1
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Zhu Q, Geng D, Li J, Zhang J, Sun H, Fan Z, He J, Hao N, Tian Y, Wen L, Li T, Qin W, Chu X, Wang Y, Yi W. A Computational and Chemical Design Strategy for Manipulating Glycan-Protein Recognition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308522. [PMID: 38582526 PMCID: PMC11199974 DOI: 10.1002/advs.202308522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/23/2024] [Indexed: 04/08/2024]
Abstract
Glycans are complex biomolecules that encode rich information and regulate various biological processes, such as fertilization, host-pathogen binding, and immune recognition, through interactions with glycan-binding proteins. A key driving force for glycan-protein recognition is the interaction between the π electron density of aromatic amino acid side chains and polarized C─H groups of the pyranose (termed the CH-π interaction). However, the relatively weak binding affinity between glycans and proteins has hindered the application of glycan detection and imaging. Here, computational modeling and molecular dynamics simulations are employed to design a chemical strategy that enhances the CH-π interaction between glycans and proteins by genetically incorporating electron-rich tryptophan derivatives into a lectin PhoSL, which specifically recognizes core fucosylated N-linked glycans. This significantly enhances the binding affinity of PhoSL with the core fucose ligand and enables sensitive detection and imaging of core fucosylated glycans in vitro and in xenograft tumors in mice. Further, the study showed that this strategy is applicable to improve the binding affinity of GafD lectin for N-acetylglucosamine-containing glycans. The approach thus provides a general and effective way to manipulate glycan-protein recognition for glycoscience applications.
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Affiliation(s)
- Qiang Zhu
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Didi Geng
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Jingchao Li
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Jinqiu Zhang
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Haofan Sun
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Zhiya Fan
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Jiahui He
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
| | - Ninghui Hao
- The Provincial International Science and Technology Cooperation Base on Engineering BiologyShanghai Institute for Advanced StudyInstitute of Quantitative BiologyInternational Campus of Zhejiang UniversityHaining314499China
| | - Yinping Tian
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Liuqing Wen
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Tiehai Li
- Carbohydrate‐Based Drug Research CenterShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China
| | - Weijie Qin
- National Center for Protein Sciences BeijingState Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of LifeomicsBeijing100026China
| | - Xiakun Chu
- Advanced Materials ThrustFunction HubThe Hong Kong University of Science and TechnologyGuangzhou511400China
| | - Yong Wang
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
- The Provincial International Science and Technology Cooperation Base on Engineering BiologyShanghai Institute for Advanced StudyInstitute of Quantitative BiologyInternational Campus of Zhejiang UniversityHaining314499China
| | - Wen Yi
- Departments of Biochemistry & BiophysicsCollege of Life SciencesZhejiang UniversityHangzhou310012China
- Cancer CentreZhejiang UniversityHangzhou310012China
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2
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Gao X, Kaluarachchi H, Zhang Y, Hwang S, Hannoush RN. A phage-displayed disulfide constrained peptide discovery platform yields novel human plasma protein binders. PLoS One 2024; 19:e0299804. [PMID: 38547072 PMCID: PMC10977726 DOI: 10.1371/journal.pone.0299804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024] Open
Abstract
Disulfide constrained peptides (DCPs) show great potential as templates for drug discovery. They are characterized by conserved cysteine residues that form intramolecular disulfide bonds. Taking advantage of phage display technology, we designed and generated twenty-six DCP phage libraries with enriched molecular diversity to enable the discovery of ligands against disease-causing proteins of interest. The libraries were designed based on five DCP scaffolds, namely Momordica charantia 1 (Mch1), gurmarin, Asteropsin-A, antimicrobial peptide-1 (AMP-1), and potato carboxypeptidase inhibitor (CPI). We also report optimized workflows for screening and producing synthetic and recombinant DCPs. Examples of novel DCP binders identified against various protein targets are presented, including human IgG Fc, serum albumin, vascular endothelial growth factor-A (VEGF-A) and platelet-derived growth factor (PDGF). We identified DCPs against human IgG Fc and serum albumin with sub-micromolar affinity from primary panning campaigns, providing alternative tools for potential half-life extension of peptides and small protein therapeutics. Overall, the molecular diversity of the DCP scaffolds included in the designed libraries, coupled with their distinct biochemical and biophysical properties, enables efficient and robust identification of de novo binders to drug targets of therapeutic relevance.
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Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
- Department of Peptide Therapeutics, Genentech, South San Francisco, California, United States of America
| | - Harini Kaluarachchi
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
| | - Yingnan Zhang
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
- Department of Biological Chemistry, Genentech, South San Francisco, California, United States of America
| | - Sunhee Hwang
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
- Department of Peptide Therapeutics, Genentech, South San Francisco, California, United States of America
| | - Rami N. Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, United States of America
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3
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Notova S, Imberty A. Tuning specificity and topology of lectins through synthetic biology. Curr Opin Chem Biol 2023; 73:102275. [PMID: 36796139 DOI: 10.1016/j.cbpa.2023.102275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 02/16/2023]
Abstract
Lectins are non-immunoglobulin and non-catalytic glycan binding proteins that are able to decipher the structure and function of complex glycans. They are widely used as biomarkers for following alteration of glycosylation state in many diseases and have application in therapeutics. Controlling and extending lectin specificity and topology is the key for obtaining better tools. Furthermore, lectins and other glycan binding proteins can be combined with additional domains, providing novel functionalities. We provide a view on the current strategy with a focus on synthetic biology approaches yielding to novel specificity, but other novel architectures with novel application in biotechnology or therapy.
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Affiliation(s)
- Simona Notova
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.
