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Soares CO, Grosso AS, Ereño-Orbea J, Coelho H, Marcelo F. Molecular Recognition Insights of Sialic Acid Glycans by Distinct Receptors Unveiled by NMR and Molecular Modeling. Front Mol Biosci 2021; 8:727847. [PMID: 34869580 PMCID: PMC8634706 DOI: 10.3389/fmolb.2021.727847] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
All cells are decorated with a highly dense and complex structure of glycan chains, which are mostly attached to proteins and lipids. In this context, sialic acids are a family of nine-carbon acidic monosaccharides typically found at the terminal position of glycan chains, modulating several physiological and pathological processes. Sialic acids have many structural and modulatory roles due to their negative charge and hydrophilicity. In addition, the recognition of sialic acid glycans by mammalian cell lectins, such as siglecs, has been described as an important immunological checkpoint. Furthermore, sialic acid glycans also play a pivotal role in host-pathogen interactions. Various pathogen receptors exposed on the surface of viruses and bacteria are responsible for the binding to sialic acid sugars located on the surface of host cells, becoming a critical point of contact in the infection process. Understanding the molecular mechanism of sialic acid glycans recognition by sialic acid-binding proteins, present on the surface of pathogens or human cells, is essential to realize the biological mechanism of these events and paves the way for the rational development of strategies to modulate sialic acid-protein interactions in diseases. In this perspective, nuclear magnetic resonance (NMR) spectroscopy, assisted with molecular modeling protocols, is a versatile and powerful technique to investigate the structural and dynamic aspects of glycoconjugates and their interactions in solution at the atomic level. NMR provides the corresponding ligand and protein epitopes, essential for designing and developing potential glycan-based therapies. In this review, we critically discuss the current state of knowledge about the structural features behind the molecular recognition of sialic acid glycans by different receptors, naturally present on human cells or pathogens, disclosed by NMR spectroscopy and molecular modeling protocols.
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Affiliation(s)
- Cátia Oliveira Soares
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Ana Sofia Grosso
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - June Ereño-Orbea
- CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Technology Park, Bilbao, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Helena Coelho
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Filipa Marcelo
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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Lim H, Lee J, You B, Oh JH, Mok HJ, Kim YS, Yoon BE, Kim BG, Back SK, Park JS, Kim KP, Schnaar RL, Lee SJ. GT1b functions as a novel endogenous agonist of toll-like receptor 2 inducing neuropathic pain. EMBO J 2020; 39:e102214. [PMID: 32030804 DOI: 10.15252/embj.2019102214] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/19/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Spinal cord microglia contribute to nerve injury-induced neuropathic pain. We have previously demonstrated that toll-like receptor 2 (TLR2) signaling is critical for nerve injury-induced activation of spinal cord microglia, but the responsible endogenous TLR2 agonist has not been identified. Here, we show that nerve injury-induced upregulation of sialyltransferase St3gal2 in sensory neurons leads to an increase in expression of the sialylated glycosphingolipid, GT1b. GT1b ganglioside is axonally transported to the spinal cord dorsal horn and contributes to characteristics of neuropathic pain such as mechanical and thermal hypersensitivity. Spinal cord GT1b functions as an TLR2 agonist and induces proinflammatory microglia activation and central sensitization. Pharmacological inhibition of GT1b synthesis attenuates nerve injury-induced spinal cord microglia activation and pain hypersensitivity. Thus, the St3gal2-GT1b-TLR2 axis may offer a novel therapeutic target for the treatment of neuropathic pain.
