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Quintana JI, Atxabal U, Unione L, Ardá A, Jiménez-Barbero J. Exploring multivalent carbohydrate-protein interactions by NMR. Chem Soc Rev 2023; 52:1591-1613. [PMID: 36753338 PMCID: PMC9987413 DOI: 10.1039/d2cs00983h] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Indexed: 02/09/2023]
Abstract
Nuclear Magnetic Resonance (NMR) has been widely employed to assess diverse features of glycan-protein molecular recognition events. Different types of qualitative and quantitative information at different degrees of resolution and complexity can be extracted from the proper application of the available NMR-techniques. In fact, affinity, structural, kinetic, conformational, and dynamic characteristics of the binding process are available. Nevertheless, except in particular cases, the affinity of lectin-sugar interactions is weak, mostly at the low mM range. This feature is overcome in biological processes by using multivalency, thus augmenting the strength of the binding. However, the application of NMR methods to monitor multivalent lectin-glycan interactions is intrinsically challenging. It is well known that when large macromolecular complexes are formed, the NMR signals disappear from the NMR spectrum, due to the existence of fast transverse relaxation, related to the large size and exchange features. Indeed, at the heart of the molecular recognition event, the associated free-bound chemical exchange process for both partners takes place in a particular timescale. Thus, these factors have to be considered and overcome. In this review article, we have distinguished, in a subjective manner, the existence of multivalent presentations in the glycan or in the lectin. From the glycan perspective, we have also considered whether multiple epitopes of a given ligand are presented in the same linear chain of a saccharide (i.e., poly-LacNAc oligosaccharides) or decorating different arms of a multiantennae scaffold, either natural (as in multiantennae N-glycans) or synthetic (of dendrimer or polymer nature). From the lectin perspective, the presence of an individual binding site at every monomer of a multimeric lectin may also have key consequences for the binding event at different levels of complexity.
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Affiliation(s)
- Jon I Quintana
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Unai Atxabal
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain.
| | - Luca Unione
- 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 Ardá
- 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, EHU-UPV, 48940 Leioa, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid, Spain
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2
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Thirunavookarasu N, Kumar S, Anandharaj A, Rawson A. Effect of ultrasonic cavitation on the formation of soy protein isolate - rice starch complexes, and the characterization and prediction of interaction sites using molecular techniques. Heliyon 2022; 8:e10942. [PMID: 36237974 PMCID: PMC9552112 DOI: 10.1016/j.heliyon.2022.e10942] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/23/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Abstract
Protein-carbohydrate interactions occur naturally in glycoproteins which are highly stable in nature and are involved in various food complexes and can enhance the quality and functional properties of foods. In the current study, we characterized the protein-carbohydrate complex formed between commercial soy protein isolate and rice starch using different treatments namely heat treatment alone, ultrasound treatment alone, combination of ultrasound and heat treatment and mixing alone. The structural data obtained using circular dichroism indicated that during the complex formation, the α-helix values were reduced by a maximum of 67% compared to soy protein isolate alone. The crystalline nature of the complexes formed by ultrasound treatment preserved the techno-functional properties as compared to complexes formed by heat treatments. The FTIR analysis of the complexes formed indicated the formation of glycosidic bond. Molecular docking analysis revealed the interaction between the complexes occurred due to hydrogen bonds which make the proteins more stable in nature thus enhancing their denaturation temperature. Glutamine, Proline and Arginine present in the D subunit of 7S 3AUP interacts with the starch molecule. The obtained results suggest that sonication combined with heat treatment led to higher interaction between the soy proteins isolate and rice starch.
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Affiliation(s)
- Nirmal Thirunavookarasu
- Department of Food Safety and Quality Testing, National Institute of Food Technology Entrepreneurship and Management - Thanjavur (NIFTEM-T), Pudukkottai Road, Thanjavur, Tamil Nadu, India,Centre of Excellence in Non-Thermal Processing, National Institute of Food Technology Entrepreneurship and Management - Thanjavur (NIFTEM-T), Pudukkottai Road, Thanjavur, Tamil Nadu, India
| | - Sumit Kumar
- Department of Food Safety and Quality Testing, National Institute of Food Technology Entrepreneurship and Management - Thanjavur (NIFTEM-T), Pudukkottai Road, Thanjavur, Tamil Nadu, India,Centre of Excellence in Non-Thermal Processing, National Institute of Food Technology Entrepreneurship and Management - Thanjavur (NIFTEM-T), Pudukkottai Road, Thanjavur, Tamil Nadu, India
| | - Arunkumar Anandharaj
- Department of Food Safety and Quality Testing, National Institute of Food Technology Entrepreneurship and Management - Thanjavur (NIFTEM-T), Pudukkottai Road, Thanjavur, Tamil Nadu, India,Corresponding author.
| | - Ashish Rawson
- Department of Food Safety and Quality Testing, National Institute of Food Technology Entrepreneurship and Management - Thanjavur (NIFTEM-T), Pudukkottai Road, Thanjavur, Tamil Nadu, India,Centre of Excellence in Non-Thermal Processing, National Institute of Food Technology Entrepreneurship and Management - Thanjavur (NIFTEM-T), Pudukkottai Road, Thanjavur, Tamil Nadu, India,Corresponding author.
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3
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Effect of ultrasonication on the protein–polysaccharide complexes: a review. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2022. [DOI: 10.1007/s11694-022-01567-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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4
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Le HT, D’Ambrosio EA, Mashayekh S, Grimes CL. Customized peptidoglycan surfaces to investigate innate immune recognition via surface plasmon resonance. Methods Enzymol 2022; 665:73-103. [PMID: 35379444 PMCID: PMC9042648 DOI: 10.1016/bs.mie.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Glycan-protein interactions facilitate some of the most important biomolecular processes in and between cells. They are involved in different cellular pathways, cell-cell interactions and associated with many diseases, making these interactions of great interest. However, their structural and functional diversity poses great challenges in studying them at the molecular level. Surface plasmon resonance (SPR) technology presents great advantages to study glycan-protein interactions due to its superior sensitivity, ability to monitor real-time interactions, relatively simple data interpretation, and most importantly, direct measurement of binding without a need for fluorescent labeling. Here, another dimensionality of SPR in studying glycan-protein interactions is demonstrated via examples of binding between human innate immune receptors and their bacterial peptidoglycan ligands. In order to best resemble interactions in solution, a novel strategy of tethering the carbohydrate at different positions to the biosensor surface is applied to represent the potential displays of the carbohydrate ligand to the receptor. Subsequent kinetic analysis provides insights into the optimized configuration of peptidoglycan fragments for binding with its receptors. The manuscript contains a "how-to guide" to help with the implementation of these methods in other glycan-protein binding systems.
