Guzmán,
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6
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Tryptophan, more than just an interfacial amino acid in the membrane activity of cationic cell-penetrating and antimicrobial peptides. Q Rev Biophys 2022; 55:e10. [PMID: 35979810 DOI: 10.1017/s0033583522000105] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Trp is unique among the amino acids since it is involved in many different types of noncovalent interactions such as electrostatic and hydrophobic ones, but also in π-π, π-cation, π-anion and π-ion pair interactions. In membranotropic peptides and proteins, Trp locates preferentially at the water-membrane interface. In antimicrobial or cell-penetrating peptides (AMPs and CPPs respectively), Trp is well-known for its strong role in the capacity of these peptides to interact and affect the membrane organisation of both bacteria and animal cells at the level of the lipid bilayer. This essential amino acid can however be involved in other types of interactions, not only with lipids, but also with other membrane partners, that are crucial to understand the functional roles of membranotropic peptides. This review is focused on this latter less known role of Trp and describes in details, both in qualitative and quantitative ways: (i) the physico-chemical properties of Trp; (ii) its effect in CPP internalisation; (iii) its importance in AMP activity; (iv) its role in the interaction of AMPs with glycoconjugates or lipids in bacteria membranes and the consequences on the activity of the peptides; (v) its role in the interaction of CPPs with negatively charged polysaccharides or lipids of animal membranes and the consequences on the activity of the peptides. We intend to bring highlights of the physico-chemical properties of Trp and describe its extensive possibilities of interactions, not only at the well-known level of the lipid bilayer, but with other less considered cell membrane components, such as carbohydrates and the extracellular matrix. The focus on these interactions will allow the reader to reevaluate reported studies. Altogether, our review gathers dedicated studies to show how unique are Trp properties, which should be taken into account to design future membranotropic peptides with expected antimicrobial or cell-penetrating activity.
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7
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Escobar C, Artigas V, Bacho M, Trujillo A. π-halogen interaction on the crystalline packing of 1,3,5-tris(4-bromophenyl)-1,3,5-triazine-2,4,6-trione·[solvate]. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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8
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9
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Abstract
Carbohydrate recognition is crucial for biological processes ranging from development to immune system function to host-pathogen interactions. The proteins that bind glycans are faced with a daunting task: to coax these hydrophilic species out of water and into a binding site. Here, we examine the forces underlying glycan recognition by proteins. Our previous bioinformatic study of glycan-binding sites indicated that the most overrepresented side chains are electron-rich aromatic residues, including tyrosine and tryptophan. These findings point to the importance of CH-π interactions for glycan binding. Studies of CH-π interactions show a strong dependence on the presence of an electron-rich π system, and the data indicate binding is enhanced by complementary electronic interactions between the electron-rich aromatic ring and the partial positive charge of the carbohydrate C-H protons. This electronic dependence means that carbohydrate residues with multiple aligned highly polarized C-H bonds, such as β-galactose, form strong CH-π interactions, whereas less polarized residues such as α-mannose do not. This information can guide the design of proteins to recognize sugars and the generation of ligands for proteins, small molecules, or catalysts that bind sugars.
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Affiliation(s)
- Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Roger C. Diehl
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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10
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Gim S, Fittolani G, Yu Y, Zhu Y, Seeberger PH, Ogawa Y, Delbianco M. Targeted Chemical Modifications Identify Key Features of Carbohydrate Assemblies and Generate Tailored Carbohydrate Materials. Chemistry 2021; 27:13139-13143. [PMID: 34251709 PMCID: PMC8518775 DOI: 10.1002/chem.202102164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 12/11/2022]
Abstract
The molecular level description of carbohydrate assemblies is hampered by their structural complexity and the lack of suitable analytical methods. Here, we employed systematic chemical modifications to identify key non-covalent interactions that triggered the supramolecular assembly of a disaccharide model. While some modifications disrupted the supramolecular organization, others were tolerated, delivering important information on the aggregation process. The screening identified new geometries, including nanotubes, and twisted ribbons that were characterized with electron tomography and electron diffraction (ED) methods. This work demonstrates that the combination of synthetic chemistry and ED methods is a powerful tool to draw correlations between the molecular structure and the nanoscale architecture of carbohydrate assemblies.
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Affiliation(s)
- Soeun Gim
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Giulio Fittolani
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Yang Yu
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Simpson Querrey InstituteNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Yuntao Zhu
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Peter H. Seeberger
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Yu Ogawa
- Univ. Grenoble AlpesCNRS, CERMAV38000GrenobleFrance
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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11
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Takemura H. Synthesis of Azacalixarenes and Development of Their Properties. Molecules 2021; 26:4885. [PMID: 34443473 PMCID: PMC8398485 DOI: 10.3390/molecules26164885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
This review focuses on the synthesis, structure, and interactions of metal ions, the detection of some weak interactions using the structure, and the construction of supramolecules of azacalixarenes that have been reported to date. Azacalixarenes are characterized by the presence of shallow or deep cavities, the simultaneous presence of a basic nitrogen atom and an acidic phenolic hydroxyl group, and the ability to introduce various side chains into the cyclic skeleton. These molecules can be given many functions by substituting groups on the benzene ring, modifying phenolic hydroxyl groups, and converting side chains. The author discusses the evidence of azacalixarene utilizing these characteristics.
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Affiliation(s)
- Hiroyuki Takemura
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Mejirodai 2-8-1, Bunkyo-ku, Tokyo 112-8681, Japan
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12
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Tamez-Fernández JF, Soto-Suárez FM, Estrada-Chavarría YD, Quijano-Quiñones RF, Toscano RA, Cuétara-Guadarrama F, Duarte-Alaniz V, Ibarra-Rivera TR, Quiroz-García B, Martínez-Otero D, Ramírez-Gualito K, Barquera-Lozada JE, Rivas-Galindo VM, Cuevas G. Effect of the n O → π* C═O Interaction on the Conformational Preference of 1,3-Diketones: A Case Study of Riolozatrione Derivatives. J Org Chem 2021; 86:9540-9551. [PMID: 34210132 DOI: 10.1021/acs.joc.1c00847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cyclopropane ring-opening reaction of riolozatrione, a natural product obtained from Jatropha dioica, afforded a 2,2-disubstituted 1,3-cyclohexandione displaying an alkyl methyl ether group at position 5. The conformational analysis of this product showed a high preference for the trans-diaxial conformation in both solution and solid state. Such conformation was possible from the noncovalent intramolecular nX → π*C═O interactions (X = an element having an unshared electron pair), allowing the determination of the interaction energies. Since the nX → π*C═O interactions can be regarded as additive, the energy values ranged from 4.52 to 6.51 kcal mol-1 for each carbonyl group with a strong dependency on the interatomic distances. The rigorous analysis of the electron density in the topological theory of atoms in molecules framework clearly shows that the origin of O-C═O interactions are through the nO → π*C═O electron transfer mechanism. Such interactions are slightly weaker than a canonical hydrogen bond but seemingly stronger than a van der Waals interaction. This interaction must be considered as a stereoelectronic effect due the electronic transfer between the interacting groups, which are limited by their relative stereochemistry and can be represented by a bond-no bond interaction, causing the pyramidalization of the carbonyl, which is the charge acceptor group.
