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Balli OI, Uversky VN, Durdagi S, Coskuner-Weber O. Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective. Proteins 2021; 90:322-339. [PMID: 34549826 DOI: 10.1002/prot.26242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/24/2021] [Accepted: 09/07/2021] [Indexed: 11/08/2022]
Abstract
Experimenters face challenges and limitations while analyzing glycoproteins due to their high flexibility, stereochemistry, anisotropic effects, and hydration phenomena. Computational studies complement experiments and have been used in characterization of the structural properties of glycoproteins. However, recent investigations revealed that computational studies face significant challenges as well. Here, we introduce and discuss some of these challenges and weaknesses in the investigations of glycoproteins. We also present requirements of future developments in computational biochemistry and computational biology areas that could be necessary for providing more accurate structural property analyses of glycoproteins using computational tools. Further theoretical strategies that need to be and can be developed are discussed herein.
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Affiliation(s)
- Oyku Irem Balli
- Molecular Biotechnology, Turkish-German University, Istanbul, Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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Stantič M, Gunčar G, Kuzman D, Mravljak R, Cvijić T, Podgornik A. Application of lectin immobilized on polyHIPE monoliths for bioprocess monitoring of glycosylated proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1174:122731. [PMID: 33971517 DOI: 10.1016/j.jchromb.2021.122731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 02/04/2023]
Abstract
In-process monitoring of glycosylated protein concentration becomes very important with the introduction of perfusion bioprocesses. Affinity chromatography based on lectins allows selective monitoring when carbohydrates are accessible on the protein surface. In this work, we immobilized lectin on polyHIPE type of monoliths and implemented it for bioprocess monitoring. A spacer was introduced to lectin, which increased binding kinetics toward Fc-fusion protein, demonstrated by bio-layer interferometry. Furthermore, complete desorption using 0.25 M galactose was shown. Affinity column exhibited linearity in the range between 0.5 and 8 mg/ml and flow-unaffected binding for the flow-rates between 0.5 and 8 ml/min. Long-term stability over at least four months period was demonstrated. No unspecific binding of culture media components, including host cell proteins and DNA, was detected. Results obtained by affinity column matched concentration values obtained by a reference method.
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Affiliation(s)
- Metka Stantič
- Faculty for Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Gregor Gunčar
- Faculty for Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Drago Kuzman
- Technical development biosimilars, Global drug development, Novartis, Kolodvorska 27, 1234 Mengeš, Slovenia
| | - Rok Mravljak
- Faculty for Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Tamara Cvijić
- Technical development biosimilars, Global drug development, Novartis, Kolodvorska 27, 1234 Mengeš, Slovenia
| | - Aleš Podgornik
- Faculty for Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia; COBIK, Tovarniška 26, 5270 Ajdovščina, Slovenia.
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Ramos-Payán M, Ocaña-González JA, Fernández-Torres R, Bello-López MÁ. A Method for the Determination of Veterinary Drugs from Different Therapeutic Classes in Animal Urine. J Chromatogr Sci 2020; 58:127-135. [PMID: 32154562 DOI: 10.1093/chromsci/bmz084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/29/2019] [Accepted: 09/10/2019] [Indexed: 11/15/2022]
Abstract
A rapid, precise and robust HPLC separation procedure has been developed and optimized for the determination of a series of drugs of different therapeutic classes: chlortetracycline, oxitetracycline, cefoperazone, diclofenac, tiamphenicol, marbofloxacin, ciprofloxacin, danofloxacin, enrofloxacin and flumequine. The chromatographic method used a monolithic C18 column and both diode array and fluorescence detection. This procedure was validated for the analysis of drugs in cow urine, using a simple and fast procedure with methanol/acetonitrile, allowing the simultaneous and efficient extraction of most of the studied drugs. The proposed method was successfully applied to the determination of enrofloxacin in cow urine, collected after the administration of this antibiotic.
