1
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Rapid differentiation of simple saccharides based on cluster ions by paper spray tandem mass spectrometry. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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2
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Mayberry CL, Maginnis MS. Taking the Scenic Route: Polyomaviruses Utilize Multiple Pathways to Reach the Same Destination. Viruses 2020; 12:v12101168. [PMID: 33076363 PMCID: PMC7602598 DOI: 10.3390/v12101168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 01/02/2023] Open
Abstract
Members of the Polyomaviridae family differ in their host range, pathogenesis, and disease severity. To date, some of the most studied polyomaviruses include human JC, BK, and Merkel cell polyomavirus and non-human subspecies murine and simian virus 40 (SV40) polyomavirus. Although dichotomies in host range and pathogenesis exist, overlapping features of the infectious cycle illuminate the similarities within this virus family. Of particular interest to human health, JC, BK, and Merkel cell polyomavirus have all been linked to critical, often fatal, illnesses, emphasizing the importance of understanding the underlying viral infections that result in the onset of these diseases. As there are significant overlaps in the capacity of polyomaviruses to cause disease in their respective hosts, recent advancements in characterizing the infectious life cycle of non-human murine and SV40 polyomaviruses are key to understanding diseases caused by their human counterparts. This review focuses on the molecular mechanisms by which different polyomaviruses hijack cellular processes to attach to host cells, internalize, traffic within the cytoplasm, and disassemble within the endoplasmic reticulum (ER), prior to delivery to the nucleus for viral replication. Unraveling the fundamental processes that facilitate polyomavirus infection provides deeper insight into the conserved mechanisms of the infectious process shared within this virus family, while also highlighting critical unique viral features.
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Affiliation(s)
- Colleen L. Mayberry
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04469, USA;
| | - Melissa S. Maginnis
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04469, USA;
- Graduate School in Biomedical Sciences and Engineering, The University of Maine, Orono, ME 04469, USA
- Correspondence:
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3
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Siow WX, Chang YT, Babič M, Lu YC, Horák D, Ma YH. Interaction of poly-l-lysine coating and heparan sulfate proteoglycan on magnetic nanoparticle uptake by tumor cells. Int J Nanomedicine 2018; 13:1693-1706. [PMID: 29599614 PMCID: PMC5866726 DOI: 10.2147/ijn.s156029] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Poly-l-lysine (PLL) enhances nanoparticle (NP) uptake, but the molecular mechanism remains unresolved. We asked whether PLL may interact with negatively charged glycoconjugates on the cell surface and facilitate uptake of magnetic NPs (MNPs) by tumor cells. Methods PLL-coated MNPs (PLL-MNPs) with positive and negative ζ-potential were prepared and characterized. Confocal and transmission electron microscopy was used to analyze cellular internalization of MNPs. A colorimetric iron assay was used to quantitate cell-associated MNPs (MNPcell). Results Coadministration of PLL and dextran-coated MNPs in culture enhanced cellular internalization of MNPs, with increased vesicle size and numbers/cell. MNPcell was increased by eight- to 12-fold in response to PLL in a concentration-dependent manner in human glioma and HeLa cells. However, the application of a magnetic field attenuated PLL-induced increase in MNPcell. PLL-coating increased MNPcell regardless of ζ-potential of PLL-MNPs, whereas magnetic force did not enhance MNPcell. In contrast, epigallocatechin gallate and magnetic force synergistically enhanced PLL-MNP uptake. In addition, heparin, but not sialic acid, greatly reduced the enhancement effects of PLL; however, removal of heparan sulfate from heparan sulfate proteoglycans of the cell surface by heparinase III significantly reduced MNPcell. Conclusion Our results suggest that PLL-heparan sulfate proteoglycan interaction may be the first step mediating PLL-MNP internalization by tumor cells. Given these results, PLL may facilitate NP interaction with tumor cells via a molecular mechanism shared by infection machinery of certain viruses.
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Affiliation(s)
- Wei Xiong Siow
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan, Republic of China.,Department of Physiology and Pharmacology and Healthy Aging Research Center, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan, Republic of China
| | - Yi-Ting Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan, Republic of China.,Department of Physiology and Pharmacology and Healthy Aging Research Center, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan, Republic of China
| | - Michal Babič
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Yi-Ching Lu
- Department of Physiology and Pharmacology and Healthy Aging Research Center, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan, Republic of China
| | - Daniel Horák
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Yunn-Hwa Ma
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan, Republic of China.,Department of Physiology and Pharmacology and Healthy Aging Research Center, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan, Republic of China.,Department of Neurology, Chang Gung Memorial Hospital, Guishan, Taoyuan, Taiwan, Republic of China
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4
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Azurmendi HF, Battistel MD, Zarb J, Lichaa F, Negrete Virgen A, Shiloach J, Freedberg DI. The β-reducing end in α(2-8)-polysialic acid constitutes a unique structural motif. Glycobiology 2017; 27:900-911. [PMID: 28369425 PMCID: PMC6283323 DOI: 10.1093/glycob/cwx025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/10/2017] [Accepted: 03/14/2017] [Indexed: 12/13/2022] Open
Abstract
Over the years, structural characterizations of α(2-8)-polysialic acid (polySia) in solution have produced inconclusive results. Efforts for obtaining detailed information in this important antigen have focused primarily on the α-linked residues and not on the distinctive characteristics of the terminal ones. The thermodynamically preferred anomeric configuration for the reducing end of sialic acids is β, which has the [I]CO2- group equatorial and the OH ([I]OH2) axial, while for all other residues the CO2- group is axial. We show that this purportedly minor difference has distinct consequences for the structure of α(2-8)-polySia near the reducing end, as the β configuration places the [I]OH2 in a favorable position for the formation of a hydrogen bond with the carboxylate group of the following residue ([II]CO2-). Molecular dynamics (MD) simulations predicted the hydrogen bond, which we subsequently directly detected by NMR. The combination of MD and residual dipolar couplings shows that the net result for the structure of Sia2-βOH is a stable conformation with well-defined hydration and charge patterns, and consistent with experimental NOE-based hydroxyl and aliphatic inter-proton distances. Moreover, we provide evidence that this distinct conformation is preserved on Sia oligosaccharides, thus constituting a motif that determines the structure and dynamics of α(2-8)-polySia for at least the first two residues of the polymer. We suggest the hypothesis that this structural motif sheds light on a longtime puzzling observation for the requirement of 10 residues of α(2-8)-polySia in order to bind effectively to specific antibodies, about four units more than for analogous cases.
