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Search for "proteins" in Full Text gives 508 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.

In-depth characterization of self-healing polymers based on π–π interactions

  • Josefine Meurer,
  • Julian Hniopek,
  • Johannes Ahner,
  • Michael Schmitt,
  • Jürgen Popp,
  • Stefan Zechel,
  • Kalina Peneva and
  • Martin D. Hager

Beilstein J. Org. Chem. 2021, 17, 2496–2504, doi:10.3762/bjoc.17.166

Graphical Abstract
  • ]. This specific process is based on reversible interactions, which are integrated in the chemical structure of the proteins of the thread [5]. Zinc–histidine metal complexes which are part of the protein’s structure enable the material to regenerate its mechanical performance after a damage event [1][6
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Published 29 Sep 2021

Post-functionalization of drug-loaded nanoparticles prepared by polymerization-induced self-assembly (PISA) with mitochondria targeting ligands

  • Janina-Miriam Noy,
  • Fan Chen and
  • Martina Stenzel

Beilstein J. Org. Chem. 2021, 17, 2302–2314, doi:10.3762/bjoc.17.148

Graphical Abstract
  • to mitochondrial protein, but also chelates other cysteine-containing species. Several hundred good binding sites for trivalent arsenicals in each organ have been proposed [6][7], and more than 50 arsenic-binding proteins could be identified and analysed by Zhang et al. [8] and Yan et al. [9] using p
  • -phenylarsenoxide-based agents. This can also lead to deactivation of the drug as these organoarsenic drugs react readily with blood proteins, in particular transferrin [10]. In order to limit premature inactivation of the arsenic drugs, a range of nanoparticles have been developed to enhance stability, thus
  • peptides and proteins have been linked to nanotechnology. DQA and TPP are both cationic and lipophilic molecules and therefore able to easily pass the mitochondrial membrane [15][16][17][18][19]. TPP is the most-studied mitochondrial targeting agent and has shown to accumulate 1000 times more in the
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Published 03 Sep 2021

(Phenylamino)pyrimidine-1,2,3-triazole derivatives as analogs of imatinib: searching for novel compounds against chronic myeloid leukemia

  • Luiz Claudio Ferreira Pimentel,
  • Lucas Villas Boas Hoelz,
  • Henayle Fernandes Canzian,
  • Frederico Silva Castelo Branco,
  • Andressa Paula de Oliveira,
  • Vinicius Rangel Campos,
  • Floriano Paes Silva Júnior,
  • Rafael Ferreira Dantas,
  • Jackson Antônio Lamounier Camargos Resende,
  • Anna Claudia Cunha,
  • Nubia Boechat and
  • Mônica Macedo Bastos

Beilstein J. Org. Chem. 2021, 17, 2260–2269, doi:10.3762/bjoc.17.144

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  • in the docking studies. Keywords: chronic myeloid leukemia; 1,3-dipolar cycloaddition; imatinib; (phenylamino)pyrimidine-pyridine; 1,2,3-triazole; Introduction Changes in tyrosine kinase proteins (TKPs), either by mutation or chromosomal translocation, can turn them into potent oncogenes
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Published 01 Sep 2021

Constrained thermoresponsive polymers – new insights into fundamentals and applications

  • Patricia Flemming,
  • Alexander S. Münch,
  • Andreas Fery and
  • Petra Uhlmann

Beilstein J. Org. Chem. 2021, 17, 2123–2163, doi:10.3762/bjoc.17.138

Graphical Abstract
  • synthetic polymers, thermoresponsivity can also be observed in biological structures and their derivatives. While LCST behavior is more frequently studied in synthetic polymers, the occurrence of UCST behavior predominates in aqueous solutions of proteins [302][303]. The thermoresponse of natural proteins
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Published 20 Aug 2021

Progress and challenges in the synthesis of sequence controlled polysaccharides

  • Giulio Fittolani,
  • Theodore Tyrikos-Ergas,
  • Denisa Vargová,
  • Manishkumar A. Chaube and
  • Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