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Affiliation(s)
- Ha T. Le
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Elizabeth A. D’Ambrosio
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Siavash Mashayekh
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Catherine Leimkuhler Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States,Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States,Correspondence to Catherine L. Grimes, The University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19716,
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5
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Unveiling Molecular Recognition of Sialoglycans by Human Siglec-10. iScience 2020; 23:101231. [PMID: 32629603 PMCID: PMC7306591 DOI: 10.1016/j.isci.2020.101231] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/20/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022] Open
Abstract
Siglec-10 is an inhibitory I-type lectin selectively recognizing sialoglycans exposed on cell surfaces, involved in several patho-physiological processes. The key role Siglec-10 plays in the regulation of immune cell functions has made it a potential target for the development of immunotherapeutics against a broad range of diseases. However, the crystal structure of the protein has not been resolved for the time being and the atomic description of Siglec-10 interactions with complex glycans has not been previously unraveled. We present here the first insights of the molecular mechanisms regulating the interaction between Siglec-10 and naturally occurring sialoglycans. We used combined spectroscopic, computational and biophysical approaches to dissect glycans' epitope mapping and conformation upon binding in order to afford a description of the 3D complexes. Our outcomes provide a structural perspective for the rational design and development of high-affinity ligands to control the receptor functionality. We unveiled the molecular basis of sialoglycans recognition by Siglec-10 The conformation of sialoglycans drives the interaction with the protein Siglec-10 is able to recognize and bind complex N-glycans Our outcomes may open the venue for the design and development of novel glycomimetics
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6
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A review on nuclear overhauser enhancement (NOE) and rotating-frame overhauser effect (ROE) NMR techniques in food science: Basic principles and applications. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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7
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Sugawara K, Kadoya T, Kuramitz H. Magnetic beads modified with an electron-transfer carbohydrate-mimetic peptide for sensing of a galactose-dependent protein. Anal Chim Acta 2018; 1001:158-167. [PMID: 29291799 DOI: 10.1016/j.aca.2017.11.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/10/2017] [Accepted: 11/17/2017] [Indexed: 12/17/2022]
Abstract
For use in the voltammetric sensing of galactose-dependent proteins, we modified magnetic beads with a peptide that had both electroactive- and molecular recognition properties. The peptide consisted of a YXY sequence and behaved as an electron-transfer carbohydrate-mimetic peptide that would combine with proteins. With this tool, the protein could be detected via a label-free system. We synthesized several penta- and hexa-peptides with a cysteine residue on the C-terminals to examine the properties of peptides. These peptides contained amino acid residues (X) of alanine, serine, or tyrosine. The peptides were immobilized on magnetic beads via N-(8-maleimidocapryloxy) succinimide. Soybean agglutinin(SBA), the in vivo function of which has been well established in animals, was selected as a model protein. The protein was detected via the changes in electrode response due to the oxidation of tyrosine residues from the phenol group to quinone. As a result, SBA was selectively accumulated on the beads modified with YYYYC. The calibration curve of SBA was linear and ranged from 2.5 × 10-12 to 1.0 × 10-10 M. With this system, SBA was recovered in human serum at values that ranged from 98 to 103%. Furthermore, the beads with peptides were regenerated five times using a protein denaturant. Accordingly, this electrochemical system was simple and could be rapidly applied to the detection of galactose-recognition proteins.
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Affiliation(s)
| | | | - Hideki Kuramitz
- Department of Environmental Biology and Chemistry, Graduate School of Science and Engineering for Research, University of Toyama, Toyama 930-8555, Japan
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8
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Kuttel MM, Cescutti P, Distefano M, Rizzo R. Fluorescence and NMR spectroscopy together with molecular simulations reveal amphiphilic characteristics of a Burkholderia biofilm exopolysaccharide. J Biol Chem 2017; 292:11034-11042. [PMID: 28468829 DOI: 10.1074/jbc.m117.785048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/26/2017] [Indexed: 01/09/2023] Open
Abstract
Biofilms are a collective mode of bacterial life in which a self-produced matrix confines cells in close proximity to each other. Biofilms confer many advantages, including protection from chemicals (including antibiotics), entrapment of useful extracellular enzymes and nutrients, as well as opportunities for efficient recycling of molecules from dead cells. Biofilm matrices are aqueous gel-like structures composed of polysaccharides, proteins, and DNA stabilized by intermolecular interactions that may include non-polar connections. Recently, polysaccharides extracted from biofilms produced by species of the Burkholderia cepacia complex were shown to possess clusters of rhamnose, a 6-deoxy sugar with non-polar characteristics. Molecular dynamics simulations are well suited to characterizing the structure and dynamics of polysaccharides, but only relatively few such studies exist of their interaction with non-polar molecules. Here we report an investigation into the hydrophobic properties of the exopolysaccharide produced by Burkholderia multivorans strain C1576. Fluorescence experiments with two hydrophobic fluorescent probes established that this polysaccharide complexes hydrophobic species, and NMR experiments confirmed these interactions. Molecular simulations to model the hydrodynamics of the polysaccharide and the interaction with guest species revealed a very flexible, amphiphilic carbohydrate chain that has frequent dynamic interactions with apolar molecules; both hexane and a long-chain fatty acid belonging to the quorum-sensing system of B. multivorans were tested. A possible role of the non-polar domains of the exopolysaccharide in facilitating the diffusion of aliphatic species toward specific targets within the biofilm aqueous matrix is proposed.
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Affiliation(s)
- Michelle M Kuttel
- From the Department of Computer Science, University of Cape Town, Rondebosch 7701, South Africa and
| | - Paola Cescutti
- the Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Marco Distefano
- the Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Roberto Rizzo
- the Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
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9
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Marchetti R, Perez S, Arda A, Imberty A, Jimenez‐Barbero J, Silipo A, Molinaro A. "Rules of Engagement" of Protein-Glycoconjugate Interactions: A Molecular View Achievable by using NMR Spectroscopy and Molecular Modeling. ChemistryOpen 2016; 5:274-96. [PMID: 27547635 PMCID: PMC4981046 DOI: 10.1002/open.201600024] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectroscopic methods permitted us to deeply dissect the fine structural details of biologically relevant molecular recognition processes with high resolution. This Review focuses on the development and use of modern nuclear magnetic resonance (NMR) techniques to dissect binding events. These spectroscopic methods, complementing X-ray crystallography and molecular modeling methodologies, will be taken into account as indispensable tools to provide a complete picture of protein-glycoconjugate binding mechanisms related to biomedicine applications against infectious diseases.
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Affiliation(s)
- Roberta Marchetti
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Serge Perez
- Department Molecular Pharmacochemistry UMR 5063CNRS and University of GrenobleAlpes, BP 5338041 Grenoble cedex 9France
| | - Ana Arda
- Bizkaia Technological ParkCIC bioGUNEBuilding 801A-148160Derio-BizkaiaSpain
| | - Anne Imberty
- Centre de Recherche sur les CNRSand University of Grenoble Macromolécules Végétales, UPR 5301Alpes, BP 5338041Grenoble cedex 9France
| | | | - Alba Silipo
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Antonio Molinaro
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
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10
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Ribeiro JP, Diercks T, Jiménez-Barbero J, André S, Gabius HJ, Cañada FJ. Fluorinated Carbohydrates as Lectin Ligands: (19)F-Based Direct STD Monitoring for Detection of Anomeric Selectivity. Biomolecules 2015; 5:3177-92. [PMID: 26580665 PMCID: PMC4693274 DOI: 10.3390/biom5043177] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 12/29/2022] Open
Abstract
The characterization of the binding of reducing carbohydrates present as mixtures of anomers in solution to a sugar recepor (lectin) poses severe difficulties. In this situation, NMR spectroscopy enables the observation of signals for each anomer in the mixture by applying approaches based on ligand observation. Saturation transfer difference (STD) NMR allows fast and efficient screening of compound mixtures for reactivity to a receptor. Owing to the exceptionally favorable properties of 19F in NMR spectroscopy and the often complex 1H spectra of carbohydrates, 19F-containing sugars have the potential to be turned into versatile sensors for recognition. Extending the recently established 1H → 1H STDre19F-NMR technique, we here demonstrate its applicability to measure anomeric selectivity of binding in a model system using the plant lectin concanavalin A (ConA) and 2-deoxy-2-fluoro-d-mannose. Indeed, it is also possible to account for the mutual inhibition between the anomers on binding to the lectin by means of a kinetic model. The monitoring of 19F-NMR signal perturbation disclosed the relative activities of the anomers in solution and thus enabled the calculation of their binding affinity towards ConA. The obtained data show a preference for the α anomer that increases with temperature. This experimental approach can be extended to others systems of biomedical interest by testing human lectins with suitably tailored glycan derivatives.