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Affiliation(s)
- Juan F Tamez-Fernández
- Facultad de Medicina, Departamento de Química Analítica, Universidad Autonoma de Nuevo Leon, 66455 Monterrey, Nuevo León, Mexico
| | - Fátima M Soto-Suárez
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Yolanda D Estrada-Chavarría
- Facultad de Medicina, Departamento de Química Analítica, Universidad Autonoma de Nuevo Leon, 66455 Monterrey, Nuevo León, Mexico
| | - Ramiro F Quijano-Quiñones
- Facultad de Química, Universidad Autónoma de Yucatán. Laboratorio de Química Teórica, Calle 43 No. 613 por calle 90, 97069 Colonia Inalámbrica, Mérida Yucatán, Mexico
| | - Rubén A Toscano
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Fabián Cuétara-Guadarrama
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Víctor Duarte-Alaniz
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Tannya R Ibarra-Rivera
- Facultad de Medicina, Departamento de Química Analítica, Universidad Autonoma de Nuevo Leon, 66455 Monterrey, Nuevo León, Mexico
| | - Beatriz Quiroz-García
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Diego Martínez-Otero
- Carretera Toluca-Atlacomulco, Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM, km 14.5, Toluca, 50200 Estado de México, Mexico
| | - Karla Ramírez-Gualito
- Facultad de Ingeniería, Universidad Anáhuac México, Avenida Universidad Anáhuac 46, Col. Lomas Anáhuac, Huixquilucan, 52786 Estado de México, Mexico
| | - José Enrique Barquera-Lozada
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
| | - Verónica M Rivas-Galindo
- Facultad de Medicina, Departamento de Química Analítica, Universidad Autonoma de Nuevo Leon, 66455 Monterrey, Nuevo León, Mexico
| | - Gabriel Cuevas
- Instituto de Química, Circuito Exterior, Ciudad Universitaria, Universidad Nacional Autónoma de México, Delegación Coyoacán, 04510 Ciudad de México, Mexico
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13
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Santana AG, Díaz-Casado L, Montalvillo L, Jiménez-Moreno E, Mann E, Asensio JL. Aromatic interactions in Glycochemistry: from molecular recognition to catalysis. Curr Med Chem 2021; 29:1208-1218. [PMID: 34254906 DOI: 10.2174/0929867328666210709120216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/05/2021] [Accepted: 05/13/2021] [Indexed: 11/22/2022]
Abstract
Aromatic platforms are ubiquitous recognition motifs occurring in protein carbohydrate binding domains (CBDs), RNA receptors and enzymes. They stabilize the glycoside/receptor complexes by participating in stacking CH/π interactions with either the α- or β- face of the corresponding pyranose units. In addition, the role played by aromatic units in the stabilization of glycoside cationic transition states has started being recognized in recent years. Extensive studies carried out during the last decade have allowed to dissect the main contributing forces that stabilize the carbohydrate/aromatic complexes, while helping delineate not only the standing relationship between the glycoside/aromatic chemical structures and the strength of this interaction, but also their potential influence on glycoside reactivity.
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Affiliation(s)
| | | | | | | | - Enrique Mann
- Instituto de Química Orgánica General (IQOG-CSIC), Madrid, Spain
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14
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Pontoni L, Roviello V, Race M, Savignano L, van Hullebusch ED, Esposito G, Pirozzi F, Fabbricino M. Supramolecular aggregation of colloidal natural organic matter masks priority pollutants released in water from peat soil. ENVIRONMENTAL RESEARCH 2021; 195:110761. [PMID: 33524333 DOI: 10.1016/j.envres.2021.110761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Natural organic matter (NOM) from Sphagnum peat soil is extracted in water and subjected to several investigations to obtain structural and conformational information. Data show that the extracted NOM is self-organized in colloidal aggregates of variable sizes (from nano to micro scales, depending on the solvent composition, i.e., ultrapure water, solutions with denaturing agents, acetone, ethanol). Aggregates are formed by highly heterogeneous classes of organic compounds. According to the results of nuclear magnetic resonance and fluorescence measurements, the three-dimensional structure of aggregates, revealed by scanning electron microscope imaging, is supposed to be stabilized by the exposition of polar functional groups to the solvent, with consequent formation of hydrogen bonds, dipole-interactions and cation bridging. In contrast, the inner part of the aggregates displays hydrophobic features and is hypothesized to be further reinforced by the establishment of π-stacking interactions. The structure is assumed to be a supramolecular aggregation of small-medium oligomeric fragments (Max 750 Da) in which priority pollutants are entrapped by dispersive forces. The structures are shown to be nanosized spheroidal particles further aggregated to form higher dimension supra-structures. Carbohydrates play primary role, stabilizing the structure and giving marked hydrophilic properties to the aggregates.
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Affiliation(s)
- Ludovico Pontoni
- Department of Civil, Architectural and Environmental Engineering (DICEA), University of Naples Federico II, Via Claudio 21, 80125, Naples, Italy; BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli "Federico II", Portici (NA), Italy.
| | - Valentina Roviello
- Department of Chemical, Materials and Industrial Production Engineering (DICMaPI), University of Naples Federico II, Piazzale V. Tecchio 80, 80125, Naples, Italy
| | - Marco Race
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, Via Di Biasio 43, Cassino, 03043, Italy
| | - Luigi Savignano
- Department of Chemical Sciences, University of Naples Federico II, Complesso di Monte S. Angelo, Via Cinthia, I-80126, Naples (NA), Italy
| | - Eric D van Hullebusch
- Université de Paris, Institut de Physique Du Globe de Paris, CNRS, UMR 7154, F-75238, Paris, France
| | - Giovanni Esposito
- Department of Civil, Architectural and Environmental Engineering (DICEA), University of Naples Federico II, Via Claudio 21, 80125, Naples, Italy
| | - Francesco Pirozzi
- Department of Civil, Architectural and Environmental Engineering (DICEA), University of Naples Federico II, Via Claudio 21, 80125, Naples, Italy; BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli "Federico II", Portici (NA), Italy
| | - Massimiliano Fabbricino
- Department of Civil, Architectural and Environmental Engineering (DICEA), University of Naples Federico II, Via Claudio 21, 80125, Naples, Italy; BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli "Federico II", Portici (NA), Italy
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15
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Syed A, Battula H, Mishra S, Jayanty S. Distinct Tetracyanoquinodimethane Derivatives: Enhanced Fluorescence in Solutions and Unprecedented Cation Recognition in the Solid State. ACS OMEGA 2021; 6:3090-3105. [PMID: 33553926 PMCID: PMC7860107 DOI: 10.1021/acsomega.0c05486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Tetracyanoquinodimethane (TCNQ) is known to react with various amines to generate substituted TCNQ derivatives with remarkable optical and nonlinear optical characteristics. The choice of amine plays a crucial role in the outcome of molecular material attributes. Especially, mono/di-substituted TCNQ's possessing strong fluorescence in solutions than solids are deficient. Furthermore, cation recognition in the solid-state TCNQ derivatives is yet undetermined. In this article, we present solution-enhanced fluorescence and exclusive solid-state recognition of K+ ion achieved through the selection of 4-(4-aminophenyl)morpholin-3-one (APM) having considerable π-conjugation and carbonyl (C=O) functionality, particularly in the ring. TCNQ when reacted with APM, in a single-step reaction, resulted in two well-defined distinct compounds, namely, 7,7-bis(4-(4-aminophenyl)morpholin-3-ono)dicyanoquinodimethane (BAPMDQ [1], yellow) and 7,7,8-(4-(4-aminophenyl)morpholin-3-ono)tricyanoquinodimethane (APMTQ [2], red), with increased fluorescence intensity in solutions than their solids. Crystal structure investigation revealed extensive C-H-π interactions and strong H-bonding in [1], whereas moderate to weak interactions in [2]. Surprisingly, simple mechanical grinding during KBr pellet preparation with [1, 2] triggered unidentified cation recognition with a profound color change (in ∼1 min) detected by the naked eye, accompanied by a drastic enhancement of fluorescence, proposed due to the presence of carbonyl functionality, noncovalent intermolecular interactions, and molecular assemblies in [1, 2] solids. Cation recognition was also noted with various other salts as well (KCl, KI, KSCN, NH4Cl, NH4Br, etc.). Currently, the recognition mechanism of K+ ion in [1, 2] is demonstrated by the strong electrostatic interaction of K+ ion with CO and simultaneously cation-π interaction of K+ with the phenyl ring of APM, supported by experimental and computational studies. Computational analysis also revealed that a strong cation-π interaction occurred between the K+ ion and the phenyl ring (APM) in [2] than in [1] (ΔG binding calculated as ∼16.3 and ∼25.2 kcal mol-1 for [1] and [2], respectively) providing additional binding free energy. Thus, both electrostatic and cation-π interactions lead to the recognition. Scanning electron microscopy of drop-cast films showed microcrystalline "roses" in [1] and micro/nano "aggregates" in [2]. Optical band gap (∼3.565 eV) indicated [1, 2] as wide-band-gap materials. The current study demonstrates fascinating novel products obtained by single-pot reaction, resulting in contrasting optical properties in solutions and experiencing cation recognition capability exclusively in the solid state.