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Published 05 Aug 2021

On the application of 3d metals for C–H activation toward bioactive compounds: The key step for the synthesis of silver bullets

  • Renato L. Carvalho,
  • Amanda S. de Miranda,
  • Mateus P. Nunes,
  • Roberto S. Gomes,
  • Guilherme A. M. Jardim and
  • Eufrânio N. da Silva Júnior

Beilstein J. Org. Chem. 2021, 17, 1849–1938, doi:10.3762/bjoc.17.126

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Published 30 Jul 2021

Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides

  • Mathias B. Danielsen and
  • Jesper Wengel

Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125

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  • hurdle that needs to be addressed before ASOs can find more widespread use [3][9][10][11][14]. A lack of efficient delivery of ASOs can be caused by various reasons such as degradation [15][16], insufficient endosomal escape [17], glomerular filtration [18], or binding to one or more proteins [19][20
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Published 29 Jul 2021

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

  • Theodore Groth,
  • Rudiyanto Gunawan and
  • Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

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  • termed glycogenes [1][2]. These glycogenes include the glycosyltransferases, glycosidases, sulfotransferases, transporters, etc. The expression of these glycogenes is in turn driven by the action of a class of proteins called transcription factors (TFs). These TFs regulate gene expression by binding
  • may regulate pathways related to sialylation, hyaluronan synthesis, as well as chondroitin and dermatan sulfate elongation. Here, STAT1, 4, and 5 proteins were enriched in the IL-21 signaling pathway. Luminal breast cancer types are known to express STAT1 and 3 as well as STATs 2 and 4. STAT5 is known
  • [24][25]. It has been found to be upregulated in breast cancer with respect to normal-like. PRDM1, also known as Blimp-1, is a transcriptional repressor, and its upregulation in cancer is known to dysregulate other proteins [26]. The increase poly-LacNAc structures have been shown to play roles in
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Published 22 Jul 2021

Volatile emission and biosynthesis in endophytic fungi colonizing black poplar leaves

  • Christin Walther,
  • Pamela Baumann,
  • Katrin Luck,
  • Beate Rothe,
  • Peter H. W. Biedermann,
  • Jonathan Gershenzon,
  • Tobias G. Köllner and
  • Sybille B. Unsicker

Beilstein J. Org. Chem. 2021, 17, 1698–1711, doi:10.3762/bjoc.17.118

Graphical Abstract
  • structures of sesquiterpenes emitted from endophytic fungi (Table 2) isolated from black poplar leaves. Terpene synthase activity of CxTPS1 and CxTPS2. A) Genes were heterologously expressed in Escherichia coli and partially purified proteins were assayed with GPP, (E,E)-FPP, or (E,E,E)-GGPP as substrates in
  • -springene (14). B) Structures of the enzyme products of CxTPS1 and CxTPS2, including (E)-β-caryophyllene (1) which was the only terpene detected from Cladosporium sp. cultures. Dendrogram analysis (rooted tree) of CxTPS1 and CxTPS2 (bold) from Cladosporium sp. and characterized TPS proteins and their main
  • amino acid substitutions per site. The alpha-domain of maize TPS4 [62] was chosen as an outgroup. TPS proteins from different Ascomycota are highlighted according to their different lifestyle: endophytic (purple), pathogenic (orange) and saprophytic (green). Fungal endophytes identified from leaves of
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Published 22 Jul 2021

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

  • Nikita Brodyagin,
  • Martins Katkevics,
  • Venubabu Kotikam,
  • Christopher A. Ryan and
  • Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