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Affiliation(s)
- João P Ribeiro
- Centre de Recherches sur les Macromolécules Végétales, UPR5301, CNRS-Université Grenoble Alpes, BP53, 38041 Grenoble cédex 09, France.
| | - Tammo Diercks
- CIC bioGUNE, Bizkaia Technological Park, Building 800, 48160 Derio, Spain.
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technological Park, Building 800, 48160 Derio, Spain.
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
| | - Sabine André
- Institut für Physiologische Chemie, Tierärztliche Fakultät der Ludwig-Maximilians-Universität, Veterinärstr. 13, 80539 München, Germany.
| | - Hans-Joachim Gabius
- Institut für Physiologische Chemie, Tierärztliche Fakultät der Ludwig-Maximilians-Universität, Veterinärstr. 13, 80539 München, Germany.
| | - Francisco Javier Cañada
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
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11
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Unione L, Galante S, Díaz D, Cañada FJ, Jiménez-Barbero J. NMR and molecular recognition. The application of ligand-based NMR methods to monitor molecular interactions. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00138a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
NMR allows the monitoring of molecular recognition processes in solution. Nowadays, a plethora of NMR methods are available to deduce the key features of the interaction from both the ligand or the receptor points of view.
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Affiliation(s)
- Luca Unione
- Chemical and Physical Biology
- Centro de Investigaciones Biológicas
- CSIC
- 28040 Madrid, Spain
| | - Silvia Galante
- Chemical and Physical Biology
- Centro de Investigaciones Biológicas
- CSIC
- 28040 Madrid, Spain
| | - Dolores Díaz
- Chemical and Physical Biology
- Centro de Investigaciones Biológicas
- CSIC
- 28040 Madrid, Spain
| | - F. Javier Cañada
- Chemical and Physical Biology
- Centro de Investigaciones Biológicas
- CSIC
- 28040 Madrid, Spain
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology
- Centro de Investigaciones Biológicas
- CSIC
- 28040 Madrid, Spain
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12
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Guo J, Catchmark JM, Mohamed MNA, Benesi AJ, Tien M, Kao TH, Watts HD, Kubicki JD. Identification and Characterization of a Cellulose Binding Heptapeptide Revealed by Phage Display. Biomacromolecules 2013; 14:1795-805. [DOI: 10.1021/bm4001876] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jing Guo
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Jeffrey M. Catchmark
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Mohamed Naseer Ali Mohamed
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Alan James Benesi
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Ming Tien
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Teh-hui Kao
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Heath D. Watts
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - James D. Kubicki
- Intercollege
Graduate Degree Program in Plant Biology, ‡Department of Agricultural and
Biological Engineering, and §School of Advanced Sciences, Crystal Growth and Crystallographic
Division, VIT University,
Vellore-632014, India
- Department
of Chemistry, ⊥Department of Biochemistry and Molecular Biology, #Department of Geosciences, ▽Center for NanoCellulosics, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
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13
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Seo Y, Andaya A, Bleiholder C, Leary JA. Differentiation of CC vs CXC Chemokine Dimers with GAG Octasaccharide Binding Partners: An Ion Mobility Mass Spectrometry Approach. J Am Chem Soc 2013; 135:4325-32. [DOI: 10.1021/ja310915m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Youjin Seo
- Departments of Chemistry and
Molecular and Cellular Biology, University of California, Davis, California 95616, United States
| | - Armann Andaya
- Departments of Chemistry and
Molecular and Cellular Biology, University of California, Davis, California 95616, United States
| | - Christian Bleiholder
- Department of Chemistry and
Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Julie A. Leary
- Departments of Chemistry and
Molecular and Cellular Biology, University of California, Davis, California 95616, United States
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14
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Eichmann SL, Meric G, Swavola JC, Bevan MA. Diffusing colloidal probes of protein-carbohydrate interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:2299-2310. [PMID: 23330828 DOI: 10.1021/la304355t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We present diffusing colloidal probe measurements of weak, multivalent, specific protein-polysaccharide interactions mediated by a competing monosaccharide. Specifically, we used integrated evanescent wave and video microscopy methods to monitor the three-dimensional Brownian excursions of conconavilin A (ConA) decorated colloids interacting with dextran-functionalized surfaces in the presence of glucose. Particle trajectories were interpreted as binding lifetime histograms, binding isotherms, and potentials of mean force. Binding lifetimes and isotherms showed clear trends of decreasing ConA-dextran-specific binding with increasing glucose concentration, consistent with expectations. Net potentials were accurately captured by superposition of a short-range, glucose-independent ConA-dextran repulsion and a longer-range, glucose-dependent dextran bridging attraction modeled as a harmonic potential. For glucose concentrations greater than 100 mM, the net ConA-dextran potential was found to have only a nonspecific repulsion, similar to that of bovine serum albumin (BSA) decorated colloids over dextran determined in control experiments. Our results demonstrate the first use of optical microscopy methods to quantify the connections between potentials of mean force and the binding behavior of ConA-decorated colloids on dextran-functionalized surfaces.
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Affiliation(s)
- Shannon L Eichmann
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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15
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Jana M, Bandyopadhyay S. Restricted dynamics of water around a protein-carbohydrate complex: computer simulation studies. J Chem Phys 2012; 137:055102. [PMID: 22894384 DOI: 10.1063/1.4739421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Water-mediated protein-carbohydrate interaction is a complex phenomenon responsible for different biological processes in cellular environment. One of the unexplored but important issues in this area is the role played by water during the recognition process and also in controlling the microscopic properties of the complex. In this study, we have carried out atomistic molecular dynamics simulations of a protein-carbohydrate complex formed between the hyaluronan binding domain of the murine Cd44 protein and the octasaccharide hyaluronan in explicit water. Efforts have been made to explore the heterogeneous influence of the complex on the dynamic properties of water present in different regions around it. It is revealed from our analyses that the heterogeneous dynamics of water around the complex are coupled with differential time scales of formation and breaking of hydrogen bonds at the interface. Presence of a highly rigid thin layer of motionally restricted water molecules bridging the protein and the carbohydrate in the common region of the complex has been identified. Such water molecules are expected to play a crucial role in controlling properties of the complex. Importantly, it is demonstrated that the formation of the protein-carbohydrate complex affects the transverse and longitudinal degrees of freedom of the interfacial water molecules in a heterogeneous manner.