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Affiliation(s)
- Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Jasmin Zarb
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Flora Lichaa
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Alejandro Negrete Virgen
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Joseph Shiloach
- Biotechnology Unit, MSC 5522, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
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5
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Gabius HJ. The sugar code: Why glycans are so important. Biosystems 2017; 164:102-111. [PMID: 28709806 DOI: 10.1016/j.biosystems.2017.07.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/05/2017] [Indexed: 02/07/2023]
Abstract
The cell surface is the platform for presentation of biochemical signals that are required for intercellular communication. Their profile necessarily needs to be responsive to internal and external factors in a highly dynamic manner. The structural features of the signals must meet the criterion of high-density information coding in a minimum of space. Thus, only biomolecules that can generate many different oligomers ('words') from few building blocks ('letters') qualify to meet this challenge. Examining the respective properties of common biocompounds that form natural oligo- and polymers comparatively, starting with nucleotides and amino acids (the first and second alphabets of life), comes up with sugars as clear frontrunner. The enzymatic machinery for the biosynthesis of sugar chains can indeed link monosaccharides, the letters of the third alphabet of life, in a manner to reach an unsurpassed number of oligomers (complex carbohydrates or glycans). Fittingly, the resulting glycome of a cell can be likened to a fingerprint. Conjugates of glycans with proteins and sphingolipids (glycoproteins and glycolipids) are ubiquitous in Nature. This implies a broad (patho)physiologic significance. By looking at the signals, at the writers and the erasers of this information as well as its readers and ensuing consequences, this review intends to introduce a broad readership to the principles of the concept of the sugar code.
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Affiliation(s)
- Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstraße 13, 80539 Munich, Germany.
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6
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Structure of a protective epitope of group B Streptococcus type III capsular polysaccharide. Proc Natl Acad Sci U S A 2017; 114:5017-5022. [PMID: 28439022 DOI: 10.1073/pnas.1701885114] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite substantial progress in the prevention of group B Streptococcus (GBS) disease with the introduction of intrapartum antibiotic prophylaxis, this pathogen remains a leading cause of neonatal infection. Capsular polysaccharide conjugate vaccines have been tested in phase I/II clinical studies, showing promise for further development. Mapping of epitopes recognized by protective antibodies is crucial for understanding the mechanism of action of vaccines and for enabling antigen design. In this study, we report the structure of the epitope recognized by a monoclonal antibody with opsonophagocytic activity and representative of the protective response against type III GBS polysaccharide. The structure and the atomic-level interactions were determined by saturation transfer difference (STD)-NMR and X-ray crystallography using oligosaccharides obtained by synthetic and depolymerization procedures. The GBS PSIII epitope is made by six sugars. Four of them derive from two adjacent repeating units of the PSIII backbone and two of them from the branched galactose-sialic acid disaccharide contained in this sequence. The sialic acid residue establishes direct binding interactions with the functional antibody. The crystal structure provides insight into the molecular basis of antibody-carbohydrate interactions and confirms that the conformational epitope is not required for antigen recognition. Understanding the structural basis of immune recognition of capsular polysaccharide epitopes can aid in the design of novel glycoconjugate vaccines.
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7
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Tan Y, Zhao N, Liu J, Li P, Stedwell CN, Yu L, Polfer NC. Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:539-550. [PMID: 28050874 DOI: 10.1007/s13361-016-1575-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 05/14/2023]
Abstract
Three lithiated N-acetyl-D-hexosamine (HexNAc) isomers, N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-galactosamine (GalNAc), and N-acetyl-D-mannosamine (ManNAc) are investigated as model monosaccharide derivatives by gas-phase infrared multiple-photon dissociation (IRMPD) spectroscopy. The hydrogen stretching region, which is attributed to OH and NH stretching modes, reveals some distinguishing spectral features of the lithium-adducted complexes that are useful in terms of differentiating these isomers. In order to understand the effect of lithium coordination on saccharide structure, and therefore anomericity, chair configuration, and hydrogen bonding networks, the conformational preferences of lithiated GlcNAc, GalNAc, and ManNAc are studied by comparing the experimental measurements with density functional theory (DFT) calculations. The experimental results of lithiated GlcNAc and GalNAc show a good match to the theoretical spectra of low-energy structures adopting a 4 C 1 chair conformation, consistent with this motif being the dominant conformation in condensed-phase monosaccharides. The epimerization effect upon going to lithiated ManNAc is significant, as in this case the 1 C 4 chair conformers give a more compelling match with the experimental results, consistent with their lower calculated energies. A contrasting computational study of these monosaccharides in their neutral form suggests that the lithium cation coordination with Lewis base oxygens can play a key role in favoring particular structural motifs (e.g., a 4 C 1 versus 1 C 4 ) and disrupting hydrogen bond networks, thus exhibiting specific IR spectral features between these closely related lithium-chelated complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Yanglan Tan
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ning Zhao
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Jinfeng Liu
- State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China
| | - Pengfei Li
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Long Yu
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Nicolas C Polfer
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
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8
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Liang K, Wang R, Boutter M, Doherty CM, Mulet X, Richardson JJ. Biomimetic mineralization of metal–organic frameworks around polysaccharides. Chem Commun (Camb) 2017; 53:1249-1252. [DOI: 10.1039/c6cc09680h] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Biomimetic mineralization exploits natural biomineralization processes for the design and fabrication of synthetic functional materials.
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Affiliation(s)
- Kang Liang
- CSIRO Manufacturing
- Clayton South
- Australia
| | - Ru Wang
- Chimie ParisTech
- ENSCP
- 75005 Paris
- France
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9
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Gu RX, Ingólfsson HI, de Vries AH, Marrink SJ, Tieleman DP. Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations. J Phys Chem B 2016; 121:3262-3275. [PMID: 27610460 PMCID: PMC5402298 DOI: 10.1021/acs.jpcb.6b07142] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from atomistic simulations are not observed at the CG level based on the Martini model, implying a difference in driving forces for ganglioside interactions in atomistic and CG simulations. For protein-ganglioside interactions, in the atomistic simulations, GM1 lipids bind to specific sites on the AQP1 surface, whereas they are depleted from WALP23. In the CG simulations, the ganglioside binding sites on the AQP1 surface are similar, but ganglioside aggregation and protein-ganglioside interactions are more prevalent than in the atomistic simulations. Using the polarizable Martini water model, results were closer to the atomistic simulations. Although experimental data for validation is lacking, we proposed modified Martini parameters for gangliosides to more closely mimic the sizes and structures of ganglioside clusters observed at the atomistic level.
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Affiliation(s)
- Ruo-Xu Gu
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
| | - Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology (GBB) Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology (GBB) Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology (GBB) Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada
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10
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Sterner E, Flanagan N, Gildersleeve JC. Perspectives on Anti-Glycan Antibodies Gleaned from Development of a Community Resource Database. ACS Chem Biol 2016; 11:1773-83. [PMID: 27220698 PMCID: PMC4949583 DOI: 10.1021/acschembio.6b00244] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Antibodies are used
extensively for a wide range of basic research
and clinical applications. While an abundant and diverse collection
of antibodies to protein antigens have been developed, good monoclonal
antibodies to carbohydrates are much less common. Moreover, it can
be difficult to determine if a particular antibody has the appropriate
specificity, which antibody is best suited for a given application,
and where to obtain that antibody. Herein, we provide an overview
of the current state of the field, discuss challenges for selecting
and using antiglycan antibodies, and summarize deficiencies in the
existing repertoire of antiglycan antibodies. This perspective was
enabled by collecting information from publications, databases, and
commercial entities and assembling it into a single database, referred
to as the Database of Anti-Glycan Reagents (DAGR). DAGR is a publicly
available, comprehensive resource for anticarbohydrate antibodies,
their applications, availability, and quality.
