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Gavade A, Nagraj AK, Patel R, Pais R, Dhanure P, Scheele J, Seiz W, Patil J. Understanding the Specific Implications of Amino Acids in the Antibody Development. Protein J 2024; 43:405-424. [PMID: 38724751 DOI: 10.1007/s10930-024-10201-4] [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] [Accepted: 04/21/2024] [Indexed: 06/01/2024]
Abstract
As the demand for immunotherapy to treat and manage cancers, infectious diseases and other disorders grows, a comprehensive understanding of amino acids and their intricate role in antibody engineering has become a prime requirement. Naturally produced antibodies may not have the most suitable amino acids at the complementarity determining regions (CDR) and framework regions, for therapeutic purposes. Therefore, to enhance the binding affinity and therapeutic properties of an antibody, the specific impact of certain amino acids on the antibody's architecture must be thoroughly studied. In antibody engineering, it is crucial to identify the key amino acid residues that significantly contribute to improving antibody properties. Therapeutic antibodies with higher binding affinity and improved functionality can be achieved through modifications or substitutions with highly suitable amino acid residues. Here, we have indicated the frequency of amino acids and their association with the binding free energy in CDRs. The review also analyzes the experimental outcome of two studies that reveal the frequency of amino acids in CDRs and provides their significant correlation between the outcomes. Additionally, it discusses the various bond interactions within the antibody structure and antigen binding. A detailed understanding of these amino acid properties should assist in the analysis of antibody sequences and structures needed for designing and enhancing the overall performance of therapeutic antibodies.
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Affiliation(s)
- Akshata Gavade
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Anil Kumar Nagraj
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Riya Patel
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Roylan Pais
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Pratiksha Dhanure
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | | | | | - Jaspal Patil
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India.
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Napiórkowska A, Szpicer A, Górska-Horczyczak E, Kurek MA. Microencapsulation of Essential Oils Using Faba Bean Protein and Chia Seed Polysaccharides via Complex Coacervation Method. Molecules 2024; 29:2019. [PMID: 38731509 PMCID: PMC11085623 DOI: 10.3390/molecules29092019] [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: 03/27/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
The aim of this study was to develop microcapsules containing juniper or black pepper essential oils, using a combination of faba bean protein and chia seed polysaccharides (in ratios of 1:1, 1:2, 2:1). By synergizing these two polymers, our goal was to enhance the efficiency of essential oil microencapsulation, opening up various applications in the food industry. Additionally, we aimed to investigate the influence of different polymer mixing ratios on the properties of the resulting microcapsules and the course of the complex coacervation process. To dissolve the essential oils and limit their evaporation, soybean and rapeseed oils were used. The powders resulting from the freeze-drying of coacervates underwent testing to assess microencapsulation efficiency (65.64-87.85%), density, flowability, water content, solubility, and hygroscopicity. Additionally, FT-IR and DSC analyses were conducted. FT-IR analysis confirmed the interactions between the components of the microcapsules, and these interactions were reflected in their high thermal resistance, especially at a protein-to-polysaccharide ratio of 2:1 (177.2 °C). The water content in the obtained powders was low (3.72-7.65%), but it contributed to their hygroscopicity (40.40-76.98%).
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Affiliation(s)
- Alicja Napiórkowska
- Department of Technique and Food Development, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (A.S.)
| | | | | | - Marcin Andrzej Kurek
- Department of Technique and Food Development, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (A.S.)
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Gan Q, Fan C. Orthogonal Translation for Site-Specific Installation of Post-translational Modifications. Chem Rev 2024; 124:2805-2838. [PMID: 38373737 PMCID: PMC11230630 DOI: 10.1021/acs.chemrev.3c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Post-translational modifications (PTMs) endow proteins with new properties to respond to environmental changes or growth needs. With the development of advanced proteomics techniques, hundreds of distinct types of PTMs have been observed in a wide range of proteins from bacteria, archaea, and eukarya. To identify the roles of these PTMs, scientists have applied various approaches. However, high dynamics, low stoichiometry, and crosstalk between PTMs make it almost impossible to obtain homogeneously modified proteins for characterization of the site-specific effect of individual PTM on target proteins. To solve this problem, the genetic code expansion (GCE) strategy has been introduced into the field of PTM studies. Instead of modifying proteins after translation, GCE incorporates modified amino acids into proteins during translation, thus generating site-specifically modified proteins at target positions. In this review, we summarize the development of GCE systems for orthogonal translation for site-specific installation of PTMs.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
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Nivet C, Custovic I, Avoscan L, Bikker FJ, Bonnotte A, Bourillot E, Briand L, Brignot H, Heydel JM, Herrmann N, Lelièvre M, Lesniewska E, Neiers F, Piétrement O, Schwartz M, Belloir C, Canon F. Development of New Models of Oral Mucosa to Investigate the Impact of the Structure of Transmembrane Mucin-1 on the Mucosal Pellicle Formation and Its Physicochemical Properties. Biomedicines 2024; 12:139. [PMID: 38255244 PMCID: PMC10812975 DOI: 10.3390/biomedicines12010139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
The mucosal pellicle (MP) is a biological film protecting the oral mucosa. It is composed of bounded salivary proteins and transmembrane mucin MUC1 expressed by oral epithelial cells. Previous research indicates that MUC1 expression enhances the binding of the main salivary protein forming the MP, MUC5B. This study investigated the influence of MUC1 structure on MP formation. A TR146 cell line, which does not express MUC1 natively, was stably transfected with genes coding for three MUC1 isoforms differing in the structure of the two main extracellular domains: the VNTR domain, exhibiting a variable number of tandem repeats, and the SEA domain, maintaining the two bound subunits of MUC1. Semi-quantification of MUC1 using dot blot chemiluminescence showed comparable expression levels in all transfected cell lines. Semi-quantification of MUC5B by immunostaining after incubation with saliva revealed that MUC1 expression significantly increased MUC5B adsorption. Neither the VNTR domain nor the SEA domain was influenced MUC5B anchoring, suggesting the key role of the MUC1 N-terminal domain. AFM-IR nanospectroscopy revealed discernible shifts indicative of changes in the chemical properties at the cell surface due to the expression of the MUC1 isoform. Furthermore, the observed chemical shifts suggest the involvement of hydrophobic effects in the interaction between MUC1 and salivary proteins.