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Affiliation(s)
- Madhurima Jana
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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16
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Jana M, Bandyopadhyay S. Conformational flexibility of a protein-carbohydrate complex and the structure and ordering of surrounding water. Phys Chem Chem Phys 2012; 14:6628-38. [PMID: 22460826 DOI: 10.1039/c2cp24104h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein-carbohydrate non-covalent interactions are important to understand various biological processes in living organisms. One of the important issues in protein-carbohydrate binding is how the protein identifies the target carbohydrate and recognizes its conformational features. Surrounding water molecules are expected to play a critical role not only in mediating the recognition process but also in maintaining the structure of the complex. We carried out atomistic molecular dynamics (MD) simulations of an aqueous solution of the protein-carbohydrate complex formed between the hyaluronan binding domain (HABD) of the murine Cd44 protein and the octasaccharide hyaluronan (HA(8)). The conformational flexibilities of the protein and the carbohydrate, and the microscopic structure and ordering of water molecules around them in the complexed form have been explored. It is revealed that the formation of the complex is associated with significant immobilization of the monosaccharide units of the carbohydrate moiety that are involved in binding. Further, reduction in water densities around the binding residues of the two molecules in the complex with respect to their free forms clearly demonstrated that the recognition between the protein and the carbohydrate is facilitated by removal of a fraction of water molecules from regions around the binding domains.
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Affiliation(s)
- Madhurima Jana
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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17
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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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18
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Martín-Santamaría S, Gabius HJ, Jiménez-Barbero J. Structural studies on the interaction of saccharides and glycomimetics with galectin-1: A 3D perspective using a combined molecular modeling and NMR approach. PURE APPL CHEM 2011. [DOI: 10.1351/pac-con-11-10-01] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The interaction of a variety of saccharides and mimetics thereof with lectin receptors has been studied using a combination of molecular modeling protocols and NMR spectroscopy techniques. It is shown that both methods complement each other in a synergistic manner to provide a detailed perspective of the conformational and structural features of the recognition process.
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Affiliation(s)
- Sonsoles Martín-Santamaría
- 1Department of Chemistry, Faculty of Pharmacy, Universidad San Pablo CEU, 28668-Boadilla del Monte, Madrid, Spain
| | - Hans-Joachim Gabius
- 2Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, München, Veterinärstrasse 13, 80539 München, Germany
| | - Jesús Jiménez-Barbero
- 3Department of Chemical and Physical Biology, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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19
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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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20
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Calle LP, Cañada FJ, Jiménez-Barbero J. Application of NMR methods to the study of the interaction of natural products with biomolecular receptors. Nat Prod Rep 2011; 28:1118-25. [DOI: 10.1039/c0np00071j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Mohamed MNA, Watts HD, Guo J, Catchmark JM, Kubicki JD. MP2, density functional theory, and molecular mechanical calculations of C–H···π and hydrogen bond interactions in a cellulose-binding module–cellulose model system. Carbohydr Res 2010; 345:1741-51. [DOI: 10.1016/j.carres.2010.05.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 05/10/2010] [Accepted: 05/22/2010] [Indexed: 10/19/2022]
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22
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Wang X, Ramström O, Yan M. Glyconanomaterials: synthesis, characterization, and ligand presentation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:1946-53. [PMID: 20301131 PMCID: PMC2940833 DOI: 10.1002/adma.200903908] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Glyconanomaterials, nanomaterials carrying surface-tethered carbohydrate ligands, have emerged and demonstrated increasing potential in biomedical imaging, therapeutics, and diagnostics. These materials combine the unique properties of nanometer-scale objects with the ability to present multiple copies of carbohydrate ligands, greatly enhancing the weak affinity of individual ligands to their binding partners. Critical to the performance of glyconanomaterials is the proper display of carbohydrate ligands, taking into consideration of the coupling chemistry, the type and length of the spacer linkage, and the ligand density. This article provides an overview of the coupling chemistry for attaching carbohydrate ligands to nanomaterials, and discusses the need for thorough characterization of glyconanomaterials, especially quantitative analyses of the ligand density and binding affinities. Using glyconanoparticles synthesized by a versatile photocoupling chemistry, methods for determining the ligand density by colorimetry and the binding affinity with lectins by a fluorescence competition assay are determined. The results show that the multivalent presentation of carbohydrate ligands significantly enhances the binding affinity by several orders of magnitude in comparison to the free ligands in solution. The effect is sizeable even at low surface ligand density. The type and length of the spacer linkage also affect the binding affinity, with the longer linkage promoting the association of bound ligands with the corresponding lectins.
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Affiliation(s)
- Xin Wang
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon, 97207-0751 (USA)
| | - Olof Ramström
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon, 97207-0751 (USA)
- Department of Chemistry, KTH - Royal Institute of Technology, Teknikringen 30, Stockholm, S-10044 (Sweden)
| | - Mingdi Yan
- Department of Chemistry Portland State University, P.O. Box 751, Portland, Oregon, 97207-0751 (USA)
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23
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Kövér KE, Szilágyi L, Batta G, Uhrín D, Jiménez-Barbero J. Biomolecular Recognition by Oligosaccharides and Glycopeptides: The NMR Point of View. COMPREHENSIVE NATURAL PRODUCTS II 2010:197-246. [DOI: 10.1016/b978-008045382-8.00193-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
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24
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Jiménez-Barbero J, L. Asensio J, Cuevas G, Canales A, Fernández-Alonso MC, Javier Cañada F. Conformational insights on the molecular recognition processes of carbohydrate molecules by proteins and enzymes: A 3D view by using NMR. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420600598103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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25
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Shpigelman A, Portnaya I, Ramon O, Livney YD. Saccharide-structure effects on polyN-isopropylacrylamide phase transition in aqueous media; Reflections on protein stability. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/polb.21562] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Preparation and evaluation of novel amphiphilic glycopeptide block copolymers as carriers for controlled drug release. POLYMER 2008. [DOI: 10.1016/j.polymer.2007.11.048] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Landström J, Nordmark EL, Eklund R, Weintraub A, Seckler R, Widmalm G. Interaction of a Salmonella enteritidis O-antigen octasaccharide with the phage P22 tailspike protein by NMR spectroscopy and docking studies. Glycoconj J 2007; 25:137-43. [PMID: 17703358 DOI: 10.1007/s10719-007-9065-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Revised: 07/02/2007] [Accepted: 07/06/2007] [Indexed: 12/01/2022]
Abstract
The tailspike protein P22 recognizes an octasaccharide derived from the O-antigen polysaccharide of Salmonella enteritidis in a shallow groove and molecular docking successfully identifies this binding region on the protein surface. Analysis by 2D (1)H,(1)H-T-ROESY and transferred NOESY NMR experiments indicate that the bound octasaccharide ligand has a conformation similar to that observed in solution. The results from a saturation transfer difference NMR experiment show that a large number of protons in the octasaccharide are in close contact with the protein as a result of binding. A comparison of the crystal structure of the complex and a molecular dynamics simulation of the octasaccharide with explicit water molecules suggest that only minor conformational changes are needed upon binding to the tailspike protein.