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4
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Lete MG, Franconetti A, Bertuzzi S, Delgado S, Azkargorta M, Elortza F, Millet O, Jiménez-Osés G, Arda A, Jiménez-Barbero J. NMR Investigation of Protein-Carbohydrate Interactions: The Recognition of Glycans by Galectins Engineered with Fluorotryptophan Residues. Chemistry 2023; 29:e202202208. [PMID: 36343278 PMCID: PMC10107428 DOI: 10.1002/chem.202202208] [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: 07/14/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
Fluorine (19 F) incorporation into glycan-binding proteins (lectins) has been achieved and exploited to monitor the binding to carbohydrate ligands by nuclear magnetic resonance (NMR) spectroscopy. Galectins are a family of lectins that bind carbohydrates, generally with weak affinities, through a combination of intermolecular interactions including a key CH-π stacking involving a conserved tryptophan residue. Herein, Galectin-3 (Gal3) and Galectin-8 (Gal8) with one and two carbohydrate recognition domains (CRDs), respectively, were selected. Gal3 contains one Trp, whereas Gal8 contains three, one at each binding site and a third one not involved in sugar binding; these were substituted by the corresponding F-Trp analogues. The presence of fluorine did not significantly modify the affinity for glycan binding, which was in slow exchange on the 19 F NMR chemical-shift timescale, even for weak ligands, and allowed binding events taking place at two different binding sites within the same lectin to be individualized.
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Affiliation(s)
- Marta G Lete
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Antonio Franconetti
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Sara Bertuzzi
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Sandra Delgado
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Félix Elortza
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Oscar Millet
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Gonzalo Jiménez-Osés
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain
| | - Ana Arda
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science Plaza Euskadi 5, 48009, Bilbao, Bizkaia, Spain.,Department of Organic Chemistry II Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940, Leioa, Spain.,Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid, Spain
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5
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Leibiger B, Stapf M, Mazik M. Cycloalkyl Groups as Building Blocks of Artificial Carbohydrate Receptors: Studies with Macrocycles Bearing Flexible Side-Arms. Molecules 2022; 27:7630. [PMID: 36364458 PMCID: PMC9654292 DOI: 10.3390/molecules27217630] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 09/29/2023] Open
Abstract
The cyclopentyl group was expected to act as a building block for artificial carbohydrate receptors and to participate in van der Waals contacts with the carbohydrate substrate in a similar way as observed for the pyrrolidine ring of proline in the crystal structures of protein-carbohydrate complexes. Systematic binding studies with a series of 1,3,5-trisubstituted 2,4,6-triethylbenzenes bearing various cycloalkyl groups as recognition units provided indications of the involvement of these groups in the complexation process and showed the influence of the ring size on the receptor efficiency. Representatives of compounds that exhibit a macrocyclic backbone and flexible side arms were now chosen as further model systems to investigate whether the previously observed effects represent a general trend. Binding studies with these macrocycles towards β-D-glucopyranoside, an all-equatorial substituted carbohydrate substrate, included 1H NMR spectroscopic titrations and microcalorimetric investigations. The performed studies confirmed the previously observed tendency and showed that the compound bearing cyclohexyl groups displays the best binding properties.
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Affiliation(s)
| | | | - Monika Mazik
- Institut für Organische Chemie, Technische Universität Bergakademie Freiberg, Leipziger Straße 29, 09596 Freiberg, Germany
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6
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Tobola F, Lepšík M, Zia SR, Leffler H, Nilsson UJ, Blixt O, Imberty A, Wiltschi B. Engineering the ligand specificity of the human galectin-1 by incorporation of tryptophan analogs. Chembiochem 2022; 23:e202100593. [PMID: 34978765 DOI: 10.1002/cbic.202100593] [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: 10/29/2021] [Revised: 12/23/2021] [Indexed: 11/05/2022]
Abstract
Galectin-1 is a β-galactoside-binding lectin with manifold biological functions. A single tryptophan residue (W68) in its carbohydrate binding site plays a major role in ligand binding and is highly conserved among galectins. To fine tune galectin-1 specificity, we introduced several non-canonical tryptophan analogs at this position of human galectin-1 and analyzed the resulting variants using glycan microarrays. Two variants containing 7-azatryptophan and 7-fluorotryptophan showed a reduced affinity for 3'-sulfated oligosaccharides. Their interaction with different ligands was further analyzed by fluorescence polarization competition assay. Using molecular modeling we provide structural clues that the change in affinities comes from modulated interactions and solvation patterns. Thus, we show that the introduction of subtle atomic mutations in the ligand binding site of galectin-1 is an attractive approach for fine-tuning its interactions with different ligands.
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Affiliation(s)
- Felix Tobola
- Graz University of Technology: Technische Universitat Graz, Institute of Molecular Biotechnology, Petersgasse 14, 8010, Graz, AUSTRIA
| | - Martin Lepšík
- Université Grenoble Alpes: Universite Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, FRANCE
| | | | - Hakon Leffler
- Lund University: Lunds Universitet, Laboratory Medicine Section MIG, Klinikgatan 28, 221 84, Lund, SWEDEN
| | - Ulf J Nilsson
- Lund University: Lunds Universitet, Centre for Analysis and Synthesis, Department of Chemistry, Box 124, 221 00, Lund, SWEDEN
| | - Ola Blixt
- Technical University of Denmark: Danmarks Tekniske Universitet, Biotechnology and Biomedicine, Søltofts Plads, 2800, Kgs. Lyngby, DENMARK
| | - Anne Imberty
- Université Grenoble Alpes: Universite Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, FRANCE
| | - Birgit Wiltschi
- Austrian Centre of Industrial Biotechnology, Synthetic Biology, Petersgasse 14, 8010, Graz, AUSTRIA
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7
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Amrhein F, Mazik M. Compounds Combining a Macrocyclic Building Block and Flexible Side‐Arms as Carbohydrate Receptors: Syntheses and Structure‐Binding Activity Relationship Studies. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Felix Amrhein
- Institut für Organische Chemie Technische Universität Bergakademie Freiberg Leipziger Strasse 29 09599 Freiberg Germany
| | - Monika Mazik
- Institut für Organische Chemie Technische Universität Bergakademie Freiberg Leipziger Strasse 29 09599 Freiberg Germany
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8
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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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9
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Chemical (neo)glycosylation of biological drugs. Adv Drug Deliv Rev 2021; 171:62-76. [PMID: 33548302 DOI: 10.1016/j.addr.2021.01.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 02/08/2023]
Abstract
Biological drugs, specifically proteins and peptides, are a privileged class of medicinal agents and are characterized with high specificity and high potency of therapeutic activity. However, biologics are fragile and require special care during storage, and are often modified to optimize their pharmacokinetics in terms of proteolytic stability and blood residence half-life. In this review, we showcase glycosylation as a method to optimize biologics for storage and application. Specifically, we focus on chemical glycosylation as an approach to modify biological drugs. We present case studies that illustrate the success of this methodology and specifically address the highly important question: does connectivity within the glycoconjugate have to be native or not? We then present the innovative methods of chemical glycosylation of biologics and specifically highlight the emerging and established protecting group-free methodologies of glycosylation. We discuss thermodynamic origins of protein stabilization via glycosylation, and analyze in detail stabilization in terms of proteolytic stability, aggregation upon storage and/or heat treatment. Finally, we present a case study of protein modification using sialic acid-containing glycans to avoid hepatic clearance of biological drugs. This review aims to spur interest in chemical glycosylation as a facile, powerful tool to optimize proteins and peptides as medicinal agents.