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  • negative charge on PNA’s backbone. Electrostatic repulsion of the negatively charged phosphates dominates the conformational properties and structure of nucleic acids. In contrast to proteins that prefer to fold in compact structures, DNA and RNA inherently prefer extended conformations that minimize the
  • electrostatic repulsion. The maintenance and function of long double-stranded DNA (dsDNA) is achieved through complex mechanisms involving histones and other proteins. Large non-coding RNAs (e.g., ribosomes) manage electrostatic repulsion using positively charged RNA-binding proteins and cations (e.g
  • covalent conjugation of PNA to delivery enhancing compounds. Cell-penetrating peptides derived from natural proteins: The initial success of PNA delivery involved PNA conjugates taken up by receptor-mediated endocytosis. Pardridge and co-workers successfully demonstrated in vivo delivery and blood-brain
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Published 19 Jul 2021

Antiviral therapy in shrimp through plant virus VLP containing VP28 dsRNA against WSSV

  • Santiago Ramos-Carreño,
  • Ivone Giffard-Mena,
  • Jose N. Zamudio-Ocadiz,
  • Alfredo Nuñez-Rivera,
  • Ricardo Valencia-Yañez,
  • Jaime Ruiz-Garcia,
  • Maria Teresa Viana and
  • Ruben D. Cadena-Nava

Beilstein J. Org. Chem. 2021, 17, 1360–1373, doi:10.3762/bjoc.17.95

Graphical Abstract
  • of interest [12][13][14][15][16]. The antiviral response of RNAi is triggered by double-stranded RNA (dsRNA) to block the synthesis of a specific viral protein, in the case of WSSV the targets being the structural proteins VP19, VP24, VP26, and VP28, as they are involved in cell recognition, virus
  • entry, binding and assembly of the virion. Previous studies have shown that silencing these structural proteins in WSSV challenge assays, increases shrimp survival [10][11][17][18][19][20][21]. The VP28 glycoprotein plays an important role in systemic infection by interacting with cell membrane proteins
  • , and it is one of the most abundant proteins along with VP26 (≈60%) in the external WSSV surface [21][22]. The RNAi trials using an intramuscular injection (IM) have shown that VP28 glycoprotein is the target of choice to block WSSV infection in shrimp [14][23][24]. However, RNAi intramuscular (IM
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Published 01 Jun 2021

Icilio Guareschi and his amazing “1897 reaction”

  • Gian Cesare Tron,
  • Alberto Minassi,
  • Giovanni Sorba,
  • Mara Fausone and
  • Giovanni Appendino

Beilstein J. Org. Chem. 2021, 17, 1335–1351, doi:10.3762/bjoc.17.93

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  • work is testified by Willstätter, who in his memoirs refers to Guareschi as “alkaloid chemist” [28]. Ptomaines (from the Greek πτωμα, cadaver) are anaerobic bacterial degradation products of proteins and choline-containing phospholipids. The formation of these is associated with putrefaction of animal
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Published 25 May 2021

A new glance at the chemosphere of macroalgal–bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry

  • Marine Vallet,
  • Filip Kaftan,
  • Veit Grabe,
  • Fatemeh Ghaderiardakani,
  • Simona Fenizia,
  • Aleš Svatoš,
  • Georg Pohnert and
  • Thomas Wichard

Beilstein J. Org. Chem. 2021, 17, 1313–1322, doi:10.3762/bjoc.17.91

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  • is an important part of the MALDI-MSI experiment. MALDI-MS can be used to identify proteins and metabolic signatures [22][23][24] from bacteria and microalgae, as well as biofilms [25]. The primary function of the applied matrix is to improve the quality of the MS spectra, particularly the signal
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Published 19 May 2021

Synthesis of multiply fluorinated N-acetyl-D-glucosamine and D-galactosamine analogs via the corresponding deoxyfluorinated glucosazide and galactosazide phenyl thioglycosides

  • Vojtěch Hamala,
  • Lucie Červenková Šťastná,
  • Martin Kurfiřt,
  • Petra Cuřínová,
  • Martin Dračínský and
  • Jindřich Karban