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Affiliation(s)
- Jens Landström
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, 106 91 Stockholm, Sweden
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28
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Konidala P, Niemeyer B. Molecular dynamics simulations of pea (Pisum sativum) lectin structure with octyl glucoside detergents: the ligand interactions and dynamics. Biophys Chem 2007; 128:215-30. [PMID: 17532552 DOI: 10.1016/j.bpc.2007.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2007] [Revised: 04/18/2007] [Accepted: 04/18/2007] [Indexed: 11/23/2022]
Abstract
The mitogenic pea (Pisum sativum) lectin is a legume protein of non-immunoglobulin nature capable of specific recognition of glucose derivatives without altering its structure. Molecular dynamics simulations were performed in a realistic environment to investigate the structure and interaction properties of pea lectin with various concentrations of n-octyl-beta-d-glucopyranoside (OG) detergent monomers distributed inside explicit solvent cell. In addition, the diffusion coefficients of the ligands (OG, Ca2+, Mn2+, and Cl-) and the water molecules were also reported. The structural flexibility of the lectin was conserved in all simulations. The self-assembly of OG monomers into a small micelle at the hydrophobic site of the lectin was noticed in the simulation with 20 OG monomers. The interaction energy analysis concludes that the lectin was appropriately termed an adaptive structure. One or rarely two binding sites were observed at an instant in each simulation that were electrostatically favoured for the OG to interact with the surface amino acid residues. Enhanced binding of OG to the pea lectin was quantified in the system containing only Ca2+ divalent ions. Interestingly, no binding was observed in the simulation without divalent ions. Furthermore, the lectin-ligand complex was stabilized by multiple hydrogen bonds and at least one water bridge. Finally, the work was also in accordance with the published work elsewhere that the simulations performed with different initial conditions and using higher nonbonded cutoffs for the van der Waals and electrostatic interactions provide more accurate information and clues than the single large simulation of the biomolecular system of interest.
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Affiliation(s)
- Praveen Konidala
- Institute of Thermodynamics, Helmut-Schmidt-University / University of the Federal Armed Forces Hamburg, Holstenhofweg 85, D-22043 Hamburg, Germany
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29
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Gerbst AG, Grachev AA, Shashkov AS, Nifantiev NE. Computation techniques in the conformational analysis of carbohydrates. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2007. [DOI: 10.1134/s1068162007010037] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Guerrini M, Guglieri S, Beccati D, Torri G, Viskov C, Mourier P. Conformational transitions induced in heparin octasaccharides by binding with antithrombin III. Biochem J 2006; 399:191-8. [PMID: 16796563 PMCID: PMC1609903 DOI: 10.1042/bj20060656] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present study deals with the conformation in solution of two heparin octasaccharides containing the pentasaccharide sequence GlcN(NAc,6S)-GlcA-GlcN(NS,3,6S)-IdoA(2S)-GlcN(NS,6S) [AGA*IA; where GlcN(NAc,6S) is N-acetylated, 6-O-sulfated alpha-D-glucosamine, GlcN(NS,3,6S) is N,3,6-O-trisulfated alpha-D-glucosamine and IdoA(2S) is 2-O-sulfated IdoA (alpha-L-iduronic acid)] located at different positions in the heparin chain and focuses on establishing geometries of IdoA residues (IdoA(2S) and IdoA) both inside and outside the AGA*IA sequence. AGA*IA constitutes the active site for AT (antithrombin) and is essential for the expression of high anticoagulant and antithrombotic activities. Analysis of NMR parameters [NOEs (nuclear Overhauser effects), transferred NOEs and coupling constants] for the two octasaccharides indicated that between the 1C4 and 2S0 conformations present in dynamic equilibrium in the free state for the IdoA(2S) residue within AGA*IA, AT selects the 2S0 form, as previously shown [Hricovini, Guerrini, Bisio, Torri, Petitou and Casu (2001) Biochem. J. 359, 265-272]. Notably, the 2S0 conformation is also adopted by the non-sulfated IdoA residue preceding AGA*IA that, in the absence of AT, adopts predominantly the 1C4 form. These results further support the concept that heparin-binding proteins influence the conformational equilibrium of iduronic acid residues that are directly or indirectly involved in binding and select one of their equi-energetic conformations for best fitting in the complex. The complete reversal of an iduronic acid conformation preferred in the free state is also demonstrated for the first time. Preliminary docking studies provided information on the octasaccharide binding location agreeing most closely with the experimental data. These results suggest a possible biological role for the non-sulfated IdoA residue preceding AGA*IA, previously thought not to influence the AT-binding properties of the pentasaccharide. Thus, for each AT binding sequence longer than AGA*IA, the interactions with the protein could differ and give to each heparin fragment a specific biological response.
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Affiliation(s)
- Marco Guerrini
- G. Ronzoni Institute for Chemical and Biochemical Research, via G. Colombo 81, 20133 Milan, Italy.
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31
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Zhuang T, Leffler H, Prestegard JH. Enhancement of bound-state residual dipolar couplings: conformational analysis of lactose bound to Galectin-3. Protein Sci 2006; 15:1780-90. [PMID: 16751604 PMCID: PMC2242564 DOI: 10.1110/ps.051994306] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Residual dipolar couplings (RDCs) have proven to be a valuable NMR tool that can provide long-range constraints for molecular structure determination. The constraints are orientational in nature and are, thus, highly complementary to conventional distance constraints from NOE data. This complementarity would seem to extend to the study of the geometry of ligands bound to proteins. However, unlike transferred NOEs, where collection, even with a large excess of free ligand, results in measurements dominated by bound contributions, RDCs of exchanging ligands can be dominated by free-state contributions. Here we present a strategy for enhancement of RDCs from bound states that is based on specifically enhancing the alignment of the protein to which a ligand will bind. The protein is modified by addition of a hydrophobic alkyl tail that anchors it to the bicelles that are a part of the ordering medium needed for RDC measurement. As an illustration, we have added a propyl chain to the C terminus of the carbohydrate recognition domain of the protein, Galectin-3, and report enhanced RDCs that prove consistent with known bound-ligand geometries for this protein.
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Affiliation(s)
- Tiandi Zhuang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
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32
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An easy access to a 3,6-branched mannopentaoside bearing one terminal [1-13C]-labeled D-mannopyranose residue. Russ Chem Bull 2005. [DOI: 10.1007/s11172-005-0396-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Yi X, Venot A, Glushka J, Prestegard JH. Glycosidic torsional motions in a bicelle-associated disaccharide from residual dipolar couplings. J Am Chem Soc 2004; 126:13636-8. [PMID: 15493919 DOI: 10.1021/ja045697t] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An analysis of torsional motions about glycosidic bonds in a disaccharide is undertaken using residual dipolar coupling measurements and selective immobilization of the reducing end sugar to provide a suitable motional reference. The immobilization is accomplished by using the short chain of an alkyl glycoside to anchor the disaccharide to a bilayer medium aligned in magnetic field. Motions about the beta-(1-4) linkage of the n-butyl-4-O-beta-d-galactopyranosyl-alpha-d-mannopyranoside are shown to be substantial (+/-40 degrees ) and in good agreement with predictions of a fully solvated molecular dynamics simulation.