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Affiliation(s)
- Clément Nivet
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Irma Custovic
- Institut Carnot de Bourgogne (ICB), UMR CNRS 6303, University of Bourgogne, 21000 Dijon, France; (I.C.); (E.B.); (E.L.); (O.P.)
| | - Laure Avoscan
- Agroécologie, UMR1347 INRAE, ERL CNRS 6300, DimaCell Platform, Center of Microscopy INRAE, University of Bourgogne, 21000 Dijon, France; (L.A.); (A.B.)
| | - Floris J. Bikker
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, 1081 LA Amsterdam, The Netherlands;
| | - Aline Bonnotte
- Agroécologie, UMR1347 INRAE, ERL CNRS 6300, DimaCell Platform, Center of Microscopy INRAE, University of Bourgogne, 21000 Dijon, France; (L.A.); (A.B.)
| | - Eric Bourillot
- Institut Carnot de Bourgogne (ICB), UMR CNRS 6303, University of Bourgogne, 21000 Dijon, France; (I.C.); (E.B.); (E.L.); (O.P.)
| | - Loïc Briand
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Hélène Brignot
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Jean-Marie Heydel
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Noémie Herrmann
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Mélanie Lelièvre
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Eric Lesniewska
- Institut Carnot de Bourgogne (ICB), UMR CNRS 6303, University of Bourgogne, 21000 Dijon, France; (I.C.); (E.B.); (E.L.); (O.P.)
| | - Fabrice Neiers
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Olivier Piétrement
- Institut Carnot de Bourgogne (ICB), UMR CNRS 6303, University of Bourgogne, 21000 Dijon, France; (I.C.); (E.B.); (E.L.); (O.P.)
| | - Mathieu Schwartz
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Christine Belloir
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
| | - Francis Canon
- Center for Taste and Feeding Behaviour (CSGA), UMR1324 INRAE, Institut Agro Dijon, Université de Bourgogne, UMR6265 CNRS, 21000 Dijon, France; (C.N.); (L.B.); (H.B.); (J.-M.H.); (N.H.); (M.L.); (F.N.); (M.S.); (C.B.)
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Johari S, Johan MR, Khaligh NG. Organocatalytic Synthesis of (Hetero)arylidene Malononitriles Using a More Sustainable, Greener, and Scalable Strategy. Curr Org Synth 2024; 21:704-716. [PMID: 38231061 DOI: 10.2174/0115701794268766231108110816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/22/2023] [Accepted: 10/03/2023] [Indexed: 01/18/2024]
Abstract
AIM AND OBJECTIVE The establishment of a green and sustainable Knoevenagel condensation reaction in organic chemistry is still crucial. This work aimed to provide a newly developed metal-free and halogen-free catalytic methodology for the synthesis of CS and (hetero-) arylidene malononitriles in the laboratory and industrial scale. The Knoevenagel condensation reaction of various carbonyl groups with malononitrile was investigated in ethanol, an ecofriendly medium, in the presence of seven nitrogen-based organocatalysts. MATERIALS AND METHODS A comparative study was conducted using two as-obtained and four commercially available nitrogen-based organocatalysts in Knoevenagel condensation reactions. The synthesis of CS gas (2-chlorobenzylidene malononitrile) using a closed catalytic system was optimized based on their efficiency and greener approach. RESULTS The conversion of 100% and excellent yields were obtained in a short time. The products could be crystallized directly from the reaction mixture. After separating pure products, the residue solution was employed directly in the next run without any concentration, activation, purification, or separation. Furthermore, the synthesis of 2-chlorobenzylidenemahmonitrile (CS) was carried out on a large scale using imidazole as a selected nitrogen-based catalyst, afforded crystalline products with 95 ± 2% yield in five consecutive runs. CONCLUSION Energy efficiency, cost saving, greener conditions, using only 5 mol% of organocatalyst, high recyclability of catalyst, prevention of waste, recycling extractant by a rotary evaporator for non-crystallized products, demonstrated the potential commercial production of CS using imidazole in ethanol as an efficient and highly recyclable catalytic system.