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10
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Linclau B, Ardá A, Reichardt NC, Sollogoub M, Unione L, Vincent SP, Jiménez-Barbero J. Fluorinated carbohydrates as chemical probes for molecular recognition studies. Current status and perspectives. Chem Soc Rev 2021; 49:3863-3888. [PMID: 32520059 DOI: 10.1039/c9cs00099b] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review provides an extensive summary of the effects of carbohydrate fluorination with regard to changes in physical, chemical and biological properties with respect to regular saccharides. The specific structural, conformational, stability, reactivity and interaction features of fluorinated sugars are described, as well as their applications as probes and in chemical biology.
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Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton SO171BJ, UK
| | - Ana Ardá
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain.
| | | | - Matthieu Sollogoub
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Stéphane P Vincent
- Department of Chemistry, Laboratory of Bio-organic Chemistry, University of Namur (UNamur), B-5000 Namur, Belgium
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain. and Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain and Department of Organic Chemistry II, Faculty of Science and Technology, UPV/EHU, 48940 Leioa, Spain
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11
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Köhler L, Hübler C, Seichter W, Mazik M. Binding modes of methyl α- d-glucopyranoside to an artificial receptor in crystalline complexes. RSC Adv 2021; 11:22221-22229. [PMID: 35480817 PMCID: PMC9034237 DOI: 10.1039/d1ra03390e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 02/28/2022] [Accepted: 06/01/2021] [Indexed: 01/04/2023] Open
Abstract
Complexes formed between methyl α-d-glucopyranoside and an artificial receptor represent a valuable source of information about the basic molecular features of carbohydrate recognition.
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Affiliation(s)
- Linda Köhler
- Institut für Organische Chemie, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany
| | - Conrad Hübler
- Institut für Organische Chemie, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany
| | - Wilhelm Seichter
- Institut für Organische Chemie, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany
| | - Monika Mazik
- Institut für Organische Chemie, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany
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12
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Köhler L, Seichter W, Mazik M. Complexes Formed between Artificial Receptors and β‐Glucopyranoside in the Crystalline State. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Linda Köhler
- Institut für Organische Chemie Technische Universität Bergakademie Freiberg Leipziger Strasse 29 09599 Freiberg Germany
| | - Wilhelm Seichter
- Institut für Organische Chemie Technische Universität Bergakademie Freiberg Leipziger Strasse 29 09599 Freiberg Germany
| | - Monika Mazik
- Institut für Organische Chemie Technische Universität Bergakademie Freiberg Leipziger Strasse 29 09599 Freiberg Germany
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13
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Atomistic simulation of carbohydrate-protein complex formation: Hevein-32 domain. Sci Rep 2019; 9:18918. [PMID: 31831756 PMCID: PMC6908686 DOI: 10.1038/s41598-019-53815-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/05/2019] [Indexed: 12/17/2022] Open
Abstract
Interactions between proteins and their small molecule ligands are of great importance for the process of drug design. Here we report an unbiased molecular dynamics simulation of systems containing hevein domain (HEV32) with N-acetylglucosamine mono-, di- or trisaccharide. Carbohydrate molecules were placed outside the binding site. Three of six simulations (6 × 2 μs) led to binding of a carbohydrate ligand into the binding mode in agreement with the experimentally determined structure. Unbinding was observed in one simulation (monosaccharide). There were no remarkable intermediates of binding for mono and disaccharide. Trisaccharide binding was initiated by formation of carbohydrate-aromatic CH/π interactions. Our results indicate that binding of ligands followed the model of conformational selection because the conformation of the protein ready for ligand binding was observed before the binding. This study extends the concept of docking by dynamics on carbohydrate-protein interactions.
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14
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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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15
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Biari KE, Gaudioso Á, Fernández-Alonso MC, Jiménez-Barbero J, Cañada FJ. Peptidoglycan Recognition by Wheat Germ Agglutinin. A View by NMR. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19849240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Wheat germ agglutinin (WGA) is a lectin composed of 4 homologous hevein domains. It has been shown that WGA binds N-acetyl glucosamine (GlcNAc)-related oligosaccharides and has applications as commercial reagent to detect glycans containing such modified residues. Peptidoglycan (PGN), the main component of the bacterial cell wall, is a polymeric material made of repeating disaccharide units of GlcNAc- N-acetylmuramic acid cross-linked with short polypeptide fragments. Wheat germ agglutinin is able to bind bacterial cells, a phenomenon that could correlate with its plant-defense capacities, but there is no information at the molecular level about how WGA binds to the PGN. Herein, we present structural data on the binding of a short PGN fragment to WGA by means of saturation transfer difference nuclear magnetic resonance studies. The results show that the GlcNAc residue establishes the major contacts with WGA, followed by the N-acetylmuramic acid residue. In contrast, the peptide moiety displays minor contacts at the binding site.