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Affiliation(s)
- Xiaobing Yi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
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34
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Chien CH, Leung MK, Su JK, Li GH, Liu YH, Wang Y. Substituent Effects on Pyrid-2-yl Ureas toward Intramolecular Hydrogen Bonding and Cytosine Complexation. J Org Chem 2004; 69:1866-71. [PMID: 15058931 DOI: 10.1021/jo0355808] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Equilibria between two conformational isomers of pyrid-2-yl ureas, the (E,Z) and (Z,Z) forms, have been studied in DMF-d(7) at -70 degrees C. Most of them show a small preference for the (E,Z) form with an equilibrium constant K(i) around 1-2. However, the K(i) value for 1-methyl-2-(3-(pyrid-2-yl)ureido)pyridinium iodide (12) was found to be 14.2 +/- 1.2. That is 1 order of magnitude larger than those of the others, which indicates that the positively charged 1-methylpyridinium-2-yl substituent would facilitate the (E,Z) form formation. Pyrid-2-yl ureas bind cytosine in DMF-d(7) with binding constants K(B) ranging from 30 to 1700 M(-1). Electron withdrawing substituents, such as the 4-O(2)NC(6)H(4)- or 1-methylpyridinium-4-yl substituent, preferentially facilitate the intermolecular cytosine complexation with large binding constants.
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Affiliation(s)
- Chia-Hui Chien
- Department of Chemistry, National Taiwan University, Taipei, Taiwan 106, Republic of China
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35
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Siebert HC, Jiménez-Barbero J, André S, Kaltner H, Gabius HJ. Describing topology of bound ligand by transferred nuclear Overhauser effect spectroscopy and molecular modeling. Methods Enzymol 2003; 362:417-34. [PMID: 12968380 DOI: 10.1016/s0076-6879(03)01029-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Hans-Christian Siebert
- Institute of Physiological Chemistry, Ludwig-Maximilians University, Veterinarstrasse 13, Munich D-80539, Germany
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36
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Watts J, Jiménez-Barbero J, Poveda A, Grindley TB. Control of disaccharide conformation by π-stacking. CAN J CHEM 2003. [DOI: 10.1139/v03-062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The conformations of a series of derivatives of the disaccharide α-L-fucopyranosyl-(1[Formula: see text]3)-2-acetamido-2-deoxy-D-glucopyranoside, part of the Lex determinant, were studied by molecular modelling using the MM3* forcefield and by 1H NMR spectroscopy. Unusually shielded O-benzyl protons were observed in the 1H NMR spectrum of phenyl 2,3,4-tri-O-benzyl-α-L-fucopyranosyl-(1[Formula: see text]3)-2-deoxy-2-phthalimido-1-thio-α-D-glucopyranoside and assigned to the 2-O-benzyl group. This observation was explained by a shift in the population of the conformational mixture present about the glycosidic linkage from the positive Ψ region in the unsubstituted disaccharide to the negative Ψ region induced by π-stacking between the phthalimide and the 2-O-benzyl phenyl ring. The experimental nuclear Overhauser enhancements confirm the accuracy of the calculations.Key words: disaccharide, conformation, π-stacking, Lex determinant, NOE measurements, MM3 calculations.
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37
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Jain NU, Noble S, Prestegard JH. Structural characterization of a mannose-binding protein-trimannoside complex using residual dipolar couplings. J Mol Biol 2003; 328:451-62. [PMID: 12691753 DOI: 10.1016/s0022-2836(03)00268-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The ligand-binding properties of a 53 kDa homomultimeric trimer from mannose-binding protein (MBP) have been investigated using residual dipolar couplings (RDCs) that are easily measured from NMR spectra of the ligand and isotopically labeled protein. Using a limited set of 1H-15N backbone amide NMR assignments for MBP and orientational information derived from the RDC measurements in aligned media, an order tensor for MBP has been determined that is consistent with symmetry-based predictions of an axially symmetric system. 13C-1H couplings for a bound trisaccharide ligand, methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside (trimannoside) have been determined at natural abundance and used as orientational constraints. The bound ligand geometry and orientational constraints allowed docking of the trimannoside ligand in the binding site of MBP to produce a structural model for MBP-oligosaccharide interactions.
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Affiliation(s)
- Nitin U Jain
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996-0840, USA
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38
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Mikkelsen LM, Krintel SL, Jiménez-Barbero J, Skrydstrup T. Application of the anomeric samarium route for the convergent synthesis of the C-linked trisaccharide alpha-D-Man-(1-->3)-[alpha-D-Man-(1-->6)]-D-Man and the disaccharides alpha-D-Man-(1-->3)-D-Man and alpha-D-Man-(1-->6)-D-Man. J Org Chem 2002; 67:6297-308. [PMID: 12201747 DOI: 10.1021/jo020339z] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Studies are reported on the assembly of the branched C-trisaccharide, alpha-D-Man-(1-->3)-[alpha-D-Man-(1-->6)]-D-Man, representing the core region of the asparagine-linked oligosaccharides. The key step in this synthesis uses a SmI(2)-mediated coupling of two mannosylpyridyl sulfones to a C3,C6-diformyl branched monosaccharide unit, thereby assembling all three sugar units in one reaction and with complete stereocontrol at the two anomeric carbon centers. Subsequent tin hydride-based deoxygenation followed by a deprotection step produces the target C-trimer. In contrast to many of the other C-glycosylation methods, this approach employes intact carbohydrate units as C-glycosyl donors and acceptors, which in many instances parallels the well-studied O-glycosylation reactions. The synthesis of the C-disaccharides alpha-D-Man-(1-->3)-D-Man and alpha-D-Man-(1-->6)-D-Man is also described, they being necessary for the following conformational studies of all three carbohydrate analogues both in solution and bound to several mannose-binding proteins.
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Affiliation(s)
- Lise Munch Mikkelsen
- Department of Chemistry, University of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark
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39
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Unger FM. The chemistry of oligosaccharide ligands of selectins: significance for the development of new immunomodulatory medicines. Adv Carbohydr Chem Biochem 2002; 57:207-435. [PMID: 11836943 DOI: 10.1016/s0065-2318(01)57018-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- F M Unger
- Institute of Chemistry and Center for Ultrastructure Research, Agricultural University, Vienna, Austria
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40
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Michels J, Geyer A, Mocanu V, Welte W, Burlingame AL, Przybylski M. Structure and functional characterization of the periplasmic N-terminal polypeptide domain of the sugar-specific ion channel protein (ScrY porin). Protein Sci 2002; 11:1565-74. [PMID: 12021455 PMCID: PMC2373611 DOI: 10.1110/ps.2760102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
The structure of the sucrose-specific porin (ScrY) from Salmonella typhimurium has been elucidated by X-ray crystallography to consist of 18 antiparallel beta-strands, associated as a trimer complex similar to ion-transport channels. However, the 71-amino-acid-residue N-terminal periplasmic domain was not determined from the crystal structure due to the absence of sufficient electron density. The N-terminal polypeptide contains a coiled-coil structural motif and has been assumed to play a role in the sugar binding of ScrY porin. In this study the proteolytic stability and a specific proteolytic truncation site at the N-terminal domain were identified by the complete primary structure characterization of ScrY porin, using MALDI mass spectrometry and post-source-decay fragmentation. The secondary structure and supramolecular association of the coiled-coil N-terminal domain were determined by chemical synthesis of the complete N-terminal polypeptide and several partial sequences and their spectroscopic, biophysical, and mass spectrometric characterization. Circular dichroism spectra revealed predominant alpha-helical conformation for the putative coiled-coil domain comprising residues 4-46. Specific association to both dimer and trimer complexes was identified by electrospray ionization mass spectra and was ascertained by dynamic light scattering and electrophoresis data. The role of the N-terminal domain in sugar binding was examined by comparative TR-NOE-NMR spectroscopy of the complete ScrY porin and a recombinant mutant, ScrY(delta1-62), lacking the N-terminal polypeptide. The TR-NOE-NMR data showed a strong influence of ScrY porin on the sugar-binding affinity and suggested a possible function of the periplasmic N terminus for supramolecular stabilization and low-affinity sugar binding.