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Affiliation(s)
- Hyoungsub Lim
- Department of Neuroscience and Physiology, Dental Research Institute, BK21-Plus, School of Dentistry, Seoul National University, Seoul, Korea
| | - Jaesung Lee
- Department of Neuroscience and Physiology, Dental Research Institute, BK21-Plus, School of Dentistry, Seoul National University, Seoul, Korea
| | - Byunghyun You
- Department of Neuroscience and Physiology, Dental Research Institute, BK21-Plus, School of Dentistry, Seoul National University, Seoul, Korea
| | - Jae Hoon Oh
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hyuck Jun Mok
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin, Korea
| | - Yoo Sung Kim
- Department of Molecular Biology, Dankook University, Cheonan, Korea
| | - Bo-Eun Yoon
- Department of Molecular Biology, Dankook University, Cheonan, Korea
| | - Byung Gon Kim
- Department of Brain Science and Neurology, Ajou University School of Medicine, Suwon, Korea
| | - Seung Keun Back
- Department of Biomedical Laboratory Science, College of Medical Science, Konyang University, Daejeon, Korea
| | - Jong-Sang Park
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin, Korea
| | - Ronald L Schnaar
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sung Joong Lee
- Department of Neuroscience and Physiology, Dental Research Institute, BK21-Plus, School of Dentistry, Seoul National University, Seoul, Korea
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Jeyaram RA, Radha CA, Gromiha MM, Veluraja K. Design of fluorinated sialic acid analog inhibitor to H5 hemagglutinin of H5N1 influenza virus through molecular dynamics simulation study. J Biomol Struct Dyn 2019; 38:3504-3513. [PMID: 31594458 DOI: 10.1080/07391102.2019.1677500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Influenza epidemics and pandemics are caused by influenza A virus. The cell surface protein of hemagglutinin and neuraminidase is responsible for viral infection and release of progeny virus on the host cell membrane. Now 18 hemagglutinin and 11 neuraminidase subtypes are identified. The avian influenza virus of H5N1 is an emergent threat to public health issues. To control the influenza viral infection it is necessary to develop antiviral inhibitors and vaccination. In the present investigation we carried out 50 ns Molecular Dynamics simulation on H5 hemagglutinin of Influenza A virus H5N1 complexed with fluorinated sialic acid by substituting fluorine atoms at any two hydroxyls of sialic acid by considering combinatorial combination. The binding affinity between the protein-ligand complex system is investigated by calculating pair interaction energy and MM-PBSA binding free energy. All the complex structures are stabilized by hydrogen bonding interactions between the H5 protein and the ligand fluorinated sialic acid. It is concluded from all the analyses that the fluorinated complexes enhance the inhibiting potency against H5 hemagglutinin and the order of inhibiting potency is SIA-F9 ≫ SIA-F2 ≈ SIA-F7 ≈ SIA-F2F4 ≈ SIA-F2F9 ≈ SIA-F7F9 > SIA-F7F8 ≈ SIA-F2F8 ≈ SIA-F8F9 > SIA-F4 ≈ SIA-F4F7 ≈ SIA-F4F8 ≈ SIA-F8 ≈ SIA-F2F7 ≈ SIA > SIA-F4F9. This study suggests that one can design the inhibitor by using the mono fluorinated models SIA-F9, SIA-F2 and SIA-F7 and difluorinated models SIA-F2F4, SIA-F2F9 and SIA-F7F9 to inhibit H5 of H5N1 to avoid Influenza A viral infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- R A Jeyaram
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - K Veluraja
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Aβ1-25-Derived Sphingolipid-Domain Tracer Peptide SBD Interacts with Membrane Ganglioside Clusters via a Coil-Helix-Coil Motif. Int J Mol Sci 2015; 16:26318-32. [PMID: 26540054 PMCID: PMC4661814 DOI: 10.3390/ijms161125955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/19/2015] [Accepted: 10/22/2015] [Indexed: 12/30/2022] Open
Abstract
The Amyloid-β (Aβ)-derived, sphingolipid binding domain (SBD) peptide is a fluorescently tagged probe used to trace the diffusion behavior of sphingolipid-containing microdomains in cell membranes through binding to a constellation of glycosphingolipids, sphingomyelin, and cholesterol. However, the molecular details of the binding mechanism between SBD and plasma membrane domains remain unclear. Here, to investigate how the peptide recognizes the lipid surface at an atomically detailed level, SBD peptides in the environment of raft-like bilayers were examined in micro-seconds-long molecular dynamics simulations. We found that SBD adopted a coil-helix-coil structural motif, which binds to multiple GT1b gangliosides via salt bridges and CH–π interactions. Our simulation results demonstrate that the CH–π and electrostatic forces between SBD monomers and GT1b gangliosides clusters are the main driving forces in the binding process. The presence of the fluorescent dye and linker molecules do not change the binding mechanism of SBD probes with gangliosides, which involves the helix-turn-helix structural motif that was suggested to constitute a glycolipid binding domain common to some sphingolipid interacting proteins, including HIV gp120, prion, and Aβ.