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Affiliation(s)
- María Ramos-Payán
- Department of Analytical Chemistry, Faculty of Chemistry, Universidad de Sevilla, c/Prof. García González s/n, 41012 Seville, Spain
| | - Juan Antonio Ocaña-González
- Department of Analytical Chemistry, Faculty of Chemistry, Universidad de Sevilla, c/Prof. García González s/n, 41012 Seville, Spain
| | - Rut Fernández-Torres
- Department of Analytical Chemistry, Faculty of Chemistry, Universidad de Sevilla, c/Prof. García González s/n, 41012 Seville, Spain
| | - Miguel Ángel Bello-López
- Department of Analytical Chemistry, Faculty of Chemistry, Universidad de Sevilla, c/Prof. García González s/n, 41012 Seville, Spain
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Role of porogenic solvent type on the performance of a monolithic imprinted column. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01399-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Waniwan JT, Chen YJ, Capangpangan R, Weng SH, Chen YJ. Glycoproteomic Alterations in Drug-Resistant Nonsmall Cell Lung Cancer Cells Revealed by Lectin Magnetic Nanoprobe-Based Mass Spectrometry. J Proteome Res 2018; 17:3761-3773. [PMID: 30261726 DOI: 10.1021/acs.jproteome.8b00433] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the functional role of glycosylation-mediated pathogenesis requires deep characterization of glycoproteome, which remains extremely challenging due to the inherently complex nature of glycoproteins. We demonstrate the utility of lectin-magnetic nanoprobe (MNP@lectin) coupled to Orbitrap HCD-CID-MS/MS for complementary glycotope-specific enrichment and site-specific glycosylation analysis of the glycoproteome. By three nanoprobes, MNP@ConA, MNP@AAL, and MNP@SNA, our results revealed the first large-scale glycoproteome of nonsmall cell lung cancer (NSCLC) with 2290 and 2767 nonredundant glycopeptides confidently identified (Byonic score ≥100) in EGFR-TKI-sensitive PC9 and -resistant PC9-IR cells, respectively, especially with more fucosylated and sialylated glycopeptides in PC9-IR cells. The complementary enrichment was demonstrated with only five glycopeptides commonly enriched in three MNP@lectins. Glycotope specificity of 79 and 62% for enrichment was achieved using MNP@AAL and MNP@SNA, respectively. Label-free quantitation revealed predominant fucosylation in PC9-IR cells, suggesting its potential role associated with NSCLC resistance. Moreover, without immunoprecipitation, this multilectin nanoprobe allows the sensitive identification of 51 glycopeptides from 10 of 12 reported sites from onco-protein EGFR. Our results not only demonstrated a sensitive approach to study the vastly under-represented N-glycoprotome but also may pave the way for a glycoproteomic atlas to further explore the site-specific function of glycoproteins associated with drug resistance in NSCLC.
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Affiliation(s)
- Juanilita T Waniwan
- Department of Chemistry , National Taiwan University , Taipei 115 , Taiwan.,Chemical Biology and Molecular Biophysics , Taiwan International Graduate Program , Taipei 115 , Taiwan.,Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
| | - Yi-Ju Chen
- Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
| | - Rey Capangpangan
- Caraga State University , Butuan City 8600 , Philippines.,Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
| | - Shao-Hsing Weng
- Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan.,Genome and Systems Biology Degree Program , National Taiwan University , Taipei 115 , Taiwan
| | - Yu-Ju Chen
- Department of Chemistry , National Taiwan University , Taipei 115 , Taiwan.,Institute of Chemistry , Academia Sinica , Taipei 115 , Taiwan
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Andjelković U, Tufegdžić S, Popović M. Use of monolithic supports for high-throughput protein and peptide separation in proteomics. Electrophoresis 2017; 38:2851-2869. [DOI: 10.1002/elps.201700260] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Uroš Andjelković
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
- Department of Biotechnology; University of Rijeka; Rijeka Croatia
| | - Srdjan Tufegdžić
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
| | - Milica Popović
- Faculty of Chemistry; University of Belgrade; Belgrade Serbia
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Dosekova E, Filip J, Bertok T, Both P, Kasak P, Tkac J. Nanotechnology in Glycomics: Applications in Diagnostics, Therapy, Imaging, and Separation Processes. Med Res Rev 2017; 37:514-626. [PMID: 27859448 PMCID: PMC5659385 DOI: 10.1002/med.21420] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/08/2016] [Accepted: 09/21/2016] [Indexed: 12/14/2022]
Abstract
This review comprehensively covers the most recent achievements (from 2013) in the successful integration of nanomaterials in the field of glycomics. The first part of the paper addresses the beneficial properties of nanomaterials for the construction of biosensors, bioanalytical devices, and protocols for the detection of various analytes, including viruses and whole cells, together with their key characteristics. The second part of the review focuses on the application of nanomaterials integrated with glycans for various biomedical applications, that is, vaccines against viral and bacterial infections and cancer cells, as therapeutic agents, for in vivo imaging and nuclear magnetic resonance imaging, and for selective drug delivery. The final part of the review describes various ways in which glycan enrichment can be effectively done using nanomaterials, molecularly imprinted polymers with polymer thickness controlled at the nanoscale, with a subsequent analysis of glycans by mass spectrometry. A short section describing an active glycoprofiling by microengines (microrockets) is covered as well.