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Affiliation(s)
- Khouzaima el Biari
- Centro de Investigaciones Biológicas, CIB CSIC, c/Ramiro de Maeztu 9, Madrid, Spain
- Département de Biologie, Faculté des Sciences, Université Ibn Zohr, Agadir, Morocco
| | - Ángel Gaudioso
- Centro de Investigaciones Biológicas, CIB CSIC, c/Ramiro de Maeztu 9, Madrid, Spain
| | | | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
- Departament of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, Bilbao, Spain
| | - F. Javier Cañada
- Centro de Investigaciones Biológicas, CIB CSIC, c/Ramiro de Maeztu 9, Madrid, Spain
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16
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Marsden SR, Mestrom L, Bento I, Hagedoorn P, McMillan DGG, Hanefeld U. CH‐π Interactions Promote the Conversion of Hydroxypyruvate in a Class II Pyruvate Aldolase. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900205] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Stefan R. Marsden
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft, The Netherlands
- EMBL Hamburg Notkestrasse 85 22607 Hamburg Germany
| | - Luuk Mestrom
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft, The Netherlands
| | - Isabel Bento
- EMBL Hamburg Notkestrasse 85 22607 Hamburg Germany
| | - Peter‐Leon Hagedoorn
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft, The Netherlands
| | - Duncan G. G. McMillan
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft, The Netherlands
| | - Ulf Hanefeld
- Biokatalyse, Afdeling Biotechnologie Technische Universiteit Delft van der Maasweg 9 2629HZ Delft, The Netherlands
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17
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Tobola F, Lelimousin M, Varrot A, Gillon E, Darnhofer B, Blixt O, Birner-Gruenberger R, Imberty A, Wiltschi B. Effect of Noncanonical Amino Acids on Protein-Carbohydrate Interactions: Structure, Dynamics, and Carbohydrate Affinity of a Lectin Engineered with Fluorinated Tryptophan Analogs. ACS Chem Biol 2018; 13:2211-2219. [PMID: 29812892 PMCID: PMC6102642 DOI: 10.1021/acschembio.8b00377] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Protein–carbohydrate
interactions play crucial roles in
biology. Understanding and modifying these interactions is of major
interest for fighting many diseases. We took a synthetic biology approach
and incorporated noncanonical amino acids into a bacterial lectin
to modulate its interactions with carbohydrates. We focused on tryptophan,
which is prevalent in carbohydrate binding sites. The exchange of
the tryptophan residues with analogs fluorinated at different positions
resulted in three distinctly fluorinated variants of the lectin from Ralstonia solanacearum. We observed differences in stability
and affinity toward fucosylated glycans and rationalized them by X-ray
and modeling studies. While fluorination decreased the aromaticity
of the indole ring and, therefore, the strength of carbohydrate–aromatic
interactions, additional weak hydrogen bonds were formed between fluorine
and the ligand hydroxyl groups. Our approach opens new possibilities
to engineer carbohydrate receptors.
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Affiliation(s)
- Felix Tobola
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | | | | | - Emilie Gillon
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Barbara Darnhofer
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
- Research Unit of Functional Proteomics and Metabolomics, Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Ola Blixt
- Department of Chemistry, Chemical Biology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Ruth Birner-Gruenberger
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
- Research Unit of Functional Proteomics and Metabolomics, Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Birgit Wiltschi
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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18
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Slavokhotova AA, Shelenkov AA, Andreev YA, Odintsova TI. Hevein-Like Antimicrobial Peptides of Plants. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523064 DOI: 10.1134/s0006297917130065] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Plant antimicrobial peptides represent one of the evolutionarily oldest innate immunity components providing the first line of host defense to pathogen attacks. This review is dedicated to a small, currently actively studied family of hevein-like peptides that can be found in various monocot and dicot plants. The review thoroughly describes all known peptides belonging to this family including data on their structures, functions, and antimicrobial activity. The main features allowing to assign these peptides to a separate family are given, and the specific characteristics of each peptide are described. Further, the mode of action for hevein-like peptides, their role in plant immune system, and the applications of these molecules in biotechnology and medicine are considered.
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Affiliation(s)
- A A Slavokhotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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19
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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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20
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21
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Schubert M. Insights into Carbohydrate Recognition by 3D Structure Determination of Protein–Carbohydrate Complexes Using NMR. NMR IN GLYCOSCIENCE AND GLYCOTECHNOLOGY 2017:101-122. [DOI: 10.1039/9781782623946-00101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
This chapter provides an overview of protein–carbohydrate complex structures determined with NMR spectroscopy and deposited in the Protein Data Bank (PDB). These 14 structures include protein–carbohydrate interactions ranging from nanomolar to millimolar affinities. Two complexes are discussed in detail, one representing a tightly bound complex and one a weak but specific interaction. This review illustrates that NMR spectroscopy is a competitive method for three-dimensional structure determination of protein–carbohydrate complexes, especially in the case of weak interactions. The number of biological functions in which protein–carbohydrate interactions are involved is steadily growing. Essential functions of the immune system such as the distinction between self and non-self, or the resolution of inflammation, involve critical protein–carbohydrate recognition events. It is therefore expected that by providing atomic details, NMR spectroscopy can make a significant contribution in the near future to unexplored pathways of the immune system and of many other biological processes.