Beilstein J. Org. Chem. 2021, 17, 1086–1095, doi:10.3762/bjoc.17.85

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  • . Keywords: amino sugars; deoxyfluorination; fluorinated carbohydrates; hexosamine hemiacetals; thioglycosides; Introduction Fluorinated carbohydrates are versatile carbohydrate mimetics used to probe or manipulate the recognition of carbohydrates by carbohydrate-binding proteins or carbohydrate-processing
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Published 11 May 2021

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

  • Christopher Liczner,
  • Kieran Duke,
  • Gabrielle Juneau,
  • Martin Egli and
  • Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

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  • , replication, splicing and other fundamental processes in biological information transfer. More specifically, they can affect chemical and thermodynamic stability, folding, secondary and tertiary structure, activity and interactions between nucleic acids, proteins and receptors. Particularly, as far as
  • production of proteins, enzymes and receptors that may be inhibited by small-molecule and antibody therapeutics. However, native RNA oligonucleotides do not possess sufficient metabolic stability for in vivo applications. Therefore, chemical modification is absolutely essential to re-engineer RNA into a
  • targeted to proviral HIV DNA [68], and as a triplex-forming oligonucleotide that selectively binds a sequence within the chromatin structure of cell nuclei [69]. Remarkably, 3'-NP DNA can also act as an RNA mimic in interactions with binding proteins despite lacking a ribose moiety, making them useful
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Published 28 Apr 2021

Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

  • Roslyn M. Ray,
  • Anders Højgaard Hansen,
  • Maria Taskova,
  • Bernhard Jandl,
  • Jonas Hansen,
  • Citra Soemardy,
  • Kevin V. Morris and
  • Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

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  • of the nature of the target proteins. CCR5, a cell surface receptor, is internalized upon ligand binding before recycling back to the cell surface or processed for degradation in the lysosome [34]. On the other hand, gp120 is a viral surface protein that is involved in viral entry through
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Published 26 Apr 2021

Synthetic reactions driven by electron-donor–acceptor (EDA) complexes

  • Zhonglie Yang,
  • Yutong Liu,
  • Kun Cao,
  • Xiaobin Zhang,
  • Hezhong Jiang and
  • Jiahong Li

Beilstein J. Org. Chem. 2021, 17, 771–799, doi:10.3762/bjoc.17.67

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  • construction of C–S bonds C–S bonds are commonly present in amino acids, proteins, glycosides, nucleic acids, and other biological macromolecules. In recent years, photocatalyst- and transition-metal strategies have been employed to construct C–S bonds [66][67][68][69]. The C–S bond synthesis via EDA-complex
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Published 06 Apr 2021

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

  • Yongdong Su,
  • Maitsetseg Bayarjargal,
  • Tracy K. Hale and
  • Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

Graphical Abstract
  • recognise and cut DNA sequences, or CRISPR-CAS9 [8][9][10] and CAS9-constructs [11][12][13][14] which rely on large proteins to open the target duplex, triplex-forming oligonucleotides (TFOs) [15] can be designed to bind in a sequence-specific manner to double-stranded DNA (dsDNA) [16]. In forming the
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Published 29 Mar 2021

Valorisation of plastic waste via metal-catalysed depolymerisation

  • Francesca Liguori,
  • Carmen Moreno-Marrodán and
  • Pierluigi Barbaro

Beilstein J. Org. Chem. 2021, 17, 589–621, doi:10.3762/bjoc.17.53

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  • oxidation, cross-linkage, bond cleavage). The term “biodegradation” indicates a “degradation caused by enzymatic processes resulting from the action of cells”. Although commonly used, also for artificial polymers, the term “biodegradable” specifically refers to biorelated polymers (i.e., proteins, nucleic
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Published 02 Mar 2021

Synthesis and physicochemical evaluation of fluorinated lipopeptide precursors of ligands for microbubble targeting