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Affiliation(s)
- Anwarhussaini Syed
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Jawaharnagar, Shameerpet Mandal, Medchal Dist., Hyderabad 500078, Telangana State, India
| | - Himabindu Battula
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Jawaharnagar, Shameerpet Mandal, Medchal Dist., Hyderabad 500078, Telangana State, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Subbalakshmi Jayanty
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Jawaharnagar, Shameerpet Mandal, Medchal Dist., Hyderabad 500078, Telangana State, India
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16
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Zhang S, Chen KY, Zou X. Carbohydrate-Protein Interactions: Advances and Challenges. COMMUNICATIONS IN INFORMATION AND SYSTEMS 2021; 21:147-163. [PMID: 34366717 DOI: 10.4310/cis.2021.v21.n1.a7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A carbohydrate, also called saccharide in biochemistry, is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms. For example, sugars are low molecular-weight carbohydrates, and starches are high molecular-weight carbohydrates. Carbohydrates are the most abundant organic substances in nature and essential constituents of all living things. Protein-carbohydrate interactions play important roles in many biological processes, such as cell growth, differentiation, and aggregation. They also have broad applications in pharmaceutical drug design. In this review, we will summarize the characteristic features of protein-carbohydrate interactions and review the computational methods for structure prediction, energy calculations, and kinetic studies of protein-carbohydrate complexes. Finally, we will discuss the challenges in this field.
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Affiliation(s)
- Shuang Zhang
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Kyle Yu Chen
- Rock Bridge High School, 4303 South Providence Rd, Columbia, MO 65203, USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
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17
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Kapros A, Balázs A, Harmat V, Háló A, Budai L, Pintér I, Menyhárd DK, Perczel A. Configuration-Controlled Crystal and/or Gel Formation of Protected d-Glucosamines Supported by Promiscuous Interaction Surfaces and a Conformationally Heterogeneous Solution State. Chemistry 2020; 26:11643-11655. [PMID: 32333713 DOI: 10.1002/chem.202000882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/17/2020] [Indexed: 11/10/2022]
Abstract
The configuration-dependent self-association mode of the two anomers of O-Ac,N-Fmoc-d-glucosamine, a foldamer building block, leading to gel and/or single crystal formation is described. The β-anomer of the sugar amino acid (2) forms a gel from various solvents (confirmed by SEM, rheology measurements, NMR, and ECD spectroscopy), whereas the α-anomer (1) does not form a gel with any solvent tested. Transition from the solution state to a gel is coupled to a concurrent shift of the Fmoc-groups: from a freely rotating (almost symmetrical) to a specific, asymmetric orientation. Whereas the crystal structure of the α-anomer is built as an evenly packed 3D system, the β-anomer forms a looser superstructure of well-packed 2D layers. Modeling indicates that in the lowest energy, but scarcely sampled conformer of the β-anomer, the Fmoc-group bends above the sugar moiety, stabilized by intramolecular CH↔π interactions between the aromatic rings. It is concluded that possessing an extended and promiscuous interaction surface and a conformationally heterogeneous solution state are among the basic requirements of gel formation for a candidate molecule.
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Affiliation(s)
- Anita Kapros
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Attila Balázs
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Veronika Harmat
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary.,MTA-ELTE Protein Modelling Research Group, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Adrienn Háló
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Lívia Budai
- Department of Pharmaceutics, Semmelweis University, Hőgyes Endre utca 7, Budapest, 1092, Hungary
| | - István Pintér
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Dóra K Menyhárd
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary.,MTA-ELTE Protein Modelling Research Group, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary.,MTA-ELTE Protein Modelling Research Group, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
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18
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Guerrero EB, de Villegas RMD, Soria MA, Santangelo MP, Campos E, Talia PM. Characterization of two GH5 endoglucanases from termite microbiome using synthetic metagenomics. Appl Microbiol Biotechnol 2020; 104:8351-8366. [DOI: 10.1007/s00253-020-10831-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
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19
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Houser J, Kozmon S, Mishra D, Hammerová Z, Wimmerová M, Koča J. The CH-π Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification. Chemistry 2020; 26:10769-10780. [PMID: 32208534 DOI: 10.1002/chem.202000593] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/18/2020] [Indexed: 12/16/2022]
Abstract
The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, and cell-cell adhesion (e.g., in cancer metastasis). Carbohydrates interact with proteins mainly through hydrogen bonding, metal-ion-mediated interaction, and non-polar dispersion interactions. The role of dispersion-driven CH-π interactions (stacking) in protein-carbohydrate recognition has been underestimated for a long time considering the polar interactions to be the main forces for saccharide interactions. However, over the last few years it turns out that non-polar interactions are equally important. In this study, we analyzed the CH-π interactions employing bioinformatics (data mining, structural analysis), several experimental (isothermal titration calorimetry (ITC), X-ray crystallography), and computational techniques. The Protein Data Bank (PDB) has been used as a source of structural data. The PDB contains over 12 000 protein complexes with carbohydrates. Stacking interactions are very frequently present in such complexes (about 39 % of identified structures). The calculations and the ITC measurement results suggest that the CH-π stacking contribution to the overall binding energy ranges from 4 up to 8 kcal mol-1 . All the results show that the stacking CH-π interactions in protein-carbohydrate complexes can be considered to be a driving force of the binding in such complexes.