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Affiliation(s)
- Erika Dosekova
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
| | - Jaroslav Filip
- Center for Advanced MaterialsQatar UniversityP.O. Box 2713DohaQatar
| | - Tomas Bertok
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
| | - Peter Both
- School of Chemistry, Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Peter Kasak
- Center for Advanced MaterialsQatar UniversityP.O. Box 2713DohaQatar
| | - Jan Tkac
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
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Tabasum S, Noreen A, Kanwal A, Zuber M, Anjum MN, Zia KM. Glycoproteins functionalized natural and synthetic polymers for prospective biomedical applications: A review. Int J Biol Macromol 2017; 98:748-776. [PMID: 28111295 DOI: 10.1016/j.ijbiomac.2017.01.078] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/05/2017] [Accepted: 01/16/2017] [Indexed: 02/06/2023]
Abstract
Glycoproteins have multidimensional properties such as biodegradability, biocompatibility, non-toxicity, antimicrobial and adsorption properties; therefore, they have wide range of applications. They are blended with different polymers such as chitosan, carboxymethyl cellulose (CMC), polyvinyl pyrrolidone (PVP), polycaprolactone (PCL), heparin, polystyrene fluorescent nanoparticles (PS-NPs) and carboxyl pullulan (PC) to improve their properties like thermal stability, mechanical properties, resistance to pH, chemical stability and toughness. Considering the versatile charateristics of glycoprotein based polymers, this review sheds light on synthesis and characterization of blends and composites of glycoproteins, with natural and synthetic polymers and their potential applications in biomedical field such as drug delivery system, insulin delivery, antimicrobial wound dressing uses, targeting of cancer cells, development of anticancer vaccines, development of new biopolymers, glycoproteome research, food product and detection of dengue glycoproteins. All the technical scientific issues have been addressed; highlighting the recent advancement.
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Affiliation(s)
- Shazia Tabasum
- Institute of Chemistry, Government College University, Faisalabad 38030, Pakistan
| | - Aqdas Noreen
- Institute of Chemistry, Government College University, Faisalabad 38030, Pakistan
| | - Arooj Kanwal
- Institute of Chemistry, Government College University, Faisalabad 38030, Pakistan
| | - Mohammad Zuber
- Institute of Chemistry, Government College University, Faisalabad 38030, Pakistan
| | | | - Khalid Mahmood Zia
- Institute of Chemistry, Government College University, Faisalabad 38030, Pakistan.