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Affiliation(s)
- Mario Schubert
- Department of Molecular Biology, University of Salzburg 5020 Salzburg Austria
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22
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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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23
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Ramaraju B, McFeeters H, Vogler B, McFeeters RL. Bacterial production of site specific 13C labeled phenylalanine and methodology for high level incorporation into bacterially expressed recombinant proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 67:23-34. [PMID: 28028744 PMCID: PMC5311020 DOI: 10.1007/s10858-016-0081-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/11/2016] [Indexed: 06/06/2023]
Abstract
Nuclear magnetic resonance spectroscopy studies of ever larger systems have benefited from many different forms of isotope labeling, in particular, site specific isotopic labeling. Site specific 13C labeling of methyl groups has become an established means of probing systems not amenable to traditional methodology. However useful, methyl reporter sites can be limited in number and/or location. Therefore, new complementary site specific isotope labeling strategies are valuable. Aromatic amino acids make excellent probes since they are often found at important interaction interfaces and play significant structural roles. Aromatic side chains have many of the same advantages as methyl containing amino acids including distinct 13C chemical shifts and multiple magnetically equivalent 1H positions. Herein we report economical bacterial production and one-step purification of phenylalanine with 13C incorporation at the Cα, Cγ and Cε positions, resulting in two isolated 1H-13C spin systems. We also present methodology to maximize incorporation of phenylalanine into recombinantly overexpressed proteins in bacteria and demonstrate compatibility with ILV-methyl labeling. Inexpensive, site specific isotope labeled phenylalanine adds another dimension to biomolecular NMR, opening new avenues of study.
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Affiliation(s)
- Bhargavi Ramaraju
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Hana McFeeters
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Bernhard Vogler
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Robert L McFeeters
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
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24
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Amrhein F, Lippe J, Mazik M. Carbohydrate receptors combining both a macrocyclic building block and flexible side arms as recognition units: binding properties of compounds with CH 2OH groups as side arms. Org Biomol Chem 2016; 14:10648-10659. [PMID: 27782281 DOI: 10.1039/c6ob01682k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
New representatives of compounds combining both a macrocyclic building block and two flexible side arms as recognition units were prepared and their binding properties toward selected carbohydrates were evaluated. The aim of this study was to examine the effects of the replacement of the heterocycle-bearing side arms by smaller units, such as hydroxy groups, on the binding capability. The design of this type of receptor was inspired by the participation of the side chain hydroxy group of serine and threonine in the biorecognition of carbohydrates. Such structural modifications enable the recognition of structure-activity relationships, which are of high importance in the development of carbohydrate receptors with predictable binding strength and selectivity.
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Affiliation(s)
- Felix Amrhein
- Institut für Organische Chemie, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany.
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25
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Tam JP, Wang S, Wong KH, Tan WL. Antimicrobial Peptides from Plants. Pharmaceuticals (Basel) 2015; 8:711-57. [PMID: 26580629 PMCID: PMC4695807 DOI: 10.3390/ph8040711] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/06/2015] [Accepted: 09/01/2015] [Indexed: 12/25/2022] Open
Abstract
Plant antimicrobial peptides (AMPs) have evolved differently from AMPs from other life forms. They are generally rich in cysteine residues which form multiple disulfides. In turn, the disulfides cross-braced plant AMPs as cystine-rich peptides to confer them with extraordinary high chemical, thermal and proteolytic stability. The cystine-rich or commonly known as cysteine-rich peptides (CRPs) of plant AMPs are classified into families based on their sequence similarity, cysteine motifs that determine their distinctive disulfide bond patterns and tertiary structure fold. Cystine-rich plant AMP families include thionins, defensins, hevein-like peptides, knottin-type peptides (linear and cyclic), lipid transfer proteins, α-hairpinin and snakins family. In addition, there are AMPs which are rich in other amino acids. The ability of plant AMPs to organize into specific families with conserved structural folds that enable sequence variation of non-Cys residues encased in the same scaffold within a particular family to play multiple functions. Furthermore, the ability of plant AMPs to tolerate hypervariable sequences using a conserved scaffold provides diversity to recognize different targets by varying the sequence of the non-cysteine residues. These properties bode well for developing plant AMPs as potential therapeutics and for protection of crops through transgenic methods. This review provides an overview of the major families of plant AMPs, including their structures, functions, and putative mechanisms.
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Affiliation(s)
- James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Shujing Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Ka H Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Wei Liang Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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26
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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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27
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Lippe J, Seichter W, Mazik M. Improved binding affinity and interesting selectivities of aminopyrimidine-bearing carbohydrate receptors in comparison with their aminopyridine analogues. Org Biomol Chem 2015; 13:11622-32. [PMID: 26467387 DOI: 10.1039/c5ob01757b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Due to the problems with the exact prediction of the binding properties of an artificial carbohydrate receptor, the identification of characteristic structural features, having the ability to influence the binding properties in a predictable way, is of high importance. The purpose of our investigation was to examine whether the previously observed higher affinity of 2-aminopyrimidine-bearing carbohydrate receptors in comparison with aminopyridine substituted analogues represents a general tendency of aminopyrimidine-bearing compounds. Systematic binding studies on new compounds consisting of 2-aminopyrimidine groups confirmed such a tendency and allowed the identification of interesting structure-activity relationships. Receptors having different symmetries showed systematic preferences for specific glycosides, which are remarkable for such simple receptor systems. Particularly suitable receptor architectures for the recognition of selected glycosides were identified and represent a valuable base for further developments in this field.
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Affiliation(s)
- Jan Lippe
- Institut für Organische Chemie, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, 09596 Freiberg, Germany.