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Chang S, He HQ, Shen L, Wan H. Understanding peptide competitive inhibition of botulinum neurotoxin a binding to SV2 protein via molecular dynamics simulations. Biopolymers 2015; 103:597-608. [DOI: 10.1002/bip.22682] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/09/2015] [Accepted: 05/18/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Shan Chang
- Institute of Bioinformatics and Medical Engineering; School of Electrical and Information Engineering, Jiangsu University of Technology; Changzhou China
| | - Hong-Qiu He
- Chongqing Center for Biomedicines and Medical Equipment; Chongqing Academy of Science and Technology; Chongqing China
| | - Lin Shen
- Institute of Bioinformatics and Medical Engineering; School of Electrical and Information Engineering, Jiangsu University of Technology; Changzhou China
| | - Hua Wan
- College of Informatics; South China Agricultural University; Guangzhou China
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Parasuraman P, Murugan V, Selvin JFA, Gromiha MM, Fukui K, Veluraja K. Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2-3)Gal: a study by in silico mutations and molecular dynamics simulations. J Mol Recognit 2015; 27:482-92. [PMID: 24984865 DOI: 10.1002/jmr.2369] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 02/02/2014] [Accepted: 02/02/2014] [Indexed: 02/06/2023]
Abstract
Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at the active site of WGA to enhance the binding specificity towards sialylglycans, and molecular dynamics simulations of 20 ns are carried out for wild type and mutated WGAs (WGA1, WGA2, and WGA3) in complex with sialylgalactose to examine the change in binding specificity. MD simulations reveal the change in binding specificity of wild type and mutated WGAs towards sialylgalactose and bound conformational flexibility of sialylgalactose. The mutated polar amino acid residues Asn114 (S114N), Lys118 (G118K), and Arg118 (G118R) make direct and water mediated hydrogen bonds and hydrophobic interactions with sialylgalactose. An analysis of possible hydrogen bonds, hydrophobic interactions, total pair wise interaction energy between active site residues and sialylgalactose and MM-PBSA free energy calculation reveals the plausible binding modes and the role of water in stabilizing different binding modes. An interesting observation is that the binding specificity of mutated WGAs (cyborg lectin) towards sialylgalactose is found to be higher in double point mutation (WGA3). One of the substituted residues Arg118 plays a crucial role in sugar binding. Based on the interactions and energy calculations, it is concluded that the order of binding specificity of WGAs towards sialylgalactose is WGA3 > WGA1 > WGA2 > WGA. On comparing with the wild type, double point mutated WGA (WGA3) exhibits increased specificity towards sialylgalactose, and thus, it can be effectively used in targeted drug delivery and as biological cell marker in cancer therapeutics.
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Affiliation(s)
- Ponnusamy Parasuraman
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, 627 012, India
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Wang F, Wan H, Hu JP, Chang S. Molecular dynamics simulations of wild type and mutants of botulinum neurotoxin A complexed with synaptic vesicle protein 2C. MOLECULAR BIOSYSTEMS 2015; 11:223-31. [DOI: 10.1039/c4mb00383g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Using molecular dynamics simulations, we investigate the relationship between the conformational changes of BoNT/A-RBD:SV2C-LD and the interfacial interactions.
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Affiliation(s)
- Feng Wang
- School of Information Science & Engineering
- Changzhou University
- Changzhou
- China
| | - Hua Wan
- College of Informatics
- South China Agricultural University
- Guangzhou
- China
| | - Jian-ping Hu
- Faculty of Biotechnology Industry
- Chengdu University
- Chengdu
- China
| | - Shan Chang
- College of Informatics
- South China Agricultural University
- Guangzhou
- China
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Molecular Modelling and Molecular Dynamics studies of GD1A, GD1B and their complexes with BoNT/B – Perspectives in interaction and specificity. J Struct Biol 2012; 180:497-508. [DOI: 10.1016/j.jsb.2012.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 08/14/2012] [Indexed: 11/23/2022]
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