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Affiliation(s)
- Eric Sterner
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Natalie Flanagan
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jeffrey C. Gildersleeve
- Chemical Biology Laboratory,
Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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11
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Multivalent Carbohydrate-Lectin Interactions: How Synthetic Chemistry Enables Insights into Nanometric Recognition. Molecules 2016; 21:molecules21050629. [PMID: 27187342 PMCID: PMC6274006 DOI: 10.3390/molecules21050629] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 12/15/2022] Open
Abstract
Glycan recognition by sugar receptors (lectins) is intimately involved in many aspects of cell physiology. However, the factors explaining the exquisite selectivity of their functional pairing are not yet fully understood. Studies toward this aim will also help appraise the potential for lectin-directed drug design. With the network of adhesion/growth-regulatory galectins as therapeutic targets, the strategy to recruit synthetic chemistry to systematically elucidate structure-activity relationships is outlined, from monovalent compounds to glyco-clusters and glycodendrimers to biomimetic surfaces. The versatility of the synthetic procedures enables to take examining structural and spatial parameters, alone and in combination, to its limits, for example with the aim to produce inhibitors for distinct galectin(s) that exhibit minimal reactivity to other members of this group. Shaping spatial architectures similar to glycoconjugate aggregates, microdomains or vesicles provides attractive tools to disclose the often still hidden significance of nanometric aspects of the different modes of lectin design (sequence divergence at the lectin site, differences of spatial type of lectin-site presentation). Of note, testing the effectors alone or in combination simulating (patho)physiological conditions, is sure to bring about new insights into the cooperation between lectins and the regulation of their activity.
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12
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Tan Y, Polfer NC. Linkage and anomeric differentiation in trisaccharides by sequential fragmentation and variable-wavelength infrared photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:359-368. [PMID: 25492690 DOI: 10.1007/s13361-014-1025-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 06/04/2023]
Abstract
Carbohydrates and their derivatives play important roles in biological systems, but their isomeric heterogeneity also presents a considerable challenge for analytical techniques. Here, a stepwise approach using infrared multiple-photon dissociation (IRMPD) via a tunable CO2 laser (9.2-10.7 μm) was employed to characterize isomeric variants of glucose-based trisaccharides. After the deprotonated trisaccharides were trapped and fragmented to disaccharide C2 fragments in a Fourier transform ion cyclotron resonance (FTICR) cell, a further variable-wavelength infrared irradiation of the C2 ion produced wavelength-dependent dissociation patterns that are represented as heat maps. The photodissociation patterns of these C2 fragments are shown to be strikingly similar to the photodissociation patterns of disaccharides with identical glycosidic bonds. Conversely, the photodissociation patterns of different glycosidic linkages exhibit considerable differences. On the basis of these results, the linkage position and anomericity of glycosidic bonds of disaccharide units in trisaccharides can be systematically differentiated and identified, providing a promising approach to characterize the structures of isomeric oligosaccharides.
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Affiliation(s)
- Yanglan Tan
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
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13
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Camilloni C, Vendruscolo M. A tensor-free method for the structural and dynamical refinement of proteins using residual dipolar couplings. J Phys Chem B 2014; 119:653-61. [PMID: 24824082 DOI: 10.1021/jp5021824] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Residual dipolar couplings (RDCs) are parameters measured in nuclear magnetic resonance spectroscopy that can provide exquisitely detailed information about the structure and dynamics of biological macromolecules. We describe here a method of using RDCs for the structural and dynamical refinement of proteins that is based on the observation that the RDC between two atomic nuclei depends directly on the angle ϑ between the internuclear vector and the external magnetic field. For every pair of nuclei for which an RDC is available experimentally, we introduce a structural restraint to minimize the deviation from the value of the angle ϑ derived from the measured RDC and that calculated in the refinement protocol. As each restraint involves only the calculation of the angle ϑ of the corresponding internuclear vector, the method does not require the definition of an overall alignment tensor to describe the preferred orientation of the protein with respect to the alignment medium. Application to the case of ubiquitin demonstrates that this method enables an accurate refinement of the structure and dynamics of this protein to be obtained.
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Affiliation(s)
- Carlo Camilloni
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
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14
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Lauc G, Krištić J, Zoldoš V. Glycans - the third revolution in evolution. Front Genet 2014; 5:145. [PMID: 24904645 PMCID: PMC4033155 DOI: 10.3389/fgene.2014.00145] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/04/2014] [Indexed: 11/13/2022] Open
Abstract
The development and maintenance of a complex organism composed of trillions of cells is an extremely complex task. At the molecular level every process requires a specific molecular structures to perform it, thus it is difficult to imagine how less than tenfold increase in the number of genes between simple bacteria and higher eukaryotes enabled this quantum leap in complexity. In this perspective article we present the hypothesis that the invention of glycans was the third revolution in evolution (the appearance of nucleic acids and proteins being the first two), which enabled the creation of novel molecular entities that do not require a direct genetic template. Contrary to proteins and nucleic acids, which are made from a direct DNA template, glycans are product of a complex biosynthetic pathway affected by hundreds of genetic and environmental factors. Therefore glycans enable adaptive response to environmental changes and, unlike other epiproteomic modifications, which act as off/on switches, glycosylation significantly contributes to protein structure and enables novel functions. The importance of glycosylation is evident from the fact that nearly all proteins invented after the appearance of multicellular life are composed of both polypeptide and glycan parts.
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Affiliation(s)
- Gordan Lauc
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb Zagreb, Croatia ; Genos Glycoscience Zagreb, Croatia
| | | | - Vlatka Zoldoš
- Department of Molecular Biology, Faculty of Science, University of Zagreb Zagreb, Croatia
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15
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Dias RP, da Hora GCA, Ramstedt M, Soares TA. Outer Membrane Remodeling: The Structural Dynamics and Electrostatics of Rough Lipopolysaccharide Chemotypes. J Chem Theory Comput 2014; 10:2488-97. [DOI: 10.1021/ct500075h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Roberta P. Dias
- Department
of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife 50740-560, Brazil
| | - Gabriel C. A. da Hora
- Department
of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife 50740-560, Brazil
| | | | - Thereza A. Soares
- Department
of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife 50740-560, Brazil
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16
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Ingólfsson HI, Lopez CA, Uusitalo JJ, de Jong DH, Gopal SM, Periole X, Marrink SJ. The power of coarse graining in biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2014; 4:225-248. [PMID: 25309628 PMCID: PMC4171755 DOI: 10.1002/wcms.1169] [Citation(s) in RCA: 325] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large-scale biomolecular processes on time scales inaccessible to all-atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state-of-the-art examples of protein folding, membrane protein gating and self-assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling.