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Affiliation(s)
- Josef Houser
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Stanislav Kozmon
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538, Bratislava, Slovak Republic
| | - Deepti Mishra
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Zuzana Hammerová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic.,Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Jaroslav Koča
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
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20
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Tian Y, Wang L, Fu G, Zhang C, Lu R, Dong X. Theoretical investigation on the substituent effects of the C–H/π interaction. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02595-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Rojo-Portillo T, Reyes-López E, Hernández-Huerta E, Quiroz-García B, Joseph-Nathan P, Sánchez-Castellanos M, Cuétara-Guadarrama F, Cuevas G. Is the VCD spectrum a fingerprint of the conformational population? The conformation of perezone in the spotlight. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Cuétara-Guadarrama F, Hernández-Huerta E, Rojo-Portillo T, Reyes-López E, Jiménez-Barbero J, Cuevas G. Experimental and theoretical study of the role of CH/π interactions in the aminolysis reaction of acetyl galactoside. Carbohydr Res 2019; 486:107821. [PMID: 31580966 DOI: 10.1016/j.carres.2019.107821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 09/02/2019] [Accepted: 09/18/2019] [Indexed: 11/16/2022]
Abstract
Molecular recognition of saccharides is a growing field, which has many implications in cancer therapy, drug discovery, and cellular communication among others. The participation of CH/π interactions in this event is well known. Nevertheless, the intrinsic role of CH/π for modulating chemical reactions is still far from being applicable. In this experimental and computational work we have evaluated the participation of CH/π interactions in the aminolysis reaction of acetyl galactoside promoted with different 6-substituted 2(1H)-pyridones. Two features have been incorporated to the promoter molecular structure, on one end the promoting pyridone group and on the other end the recognition moiety, joined together by an alkyne spacer. The small increment in the observed pseudo-first-order rate constant values (kobs) was related to the stability of the transition state provided by noncovalent interactions, including CH/π interactions. A longer alkyne spacer was necessary to improve the molecular recognition of the galactoside substrate. The trend of the calculated activation energy values (ΔERTS) was in good accordance with the experimental rate constant values.
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Affiliation(s)
- Fabián Cuétara-Guadarrama
- Departamento de Fisicoquímica, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Eduardo Hernández-Huerta
- Departamento de Fisicoquímica, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Tania Rojo-Portillo
- Departamento de Fisicoquímica, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Elizabeth Reyes-López
- Departamento de Fisicoquímica, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Jesús Jiménez-Barbero
- Centro de Investigaciones Biológicas (CIB-CSIC), 28040, Madrid, Spain; Center for Cooperative Research in Biosciences (CIC-bioGUNE), 48160, Derio-Bizkaia, Spain; Basque Foundation for Science, Ikerbasque, 48013, Bilbao, Spain
| | - Gabriel Cuevas
- Departamento de Fisicoquímica, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico.
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23
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Montalvillo-Jiménez L, Santana AG, Corzana F, Jiménez-Osés G, Jiménez-Barbero J, Gómez AM, Asensio JL. Impact of Aromatic Stacking on Glycoside Reactivity: Balancing CH/π and Cation/π Interactions for the Stabilization of Glycosyl-Oxocarbenium Ions. J Am Chem Soc 2019; 141:13372-13384. [PMID: 31390207 DOI: 10.1021/jacs.9b03285] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Carbohydrate/aromatic stacking represents a recurring key motif for the molecular recognition of glycosides, either by protein binding domains, enzymes, or synthetic receptors. Interestingly, it has been proposed that aromatic residues might also assist in the formation/cleavage of glycosidic bonds by stabilizing positively charged oxocarbenium-like intermediates/transition states through cation/π interactions. While the significance of aromatic stacking on glycoside recognition is well stablished, its impact on the reactivity of glycosyl donors is yet to be explored. Herein, we report the first experimental study on this relevant topic. Our strategy is based on the design, synthesis, and reactivity evaluation of a large number of model systems, comprising a wide range of glycosidic donor/aromatic complexes. Different stacking geometries and dynamic features, anomeric leaving groups, sugar configurations, and reaction conditions have been explicitly considered. The obtained results underline the opposing influence exerted by van der Waals and Coulombic forces on the reactivity of the carbohydrate/aromatic complex: depending on the outcome of this balance, aromatic platforms can indeed exert a variety of effects, stretching from reaction inhibition all the way to rate enhancements. Although aromatic/glycosyl cation contacts are highly dynamic, the conclusions of our study suggest that aromatic assistance to glycosylation processes must indeed be feasible, with far reaching implications for enzyme engineering and organocatalysis.
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Affiliation(s)
| | - Andrés G Santana
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain
| | - Francisco Corzana
- Departamento Quı́mica and Centro de Investigación en Sı́ntesis Quı́mica , Universidad de La Rioja , 26006 Logroño , Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC-bioGUNE) , 48160 Derio , Spain
| | - Jesús Jiménez-Barbero
- Center for Cooperative Research in Biosciences (CIC-bioGUNE) , 48160 Derio , Spain.,Basque Foundation for Science, Ikerbasque , 48013 Bilbo , Spain
| | - Ana M Gómez
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain
| | - Juan Luis Asensio
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain
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24
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Kanao E, Kubo T, Naito T, Matsumoto T, Sano T, Yan M, Otsuka K. Differentiating π Interactions by Constructing Concave/Convex Surfaces Using a Bucky Bowl Molecule, Corannulene in Liquid Chromatography. Anal Chem 2018; 91:2439-2446. [DOI: 10.1021/acs.analchem.8b05260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Eisuke Kanao
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takuya Kubo
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Toyohiro Naito
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takatoshi Matsumoto
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Tomoharu Sano
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts Lowell, One University Avenue, Lowell, Massachusetts 01854, United States
| | - Koji Otsuka
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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25
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Rabon AM, Goolsby KL, Young MC. One-dimensional networks formed via the self-assembly of anthracenedibenzoic acid with zinc(II). ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2018; 74:1774-1780. [PMID: 30516164 DOI: 10.1107/s2053229618016649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/22/2018] [Indexed: 11/10/2022]
Abstract
Self-assembly of metal-organic coordination polymers occurs because of enthalpically favorable interactions. In the case of the bulky 4,4'-(anthracene-9,10-diyl)dibenzoic acid ligand (abdH2), we demonstrate that the presence of numerous π-π and C-H...π interactions outweigh the formation of saturated coordination complexes with zinc, leading to the formation of a dimethylformamide (DMF) solvate, namely 4,4'-(anthracene-9,10-diyl)dibenzoic acid dimethylformamide disolvate, C28H18O4·2C3H7NO or [(abdH2)(DMF)2], at low concentrations of zinc. Meanwhile, at higher zinc concentrations, the abdH2 ligand gives rise to the nonporous one-dimensional coordination polymer catena-poly[[bis(dimethylformamide-κO)zinc(II)]-μ-4,4'-(anthracene-9,10-diyl)dibenzoato-κ2O:O'], [Zn(C28H16O4)(C3H7NO)2]n or [Zn(abd)(DMF)2]n, when assembled in dimethylformamide, while a related compound is observed when N,N-dimethylacetamide (DMA) is used as the solvent, namely catena-poly[[[bis(N,N-dimethylacetamide-κO)zinc(II)]-μ-4,4'-(anthracene-9,10-diyl)dibenzoato-κ2O:O'] N,N-dimethylacetamide monosolvate], {[Zn(C28H16O4)(C4H9NO)2]·C4H9NO}n or {[Zn(abd)(DMA)2]·DMA}n. Attempts to use other amide-based solvents did not give rise to any other assembled structures.