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Affiliation(s)
- Suzaimi Johari
- Nanotechnology and Catalysis Research Center, Institute for Advanced Studies (IAS), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mohd Rafie Johan
- Nanotechnology and Catalysis Research Center, Institute for Advanced Studies (IAS), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nader Ghaffari Khaligh
- Nanotechnology and Catalysis Research Center, Institute for Advanced Studies (IAS), University of Malaya, 50603, Kuala Lumpur, Malaysia
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Pandey AK, Ganguly HK, Sinha SK, Daniels KE, Yap GPA, Patel S, Zondlo NJ. An Inherent Difference between Serine and Threonine Phosphorylation: Phosphothreonine Strongly Prefers a Highly Ordered, Compact, Cyclic Conformation. ACS Chem Biol 2023; 18:1938-1958. [PMID: 37595155 DOI: 10.1021/acschembio.3c00068] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Phosphorylation and dephosphorylation of proteins by kinases and phosphatases are central to cellular responses and function. The structural effects of serine and threonine phosphorylation were examined in peptides and in proteins, by circular dichroism, NMR spectroscopy, bioinformatics analysis of the PDB, small-molecule X-ray crystallography, and computational investigations. Phosphorylation of both serine and threonine residues induces substantial conformational restriction in their physiologically more important dianionic forms. Threonine exhibits a particularly strong disorder-to-order transition upon phosphorylation, with dianionic phosphothreonine preferentially adopting a cyclic conformation with restricted ϕ (ϕ ∼ -60°) stabilized by three noncovalent interactions: a strong intraresidue phosphate-amide hydrogen bond, an n → π* interaction between consecutive carbonyls, and an n → σ* interaction between the phosphate Oγ lone pair and the antibonding orbital of C-Hβ that restricts the χ2 side-chain conformation. Proline is unique among the canonical amino acids for its covalent cyclization on the backbone. Phosphothreonine can mimic proline's backbone cyclization via noncovalent interactions. The preferred torsions of dianionic phosphothreonine are ϕ,ψ = polyproline II helix > α-helix (ϕ ∼ -60°); χ1 = g-; χ2 ∼ +115° (eclipsed C-H/O-P bonds). This structural signature is observed in diverse proteins, including in the activation loops of protein kinases and in protein-protein interactions. In total, these results suggest a structural basis for the differential use and evolution of threonine versus serine phosphorylation sites in proteins, with serine phosphorylation typically inducing smaller, rheostat-like changes, versus threonine phosphorylation promoting larger, step function-like switches, in proteins.
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Affiliation(s)
- Anil K Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Himal K Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Sudipta Kumar Sinha
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Chemistry, Indian Institute of Technology Ropar, Nangal Road, Rupnagar 140001, India
| | - Kelly E Daniels
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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Wawrzkiewicz-Jałowiecka A, Lalik A, Lukasiak A, Richter-Laskowska M, Trybek P, Ejfler M, Opałka M, Wardejn S, Delfino DV. Potassium Channels, Glucose Metabolism and Glycosylation in Cancer Cells. Int J Mol Sci 2023; 24:ijms24097942. [PMID: 37175655 PMCID: PMC10178682 DOI: 10.3390/ijms24097942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Potassium channels emerge as one of the crucial groups of proteins that shape the biology of cancer cells. Their involvement in processes like cell growth, migration, or electric signaling, seems obvious. However, the relationship between the function of K+ channels, glucose metabolism, and cancer glycome appears much more intriguing. Among the typical hallmarks of cancer, one can mention the switch to aerobic glycolysis as the most favorable mechanism for glucose metabolism and glycome alterations. This review outlines the interconnections between the expression and activity of potassium channels, carbohydrate metabolism, and altered glycosylation in cancer cells, which have not been broadly discussed in the literature hitherto. Moreover, we propose the potential mediators for the described relations (e.g., enzymes, microRNAs) and the novel promising directions (e.g., glycans-orinented drugs) for further research.
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Affiliation(s)
- Agata Wawrzkiewicz-Jałowiecka
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Anna Lalik
- Department of Systems Biology and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland
- Biotechnology Center, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Agnieszka Lukasiak
- Department of Physics and Biophysics, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Monika Richter-Laskowska
- The Centre for Biomedical Engineering, Łukasiewicz Research Network-Krakow Institute of Technology, 30-418 Krakow, Poland
| | - Paulina Trybek
- Institute of Physics, University of Silesia in Katowice, 41-500 Chorzów, Poland
| | - Maciej Ejfler
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Maciej Opałka
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Sonia Wardejn
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Domenico V Delfino
- Section of Pharmacology, Department of Medicine and Surgery, University of Perugia, 06129 Perugia, Italy
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