1
|
de Barros MC, de Oliveira APS, dos Santos FG, Silva FAC, Menezes TM, Seabra GDM, Yoneda JS, Coelho LCBB, Macedo MLR, Napoleão TH, Lima TDA, Neves JL, Paiva PMG. Carbohydrate-Binding Mechanism of the Coagulant Lectin from Moringa oleifera Seeds (cMoL) Is Related to the Dimeric Protein Structure. Molecules 2024; 29:4615. [PMID: 39407546 PMCID: PMC11477877 DOI: 10.3390/molecules29194615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/21/2024] [Accepted: 09/03/2024] [Indexed: 10/19/2024] Open
Abstract
This study characterized the binding mechanisms of the lectin cMoL (from Moringa oleifera seeds) to carbohydrates using spectroscopy and molecular dynamics (MD). The interaction with carbohydrates was studied by evaluating lectin fluorescence emission after titration with glucose or galactose (2.0-11 mM). The Stern-Volmer constant (Ksv), binding constant (Ka), Gibbs free energy (∆G), and Hill coefficient were calculated. After the urea-induced denaturation of cMoL, evaluations were performed using fluorescence spectroscopy, circular dichroism (CD), and hemagglutinating activity (HA) evaluations. The MD simulations were performed using the Amber 20 package. The decrease in Ksv revealed that cMoL interacts with carbohydrates via a static mechanism. The cMoL bound carbohydrates spontaneously (ΔG < 0) and presented a Ka on the order of 102, with high selectivity for glucose. Protein-ligand complexes were stabilized by hydrogen bonds and hydrophobic interactions. The Hill parameter (h~2) indicated that the binding occurs through the cMoL dimer. The loss of HA at urea concentrations at which the fluorescence and CD spectra indicated protein monomerization confirmed these results. The MD simulations revealed that glucose bound to the large cavity formed between the monomers. In conclusion, the biotechnological application of cMoL lectin requires specific methods or media to improve its dimeric protein structure.
Collapse
Affiliation(s)
- Matheus Cavalcanti de Barros
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Recife 50670-901, PE, Brazil; (M.C.d.B.); (L.C.B.B.C.); (T.H.N.); (T.d.A.L.); (P.M.G.P.)
| | - Ana Patrícia Silva de Oliveira
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Recife 50670-901, PE, Brazil; (M.C.d.B.); (L.C.B.B.C.); (T.H.N.); (T.d.A.L.); (P.M.G.P.)
| | - Franciane Gonçalves dos Santos
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife 50670-901, PE, Brazil; (F.G.d.S.); (T.M.M.); (J.L.N.)
| | | | - Thais Meira Menezes
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife 50670-901, PE, Brazil; (F.G.d.S.); (T.M.M.); (J.L.N.)
| | - Gustavo de Miranda Seabra
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainseville, FL 32611, USA;
| | - Juliana Sakamoto Yoneda
- Laboratório Nacional de Luz Síncrotron, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-100, SP, Brazil;
| | | | - Maria Lígia Rodrigues Macedo
- Departamento de Tecnologia de Alimentos e da Saúde, Faculdade de Ciências Farmacêuticas, Alimentos e 22 Nutrição, Universidade Federal do Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil;
| | - Thiago Henrique Napoleão
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Recife 50670-901, PE, Brazil; (M.C.d.B.); (L.C.B.B.C.); (T.H.N.); (T.d.A.L.); (P.M.G.P.)
| | - Thâmarah de Albuquerque Lima
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Recife 50670-901, PE, Brazil; (M.C.d.B.); (L.C.B.B.C.); (T.H.N.); (T.d.A.L.); (P.M.G.P.)
| | - Jorge Luiz Neves
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Recife 50670-901, PE, Brazil; (F.G.d.S.); (T.M.M.); (J.L.N.)
| | - Patrícia Maria Guedes Paiva
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Recife 50670-901, PE, Brazil; (M.C.d.B.); (L.C.B.B.C.); (T.H.N.); (T.d.A.L.); (P.M.G.P.)