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28
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Docking polysaccharide to proteins that have a Tryptophan box in the binding pocket. Carbohydr Res 2015; 414:78-84. [DOI: 10.1016/j.carres.2015.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/09/2015] [Accepted: 07/12/2015] [Indexed: 11/20/2022]
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29
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Calle LP, Echeverria B, Franconetti A, Serna S, Fernández‐Alonso MC, Diercks T, Cañada FJ, Ardá A, Reichardt N, Jiménez‐Barbero J. Monitoring Glycan–Protein Interactions by NMR Spectroscopic Analysis: A Simple Chemical Tag That Mimics Natural CH–π Interactions. Chemistry 2015; 21:11408-16. [DOI: 10.1002/chem.201501248] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Luis P. Calle
- Department of Chemical and Physical Biology, CIB‐CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Begoña Echeverria
- Department of Glycotechnology, CICbiomaGUNE, Paseo Miramón 182, 20009 San Sebastián (Spain)
| | - Antonio Franconetti
- Department of Organic Chemistry, University of Sevilla, Profesor García González 1, 41012 Sevilla (Spain)
| | - Sonia Serna
- Department of Glycotechnology, CICbiomaGUNE, Paseo Miramón 182, 20009 San Sebastián (Spain)
| | | | - Tammo Diercks
- Structural Biology Unit, CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801a, 48160 Derio (Spain)
| | - F. Javier Cañada
- Department of Chemical and Physical Biology, CIB‐CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Ana Ardá
- Structural Biology Unit, CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801a, 48160 Derio (Spain)
| | | | - Jesús Jiménez‐Barbero
- Structural Biology Unit, CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801a, 48160 Derio (Spain)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao (Spain)
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30
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Nahalka J, Hrabarova E, Talafova K. Protein-RNA and protein-glycan recognitions in light of amino acid codes. Biochim Biophys Acta Gen Subj 2015; 1850:1942-52. [PMID: 26145579 DOI: 10.1016/j.bbagen.2015.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND RNA-binding proteins, in cooperation with non-coding RNAs, play important roles in post-transcriptional regulation. Non-coding micro-RNAs control information flow from the genome to the glycome by interacting with glycan-synthesis enzymes. Glycan-binding proteins read the cell surface and cytoplasmic glycome and transfer signals back to the nucleus. The profiling of the protein-RNA and protein-glycan interactomes is of significant medicinal importance. SCOPE OF REVIEW This review discusses the state-of-the-art research in the protein-RNA and protein-glycan recognition fields and proposes the application of amino acid codes in profiling and programming the interactomes. MAJOR CONCLUSIONS The deciphered PUF-RNA and PPR-RNA amino acid recognition codes can be explained by the protein-RNA amino acid recognition hypothesis based on the genetic code. The tripartite amino acid code is also involved in protein-glycan interactions. At present, the results indicate that a system of four codons ("gnc", where n=g - guanine, c - cytosine, u - uracil or a - adenine) and four amino acids (G - glycine, A - alanine, V - valine, D - aspartic acid) could be the original genetic code that imprinted "rules" into both recognition processes. GENERAL SIGNIFICANCE Amino acid recognition codes have provocative potential in the profiling and programming of the protein-RNA and protein-glycan interactomes. The profiling and even programming of the interactomes will play significant roles in diagnostics and the development of therapeutic procedures against cancer and neurodegenerative, developmental and other diseases.
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Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic.
| | - Eva Hrabarova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic
| | - Klaudia Talafova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dubravska cesta 9, SK-84538 Bratislava, Slovak Republic; Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Trieda Andreja Hlinku 2, SK-94976 Nitra, Slovak Republic
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31
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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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Molecular simulations of hevein/(GlcNAc)3 complex with weakened OH/O and CH/π hydrogen bonds: implications for their role in complex stabilization. Carbohydr Res 2015; 408:1-7. [PMID: 25816996 DOI: 10.1016/j.carres.2015.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 11/23/2022]
Abstract
Carbohydrate-protein complexes are often characterized by interactions via aromatic amino acid residues. Several mechanisms have been proposed to explain these stacking-like interactions between pyranose sugars and aromatic moieties. The physical basis of these interactions is being explained as either dispersion CH/π or hydrophobic. In order to elucidate the nature of these interactions, we performed a series of molecular dynamics simulation of hevein domain (HEV32) in complex with (β-D-GlcNAc)3. Selected OH/O and CH/π hydrogen bonds involved in carbohydrate recognition were artificially weakened in 100 ns molecular dynamics simulations. Separate weakening of either OH/O or CH/π hydrogen bonds was not sufficient to destabilize the complex. This indicates that other effects, not solely CH/π dispersion interactions, contribute significantly to the stability of the complex. Significant destabilization of complexes was reached only by simultaneous weakening of OH/O and CH/π hydrogen bonds. This also shows that classical hydrogen bonds and CH/π interactions are working in concert to stabilize this carbohydrate-protein test case.
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33
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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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34
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Synthesis of compounds based on a dimesitylmethane scaffold and representative binding studies showing di- vs monosaccharide preference. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.09.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Lucas R, Peñalver P, Gómez-Pinto I, Vengut-Climent E, Mtashobya L, Cousin J, Maldonado OS, Perez V, Reynes V, Aviñó A, Eritja R, González C, Linclau B, Morales JC. Effects of sugar functional groups, hydrophobicity, and fluorination on carbohydrate-DNA stacking interactions in water. J Org Chem 2014; 79:2419-29. [PMID: 24552250 DOI: 10.1021/jo402700y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Carbohydrate-aromatic interactions are highly relevant for many biological processes. Nevertheless, experimental data in aqueous solution relating structure and energetics for sugar-arene stacking interactions are very scarce. Here, we evaluate how structural variations in a monosaccharide including carboxyl, N-acetyl, fluorine, and methyl groups affect stacking interactions with aromatic DNA bases. We find small differences on stacking interaction among the natural carbohydrates examined. The presence of fluorine atoms within the pyranose ring slightly increases the interaction with the C-G DNA base pair. Carbohydrate hydrophobicity is the most determinant factor. However, gradual increase in hydrophobicity of the carbohydrate does not translate directly into a steady growth in stacking interaction. The energetics correlates better with the amount of apolar surface buried upon sugar stacking on top of the aromatic DNA base pair.
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Affiliation(s)
- Ricardo Lucas
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla , 49 Américo Vespucio, 41092, Sevilla, Spain
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36
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del Carmen Fernández-Alonso M, Díaz D, Berbis MÁ, Marcelo F, Cañada J, Jiménez-Barbero J. Protein-carbohydrate interactions studied by NMR: from molecular recognition to drug design. Curr Protein Pept Sci 2013; 13:816-30. [PMID: 23305367 PMCID: PMC3706953 DOI: 10.2174/138920312804871175] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/12/2012] [Accepted: 07/25/2012] [Indexed: 02/04/2023]
Abstract
Diseases that result from infection are, in general, a consequence of specific interactions between a pathogenic organism and the cells. The study of host-pathogen interactions has provided insights for the design of drugs with therapeutic properties. One area that has proved to be promising for such studies is the constituted by carbohydrates which participate in biological processes of paramount importance. On the one hand, carbohydrates have shown to be information carriers with similar, if not higher, importance than traditionally considered carriers as amino acids and nucleic acids. On the other hand, the knowledge on molecular recognition of sugars by lectins and other carbohydrate-binding proteins has been employed for the development of new biomedical strategies. Biophysical techniques such as X-Ray crystallography and NMR spectroscopy lead currently the investigation on this field. In this review, a description of traditional and novel NMR methodologies employed in the study of sugar-protein interactions is briefly presented in combination with a palette of NMR-based studies related to biologically and/or pharmaceutically relevant applications.