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Affiliation(s)
- Jenny Michels
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
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41
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Abstract
NOESY and ROESY cross-peak intensities depend on internuclear distances and internal motion. Internal motion is usually ignored, and NOESY cross-peak intensities are interpreted in terms of internuclear distances only. Off-resonance ROESY experiments measure a weighted average of NOE and ROE. The weight can be described and experimentally set by an angle theta;. For large enough molecules, NOE and ROE have opposite signs. Therefore, each cross-peak intensity becomes zero for an angle theta;(0). For any sample, the maximum angle theta;(0) is determined by the overall motion of the molecule. Smaller theta;(0) values reflect the angular component of internal motions. Because individual cross-peaks are analyzed, the method evaluates internal motions of individual H,H vectors. The reduction of theta;(0) is largest for internal motions on a time scale of 100-300 ps. The sensitivity of theta;(0) for internal motions decreases with increasing molecular weight. We estimate that detecting internal motions will be practicable for molecules up to about 15 kDa. We describe a protocol to measure theta;(0) from a series of off-resonance ROESY spectra. For such a series, we describe the choice of experimental parameters, a procedure to extract theta;(0) from the raw data, and the interpretation of theta;(0) in terms of internal motions. In the small protein BPTI, we analyzed 75 cross-peaks. The precision of theta;(0) was 0.25 degrees, as compared to typical reductions of theta;(0) of 3 degrees. We found a well-defined maximum theta;(0) for cross-peaks in rigid parts of the molecule, which reflects the overall motion of the molecule. For BPTI, also many structurally important long-range cross-peaks appear rigid. The lower theta;(0) values of long-range contacts involving methyl groups are consistent with methyl rotation on the 25-ps time scale. The lower theta;(0) values of the flexible C-terminus and of flexible side chains translate into upper limits for the angular order parameter of 0.4 and 0.5-0.8, respectively. Off-resonance ROESY can monitor internal motions of H,H contacts that are used in a structure calculation. Because no isotope labeling is needed, off-resonance ROESY can be used to detect internal motions in a wide range of natural products.
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Affiliation(s)
- Jürgen Schleucher
- Department of Medical Biochemistry and Biophysics, and Department of Organic Chemistry, Umeå University, S-90187 Umeå, Sweden.
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42
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Azurmendi HF, Bush CA. Conformational studies of blood group A and blood group B oligosaccharides using NMR residual dipolar couplings. Carbohydr Res 2002; 337:905-15. [PMID: 12007473 DOI: 10.1016/s0008-6215(02)00070-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformations of two synthetic trisaccharides of blood group A and B (alpha-L-Fucp-(1-->2)-[alpha-D-GalpNAc-(1-->3)]-alpha-D-Galp and alpha-L-Fucp-(1-->2)-[alpha-D-Galp-(1-->3)]-alpha-D-Galp, respectively) and of a type A tetrasaccharide alditol, Fucp-(1-->2)-[alpha-D-GalpNAc-(1-->3)]-beta-D-Galp-(1-->3)-GalNAc-ol, were studied by NMR measurements of one-bond C-H residual dipolar couplings in partially oriented liquid crystal solutions. The conformations of the three oligosaccharides were analyzed by generating thousands of structures using a Monte-Carlo method. Two different strategies were applied to calculate theoretical dipolar couplings for these structures. In the first method, the orientation of the molecule was calculated from the optimal fit of the molecular model to the experimental data, while in the second method the orientation tensor was calculated directly from the moment of inertia of the molecular model. Both methods of analysis give similar results but with slightly better agreement with experiment for the former one. The analysis of the results implies a single unique conformation for both blood group epitopes in solution in disagreement with theoretical models suggesting the existence of two conformers in solution.
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Affiliation(s)
- Hugo F Azurmendi
- Department of Chemistry and Biochemistry, University of Maryland-Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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43
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García-Herrero A, Montero E, Muñoz JL, Espinosa JF, Vián A, García JL, Asensio JL, Cañada FJ, Jiménez-Barbero J. Conformational selection of glycomimetics at enzyme catalytic sites: experimental demonstration of the binding of distinct high-energy distorted conformations of C-, S-, and O-glycosides by E. Coli beta-galactosidases. J Am Chem Soc 2002; 124:4804-10. [PMID: 11971730 DOI: 10.1021/ja0122445] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We show that the conformational features of the molecular complexes of E. coli beta-galactosidase and O-glycosides may differ from those formed with closely related compounds in their chemical nature, such as C- and S-glycosyl analogues. In the particular case presented here, NMR and ab initio quantum mechanical results show that the 3D-shapes of the ligand/inhibitor within the enzyme binding site depend on the chemical nature of the compounds. In fact, they depend on the relative size of the stereoelectronic barriers for chair deformation or for rotation around Phi glycosidic linkage.
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Affiliation(s)
- Alicia García-Herrero
- Department Bioorganic Chemistry, Instituto Quimica Organica, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
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44
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Comparative analysis of ganglioside conformations by MD simulations: implications for specific recognition by proteins. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(01)00813-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Vasudevan SV, Balaji PV. Molecular dynamics simulations of alpha2 --> 8-linked disialoside: conformational analysis and implications for binding to proteins. Biopolymers 2002; 63:168-80. [PMID: 11787005 DOI: 10.1002/bip.10019] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Computational methods have played a key role in elucidating the various three-dimensional structures of oligosaccharides. Such structural information, together with other experimental data, leads to a better understanding of the role of oligosaccharide in various biological processes. The disialoside Neu5Ac-alpha2-->8-Neu5Ac appears as the terminal glycan in glycoproteins and glycolipids, and is known to play an important role in various events of cellular communication. Neurotoxins such as botulinum and tetanus require Neu5Ac-alpha2 --> 8-Neu5Ac for infecting the host. Glycoconjugates containing this disialoside and the enzymes catalyzing their biosynthesis are also regulated during cell growth, development, and differentiation. Unlike other biologically relevant disaccharides that have only two linkage bonds, the alpha2-->8-linked disialoside has four: C2-O, O-C8', C8'-C7', and C7'-C6'. The present report describes the results from nine 1 ns MD simulations of alpha2-->8-linked disialoside (Neu5Ac-alpha2-->8-Neu5Ac); simulations were run using GROMOS96 by explicitly considering the solvent molecules. Conformations around the O-C8' bond are restricted to the +sc/+ap regions due to stereochemical reasons. In contrast, conformations around the C2-O and C8'-C7' bonds were found to be largely unrestricted and all the three staggered regions are accessible. The conformations around the C7'-C6' bond were found to be in either the -sc or the anti region. These results are in excellent agreement with the available NMR and potential energy calculation studies. Overall, the disaccharide is flexible and adopts mainly two ensembles of conformations differing in the conformation around the C7'-C6' bond. The flexibility associated with this disaccharide allows for better optimization of intermolecular contacts while binding to proteins and this may partially compensate for the loss of conformational entropy that may be incurred due to disaccharide's flexibility.