| |
Collapse
|
2
|
Nieto-Fabregat F, Lenza MP, Marseglia A, Di Carluccio C, Molinaro A, Silipo A, Marchetti R. Computational toolbox for the analysis of protein-glycan interactions. Beilstein J Org Chem 2024; 20:2084-2107. [PMID: 39189002 PMCID: PMC11346309 DOI: 10.3762/bjoc.20.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 08/01/2024] [Indexed: 08/28/2024] Open
Abstract
Protein-glycan interactions play pivotal roles in numerous biological processes, ranging from cellular recognition to immune response modulation. Understanding the intricate details of these interactions is crucial for deciphering the molecular mechanisms underlying various physiological and pathological conditions. Computational techniques have emerged as powerful tools that can help in drawing, building and visualising complex biomolecules and provide insights into their dynamic behaviour at atomic and molecular levels. This review provides an overview of the main computational tools useful for studying biomolecular systems, particularly glycans, both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein-glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein-ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein-glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural determinants that govern specific molecular interactions.
Collapse
Affiliation(s)
- Ferran Nieto-Fabregat
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Maria Pia Lenza
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Angela Marseglia
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Cristina Di Carluccio
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| |
Collapse
|
3
|
Rudra S, Mondal S, Chakraborty M, Swamy MJ, Jana T. Galactose Glycopolymer- Grafted Silica Nanoparticles: Synthesis and Binding Studies with Lectin. ACS APPLIED BIO MATERIALS 2024; 7:5689-5701. [PMID: 39116418 DOI: 10.1021/acsabm.4c00759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Weak binding of carbohydrates with protein receptors possesses serious drawbacks in the advancement of therapeutics; however, the development of strategies for multipoint interactions between carbohydrates and protein can overcome these challenges. One such method is developed in this work where glycopolymer-grafted silica nanoparticles with a large number of carbohydrate units are prepared for the interactions with multiple binding sites of the protein. First, a glycomonomer, β-d-galactose-hydroxyethyl methacrylate (β-GEMA), was synthesized in a two-step process by coupling β-d-galactose pentaacetate and hydroxyethyl methacrylate (HEMA), followed by deacetylation for the preparation of poly(β-GEMA) glycopolymers (GPs). Further, the poly(β-GEMA) chains were grafted onto the silica nanoparticle (SiNP) surface by utilizing the "grafting-from" strategy of surface-initiated reversible addition-fragmentation chain transfer (RAFT) polymerization to prepare p(β-GEMA)-grafted SiNPs (GNPs). Five different chain lengths ranging from 10 to 40 kDa of the GPs and the GNPs were prepared, and various characterization techniques confirmed the formation of GPs and grafting of the GPs on the SiNP surface. The particle size of GNPs and the number of GPs grafted on the SiNP surface showed a strong dependence on the chain length of the GPs. Further, the GNPs were subjected to a binding study with β-galactose-specific protein peanut agglutinin (PNA). A much stronger binding in the case of GNPs was observed with an association constant ∼320 times and ∼53 times than that of the monomeric methyl-β-d-galactopyranoside and the GPs, respectively. Additionally, the binding of the PNA with GNPs and GPs was also studied with varying chain lengths to understand the effects of the chain length on the binding affinity. A clear increase in binding constants was observed in the case of GNPs with increasing chain length of grafted GPs, attributed to the enhanced enthalpic and entropic contributions. This work holds its uniqueness in these improved interactions between carbohydrates and proteins, which can be used for carbohydrate-based targeted therapeutics.
Collapse
Affiliation(s)
- Somdatta Rudra
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Saradamoni Mondal
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | | | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Tushar Jana
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| |
Collapse
|
4
|
Beigtan M, Haddadnezhad M, Weon BM. Altering Mechanical and Dissolution Properties of Coffee Deposit by Adding Glucose. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:15188-15195. [PMID: 39004894 DOI: 10.1021/acs.langmuir.4c01608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Glucose modifies the mechanical stability of coffee films and facilitates their dissolution dynamics at the microscale, rendering glucose-coffee a valuable natural biomaterial system for studying pharmaceutical applications. We show the glucose-dependent inhibition of crack propagation during the evaporation of glucose-coffee droplets. The addition of glucose increases the hardness, stiffness, and shear modulus of films, as measured by surface nanomechanical testing. The glucose-coffee film dissolves faster and more evenly than the pure coffee film through interfaces. The water penetrates through well-dissolved glucose channels. The modified mechanical properties and adjustable dissolution time, coupled with edibility, position the glucose-modified coffee as an excellent candidate for developing pharmaceutical inks for personalized medicine droplet-based printing.