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Affiliation(s)
- Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Cesar A Lopez
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Djurre H de Jong
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Srinivasa M Gopal
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
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17
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Solís D, Bovin NV, Davis AP, Jiménez-Barbero J, Romero A, Roy R, Smetana K, Gabius HJ. A guide into glycosciences: How chemistry, biochemistry and biology cooperate to crack the sugar code. Biochim Biophys Acta Gen Subj 2014; 1850:186-235. [PMID: 24685397 DOI: 10.1016/j.bbagen.2014.03.016] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 01/17/2023]
Abstract
BACKGROUND The most demanding challenge in research on molecular aspects within the flow of biological information is posed by the complex carbohydrates (glycan part of cellular glycoconjugates). How the 'message' encoded in carbohydrate 'letters' is 'read' and 'translated' can only be unraveled by interdisciplinary efforts. SCOPE OF REVIEW This review provides a didactic step-by-step survey of the concept of the sugar code and the way strategic combination of experimental approaches characterizes structure-function relationships, with resources for teaching. MAJOR CONCLUSIONS The unsurpassed coding capacity of glycans is an ideal platform for generating a broad range of molecular 'messages'. Structural and functional analyses of complex carbohydrates have been made possible by advances in chemical synthesis, rendering production of oligosaccharides, glycoclusters and neoglycoconjugates possible. This availability facilitates to test the glycans as ligands for natural sugar receptors (lectins). Their interaction is a means to turn sugar-encoded information into cellular effects. Glycan/lectin structures and their spatial modes of presentation underlie the exquisite specificity of the endogenous lectins in counterreceptor selection, that is, to home in on certain cellular glycoproteins or glycolipids. GENERAL SIGNIFICANCE Understanding how sugar-encoded 'messages' are 'read' and 'translated' by lectins provides insights into fundamental mechanisms of life, with potential for medical applications.
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Affiliation(s)
- Dolores Solís
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 07110 Bunyola, Mallorca, Illes Baleares, Spain.
| | - Nicolai V Bovin
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho-Maklaya 16/10, 117871 GSP-7, V-437, Moscow, Russian Federation.
| | - Anthony P Davis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - Antonio Romero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - René Roy
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada.
| | - Karel Smetana
- Charles University, 1st Faculty of Medicine, Institute of Anatomy, U nemocnice 3, 128 00 Prague 2, Czech Republic.
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 München, Germany.
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18
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Ochoa L, Paniagua Michel JDJ, Olmos-Soto J. Complex carbohydrates as a possible source of high energy to formulate functional feeds. ADVANCES IN FOOD AND NUTRITION RESEARCH 2014; 73:259-288. [PMID: 25300550 DOI: 10.1016/b978-0-12-800268-1.00012-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Carbohydrates (CHOs) are the most abundant organic compounds found in living organisms and are a great source of metabolic energy, both for plants and animals. Besides of CHOs great potential to solve animal's energy requirements and diminishing high feed cost, we first must to understand its digestibility and assimilation to avoid several inconvenients. Today, CHOs feed animal inclusions are of great concern about cost-benefits, animal's health status, and environmental pollution. In this chapter, we make a brief description about sugars (DP1-2), oligosaccharides (DP3-9), polysaccharides (DP ≥10), and their essential characteristics to understand the role of marine and terrestrial CHOs in animal nutrition. Subsequently, we talk about basic concepts, CHOs functional benefits, suggestions about their application and successful cases. This information will contribute to produce a new generation of high-quality and energetic functional feed formulations for livestock and aquaculture farms; which must be of low cost, healthy, and environmentally friendly, with the inclusion of prebiotics and probiotics.
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Affiliation(s)
- Leonel Ochoa
- Centro de Innovación Biotecnológica AC (CENBIOTEC), Ensenada, Baja California, Mexico
| | - José de Jesús Paniagua Michel
- Bioactive Compounds and Biorremediation Laboratory, Department of Marine Biotechnology, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico
| | - Jorge Olmos-Soto
- Laboratory for Molecular Microbiology, Department of Marine Biotechnology, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico.
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19
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BSA-boronic acid conjugate as lectin mimetics. Biochem Biophys Res Commun 2013; 443:562-7. [PMID: 24326067 DOI: 10.1016/j.bbrc.2013.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/02/2013] [Indexed: 11/21/2022]
Abstract
We report bovine serum albumin (BSA)-boronic acid (BA) conjugates as lectin mimetics and their glyco-capturing capacity. The BSA-BA conjugates were synthesized by amidation of carboxylic acid groups in BSA with aminophenyl boronic acid in the presence of EDC, and were characterized by Alizarin Red S (ARS) assay and SDS-PAGE gel. The BSA-BA conjugates were immobilized onto maleimide-functionalized silica beads and their sugar capturing capacity and specificity were confirmed by ARS displacement assay. Further, surface plasmon resonance (SPR) analysis of the glyco-capturing activity of the BSA-BA conjugates was conducted by immobilizing BSA-BA onto SPR gold chip. Overall, we demonstrated a BSA-BA-based lectin mimetics for glyco-capturing applications. These lectin mimetics are expected to provide an important tool for glycomics and biosensor research and applications.
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20
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Pendrill R, Säwén E, Widmalm G. Conformation and dynamics at a flexible glycosidic linkage revealed by NMR spectroscopy and molecular dynamics simulations: analysis of β-L-Fucp-(1→6)-α-D-Glcp-OMe in water solution. J Phys Chem B 2013; 117:14709-22. [PMID: 24175957 DOI: 10.1021/jp409985h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The intrinsic flexibility of carbohydrates facilitates different 3D structures in response to altered environments. At glycosidic (1→6)-linkages, three torsion angles are variable, and herein the conformation and dynamics of β-L-Fucp-(1→6)-α-D-Glcp-OMe are investigated using a combination of NMR spectroscopy and molecular dynamics (MD) simulations. The disaccharide shows evidence of conformational averaging for the ψ and ω torsion angles, best explained by a four-state conformational distribution. Notably, there is a significant population of conformations having ψ = 85° (clinal) in addition to those having ψ = 180° (antiperiplanar). Moderate differences in (13)C R1 relaxation rates are found to be best explained by axially symmetric tumbling in combination with minor differences in librational motion for the two residues, whereas the isomerization motions are occurring too slowly to be contributing significantly to the observed relaxation rates. The MD simulation was found to give a reasonably good agreement with experiment, especially with respect to diffusive properties, among which the rotational anisotropy, D∥/D⊥, is found to be 2.35. The force field employed showed too narrow ω torsion angles in the gauche-trans and gauche-gauche states as well as overestimating the population of the gauche-trans conformer. This information can subsequently be used in directing parameter developments and emphasizes the need for refinement of force fields for (1→6)-linked carbohydrates.