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Stine KJ. Application of Porous Materials to Carbohydrate Chemistry and Glycoscience. Adv Carbohydr Chem Biochem 2017; 74:61-136. [PMID: 29173727 DOI: 10.1016/bs.accb.2017.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
There is a growing interest in using a range of porous materials to meet research needs in carbohydrate chemistry and glycoscience in general. Among the applications of porous materials reviewed in this chapter, enrichment of glycans from biological samples prior to separation and analysis by mass spectrometry is a major emphasis. Porous materials offer high surface area, adjustable pore sizes, and tunable surface chemistry for interacting with glycans, by boronate affinity, hydrophilic interactions, molecular imprinting, and polar interactions. Among the materials covered in this review are mesoporous silica and related materials, porous graphitic carbon, mesoporous carbon, porous polymers, and nanoporous gold. In some applications, glycans are enzymatically or chemically released from glycoproteins or glycopeptides, and the porous materials have the advantage of size selectivity admitting only the glycans into the pores and excluding proteins. Immobilization of lectins onto porous materials of suitable pore size allows for the use of lectin-carbohydrate interactions in capture or separation of glycoproteins. Porous material surfaces modified with carbohydrates can be used for the selective capture of lectins. Controlled release of therapeutics from porous materials mediated by glycans has been reported, and so has therapeutic targeting using carbohydrate-modified porous particles. Additional applications of porous materials in glycoscience include their use in the supported synthesis of oligosaccharides and in the development of biosensors for glycans.
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Boronic acid-fumed silica nanoparticles incorporated large surface area monoliths for protein separation by nano-liquid chromatography. Anal Bioanal Chem 2016; 408:8457-8466. [DOI: 10.1007/s00216-016-9968-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/26/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022]
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Alla AJ, D' Andrea FB, Bhattarai JK, Cooper JA, Tan YH, Demchenko AV, Stine KJ. Selective capture of glycoproteins using lectin-modified nanoporous gold monolith. J Chromatogr A 2015; 1423:19-30. [PMID: 26554297 DOI: 10.1016/j.chroma.2015.10.060] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 10/14/2015] [Accepted: 10/17/2015] [Indexed: 11/25/2022]
Abstract
The surface of nanoporous gold (np-Au) monoliths was modified via a flow method with the lectin Concanavalin A (Con A) to develop a substrate for separation and extraction of glycoproteins. Self-assembled monolayers (SAMs) of α-lipoic acid (LA) on the np-Au monoliths were prepared followed by activation of the terminal carboxyl groups to create amine reactive esters that were utilized in the immobilization of Con A. Thermogravimetric analysis (TGA) was used to determine the surface coverages of LA and Con A on np-Au monoliths which were found to be 1.31×10(18) and 1.85×10(15)moleculesm(-2), respectively. An in situ solution depletion method was developed that enabled surface coverage characterization without damaging the substrate and suggesting the possibility of regeneration. Using this method, the surface coverages of LA and Con A were found to be 0.989×10(18) and 1.32×10(15)moleculesm(-2), respectively. The selectivity of the Con A-modified np-Au monolith for the high mannose-containing glycoprotein ovalbumin (OVA) versus negative control non-glycosylated bovine serum albumin (BSA) was demonstrated by the difference in the ratio of the captured molecules to the immobilized Con A molecules, with OVA:Con A=2.3 and BSA:Con A=0.33. Extraction of OVA from a 1:3 mole ratio mixture with BSA was demonstrated by the greater amount of depletion of OVA concentration during the circulation with the developed substrate. A significant amount of captured OVA was eluted using α-methyl mannopyranoside as a competitive ligand. This work is motivated by the need to develop new materials for chromatographic separation and extraction substrates for use in preparative and analytical procedures in glycomics.
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Affiliation(s)
- Allan J Alla
- Department of Chemistry and Biochemistry, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121 USA; Center for Nanoscience, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121, USA
| | - Felipe B D' Andrea
- Department of Chemistry and Biochemistry, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121 USA; Center for Nanoscience, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121, USA
| | - Jay K Bhattarai
- Department of Chemistry and Biochemistry, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121 USA; Center for Nanoscience, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121, USA
| | - Jared A Cooper
- Department of Chemistry and Biochemistry, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121 USA; Center for Nanoscience, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121, USA
| | - Yih Horng Tan
- Department of Chemistry and Biochemistry, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121 USA; Center for Nanoscience, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121, USA
| | - Alexei V Demchenko
- Department of Chemistry and Biochemistry, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121 USA
| | - Keith J Stine
- Department of Chemistry and Biochemistry, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121 USA; Center for Nanoscience, One University Boulevard, University of Missouri-St. Louis, Saint Louis, MO 63121, USA.
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