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37
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Asensio JL, Ardá A, Cañada FJ, Jiménez-Barbero J. Carbohydrate-aromatic interactions. Acc Chem Res 2013; 46:946-54. [PMID: 22704792 DOI: 10.1021/ar300024d] [Citation(s) in RCA: 359] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recognition of saccharides by proteins has far reaching implications in biology, technology, and drug design. Within the past two decades, researchers have directed considerable effort toward a detailed understanding of these processes. Early crystallographic studies revealed, not surprisingly, that hydrogen-bonding interactions are usually involved in carbohydrate recognition. But less expectedly, researchers observed that despite the highly hydrophilic character of most sugars, aromatic rings of the receptor often play an important role in carbohydrate recognition. With further research, scientists now accept that noncovalent interactions mediated by aromatic rings are pivotal to sugar binding. For example, aromatic residues often stack against the faces of sugar pyranose rings in complexes between proteins and carbohydrates. Such contacts typically involve two or three CH groups of the pyranoses and the π electron density of the aromatic ring (called CH/π bonds), and these interactions can exhibit a variety of geometries, with either parallel or nonparallel arrangements of the aromatic and sugar units. In this Account, we provide an overview of the structural and thermodynamic features of protein-carbohydrate interactions, theoretical and experimental efforts to understand stacking in these complexes, and the implications of this understanding for chemical biology. The interaction energy between different aromatic rings and simple monosaccharides based on quantum mechanical calculations in the gas phase ranges from 3 to 6 kcal/mol range. Experimental values measured in water are somewhat smaller, approximately 1.5 kcal/mol for each interaction between a monosaccharide and an aromatic ring. This difference illustrates the dependence of these intermolecular interactions on their context and shows that this stacking can be modulated by entropic and solvent effects. Despite their relatively modest influence on the stability of carbohydrate/protein complexes, the aromatic platforms play a major role in determining the specificity of the molecular recognition process. The recognition of carbohydrate/aromatic interactions has prompted further analysis of the properties that influence them. Using a variety of experimental and theoretical methods, researchers have worked to quantify carbohydrate/aromatic stacking and identify the features that stabilize these complexes. Researchers have used site-directed mutagenesis, organic synthesis, or both to incorporate modifications in the receptor or ligand and then quantitatively analyzed the structural and thermodynamic features of these interactions. Researchers have also synthesized and characterized artificial receptors and simple model systems, employing a reductionistic chemistry-based strategy. Finally, using quantum mechanics calculations, researchers have examined the magnitude of each property's contribution to the interaction energy.
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Affiliation(s)
- Juan Luis Asensio
- Chemical & Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid
| | - Ana Ardá
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Jesús Jiménez-Barbero
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
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38
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Meyer D, Mutschler C, Robertson I, Batt A, Tatko C. Aromatic interactions with naphthylalanine in a β
-hairpin peptide. J Pept Sci 2013; 19:277-82. [DOI: 10.1002/psc.2496] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 01/22/2013] [Accepted: 01/25/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Meyer
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Caleb Mutschler
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Ian Robertson
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Alexandra Batt
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Chad Tatko
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
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39
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Rosien JR, Seichter W, Mazik M. Trimethoxybenzene- and trimethylbenzene-based compounds bearing imidazole, indole and pyrrole groups as recognition units: synthesis and evaluation of the binding properties towards carbohydrates. Org Biomol Chem 2013; 11:6569-79. [DOI: 10.1039/c3ob41540f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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40
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Ke C, Destecroix H, Crump MP, Davis AP. A simple and accessible synthetic lectin for glucose recognition and sensing. Nat Chem 2012; 4:718-23. [DOI: 10.1038/nchem.1409] [Citation(s) in RCA: 215] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 06/19/2012] [Indexed: 01/23/2023]
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41
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Ellis CR, Maiti B, Noid WG. Specific and nonspecific effects of glycosylation. J Am Chem Soc 2012; 134:8184-93. [PMID: 22524526 DOI: 10.1021/ja301005f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Glycosylation regulates vital cellular processes and dramatically influences protein folding and stability. In particular, experiments have demonstrated that asparagine (N)-linked disaccharides drive a "conformational switch" in a model peptide. The present work investigates this conformational switch via extensive atomically detailed replica exchange molecular dynamics simulations in explicit solvent. To distinguish the effects of specific and nonspecific interactions upon the peptide conformational ensemble, these simulations considered model peptides that were N-linked to a disaccharide and to a steric crowder of the same shape. The simulations are remarkably consistent with experiment and provide detailed insight into the peptide structure ensemble. They suggest that steric crowding by N-linked disaccharides excludes extended conformations, but does not significantly impact the tetrahedral structure of the surrounding solvent or otherwise alter the peptide free energy surface. However, the combination of steric crowding with specific hydrogen bonds and hydrophobic stacking interactions more dramatically impacts the peptide ensemble and stabilizes new structures.
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Affiliation(s)
- Christopher R Ellis
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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42
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Pace CJ, Kim D, Gao J. Experimental evaluation of CH-π interactions in a protein core. Chemistry 2012; 18:5832-6. [PMID: 22473937 DOI: 10.1002/chem.201200334] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Indexed: 11/08/2022]
Abstract
CH-π stacks up! Using the protein α(2) D as a model system, we estimate that a CH-π contact between cyclohexylalanine (Cha) and phenylalanine (F) contributes approximately -0.7 kcal mol(-1) to the protein stability. The stacking F-Cha pairs are sequestered in the core of the protein, where water interference does not exist (see figure). Therefore, the observed energetic gain should represent the inherent magnitude and upper limit of the CH-π interactions.