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Affiliation(s)
- Allison M Rabon
- Department of Chemistry and Biochemistry, School of Green Chemistry and Engineering, University of Toledo, 2801 W. Bancroft St., Toledo, OH 43606, USA
| | - Kayla L Goolsby
- Department of Chemistry and Biochemistry, School of Green Chemistry and Engineering, University of Toledo, 2801 W. Bancroft St., Toledo, OH 43606, USA
| | - Michael C Young
- Department of Chemistry and Biochemistry, School of Green Chemistry and Engineering, University of Toledo, 2801 W. Bancroft St., Toledo, OH 43606, USA
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26
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Blaum BS, Neu U, Peters T, Stehle T. Spin ballet for sweet encounters: saturation-transfer difference NMR and X-ray crystallography complement each other in the elucidation of protein-glycan interactions. Acta Crystallogr F Struct Biol Commun 2018; 74:451-462. [PMID: 30084394 PMCID: PMC6096479 DOI: 10.1107/s2053230x18006581] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/28/2018] [Indexed: 03/11/2023] Open
Abstract
Biomolecular NMR spectroscopy has limitations in the determination of protein structures: an inherent size limit and the requirement for expensive and potentially difficult isotope labelling pose considerable hurdles. Therefore, structural analysis of larger proteins is almost exclusively performed by crystallography. However, the diversity of biological NMR applications outperforms that of any other structural biology technique. For the characterization of transient complexes formed by proteins and small ligands, notably oligosaccharides, one NMR technique has recently proven to be particularly powerful: saturation-transfer difference NMR (STD-NMR) spectroscopy. STD-NMR experiments are fast and simple to set up, with no general protein size limit and no requirement for isotope labelling. The method performs best in the moderate-to-low affinity range that is of interest in most of glycobiology. With small amounts of unlabelled protein, STD-NMR experiments can identify hits from mixtures of potential ligands, characterize mutant proteins and pinpoint binding epitopes on the ligand side. STD-NMR can thus be employed to complement and improve protein-ligand complex models obtained by other structural biology techniques or by purely computational means. With a set of protein-glycan interactions from our own work, this review provides an introduction to the technique for structural biologists. It exemplifies how crystallography and STD-NMR can be combined to elucidate protein-glycan (and other protein-ligand) interactions in atomic detail, and how the technique can extend structural biology from simplified systems amenable to crystallization to more complex biological entities such as membranes, live viruses or entire cells.
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Affiliation(s)
- Bärbel S. Blaum
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Ursula Neu
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Thomas Peters
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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27
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Molecular dynamics simulations of theoretical cellulose nanotube models. Carbohydr Polym 2018; 190:331-338. [PMID: 29628255 DOI: 10.1016/j.carbpol.2018.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/26/2018] [Accepted: 03/05/2018] [Indexed: 11/23/2022]
Abstract
Nanotubes are remarkable nanoscale architectures for a wide range of potential applications. In the present paper, we report a molecular dynamics (MD) study of the theoretical cellulose nanotube (CelNT) models to evaluate their dynamic behavior in solution (either chloroform or benzene). Based on the one-quarter chain staggering relationship, we constructed six CelNT models by combining the two chain polarities (parallel (P) and antiparallel (AP)) and three symmetry operations (helical right (HR), helical left (HL), and rotation (R)) to generate a circular arrangement of molecular chains. Among the four models that retained the tubular form (P-HR, P-HL, P-R, and AP-R), the P-R and AP-R models have the lowest steric energies in benzene and chloroform, respectively. The structural features of the CelNT models were characterized in terms of the hydroxymethyl group conformation and intermolecular hydrogen bonds. Solvent structuring more clearly occurred with benzene than chloroform, suggesting that the CelNT models may disperse in benzene.
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28
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Analysis of Physicochemical Interaction of Aβ40 with a GM1 Ganglioside-Containing Lipid Membrane. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.8b00139] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Jütten L, Ramírez-Gualito K, Weilhard A, Albrecht B, Cuevas G, Fernández-Alonso MD, Jiménez-Barbero J, Schlörer NE, Diaz D. Exploring the Role of Solvent on Carbohydrate-Aryl Interactions by Diffusion NMR-Based Studies. ACS OMEGA 2018; 3:536-543. [PMID: 31457911 PMCID: PMC6641296 DOI: 10.1021/acsomega.7b01630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/28/2017] [Indexed: 05/26/2023]
Abstract
Carbohydrate-protein interactions play an important role in many molecular recognition processes. An exquisite combination of multiple factors favors the interaction of the receptor with one specific type of sugar, whereas others are excluded. Stacking CH-aromatic interactions within the binding site provide a relevant contribution to the stabilization of the resulting sugar-protein complex. Being experimentally difficult to detect and analyze, the key CH-π interaction features have been very often dissected using a variety of techniques and simple model systems. In the present work, diffusion NMR spectroscopy has been employed to separate the components of sugar mixtures in different solvents on the basis of their differential ability to interact through CH-π interactions with one particular aromatic cosolute in solution. The experimental data show that the properties of the solvent did also influence the diffusion behavior of the sugars present in the mixture, inhibiting or improving their separation. Overall, the results showed that, for the considered monosaccharide derivatives, their diffusion coefficient values and, consequently, their apparent molecular sizes and/or shapes depend on the balance between solute/cosolute as well as solute/solvent interactions. Thus, in certain media and in the presence of the aromatic cosolute, the studied saccharides that are more suited to display CH-π interactions exhibited a lower diffusion coefficient than the noncomplexing sugars in the mixture. However, when dissolved in another medium, the interaction with the solvent strongly competes with that of the aromatic cosolute.
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Affiliation(s)
- Linda Jütten
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Karla Ramírez-Gualito
- Centro
de Nanociencias y Micro y Nanotecnología, Instituto Politécnico Nacional, Avenida Luis Enrique Erro S/N, Unidad Profesional
Adolfo López Mateos, Zacatenco, C.P. 07738 Ciudad de México, México
| | - Andreas Weilhard
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Benjamin Albrecht
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Gabriel Cuevas
- Instituto
de Química, Universidad Nacional Autónoma de México,
Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán, C.P. 04510 Ciudad de México, México
| | | | - Jesús Jiménez-Barbero
- Centro
de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
- CIC
bioGUNE, Science and
Technology Park bld 801 A, 48160 Derio, Spain
- Basque Foundation
for Science, Ikerbasque, Maria Diaz de Haro 3, 48013 Bilbao, Spain
- Department
of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Spain
| | - Nils E. Schlörer
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
| | - Dolores Diaz
- Department
für Chemie, NMR-Abteilung, Universität
zu Köln, Greinstr.
4, 50939 Köln, Germany
- Centro
de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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Lacetera A, Berbís MÁ, Nurisso A, Jiménez-Barbero J, Martín-Santamaría S. Computational Chemistry Tools in Glycobiology: Modelling of Carbohydrate–Protein Interactions. COMPUTATIONAL TOOLS FOR CHEMICAL BIOLOGY 2017. [DOI: 10.1039/9781788010139-00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular modelling provides a major impact in the field of glycosciences, helping in the characterisation of the molecular basis of the recognition between lectins from pathogens and human glycoconjugates, and in the design of glycocompounds with anti-infectious properties. The conformational properties of oligosaccharides are complex, and therefore, the simulation of these properties is a challenging task. Indeed, the development of suitable force fields is required for the proper simulation of important problems in glycobiology, such as the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics, including O-linkages in oligo- and polysaccharides, and N- and O-linkages in glycoproteins. The computational description of representative examples is discussed, herein, related to biologically active oligosaccharides and their interaction with lectins and other proteins, and the new routes open for the design of glycocompounds with promising biological activities.