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Affiliation(s)
- Robert Pendrill
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
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21
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Sattelle BM, Almond A. Shaping up for structural glycomics: a predictive protocol for oligosaccharide conformational analysis applied to N-linked glycans. Carbohydr Res 2013; 383:34-42. [PMID: 24252626 PMCID: PMC3909462 DOI: 10.1016/j.carres.2013.10.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/17/2013] [Accepted: 10/19/2013] [Indexed: 11/28/2022]
Abstract
Aqueous 10 μs simulations of N-linked mannosyl cores and sialyl Lewis (sLe) antennae are validated. Sequence dependent glycosidic linkage and pyranose ring μs motions are implicated in bioactivity. Stacked pyranoses in sLea and sLex are predicted to be atypically rigid on μs timescales. In a 25 μs simulation of sLex, all known conformers were sampled within the initial 10 μs of dynamics. Unbiased 10 μs simulations are proposed as a route to systematic and accurate glycomic 3D-analysis.
The human glycome comprises a vast untapped repository of 3D-structural information that holds the key to glycan recognition and a new era of rationally designed mimetic chemical probes, drugs, and biomaterials. Toward routine prediction of oligosaccharide conformational populations and exchange rates at thermodynamic equilibrium, we apply hardware-accelerated aqueous molecular dynamics to model μs motions in N-glycans that underpin inflammation and immunity. In 10 μs simulations, conformational equilibria of mannosyl cores, sialyl Lewis (sLe) antennae, and constituent sub-sequences agreed with prior refinements (X-ray and NMR). Glycosidic linkage and pyranose ring flexing were affected by branching, linkage position, and secondary structure, implicating sequence dependent motions in glycomic functional diversity. Linkage and ring conformational transitions that have eluded precise quantification by experiment and conventional (ns) simulations were predicted to occur on μs timescales. All rings populated non-chair shapes and the stacked galactose and fucose pyranoses of sLea and sLex were rigidified, suggesting an exploitable 3D-signature of cell adhesion protein binding. Analyses of sLex dynamics over 25 μs revealed that only 10 μs were sufficient to explore all aqueous conformers. This simulation protocol, which yields conformational ensembles that are independent of initial 3D-structure, is proposed as a route to understanding oligosaccharide recognition and structure–activity relationships, toward development of carbohydrate-based novel chemical entities.
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Affiliation(s)
- Benedict M Sattelle
- Faculty of Life Sciences, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
| | - Andrew Almond
- Faculty of Life Sciences, The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK.
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22
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Kumar S, Frank M, Schwartz-Albiez R. Understanding the specificity of human Galectin-8C domain interactions with its glycan ligands based on molecular dynamics simulations. PLoS One 2013; 8:e59761. [PMID: 23555773 PMCID: PMC3612102 DOI: 10.1371/journal.pone.0059761] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 02/18/2013] [Indexed: 11/18/2022] Open
Abstract
Human Galectin-8 (Gal-8) is a member of the galectin family which shares an affinity for β-galactosides. The tandem-repeat Gal-8 consists of a N- and a C-terminal carbohydrate recognition domain (N- and C-CRD) joined by a linker peptide of various length. Despite their structural similarity both CRDs recognize different oligosaccharides. While the molecular requirements of the N-CRD for high binding affinity to sulfated and sialylated glycans have recently been elucidated by crystallographic studies of complexes with several oligosaccharides, the binding specificities of the C-CRD for a different set of oligosaccharides, as derived from experimental data, has only been explained in terms of the three-dimensional structure for the complex C-CRD with lactose. In this study we performed molecular dynamics (MD) simulations using the recently released crystal structure of the Gal-8C-CRD to analyse the three-dimensional conditions for its specific binding to a variety of oligosaccharides as previously defined by glycan-microarray analysis. The terminal β-galactose of disaccharides (LacNAc, lacto-N-biose and lactose) and the internal β-galactose moiety of blood group antigens A and B (BGA, BGB) as well as of longer linear oligosaccharide chains (di-LacNAc and lacto-N-neotetraose) are interacting favorably with conserved amino acids (H53, R57, N66, W73, E76). Lacto-N-neotetraose and di-LacNAc as well as BGA and BGB are well accommodated. BGA and BGB showed higher affinity than LacNAc and lactose due to generally stronger hydrogen bond interactions and water mediated hydrogen bonds with α1-2 fucose respectively. Our results derived from molecular dynamics simulations are able to explain the glycan binding specificities of the Gal-8C-CRD in comparison to those of the Gal-8N -CRD.
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Affiliation(s)
- Sonu Kumar
- D015, Translational Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, Germany
| | | | - Reinhard Schwartz-Albiez
- D015, Translational Immunology, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, Germany
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23
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López CA, Sovova Z, van Eerden FJ, de Vries AH, Marrink SJ. Martini Force Field Parameters for Glycolipids. J Chem Theory Comput 2013; 9:1694-708. [DOI: 10.1021/ct3009655] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- César A. López
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Zofie Sovova
- Faculty
of Science, University
of South Bohemia, Czech Republic, and Institute of Nanobiology and
Structural Biology GCRC ASCR, v.v.i. Nove Hrady, Czech Republic
| | - Floris J. van Eerden
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Alex H. de Vries
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
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24
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Zambre VP, Giridhar R, Yadav MR. Pharmacophore modeling and 3D-QSAR (CoMSIA) studies for structural requirements of some triazine derivatives as G-quadruplex binders for telomerase inhibition. Med Chem Res 2013. [DOI: 10.1007/s00044-012-0447-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Andres D, Gohlke U, Broeker NK, Schulze S, Rabsch W, Heinemann U, Barbirz S, Seckler R. An essential serotype recognition pocket on phage P22 tailspike protein forces Salmonella enterica serovar Paratyphi A O-antigen fragments to bind as nonsolution conformers. Glycobiology 2013; 23:486-94. [DOI: 10.1093/glycob/cws224] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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26
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Toukach FV, Ananikov VP. Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations. Chem Soc Rev 2013; 42:8376-415. [DOI: 10.1039/c3cs60073d] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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27
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Fasciotti M, Sanvido GB, Santos VG, Lalli PM, McCullagh M, de Sá GF, Daroda RJ, Peter MG, Eberlin MN. Separation of isomeric disaccharides by traveling wave ion mobility mass spectrometry using CO2 as drift gas. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1643-7. [PMID: 23280753 DOI: 10.1002/jms.3089] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 08/10/2012] [Accepted: 08/15/2012] [Indexed: 05/16/2023]
Abstract
The use of CO(2) as a massive and polarizable drift gas is shown to greatly improve peak-to-peak resolution (R(p-p) ), as compared with N(2) , for the separation of disaccharides in a Synapt G2 traveling wave ion mobility cell. Near or baseline R(p-p) was achieved for three pairs of sodiated molecules of disaccharide isomers, that is, cellobiose and sucrose (R(p-p) = 0.76), maltose and sucrose (R(p-p) = 1.04), and maltose and lactose (R(p-p) = 0.74). Ion mobility mass spectrometry using CO(2) as the drift gas offers therefore an attractive alternative for fast and efficient separation of isomeric disaccharides.