Collapse
Affiliation(s)
- Mohadese Beigtan
- Soft Matter Physics Laboratory, School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon 16419, South Korea
| | | | - Byung Mook Weon
- Soft Matter Physics Laboratory, School of Advanced Materials Science and Engineering, Sungkyunkwan University, Suwon 16419, South Korea
| |
Collapse
|
5
|
De Coninck T, Gippert GP, Henrissat B, Desmet T, Van Damme EJM. Investigating diversity and similarity between CBM13 modules and ricin-B lectin domains using sequence similarity networks. BMC Genomics 2024; 25:643. [PMID: 38937673 PMCID: PMC11212257 DOI: 10.1186/s12864-024-10554-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND The CBM13 family comprises carbohydrate-binding modules that occur mainly in enzymes and in several ricin-B lectins. The ricin-B lectin domain resembles the CBM13 module to a large extent. Historically, ricin-B lectins and CBM13 proteins were considered completely distinct, despite their structural and functional similarities. RESULTS In this data mining study, we investigate structural and functional similarities of these intertwined protein groups. Because of the high structural and functional similarities, and differences in nomenclature usage in several databases, confusion can arise. First, we demonstrate how public protein databases use different nomenclature systems to describe CBM13 modules and putative ricin-B lectin domains. We suggest the introduction of a novel CBM13 domain identifier, as well as the extension of CAZy cross-references in UniProt to guard the distinction between CAZy and non-CAZy entries in public databases. Since similar problems may occur with other lectin families and CBM families, we suggest the introduction of novel CBM InterPro domain identifiers to all existing CBM families. Second, we investigated phylogenetic, nomenclatural and structural similarities between putative ricin-B lectin domains and CBM13 modules, making use of sequence similarity networks. We concluded that the ricin-B/CBM13 superfamily may be larger than initially thought and that several putative ricin-B lectin domains may display CAZyme functionalities, although biochemical proof remains to be delivered. CONCLUSIONS Ricin-B lectin domains and CBM13 modules are associated groups of proteins whose database semantics are currently biased towards ricin-B lectins. Revision of the CAZy cross-reference in UniProt and introduction of a dedicated CBM13 domain identifier in InterPro may resolve this issue. In addition, our analyses show that several proteins with putative ricin-B lectin domains show very strong structural similarity to CBM13 modules. Therefore ricin-B lectin domains and CBM13 modules could be considered distant members of a larger ricin-B/CBM13 superfamily.
Collapse
Affiliation(s)
- Tibo De Coninck
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Proeftuinstraat 86, Ghent, 9000, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Garry P Gippert
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology & Biomedicine, Technical University of Denmark, Søltofts Plads 224, Kgs. Lyngby, 2800, Denmark
| | - Bernard Henrissat
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology & Biomedicine, Technical University of Denmark, Søltofts Plads 224, Kgs. Lyngby, 2800, Denmark
| | - Tom Desmet
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Proeftuinstraat 86, Ghent, 9000, Belgium.