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Affiliation(s)
- Alessandra Lacetera
- Center for Biological Research CIB-CSIC. Ramiro de Maeztu, 9 28040-Madrid Spain
| | - M. Álvaro Berbís
- Center for Biological Research CIB-CSIC. Ramiro de Maeztu, 9 28040-Madrid Spain
| | - Alessandra Nurisso
- School of Pharmaceutical Sciences University of Geneva, University of Lausanne, Rue Michel Servet 1 CH-1211 Geneva 4 Switzerland
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31
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Cruz-Vásquez O, Bernal-Sánchez LJ, Cervantes R, Tiburcio J, Rojas A. Energetics and the molecular structure of an ion-paired supramolecular system in water. Phys Chem Chem Phys 2017; 19:19334-19340. [PMID: 28703831 DOI: 10.1039/c7cp02955a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The forces that bind the components of a host-guest complex to generate a stable supramolecular system are noncovalent interactions. The enthalpy of this association, ΔasH°, usually measured using calorimetry, quantifies the magnitude of such interactions and is directly related to the stability of the supramolecular complex formed. Using Calvet calorimetry to determine the enthalpies of solution and reaction in water, the enthalpy of association was derived for a supramolecular system formed by the anionic macrocycle anti-disulfodibenzo[24]crown-8 ([DSDB24C8]2-) and the dicationic guest paraquat [PQT]2+. The calorimetric results show an exothermic association process, which indicates the generation of strong interactions between the components of the ion pair. This is consistent with the formation of a stable supramolecular complex [PQT][DSDB24C8], whose spatial arrangement in aqueous solution is proposed based on spectroscopic analysis.
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Affiliation(s)
- Octavio Cruz-Vásquez
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), Ciudad de México, Mexico.
| | - Lan Jade Bernal-Sánchez
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), Ciudad de México, Mexico.
| | - Ruy Cervantes
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), Ciudad de México, Mexico.
| | - Jorge Tiburcio
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), Ciudad de México, Mexico.
| | - Aarón Rojas
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), Ciudad de México, Mexico.
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32
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Díaz-Gómez DG, Galindo-Murillo R, Cortés-Guzmán F. The Role of the DNA Backbone in Minor-Groove Ligand Binding. Chemphyschem 2017; 18:1909-1915. [PMID: 28463411 DOI: 10.1002/cphc.201700260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 11/08/2022]
Abstract
Molecular recognition between ligands and nucleic acids plays a key role in therapeutic activity. Some molecules interact with DNA in a nonbonded manner through intercalation or through the DNA grooves. The recognition of minor-groove binders is attributed to a set of hydrogen-bonding interactions between the binders and the hydrogen-bond-acceptor groups on the groove floor and walls. It is commonly considered that interactions with the sugar groups of the DNA backbone are insignificant and do not contribute to the binding affinity or the specificity. However, our group has found that the deoxyribose rings have a central function in the recognition and the intercalation of metal complexes into DNA. Herein, we determined the specific interactions between the binder CGP 40215A and the minor-groove atoms, based on the local properties of electron density. We found that specific interactions between the deoxyribose moiety within the backbone of DNA and the binder are essential for molecular recognition, and they are responsible for one third of the interaction energy.
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Affiliation(s)
- Dalia G Díaz-Gómez
- Instituto de Quimica, Universidad Nacional Autonoma de Mexico, Av. Universidad 3000, Col. Copilco Bajo, 4510, Mexico, Mexico
| | | | - Fernando Cortés-Guzmán
- Instituto de Quimica, Universidad Nacional Autonoma de Mexico, Av. Universidad 3000, Col. Copilco Bajo, 4510, Mexico, Mexico
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Unione L, Alcalá M, Echeverria B, Serna S, Ardá A, Franconetti A, Cañada FJ, Diercks T, Reichardt N, Jiménez-Barbero J. Fluoroacetamide Moieties as NMR Spectroscopy Probes for the Molecular Recognition of GlcNAc-Containing Sugars: Modulation of the CH-π Stacking Interactions by Different Fluorination Patterns. Chemistry 2017; 23:3957-3965. [PMID: 28124793 PMCID: PMC5484281 DOI: 10.1002/chem.201605573] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Indexed: 12/13/2022]
Abstract
We herein propose the use of fluoroacetamide and difluoroacetamide moieties as sensitive tags for the detection of sugar–protein interactions by simple 1H and/or 19F NMR spectroscopy methods. In this process, we have chosen the binding of N,N′‐diacetyl chitobiose, a ubiquitous disaccharide fragment in glycoproteins, by wheat‐germ agglutinin (WGA), a model lectin. By using saturation‐transfer difference (STD)‐NMR spectroscopy, we experimentally demonstrate that, under solution conditions, the molecule that contained the CHF2CONH‐ moiety is the stronger aromatic binder, followed by the analogue with the CH2FCONH‐ group and the natural molecule (with the CH3CONH‐ fragment). In contrast, the molecule with the CF3CONH‐ isoster displayed the weakest intermolecular interaction (one order of magnitude weaker). Because sugar–aromatic CH–π interactions are at the origin of these observations, these results further contribute to the characterization and exploration of these forces and offer an opportunity to use them to unravel complex recognition processes.
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Affiliation(s)
- Luca Unione
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 801 A, 48170, Derio, Spain
| | - Maria Alcalá
- Glycotechnology Laboratory, CICbiomaGUNE, Paseo Miramón, 20014, Donostia-San Sebastian, Spain
| | - Begoña Echeverria
- Glycotechnology Laboratory, CICbiomaGUNE, Paseo Miramón, 20014, Donostia-San Sebastian, Spain
| | - Sonia Serna
- Glycotechnology Laboratory, CICbiomaGUNE, Paseo Miramón, 20014, Donostia-San Sebastian, Spain
| | - Ana Ardá
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 801 A, 48170, Derio, Spain
| | - Antonio Franconetti
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, Profesor García González 1, 41012, Sevilla, Spain
| | - F Javier Cañada
- Department of Chemical and Physical Biology, CIB-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Tammo Diercks
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 801 A, 48170, Derio, Spain
| | - Niels Reichardt
- Glycotechnology Laboratory, CICbiomaGUNE, Paseo Miramón, 20014, Donostia-San Sebastian, Spain.,CIBER-BBN, Paseo Miramón, 20009, Donostia-San Sebastián, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 801 A, 48170, Derio, Spain.,Basque Foundation for Science, Maria Diaz de Haro 13, 48009, Bilbao, Spain.,Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, 48940, Leioa, Bizkaia, Spain
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Bhattacharya A, Naskar JP, Saha P, Ganguly R, Saha B, Choudhury ST, Chowdhury S. A new oxorhenium(V) complex with benzothiazole derived ligand: Relative stability and global chemical reactivity indices. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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35
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Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
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Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
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36
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Jana S, Hamre AG, Wildberger P, Holen MM, Eijsink VGH, Beckham GT, Sørlie M, Payne CM. Aromatic-Mediated Carbohydrate Recognition in Processive Serratia marcescens Chitinases. J Phys Chem B 2016; 120:1236-49. [PMID: 26824449 DOI: 10.1021/acs.jpcb.5b12610] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microorganisms use a host of enzymes, including processive glycoside hydrolases, to deconstruct recalcitrant polysaccharides to sugars. Processive glycoside hydrolases closely associate with polymer chains and repeatedly cleave glycosidic linkages without dissociating from the crystalline surface after each hydrolytic step; they are typically the most abundant enzymes in both natural secretomes and industrial cocktails by virtue of their significant hydrolytic potential. The ubiquity of aromatic residues lining the enzyme catalytic tunnels and clefts is a notable feature of processive glycoside hydrolases. We hypothesized that these aromatic residues have uniquely defined roles, such as substrate chain acquisition and binding in the catalytic tunnel, that are defined by their local environment and position relative to the substrate and the catalytic center. Here, we investigated this hypothesis with variants of Serratia marcescens family 18 processive chitinases ChiA and ChiB. We applied molecular simulation and free energy calculations to assess active site dynamics and ligand binding free energies. Isothermal titration calorimetry provided further insight into enthalpic and entropic contributions to ligand binding free energy. Thus, the roles of six aromatic residues, Trp-167, Trp-275, and Phe-396 in ChiA, and Trp-97, Trp-220, and Phe-190 in ChiB, have been examined. We observed that point mutation of the tryptophan residues to alanine results in unfavorable changes in the free energy of binding relative to wild-type. The most drastic effects were observed for residues positioned at the "entrances" of the deep substrate-binding clefts and known to be important for processivity. Interestingly, phenylalanine mutations in ChiA and ChiB had little to no effect on chito-oligomer binding, in accordance with the limited effects of their removal on chitinase functionality.