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Affiliation(s)
- Maíra Fasciotti
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, UNICAMP 13083-970, Campinas, SP, Brazil
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28
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Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012; 2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
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Affiliation(s)
- B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- School of Chemistry, National University of Ireland, Galway, Ireland
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29
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Zhang Z, Khan NM, Nunez KM, Chess EK, Szabo CM. Complete Monosaccharide Analysis by High-Performance Anion-Exchange Chromatography with Pulsed Amperometric Detection. Anal Chem 2012; 84:4104-10. [DOI: 10.1021/ac300176z] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhenqing Zhang
- Baxter Healthcare Corporation, Round Lake, Illinois
60073, United States
| | - Nazeer M. Khan
- Baxter Healthcare Corporation, Round Lake, Illinois
60073, United States
| | - Karen M. Nunez
- Baxter Healthcare Corporation, Round Lake, Illinois
60073, United States
| | - Edward K. Chess
- Baxter Healthcare Corporation, Round Lake, Illinois
60073, United States
| | - Christina M. Szabo
- Baxter Healthcare Corporation, Round Lake, Illinois
60073, United States
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30
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31
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Bauer BA, Patel S. Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1153-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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32
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Konda C, Bendiak B, Xia Y. Differentiation of the stereochemistry and anomeric configuration for 1-3 linked disaccharides via tandem mass spectrometry and 18O-labeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:347-358. [PMID: 22095166 DOI: 10.1007/s13361-011-0287-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 10/20/2011] [Accepted: 10/21/2011] [Indexed: 05/31/2023]
Abstract
Collision-induced dissociation (CID) of deprotonated hexose-containing disaccharides (m/z 341) with 1-2, 1-4, and 1-6 linkages yields product ions at m/z 221, which have been identified as glycosyl-glycolaldehyde anions. From disaccharides with these linkages, CID of m/z 221 ions produces distinct fragmentation patterns that enable the stereochemistries and anomeric configurations of the non-reducing sugar units to be determined. However, only trace quantities of m/z 221 ions can be generated for 1-3 linkages in Paul or linear ion traps, preventing further CID analysis. Here we demonstrate that high intensities of m/z 221 ions can be built up in the linear ion trap (Q3) from beam-type CID of a series of 1-3 linked disaccharides conducted on a triple quadrupole/linear ion trap mass spectrometer. (18)O-labeling at the carbonyl position of the reducing sugar allowed mass-discrimination of the "sidedness" of dissociation events to either side of the glycosidic linkage. Under relatively low energy beam-type CID and ion trap CID, an m/z 223 product ion containing (18)O predominated. It was a structural isomer that fragmented quite differently than the glycosyl-glycolaldehydes and did not provide structural information about the non-reducing sugar. Under higher collision energy beam-type CID conditions, the formation of m/z 221 ions, which have the glycosyl-glycolaldehyde structures, were favored. Characteristic fragmentation patterns were observed for each m/z 221 ion from higher energy beam-type CID of 1-3 linked disaccharides and the stereochemistry of the non-reducing sugar, together with the anomeric configuration, were successfully identified both with and without (18)O-labeling of the reducing sugar carbonyl group.
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Affiliation(s)
- Chiharu Konda
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-1393, USA
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33
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Lin Z, Bendiak B, Rubtsov IV. Discrimination between coupling networks of glucopyranosides varying at a single stereocenter using two-dimensional vibrational correlation spectroscopy. Phys Chem Chem Phys 2012; 14:6179-91. [DOI: 10.1039/c2cp23245f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Zeng X, Andrade CAS, Oliveira MDL, Sun XL. Carbohydrate–protein interactions and their biosensing applications. Anal Bioanal Chem 2011; 402:3161-76. [DOI: 10.1007/s00216-011-5594-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 11/02/2011] [Accepted: 11/20/2011] [Indexed: 01/16/2023]
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35
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Zhong Y, Bauer BA, Patel S. Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization. J Comput Chem 2011; 32:3339-53. [PMID: 21898464 PMCID: PMC3193586 DOI: 10.1002/jcc.21873] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 04/25/2011] [Accepted: 05/28/2011] [Indexed: 12/13/2022]
Abstract
N-Acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural properties of NAG and NAG-containing macromolecules, like peptidoglycans and polymeric chitin, at the atomic level using molecular dynamics simulations. In this work, we develop a polarizable carbohydrate force field for NAG and contrast simulation results of various properties using this novel force field and an analogous nonpolarizable (fixed charge) model. Aqueous solutions of NAG and its oligomers are investigated; we explore conformational properties (rotatable bond geometry), electrostatic properties (dipole moment distribution), dynamical properties (self-diffusion coefficient), hydrogen bonding (water bridge structure and dynamics), and free energy of hydration. The fixed-charge carbohydrate force field exhibits deviations from the gas phase relative rotation energy of exocyclic hydroxymethyl side chain and of chair/boat ring distortion. The polarizable force field predicts conformational properties in agreement with corresponding first-principles results. NAG-water hydrogen bonding pattern is studied through radial distribution functions (RDFs) and correlation functions. Intermolecular hydrogen bonding between solute and solvent is found to stabilize NAG solution structures while intramolecular hydrogen bonds define glycosidic linkage geometry of NAG oligomers. The electrostatic component of hydration free energy is highly dependent on force field atomic partial charges, influencing a more favorable free energy of hydration in the fixed-charge model compared to the polarizable model.
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Affiliation(s)
- Yang Zhong
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Brad A. Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Kadirvelraj R, Grant OC, Goldstein IJ, Winter HC, Tateno H, Fadda E, Woods RJ. Structure and binding analysis of Polyporus squamosus lectin in complex with the Neu5Ac{alpha}2-6Gal{beta}1-4GlcNAc human-type influenza receptor. Glycobiology 2011; 21:973-84. [PMID: 21436237 DOI: 10.1093/glycob/cwr030] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Glycan chains that terminate in sialic acid (Neu5Ac) are frequently the receptors targeted by pathogens for initial adhesion. Carbohydrate-binding proteins (lectins) with specificity for Neu5Ac are particularly useful in the detection and isolation of sialylated glycoconjugates, such as those associated with pathogen adhesion as well as those characteristic of several diseases including cancer. Structural studies of lectins are essential in order to understand the origin of their specificity, which is particularly important when employing such reagents as diagnostic tools. Here, we report a crystallographic and molecular dynamics (MD) analysis of a lectin from Polyporus squamosus (PSL) that is specific for glycans terminating with the sequence Neu5Acα2-6Galβ. Because of its importance as a histological reagent, the PSL structure was solved (to 1.7 Å) in complex with a trisaccharide, whose sequence (Neu5Acα2-6Galβ1-4GlcNAc) is exploited by influenza A hemagglutinin for viral adhesion to human tissue. The structural data illuminate the origin of the high specificity of PSL for the Neu5Acα2-6Gal sequence. Theoretical binding free energies derived from the MD data confirm the key interactions identified crystallographically and provide additional insight into the relative contributions from each amino acid, as well as estimates of the importance of entropic and enthalpic contributions to binding.