| |
Collapse
|
6
|
Deb B, Das A, Vilvadrinath R, Jangra A, Shukla MS, Akhouri RR, Goel S. Glycophorin B-PfEMP1 interaction mediates robust rosetting in Plasmodium falciparum. Int J Biol Macromol 2024; 262:129868. [PMID: 38309398 DOI: 10.1016/j.ijbiomac.2024.129868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/15/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
P. falciparumerythrocyte membrane protein 1 (PfEMP1) is the major parasite protein responsible for rosetting by binding to host receptors such as heparan sulfate, CR1 on RBC surface. Usually monomeric protein-carbohydrate interactions are weak [1], therefore PfEMP1 binds to plasma proteins like IgM or α2-macroglobulin that facilitate its clustering on parasitized RBC surface and augment rosetting [2,3]. We show that 3D7A expresses PfEMP1, PF3D7_0412900, and employs its CIDRγ2 domain to interact with glycophorin B on uninfected RBC to form large rosettes but more importantly even in the absence of plasma proteins. Overall, we established the role of PF3D7_0412900 in rosetting as antibodies against CIDRγ2 domain reduced rosetting and also identified its receptor, glycophorin B which could provide clue why glycophorin B null phenotype, S-s-U- RBCs prevalent in malaria endemic areas is protective against severe malaria.
Collapse
Affiliation(s)
- Bijayeeta Deb
- Indian Institute of Science Education and Research (IISER) Tirupati, India
| | - Adrita Das
- Indian Institute of Science Education and Research (IISER) Tirupati, India
| | - Ramya Vilvadrinath
- Indian Institute of Science Education and Research (IISER) Tirupati, India
| | - Arvind Jangra
- Indian Institute of Science Education and Research (IISER) Tirupati, India
| | | | | | - Suchi Goel
- Indian Institute of Science Education and Research (IISER) Tirupati, India.
| |
Collapse
|
7
|
Oliva R, Ostermeier L, Jaworek MW, Del Vecchio P, Gajardo-Parra N, Cea-Klapp E, Held C, Petraccone L, Winter R. Modulation of protein-saccharide interactions by deep-sea osmolytes under high pressure stress. Int J Biol Macromol 2024; 255:128119. [PMID: 37977458 DOI: 10.1016/j.ijbiomac.2023.128119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Deep-sea organisms must cope with high hydrostatic pressures (HHP) up to the kbar regime to control their biomolecular processes. To alleviate the adverse effects of HHP on protein stability most organisms use high amounts of osmolytes. Little is known about the effects of these high concentrations on ligand binding. We studied the effect of the deep-sea osmolytes trimethylamine-N-oxide, glycine, and glycine betaine on the binding between lysozyme and the tri-saccharide NAG3, employing experimental and theoretical tools to reveal the combined effect of osmolytes and HHP on the conformational dynamics, hydration changes, and thermodynamics of the binding process. Due to their different chemical makeup, these cosolutes modulate the protein-sugar interaction in different ways, leading to significant changes in the binding constant and its pressure dependence. These findings suggest that deep-sea organisms may down- and up-regulate reactions in response to HHP stress by altering the concentration and type of the intracellular osmolyte.
Collapse
Affiliation(s)
- Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 26, 80126 Naples, Italy.
| | - Lena Ostermeier
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Michel W Jaworek
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 26, 80126 Naples, Italy
| | - Nicolas Gajardo-Parra
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Esteban Cea-Klapp
- Departamento de Ingeniería Química, Faculty of Engineering, Universidad de Concepción, Concepción, Chile
| | - Christoph Held
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 26, 80126 Naples, Italy
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany.