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Affiliation(s)
- Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
| | - Anne Grethe Hamre
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Patricia Wildberger
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Matilde Mengkrog Holen
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
| | - Morten Sørlie
- Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences , Ås 1430, Norway
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States
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37
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Zhang X, Wang S, Wu X, Liu S, Li D, Xu H, Gao P, Chen G, Wang L. Subsite-specific contributions of different aromatic residues in the active site architecture of glycoside hydrolase family 12. Sci Rep 2015; 5:18357. [PMID: 26670009 PMCID: PMC4680936 DOI: 10.1038/srep18357] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/16/2015] [Indexed: 01/22/2023] Open
Abstract
The active site architecture of glycoside hydrolase (GH) is a contiguous subregion of the enzyme constituted by residues clustered in the three-dimensional space, recognizing the monomeric unit of ligand through hydrogen bonds and hydrophobic interactions. Mutations of the key residues in the active site architecture of the GH12 family exerted different impacts on catalytic efficiency. Binding affinities between the aromatic amino acids and carbohydrate rings were quantitatively determined by isothermal titration calorimetry (ITC) and the quantum mechanical (QM) method, showing that the binding capacity order of Tyr>Trp>His (and Phe) was determined by their side-chain properties. The results also revealed that the binding constant of a certain residue remained unchanged when altering its location, while the catalytic efficiency changed dramatically. Increased binding affinity at a relatively distant subsite, such as the mutant of W7Y at the -4 subsite, resulted in a marked increase in the intermediate product of cellotetraose and enhanced the reactivity of endoglucanase by 144%; while tighter binding near the catalytic center, i.e. W22Y at the -2 subsite, enabled the enzyme to bind and hydrolyze smaller oligosaccharides. Clarification of the specific roles of the aromatics at different subsites may pave the way for a more rational design of GHs.
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Affiliation(s)
- Xiaomei Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Shuai Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Xiuyun Wu
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Shijia Liu
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Dandan Li
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Hao Xu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P.R. China
| | - Peiji Gao
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Guanjun Chen
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Lushan Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
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38
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Jiménez-Moreno E, Jiménez-Osés G, Gómez AM, Santana AG, Corzana F, Bastida A, Jiménez-Barbero J, Asensio JL. A thorough experimental study of CH/π interactions in water: quantitative structure-stability relationships for carbohydrate/aromatic complexes. Chem Sci 2015; 6:6076-6085. [PMID: 28717448 PMCID: PMC5504637 DOI: 10.1039/c5sc02108a] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/29/2015] [Indexed: 12/01/2022] Open
Abstract
CH/π interactions play a key role in a large variety of molecular recognition processes of biological relevance. However, their origins and structural determinants in water remain poorly understood. In order to improve our comprehension of these important interaction modes, we have performed a quantitative experimental analysis of a large data set comprising 117 chemically diverse carbohydrate/aromatic stacking complexes, prepared through a dynamic combinatorial approach recently developed by our group. The obtained free energies provide a detailed picture of the structure-stability relationships that govern the association process, opening the door to the rational design of improved carbohydrate-based ligands or carbohydrate receptors. Moreover, this experimental data set, supported by quantum mechanical calculations, has contributed to the understanding of the main driving forces that promote complex formation, underlining the key role played by coulombic and solvophobic forces on the stabilization of these complexes. This represents the most quantitative and extensive experimental study reported so far for CH/π complexes in water.
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Affiliation(s)
- Ester Jiménez-Moreno
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain . ; ; Tel: +34 915622900
| | - Gonzalo Jiménez-Osés
- Dept. Química and Centro de Investigación en Síntesis Química , Universidad de La Rioja , Logroño , Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI) , University of Zaragoza , BIFI-IQFR (CSIC) , Zaragoza , Spain
| | - Ana M Gómez
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain . ; ; Tel: +34 915622900
| | - Andrés G Santana
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain . ; ; Tel: +34 915622900
| | - Francisco Corzana
- Dept. Química and Centro de Investigación en Síntesis Química , Universidad de La Rioja , Logroño , Spain
| | - Agatha Bastida
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain . ; ; Tel: +34 915622900
| | - Jesus Jiménez-Barbero
- Centro de Investigaciones Biológicas (CIB-CSIC) , Madrid , Spain
- Center for Cooperative Research in Biosciences (CIC-bioGUNE) , Derio-Bizkaia , Spain
- Basque Foundation for Science , Ikerbasque , Bilbao , Spain
| | - Juan Luis Asensio
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain . ; ; Tel: +34 915622900
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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40
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Abstract
Dispersive interactions are known to play a major role in molecular associations in the gas phase and in the solid state. In solution, however, their significance has been disputed in recent years on the basis of several arguments. A major problem until now has been the separation of dispersive and hydrophobic effects, which are both maximized in water due the low polarizability of this most important medium. Analyses of complexes between porphyrins and systematically varied substrates in water have allowed us to discriminate dispersive from hydrophobic effects, as the latter turned out to be negligible for complexations with flat surfaces such as porphyrins. Also, for the first time, it has become possible to obtain binding free energy increments ΔΔG for a multitude of organic residues including halogen, amide, amino, ether, carbonyl, ester, nitro, sulfur, unsatured, and cyclopropane groups, which turned out to be additive. Binding contributions for saturated residues are unmeasurably small, with ΔΔG > 1 kJ/mol, but they increase to, e.g., ΔΔG = 5 kJ/mol for a nitro group, a value not far from, e.g., that of a stacking pyridine ring. Stacking interactions of heteroarenes with porphyrins depend essentially on the size of the arenes, in line with polarizabilities, and seem to be rather independent of the position of nitrogen within the rings. Measurements of halogen derivatives indicate that complexes with porphyrins, cyclodextrins, and pillarenes as hosts in different media consistently show increasing stability from fluorine to iodine as the substituent. This, and the observed sequence with other substrates, is in line with the expected increase in dispersive forces with increasing polarizability. Induced dipoles, which also would increase with polarizability, can be ruled out as providing the driving source in view of the data with halides: the observed stability sequence is opposite the change of electronegativity from fluorine to iodine. The same holds for the solvent effect observed in ethanol-water mixtures. Dispersive contributions vary not only with the polarizability of the used media but also with the interacting receptor sites; it has been shown that for cucurbiturils the polarizability inside the cavity is extremely low, which also explains why hydrophobic effects are maximized with these hosts. Complexations with other known host compounds, however, such as those between cryptands or cavitands with, e.g., noble gases, bear the signature of dominating dispersive forces. Some recent examples illustrate that such van der Waals forces can also play an important role in complexations with proteins. Again, a clue for this is the increase in ΔG for inhibitor binding by 7 kJ/mol for, e.g., a bromine in comparison to a fluorine derivative.