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Affiliation(s)
- Renuka Kadirvelraj
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
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Jang JW, Song CM, Choi KH, Cho YS, Baek DJ, Shin KJ, Pae AN. In silico Analysis on hERG Channel Blocking Effect of a Series of T-type Calcium Channel Blockers. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.1.251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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38
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Li WW, Claridge TDW, Li Q, Wormald MR, Davis BG, Bayley H. Tuning the cavity of cyclodextrins: altered sugar adaptors in protein pores. J Am Chem Soc 2011; 133:1987-2001. [PMID: 21244029 DOI: 10.1021/ja1100867] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclodextrins (CDs) have been widely used in host-guest molecular recognition because of their chiral and hydrophobic cavities. For example, β-cyclodextrin (βCD) lodged as a molecular adaptor in protein pores such as α-hemolysin (αHL) is used for stochastic sensing. Here, we have tuned the cavity and overall size of βCD by replacing a single oxygen atom in its ring skeleton by a disulfide unit in two different configurations to both expand our ability to detect analytes and understand the interactions of βCD with protein pores. The three-dimensional structures of the two stereoisomeric CDs have been determined by the combined application of NMR spectroscopy and molecular simulation and show distorted conformations as compared to natural βCD. The interactions of these synthetic βCD analogues with mutant αHL protein pores and guest molecules were studied by single-channel electrical recording. The dissociation rate constants for both disulfide CDs from the mutant pores show ∼1000-fold increase as compared to those of unaltered βCD, but are ∼10-fold lower than the dissociation rate constants for βCD from wild-type αHL. Both of the skeleton-modified CDs show altered selectivity toward guest molecules. Our approach expands the breadth in sensitivity and diversity of sensing with protein pores and suggests structural parameters useful for CD design, particularly in the creation of asymmetric cavities.
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Affiliation(s)
- Wen-Wu Li
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
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Yang Z, Nie Y, Yang G, Zu Y, Fu Y, Zhou L. Synergistic effects in the designs of neuraminidase ligands: Analysis from docking and molecular dynamics studies. J Theor Biol 2010; 267:363-74. [DOI: 10.1016/j.jtbi.2010.08.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 07/29/2010] [Accepted: 08/25/2010] [Indexed: 10/19/2022]
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41
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Assignment of the stereochemistry and anomeric configuration of structurally informative product ions derived from disaccharides: infrared photodissociation of glycosyl-glycolaldehydes in the negative ion mode. Carbohydr Res 2010; 345:2390-400. [DOI: 10.1016/j.carres.2010.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2010] [Revised: 08/29/2010] [Accepted: 09/01/2010] [Indexed: 12/30/2022]
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42
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Raffaini G, Ganazzoli F. A molecular dynamics study of the inclusion complexes of C60 with some cyclodextrins. J Phys Chem B 2010; 114:7133-9. [PMID: 20450215 DOI: 10.1021/jp911812j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The strongly hydrophobic C(60) fullerene is a carbon allotrope of huge interest in materials science and in pharmaceutical chemistry that can be solubilized in water either by extensive chemical functionalization or by inclusion in appropriate carriers such as the cyclodextrins with formation of host-guest complexes. Here we report a molecular dynamics study of the complexes formed in solution by C(60) with gamma- and delta-cyclodextrins. The most stable host-guest complex stoichiometry is determined to be 2:1 through simulations in vacuo and in explicit water by the stepwise addition of the cyclodextrins to C(60). No a priori assumption about the inclusion stoichiometry and geometry is made. The equilibrium fluctuations of the complexes that can affect the system stability are also investigated within the molecular dynamics runs.
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Affiliation(s)
- Giuseppina Raffaini
- Dipartimento di Chimica, Materiali e Ingegneria Chimica G. Natta, Politecnico di Milano, via L. Mancinelli 7, 20131 Milano, Italy.
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Faivre V, Rosilio V. Interest of glycolipids in drug delivery: from physicochemical properties to drug targeting. Expert Opin Drug Deliv 2010; 7:1031-48. [DOI: 10.1517/17425247.2010.511172] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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44
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Less is more when simulating unsulfated glycosaminoglycan 3D-structure: Comparison of GLYCAM06/TIP3P, PM3-CARB1/TIP3P, and SCC-DFTB-D/TIP3P predictions with experiment. J Comput Chem 2010; 31:2932-47. [DOI: 10.1002/jcc.21589] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Perić-Hassler L, Hansen HS, Baron R, Hünenberger PH. Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling. Carbohydr Res 2010; 345:1781-801. [PMID: 20576257 DOI: 10.1016/j.carres.2010.05.026] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 05/20/2010] [Accepted: 05/22/2010] [Indexed: 10/19/2022]
Abstract
Explicit-solvent molecular dynamics (MD) simulations of the 11 glucose-based disaccharides in water at 300K and 1bar are reported. The simulations were carried out with the GROMOS 45A4 force-field and the sampling along the glycosidic dihedral angles phi and psi was artificially enhanced using the local elevation umbrella sampling (LEUS) method. The trajectories are analyzed in terms of free-energy maps, stable and metastable conformational states (relative free energies and estimated transition timescales), intramolecular H-bonds, single molecule configurational entropies, and agreement with experimental data. All disaccharides considered are found to be characterized either by a single stable (overwhelmingly populated) state ((1-->n)-linked disaccharides with n=1, 2, 3, or 4) or by two stable (comparably populated and differing in the third glycosidic dihedral angle omega ; gg or gt) states with a low interconversion barrier ((1-->6)-linked disaccharides). Metastable (anti-phi or anti-psi) states are also identified with relative free energies in the range of 8-22 kJ mol(-1). The 11 compounds can be classified into four families: (i) the alpha(1-->1)alpha-linked disaccharide trehalose (axial-axial linkage) presents no metastable state, the lowest configurational entropy, and no intramolecular H-bonds; (ii) the four alpha(1-->n)-linked disaccharides (n=1, 2, 3, or 4; axial-equatorial linkage) present one metastable (anti-psi) state, an intermediate configurational entropy, and two alternative intramolecular H-bonds; (iii) the four beta(1-->n)-linked disaccharides (n=1, 2, 3, or 4; equatorial-equatorial linkage) present two metastable (anti-phi and anti-psi) states, an intermediate configurational entropy, and one intramolecular H-bond; (iv) the two (1-->6)-linked disaccharides (additional glycosidic dihedral angle) present no (isomaltose) or a pair of (gentiobiose) metastable (anti-phi) states, the highest configurational entropy, and no intramolecular H-bonds. The observed conformational preferences appear to be dictated by four main driving forces (ring conformational preferences, exo-anomeric effect, steric constraints, and possible presence of a third glycosidic dihedral angle), leaving a secondary role to intramolecular H-bonding and specific solvation effects. In spite of the weak conformational driving force attributed to solvent-exposed H-bonds in water (highly polar protic solvent), intramolecular H-bonds may still have a significant influence on the physico-chemical properties of the disaccharide by decreasing its hydrophilicity. Along with previous work, the results also complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups, glycosidic dihedral angleomega in (1-->6)-linked disaccharides), approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi). The calculated average values of the glycosidic torsional angles agree well with the available experimental data, providing validation for the force-field and simulation methodology employed.