| |
Collapse
|
8
|
Nurujjaman M, Mashhoor T, Pronoy TUH, Auwal A, Hasan MR, Islam SS, Hasan I, Asaduzzaman AKM, Uddin MB, Kabir SR, Islam F. Antitumor Activity of a Lectin Purified from Punica granatum Pulps against Ehrlich Ascites Carcinoma (EAC) Cells. Anticancer Agents Med Chem 2024; 24:193-202. [PMID: 38037833 DOI: 10.2174/0118715206269394231124093423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Lectins are carbohydrate-binding proteins with various pharmacological activities, such as antimicrobial, antidiabetic, antioxidant, and anticancer. Punica granatum fruit extract has traditional uses, however, the anti-cancer activity of purified lectin isolated from P. granatum pulp is yet to be reported. OBJECTIVE The goals of this study are purification, characterization of the lectin from P. granatum, and examination of the purified lectin's anticancer potential. METHODS Diethylaminoethyl (DEAE) ion-exchange chromatography was used to purify the lectin, and SDSPAGE was used to check the purity and homogeneity of the lectin. Spectrometric and chemical analysis were used to characterize the lectin. The anticancer activity of the lectin was examined using in vivo and in vitro functional assays. RESULTS A lectin, designated as PgL of 28.0 ± 1.0 kDa molecular mass, was isolated and purified from the pulps of P. granatum and the lectin contains 40% sugar. Also, it is a bivalent ion-dependent lectin and lost its 75% activity in the presence of urea (8M). The lectin agglutinated blood cells of humans and rats, and sugar molecules such as 4-nitrophenyl-α-D-manopyranoside and 2- nitrophenyl -β- D-glucopyranoside inhibited PgL's hemagglutination activity. At pH ranges of 6.0-8.0 and temperature ranges of 30°C -80°C, PgL exhibited the highest agglutination activity. In vitro MTT assay showed that PgL inhibited Ehrlich ascites carcinoma (EAC) cell growth in a dose-dependent manner. PgL exhibited 39 % and 58.52 % growth inhibition of EAC cells in the mice model at 1.5 and 3.0 mg/kg/day (i.p.), respectively. In addition, PgL significantly increased the survival time (32.0 % and 49.3 %) of EAC-bearing mice at 1.5 and 3.0 mg/kg/day doses (i.p.), respectively, in comparison to untreated EAC-bearing animals (p < 0.01). Also, PgL reduced the tumor weight of EAC-bearing mice (66.6 versus 39.13%; p < 0.01) at the dose of 3.0 mg/kg/day treatment. Furthermore, supplementation of PgL restored the haematological parameters toward normal levels deteriorated in EAC-bearing animals by the toxicity of EAC cells. CONCLUSION The results indicated that the purified lectin has anticancer activity and has the potential to be developed as an effective chemotherapy agent.
Collapse
Affiliation(s)
- Md Nurujjaman
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Tanjila Mashhoor
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Tasfik Ul Haque Pronoy
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Abdul Auwal
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Robiul Hasan
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Shaikh Shohidul Islam
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Imtiaj Hasan
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - A K M Asaduzzaman
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md Belal Uddin
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Syed Rashel Kabir
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Farhadul Islam
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh
| |
Collapse
|
9
|
Ravindra Bhoge P, Chandra A, Kikkeri R. The Impact of Nanomaterial Morphology on Modulation of Carbohydrate-Protein Interactions. ChemMedChem 2023; 18:e202300262. [PMID: 37403554 DOI: 10.1002/cmdc.202300262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/06/2023]
Abstract
Carbohydrate-protein interactions (CPIs) play a crucial role in the regulation of various physiological and pathological processes within living systems. However, these interactions are typically weak, prompting the development of multivalent probes, including nanoparticles and polymer scaffolds, to enhance the avidity of CPIs. Additionally, the morphologies of glyco-nanostructures can significantly impact protein binding, bacterial adhesion, cellular internalization, and immune responses. In this review, we have examined the advancements in glyco-nanostructures of different shapes that modulate CPIs. We specifically emphasize glyco-nanostructures constructed from small-molecule amphiphilic carbohydrates, block copolymers, metal-based nanoparticles, and carbon-based materials, highlighting their potential applications in glycobiology.
Collapse
Affiliation(s)
- Preeti Ravindra Bhoge
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Ankita Chandra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Raghavendra Kikkeri
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| |
Collapse
|
10
|
Liu C, Pfister B, Osman R, Ritter M, Heutinck A, Sharma M, Eicke S, Fischer-Stettler M, Seung D, Bompard C, Abt MR, Zeeman SC. LIKE EARLY STARVATION 1 and EARLY STARVATION 1 promote and stabilize amylopectin phase transition in starch biosynthesis. SCIENCE ADVANCES 2023; 9:eadg7448. [PMID: 37235646 DOI: 10.1126/sciadv.adg7448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Starch, the most abundant carbohydrate reserve in plants, primarily consists of the branched glucan amylopectin, which forms semi-crystalline granules. Phase transition from a soluble to an insoluble form depends on amylopectin architecture, requiring a compatible distribution of glucan chain lengths and a branch-point distribution. Here, we show that two starch-bound proteins, LIKE EARLY STARVATION 1 (LESV) and EARLY STARVATION 1 (ESV1), which have unusual carbohydrate-binding surfaces, promote the phase transition of amylopectin-like glucans, both in a heterologous yeast system expressing the starch biosynthetic machinery and in Arabidopsis plants. We propose a model wherein LESV serves as a nucleating role, with its carbohydrate-binding surfaces helping align glucan double helices to promote their phase transition into semi-crystalline lamellae, which are then stabilized by ESV1. Because both proteins are widely conserved, we suggest that protein-facilitated glucan crystallization may be a general and previously unrecognized feature of starch biosynthesis.