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Affiliation(s)
- Sheeja V Vasudevan
- Biotechnology Center, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
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Azurmendi HF, Martin-Pastor M, Bush CA. Conformational studies of Lewis X and Lewis A trisaccharides using NMR residual dipolar couplings. Biopolymers 2002; 63:89-98. [PMID: 11786997 DOI: 10.1002/bip.10015] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The conformations of the histo-blood group carbohydrate antigens Lewis X (Le(x)) and Lewis A (Le(a)) were studied by NMR measurements of one-bond C-H residual dipolar couplings in partially oriented liquid crystal solutions. A strategy for rapid calculation of the difference between theoretical and experimental dipolar couplings of a large number of model structures generated by computer simulations was developed, resulting in an accurate model structure for the compounds. Monte Carlo simulations were used to generate models for the trisaccharides, and orientations of each model were sought that could reproduce the experimental residual dipolar coupling values. For both, Le(a) and Le(x), single low energy models giving excellent agreement with experiment were found, implying a compact rigidly folded conformation for both trisaccharides. The new approach was also applied to the pentasaccharides lacto-N-fucopentaose 2 (LNF-2) and lacto-N-fucopentaose 3 (LNF-3) proving its consistency and robustness. For describing the conformation of tightly folded oligosaccharides, a definition for characterization of ring planes in pyranoside chairs is proposed and applied to the analysis of the relation between the fucose and galactose residues in the epitopes, revealing the structural similarity between them.
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Affiliation(s)
- Hugo F Azurmendi
- Department of Chemistry and Biochemistry, University of Maryland-Baltimore County, Baltimore, MD 21250, USA
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47
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Affiliation(s)
- Yehia Mechref
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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48
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Vishnyakov A, Laaksonen A, Widmalm G. Molecular dynamics simulations of alpha-D-Manp-(1-->3)-beta-D-Glcp-OMe in methanol and in dimethyl sulfoxide solutions. J Mol Graph Model 2002; 19:338-42, 396-7. [PMID: 11449573 DOI: 10.1016/s1093-3263(00)00082-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations have been performed of the disaccharide alpha-D-Manp-(1-->3)-beta-D-Glcp-OMe in two different solvents, namely in methanol and in dimethyl sulfoxide. The conformation of the disaccharide is similar to that previously determined in water. The three-dimensional structure around the solute was investigated by geometric hydrogen bonding criteria, radial distribution functions, coordination number analysis, residence times for hydrogen bonds, and spatial distribution functions. Differences and similarities between methanol and the aprotic dimethyl sulfoxide as solvent are analyzed.
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Affiliation(s)
- A Vishnyakov
- TRI/Princeton, 601 Prospect Ave, Princeton, NJ 08542, USA
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49
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Alonso-Plaza JM, Canales MA, Jiménez M, Roldán JL, García-Herrero A, Iturrino L, Asensio JL, Cañada FJ, Romero A, Siebert HC, André S, Solís D, Gabius HJ, Jiménez-Barbero J. NMR investigations of protein-carbohydrate interactions: insights into the topology of the bound conformation of a lactose isomer and beta-galactosyl xyloses to mistletoe lectin and galectin-1. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1568:225-36. [PMID: 11786229 DOI: 10.1016/s0304-4165(01)00224-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A hallmark of oligosaccharides is their often limited spatial flexibility, allowing them to access a distinct set of conformers in solution. Viewing each individual or even the complete ensemble of conformations as potential binding partner(s) for lectins in protein-carbohydrate interactions, it is pertinent to address the question on the characteristics of bound state conformation(s) in solution. Also, it is possible that entering the lectin's binding site distorts the low-energy topology of a glycosidic linkage. As a step to delineate the strategy of ligand selection for galactosides, a common physiological docking point, we have performed a NMR study on two non-homologous lectins showing identical monosaccharide specificity. Thus, the conformation of lactose analogues bound to bovine heart galectin-1 and to mistletoe lectin in solution has been determined by transferred nuclear Overhauser effect measurements. It is demonstrated that the lectins select the syn conformation of lactose and various structural analogues (Galbeta(1-->4)Xyl, Galbeta(1-->3)Xyl, Galbeta(1-->2)Xyl, and Galbeta(1-->3)Glc) from the ensemble of presented conformations. No evidence for conformational distortion was obtained. Docking of the analogues to the modeled binding sites furnishes explanations, in structural terms, for exclusive recognition of the syn conformer despite the non-homologous design of the binding sites.
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50
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Höög C, Landersjö C, Widmalm G. Oligosaccharides display both rigidity and high flexibility in water as determined by 13C NMR relaxation and 1H,1H NOE spectroscopy: evidence of anti-phi and anti-psi torsions in the same glycosidic linkage. Chemistry 2001; 7:3069-77. [PMID: 11495434 DOI: 10.1002/1521-3765(20010716)7:14<3069::aid-chem3069>3.0.co;2-a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The trisaccharide beta-D-Glcp-(1-->2)-beta-D-Glcp-(1-->3)-alpha-D-Glcp-OMe has been investigated by molecular dynamics (MD) simulations and NMR experiments in water. 13C spin-lattice (T1) and spin-spin (T2) relaxation times, together with 1H,13C NOE data were measured at two magnetic field strengths (9.4 and 14.1 T) in a 277 K D2O solution. Relaxation data interpreted by means of the model-free formalism revealed a rigid (S2 approximately 0.9) oligosaccharide tumbling in solution. 1H,1H Cross-relaxation rates were determined at 600 MHz by 1D DPFGSE NOESY and T-ROESY experiments, which provided high quality data and subsequently proton-proton distances within the trisaccharide. The presence of anti conformers at both torsions of a glycosidic linkage is demonstrated for the first time. MD simulations were carried out to facilitate analysis of the NOE data. In total, 15 simulations-starting from five different conformational states--were performed, with production runs of up to 10 ns, resulting in 83 ns of oligosaccharide dynamics in water. anti Conformers were populated to different degrees in the simulations, especially at the phi2 torsion angle. By combining the results from the NOE experiments and the MD simulations, the anti conformers at the (1-->2)-linkage were quantified as 7% anti-phi2 and 2% anti-psi2, revealing a highly flexible trisaccharide in which large conformational changes occur. From the MD simulations, interresidue hydrogen bonding, from HO2" to O2 or O3, was significantly populated (approximately 40%) in both of the anti conformational states. The contentious issue over rigidity versus flexibility in oligosaccharides has thus been thoroughly examined, showing that the dynamics should be taken into account for a relevant description of the molecular system.
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Affiliation(s)
- C Höög
- Department of Organic Chemistry, Arrhenius Laboratory Stockholm University, Sweden
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