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Affiliation(s)
- Christopher J Pace
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
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43
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Lindhorst TK, Kubik S. Supramolecular Approaches to the Study of Glycobiology. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Tsuzuki S, Uchimaru T, Mikami M. Magnitude of CH/O interactions between carbohydrate and water. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1192-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Kumari M, Sunoj RB, Balaji PV. Conformational mapping and energetics of saccharide–aromatic residue interactions: implications for the discrimination of anomers and epimers and in protein engineering. Org Biomol Chem 2012; 10:4186-200. [DOI: 10.1039/c2ob25182e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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46
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Tsuzuki S, Uchimaru T, Mikami M. Magnitude and nature of carbohydrate-aromatic interactions in fucose-phenol and fucose-indole complexes: CCSD(T) level interaction energy calculations. J Phys Chem A 2011; 115:11256-62. [PMID: 21812469 DOI: 10.1021/jp2045756] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The CH/π contact structures of the fucose-phenol and fucose-indole complexes and the stabilization energies by formation of the complexes (E(form)) were studied by ab initio molecular orbital calculations. The three types of interactions (CH/π and OH/π interactions and OH/O hydrogen bonds) were compared and evaluated in a single molecular system and at the same level of theory. The E(form) calculated for the most stable CH/π contact structure of the fucose-phenol complex at the CCSD(T) level (-4.9 kcal/mol) is close to that for the most stable CH/π contact structure of the fucose-benzene complex (-4.5 kcal/mol). On the other hand the most stable CH/π contact structure of the fucose-indole complex has substantially larger E(form) (-6.5 kcal/mol). The dispersion interaction is the major source of the attraction in the CH/π contact structures of the fucose-phenol and fucose-indole complexes as in the case of the fucose-benzene complex. The electrostatic interactions in the CH/π contact structures are small (less than 1.5 kcal/mol). The nature of the interactions between the nonpolar surface of the carbohydrate and aromatic rings is completely different from that of the conventional hydrogen bonds where the electrostatic interaction is the major source of the attraction. The distributed multipole analysis and DFT-SATP analysis show that the dispersion interactions in the CH/π contact structure of fucose-indole complex are substantially larger than those in the CH/π contact structures of fucose-benzene and fucose-phenol complexes. The large dispersion interactions are responsible for the large E(form) for the fucose-indole complex.
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Affiliation(s)
- Seiji Tsuzuki
- CREST, JST, and Research Initiative of Computational Sciences (RICS), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
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47
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Barwell NP, Davis AP. Substituent Effects in Synthetic Lectins - Exploring the Role of CH−π Interactions in Carbohydrate Recognition. J Org Chem 2011; 76:6548-57. [DOI: 10.1021/jo200755z] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicholas P. Barwell
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, U.K. BS8 1TS
| | - Anthony P. Davis
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, U.K. BS8 1TS
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48
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Kozmon S, Matuška R, Spiwok V, Koča J. Dispersion interactions of carbohydrates with condensate aromatic moieties: theoretical study on the CH-π interaction additive properties. Phys Chem Chem Phys 2011; 13:14215-22. [PMID: 21755090 DOI: 10.1039/c1cp21071h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this article we present the first systematic study of the additive properties (i.e. degree of additivity) of the carbohydrate-aromatic moiety CH-π dispersion interaction. The additive properties were studied on the β-D-glucopyranose, β-D-mannopyranose and α-L-fucopyranose complexes with the naphthalene molecule by comparing the monodentate (single CH-π) and bidentate (two CH-π) complexes. All model complexes were optimized using the DFT-D approach, at the BP/def2-TZVPP level of theory. The interaction energies were refined using single point calculations at highly correlated ab initio methods at the CCSD(T)/CBS level, calculated as E + (E(CCSD(T))-E(MP2))(Small Basis). Bidentate complexes show very strong interactions in the range from -10.79 up to -7.15 and -8.20 up to -6.14 kcal mol(-1) for the DFT-D and CCSD(T)/CBS level, respectively. These values were compared with the sum of interaction energies of the appropriate monodentate carbohydrate-naphthalene complexes. The comparison reveals that the bidentate complex interaction energy is higher (interaction is weaker) than the sum of monodentate complex interaction energies. Bidentate complex interaction energy corresponds to 2/3 of the sum of the appropriate monodentate complex interaction energies (averaging over all modeled carbohydrate complexes). The observed interaction energies were also compared with the sum of interaction energies of the corresponding previously published carbohydrate-benzene complexes. Also in this case the interaction energy of the bidentate complex was higher (i.e. weaker interaction) than the sum of interaction energies of the corresponding benzene complexes. However, the obtained difference is lower than before, while the bidentate complex interaction energy corresponds to 4/5 of the sum of interaction energy of the benzene complexes, averaged over all structures. The mentioned comparison might aid protein engineering efforts where amino acid residues phenylalanine or tyrosine are to be replaced by a tryptophan and can help to predict the changes in the interactions. The observed results also show that DFT-D correctly describes the CH-π interaction energy and their additive properties in comparison to CCSD(T)/CBS calculated interaction energies. Thus, the DFT-D approach might be used for calculation of larger complexes of biological interest, where dispersion interaction plays an important role.
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Affiliation(s)
- Stanislav Kozmon
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
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49
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Nishio M. The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates. Phys Chem Chem Phys 2011; 13:13873-900. [PMID: 21611676 DOI: 10.1039/c1cp20404a] [Citation(s) in RCA: 624] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.
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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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50
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Roldós V, Cañada FJ, Jiménez-Barbero J. Carbohydrate-Protein Interactions: A 3D View by NMR. Chembiochem 2011; 12:990-1005. [DOI: 10.1002/cbic.201000705] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Indexed: 12/29/2022]
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