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Affiliation(s)
- Hans-Jörg Schneider
- FR Organische Chemie, Universität des Saarlandes, D-66041 Saarbrücken, Germany
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41
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Saha S, Sastry GN. Cooperative or Anticooperative: How Noncovalent Interactions Influence Each Other. J Phys Chem B 2015; 119:11121-35. [DOI: 10.1021/acs.jpcb.5b03005] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Soumen Saha
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, Andhra Pradesh, India
| | - G. Narahari Sastry
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, Andhra Pradesh, India
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42
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Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
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Destecroix H, Renney CM, Mooibroek TJ, Carter TS, Stewart PFN, Crump MP, Davis AP. Affinity enhancement by dendritic side chains in synthetic carbohydrate receptors. Angew Chem Int Ed Engl 2015; 54:2057-61. [PMID: 25645064 PMCID: PMC4506558 DOI: 10.1002/anie.201409124] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/01/2014] [Indexed: 01/23/2023]
Abstract
Dendritic side chains have been used to modify the binding environment in anthracene-based synthetic carbohydrate receptors. Control of length, charge, and branching enabled the positioning of side-chain carboxylate groups in such a way that they assisted in binding substrates rather than blocking the cavity. Conformational degeneracy in the dendrimers resulted in effective preorganization despite the flexibility of the system. Strong binding was observed to glucosammonium ions in water, with Ka values up to 7000 M(-1) . Affinities for uncharged substrates (glucose and N-acetylglucosamine) were also enhanced, despite competition from solvent and the absence of electrostatic interactions.
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Affiliation(s)
- Harry Destecroix
- School of Chemistry, University of Bristol, Cantock's CloseBristol, BS8 1TS (UK)
| | - Charles M Renney
- School of Chemistry, University of Bristol, Cantock's CloseBristol, BS8 1TS (UK)
| | - Tiddo J Mooibroek
- School of Chemistry, University of Bristol, Cantock's CloseBristol, BS8 1TS (UK)
| | - Tom S Carter
- School of Chemistry, University of Bristol, Cantock's CloseBristol, BS8 1TS (UK)
| | - Patrick F N Stewart
- School of Chemistry, University of Bristol, Cantock's CloseBristol, BS8 1TS (UK)
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Cantock's CloseBristol, BS8 1TS (UK)
| | - Anthony P Davis
- School of Chemistry, University of Bristol, Cantock's CloseBristol, BS8 1TS (UK)
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44
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Destecroix H, Renney CM, Mooibroek TJ, Carter TS, Stewart PFN, Crump MP, Davis AP. Affinity Enhancement by Dendritic Side Chains in Synthetic Carbohydrate Receptors. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409124] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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45
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Lippe J, Mazik M. Carbohydrate Receptors Combining Both a Macrocyclic Building Block and Flexible Side Arms as Recognition Units: Design, Syntheses, and Binding Studies. J Org Chem 2015; 80:1427-39. [DOI: 10.1021/jo502335u] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jan Lippe
- Institut für Organische
Chemie, Technische Universität Bergakademie Freiberg, Leipziger Strasse
29, 09596 Freiberg, Germany
| | - Monika Mazik
- Institut für Organische
Chemie, Technische Universität Bergakademie Freiberg, Leipziger Strasse
29, 09596 Freiberg, Germany
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46
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Cecioni S, Imberty A, Vidal S. Glycomimetics versus Multivalent Glycoconjugates for the Design of High Affinity Lectin Ligands. Chem Rev 2014; 115:525-61. [DOI: 10.1021/cr500303t] [Citation(s) in RCA: 381] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Samy Cecioni
- CERMAV, Université Grenoble Alpes and CNRS, BP 53, F-38041 Grenoble Cedex 9, France
- Institut
de Chimie et Biochimie Moléculaires et Supramoléculaires,
Laboratoire de Chimie Organique 2 - Glycochimie, UMR 5246, Université Lyon 1 and CNRS, 43 Boulevard du 11 Novembre 1918, F-69622, Villeurbanne, France
| | - Anne Imberty
- CERMAV, Université Grenoble Alpes and CNRS, BP 53, F-38041 Grenoble Cedex 9, France
| | - Sébastien Vidal
- Institut
de Chimie et Biochimie Moléculaires et Supramoléculaires,
Laboratoire de Chimie Organique 2 - Glycochimie, UMR 5246, Université Lyon 1 and CNRS, 43 Boulevard du 11 Novembre 1918, F-69622, Villeurbanne, France
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47
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von Schantz L, Håkansson M, Logan DT, Nordberg-Karlsson E, Ohlin M. Carbohydrate binding module recognition of xyloglucan defined by polar contacts with branching xyloses and CH-Π interactions. Proteins 2014; 82:3466-75. [PMID: 25302425 DOI: 10.1002/prot.24700] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 09/03/2014] [Accepted: 09/19/2014] [Indexed: 12/13/2022]
Abstract
Engineering of novel carbohydrate-binding proteins that can be utilized in various biochemical and biotechnical applications would benefit from a deeper understanding of the biochemical interactions that determine protein-carbohydrate specificity. In an effort to understand further the basis for specificity we present the crystal structure of the multi-specific carbohydrate-binding module (CBM) X-2 L110F bound to a branched oligomer of xyloglucan (XXXG). X-2 L110F is an engineered CBM that can recognize xyloglucan, xylans and β-glucans. The structural observations of the present study compared with previously reported structures of X-2 L110F in complex with linear oligomers, show that the π-surface of a phenylalanine, F110, allows for interactions with hydrogen atoms on both linear (xylopentaose and cellopentaose) and branched ligands (XXXG). Furthermore, X-2 L110F is shown to have a relatively flexible binding cleft, as illustrated in binding to XXXG. This branched ligand requires a set of reorientations of protein side chains Q72, N31, and R142, although these residues have previously been determined as important for binding to xylose oligomers by mediating polar contacts. The loss of these polar contacts is compensated for in binding to XXXG by polar interactions mediated by other protein residues, T74, R115, and Y149, which interact mainly with the branching xyloses of the xyloglucan oligomer. Taken together, the present study illustrates in structural detail how CH-π interactions can influence binding specificity and that flexibility is a key feature for the multi-specificity displayed by X-2 L110F, allowing for the accommodation of branched ligands.
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Affiliation(s)
- Laura von Schantz
- Department of Immunotechnology, Lund University, Medicon Village, SE-223 81 Lund, Sweden
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48
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Nepal B, Scheiner S. Effect of Ionic Charge on the CH···π Hydrogen Bond. J Phys Chem A 2014; 118:9575-87. [DOI: 10.1021/jp5070598] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Binod Nepal
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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49
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Li P, Parker TM, Hwang J, Deng F, Smith MD, Pellechia PJ, Sherrill CD, Shimizu KD. The CH−π Interactions of Methyl Ethers as a Model for Carbohydrate–N-Heteroarene Interactions. Org Lett 2014; 16:5064-7. [DOI: 10.1021/ol502418k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ping Li
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Trent M. Parker
- Center
for Computational Molecular Science and Technology, School of Chemistry
and Biochemistry and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jungwun Hwang
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Fengyuan Deng
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - C. David Sherrill
- Center
for Computational Molecular Science and Technology, School of Chemistry
and Biochemistry and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ken D. Shimizu
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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50
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Wilson KA, Kellie JL, Wetmore SD. DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar. Nucleic Acids Res 2014; 42:6726-41. [PMID: 24744240 PMCID: PMC4041443 DOI: 10.1093/nar/gku269] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π-π stacking, π-π T-shaped or sugar-π contacts. Three hundred forty-four nucleobase-amino acid π-π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA-protein sugar-π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C-H···π and/or lone-pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π-π and sugar-π interactions display a range of relative monomer orientations and therefore interaction energies (up to -50 (-70) kJ mol(-1) for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA-protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
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