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Affiliation(s)
- Lovorka Perić-Hassler
- Laboratory of Physical Chemistry, ETH Zürich, ETH Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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Hawkes CA, Deng LH, Shaw JE, Nitz M, McLaurin J. Small molecule beta-amyloid inhibitors that stabilize protofibrillar structures in vitro improve cognition and pathology in a mouse model of Alzheimer's disease. Eur J Neurosci 2010; 31:203-13. [PMID: 20074226 DOI: 10.1111/j.1460-9568.2009.07052.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Beta-amyloid (Abeta) peptides are thought to play a major role in the pathogenesis of Alzheimer's disease. Compounds that disrupt the kinetic pathways of Abeta aggregation may be useful in elucidating the role of oligomeric, protofibrillar and fibrillar Abeta in the etiology of the disease. We have previously reported that scyllo-inositol inhibits Abeta(42) fibril formation but the mechanism(s) by which this occurs has not been investigated in detail. Using a series of scyllo-inositol derivatives in which one or two hydroxyl groups were replaced with hydrogen, chlorine or methoxy substituents, we examined the role of hydrogen bonding and hydrophobicity in the structure-function relationship of scyllo-inositol-Abeta binding. We report here that all scyllo-inositol derivatives demonstrated reduced effectiveness in preventing Abeta(42) fibrillization compared with scyllo-inositol, suggesting that scyllo-inositol interacts with Abeta(42) via key hydrogen bonds that are formed by all hydroxyl groups. Increasing the hydrophobicity of scyllo-inositol by the addition of two methoxy groups (1,4-di-O-methyl-scyllo-inositol) produced a derivative that stabilized Abeta(42) protofibrils in vitro. Prophylactic administration of 1,4-di-O-methyl-scyllo-inositol to TgCRND8 mice attenuated spatial memory impairments and significantly decreased cerebral amyloid pathology. These results suggest that Abeta aggregation can be targeted at multiple points along the kinetic pathway for the improvement of Alzheimer's disease-like pathology.
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Affiliation(s)
- Cheryl A Hawkes
- Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
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47
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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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48
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Sattelle BM, Shakeri J, Roberts IS, Almond A. A 3D-structural model of unsulfated chondroitin from high-field NMR: 4-sulfation has little effect on backbone conformation. Carbohydr Res 2009; 345:291-302. [PMID: 20022001 PMCID: PMC3098369 DOI: 10.1016/j.carres.2009.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 11/06/2009] [Accepted: 11/10/2009] [Indexed: 11/26/2022]
Abstract
The glycosaminoglycan chondroitin sulfate is essential in human health and disease but exactly how sulfation dictates its 3D-structure at the atomic level is unclear. To address this, we have purified homogenous oligosaccharides of unsulfated chondroitin (with and without (15)N-enrichment) and analysed them by high-field NMR to make a comparison published chondroitin sulfate and hyaluronan 3D-structures. The result is the first full assignment of the tetrasaccharide and an experimental 3D-model of the hexasaccharide (PDB code 2KQO). In common with hyaluronan, we confirm that the amide proton is not involved in strong, persistent inter-residue hydrogen bonds. However, in contrast to hyaluronan, a hydrogen bond is not inferred between the hexosamine OH-4 and the glucuronic acid O5 atoms across the beta(1-->3) glycosidic linkage. The unsulfated chondroitin bond geometry differs slightly from hyaluronan by rotation about the beta(1-->3) psi dihedral (as previously predicted by simulation), while the beta(1-->4) linkage is unaffected. Furthermore, comparison shows that this glycosidic linkage geometry is similar in chondroitin-4-sulfate. We therefore hypothesise that both hexosamine OH-4 and OH-6 atoms are solvent exposed in chondroitin, explaining why it is amenable to sulfation and hyaluronan is not, and also that 4-sulfation has little effect on backbone conformation. Our conclusions exemplify the value of the 3D-model presented here and progress our understanding of glycosaminoglycan molecular properties.
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Affiliation(s)
- Benedict M Sattelle
- Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester, M1 7DN, UK
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López CA, Rzepiela AJ, de Vries AH, Dijkhuizen L, Hünenberger PH, Marrink SJ. Martini Coarse-Grained Force Field: Extension to Carbohydrates. J Chem Theory Comput 2009; 5:3195-210. [DOI: 10.1021/ct900313w] [Citation(s) in RCA: 307] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cesar A. López
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Centre for Carbohydrate Bioprocessing, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands, and Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Andrzej J. Rzepiela
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Centre for Carbohydrate Bioprocessing, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands, and Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Alex H. de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Centre for Carbohydrate Bioprocessing, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands, and Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Lubbert Dijkhuizen
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Centre for Carbohydrate Bioprocessing, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands, and Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Philippe H. Hünenberger
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Centre for Carbohydrate Bioprocessing, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands, and Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Centre for Carbohydrate Bioprocessing, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands, and Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland
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50
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Raffaini G, Ganazzoli F, Malpezzi L, Fuganti C, Fronza G, Panzeri W, Mele A. Validating a strategy for molecular dynamics simulations of cyclodextrin inclusion complexes through single-crystal X-ray and NMR experimental data: a case study. J Phys Chem B 2009; 113:9110-22. [PMID: 19526998 DOI: 10.1021/jp901581e] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A theoretical and experimental study about the formation and structure of the inclusion complex (-)-menthyl-O-beta-D-glucopyranoside 1 with beta-cyclodextrin (beta-CD) 2 is presented as paradigmatic case study to test the results of molecular dynamics (MD) simulations. The customary methodological approach-the use of experimental geometrical parameters as restraints for MD runs-is logically reversed and the calculated structures are a posteriori compared with those obtained from NMR spectroscopy in D(2)O solution and single crystal X-ray diffraction so as to validate the simulation procedure. The guest molecule 1 allows for a broad repertoire of intermolecular interactions (dipolar, hydrophobic, hydrogen bonds) concurring to stabilize the host-guest complex, thus providing the general applicability of the simulation procedure to cyclodextrin physical chemistry. Many starting geometries of the host-guest association were chosen, not assuming any a priori inclusion. The simulation protocol, involving energy minimization and MD runs in explicit water, yielded four possible inclusion geometries, ruling out higher-energy outer adducts. By analysis of the average energy at room temperature, the most stable geometry in solution was eventually obtained, while the kinetics of formation showed that it is also kinetically favored. The reliability of such geometry was thoroughly checked against the NOE distances via the pair distribution functions, that is, the statistical distribution of intermolecular distances among selected diagnostic atoms calculated from the MD trajectories at room temperature. An analogous procedure was adopted both with implicit solvent and in vacuo. The most stable geometry matched that found with explicit solvent but major differences were observed in the relative stability of the metastable complexes as a consequence of the lack of hydration on the polar moiety of the guest. Finally, a control set of geometrical parameters of the thermodynamically favored complex matched the corresponding one obtained from the X-ray structure, while local conformational differences were indicative of packing effects.
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Affiliation(s)
- Giuseppina Raffaini
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via L. Mancinelli 7, 20131 Milano, Italy.
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