Collapse
Affiliation(s)
- Chun Liu
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Barbara Pfister
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Rayan Osman
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Maximilian Ritter
- Institute for Building Materials, ETH Zurich, Stefano-Franscini-Platz 3, 8093 Zurich, Switzerland
| | - Arvid Heutinck
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Mayank Sharma
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Simona Eicke
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | | | - David Seung
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Coralie Bompard
- Université de Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Melanie R Abt
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland
| |
Collapse
|
11
|
STARK RYAN. Protein-mediated interactions in the dynamic regulation of acute inflammation. BIOCELL 2023; 47:1191-1198. [PMID: 37261220 PMCID: PMC10231872 DOI: 10.32604/biocell.2023.027838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/09/2023] [Indexed: 06/02/2023]
Abstract
Protein-mediated interactions are the fundamental mechanism through which cells regulate health and disease. These interactions require physical contact between proteins and their respective targets of interest. These targets include not only other proteins but also nucleic acids and other important molecules as well. These proteins are often involved in multibody complexes that work dynamically to regulate cellular health and function. Various techniques have been adapted to study these important interactions, such as affinity-based assays, mass spectrometry, and fluorescent detection. The application of these techniques has led to a greater understanding of how protein interactions are responsible for both the instigation and resolution of acute inflammatory diseases. These pursuits aim to provide opportunities to target specific protein interactions to alleviate acute inflammation.
Collapse
Affiliation(s)
- RYAN STARK
- Department of Pediatric Critical Care Medicine, Vanderbilt University Medical Center, 2200 Children’s Way, 5121 Doctors’ Office Tower, Nashville, TN 37232-9075
| |
Collapse
|
12
|
Kassem S, McPhee SA, Berisha N, Ulijn RV. Emergence of Cooperative Glucose-Binding Networks in Adaptive Peptide Systems. J Am Chem Soc 2023; 145:9800-9807. [PMID: 37075194 DOI: 10.1021/jacs.3c01620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Minimalistic peptide-based systems that bind sugars in water are challenging to design due to the weakness of interactions and required cooperative contributions from specific amino-acid side chains. Here, we used a bottom-up approach to create peptide-based adaptive glucose-binding networks by mixing glucose with selected sets of input dipeptides (up to 4) in the presence of an amidase to enable in situ reversible peptide elongation, forming mixtures of up to 16 dynamically interacting tetrapeptides. The choice of input dipeptides was based on amino-acid abundance in glucose-binding sites found in the protein data bank, with side chains that can support hydrogen bonding and CH-π interactions. Tetrapeptide sequence amplification patterns, determined through LC-MS analysis, served as a readout for collective interactions and led to the identification of optimized binding networks. Systematic variation of dipeptide input revealed the emergence of two networks of non-covalent hydrogen bonding and CH-π interactions that can co-exist, are cooperative and context-dependent. A cooperative binding mode was determined by studying the binding of the most amplified tetrapeptide (AWAD) with glucose in isolation. Overall, these results demonstrate that the bottom-up design of complex systems can recreate emergent behaviors driven by covalent and non-covalent self-organization that are not observed in reductionist designs and lead to the identification of system-level cooperative binding motifs.
Collapse
Affiliation(s)
- Salma Kassem
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Scott A McPhee
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Naxhije Berisha
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
| |
Collapse
|