  • Masayori Hagimori,
  • Estefanía E. Mendoza-Ortega and
  • Marie Pierre Krafft

Beilstein J. Org. Chem. 2021, 17, 511–518, doi:10.3762/bjoc.17.45

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  • , which involves the use of targeting ligands, such as monoclonal antibodies, antibody fragments, proteins, peptides, and other small molecules, including vitamins and carbohydrates [7][8]. The targeting ligands are coupled to the surface of the carrier to selectively target tumor cells that overexpress a
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Published 19 Feb 2021

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

  • Vladimir Kubyshkin,
  • Rebecca Davis and
  • Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

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  • structure and distinct conformational profile, proline is unique in the repertoire of the 20 amino acids coded into proteins. Here, we summarize the biochemical work on the replacement of proline with (4R)- and (4S)-fluoroproline as well as 4,4-difluoroproline in proteins done mainly in the last two decades
  • proline replacements are able to elevate the protein expression speed and yields and improve the thermodynamic and kinetic folding profiles of individual proteins. In this context, fluoroprolines can be viewed as useful tools in the biotechnological toolbox. As a prospect, we envision that proteome-wide
  • biodiversity, containing fluorine as a bioelement. Keywords: amino acids; evolution; fluorine; proline; proteins; Introduction Nature employs a rather small set of chemical elements for constructing the core biochemical makeup. Most elements of the periodic table are excluded from the biochemical world. Not
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Published 15 Feb 2021

Synthesis of legonmycins A and B, C(7a)-hydroxylated bacterial pyrrolizidines

  • Wilfred J. M. Lewis,
  • David M. Shaw and
  • Jeremy Robertson

Beilstein J. Org. Chem. 2021, 17, 334–342, doi:10.3762/bjoc.17.31

Graphical Abstract
  • ]. Proteins coded by three of these genes (LgnA, LgnB, and LgnD) were shown to assemble legonindolizidines A (1) and B (2) – from proline, threonine, and a fatty acid component – which are then converted by LgnC, a flavin-dependent monooxygenase, into the corresponding legonmycins (3 and 4) via a sequence of
  • was established with, in this case, PxaB achieving the oxidative steps from indolizidine intermediates 5–8 produced by PxaA. An important aspect of this work was the finding that at least 90 different bacterial strains, spanning 23 species, contain gene sequences encoding proteins related to PxaB
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Published 02 Feb 2021

19F NMR as a tool in chemical biology

  • Diana Gimenez,
  • Aoife Phelan,
  • Cormac D. Murphy and
  • Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

Graphical Abstract
  • fluorinated probes and their incorporation into macromolecules, the application of 19F NMR to monitor protein–protein interactions, protein–ligand interactions, physiologically relevant ions and in the structural analysis of proteins and nucleic acids. The continued relevance of the technique to investigate
  • labelling 19F NMR offers an attractive option for investigating the interactions between proteins and other biomolecules such as nucleic acids. Many of the advantages of 19F NMR have already been discussed but it is worth highlighting that it is a particularly useful technique to study large proteins that
  • cannot easily be probed by conventional NMR experiments. Given that fluorine atoms (e.g., 19F labels) are not naturally present in proteins, a key element to establishing 19F NMR in this area has been the development of methods that can be used to give access to 19F-labelled proteins. Methods for the
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Published 28 Jan 2021

The preparation and properties of 1,1-difluorocyclopropane derivatives

  • Kymbat S. Adekenova,
  • Peter B. Wyatt and
  • Sergazy M. Adekenov

Beilstein J. Org. Chem. 2021, 17, 245–272, doi:10.3762/bjoc.17.25

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Published 26 Jan 2021

Molecular basis for protein–protein interactions

  • Brandon Charles Seychell and
  • Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

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  • design. Protein–protein interactions and their discovery are thus an interesting avenue for understanding how protein complexes, which make up the majority of proteins, work. Keywords: characterisation methods; heterooligomeric complex; homooligomeric complex; molecular interactions; protein–protein
  • interactions; Introduction From signalling over transport to catalysis, the broad functionality of proteins is essential in the cellular machinery. To this effect, proteins can be seen as the workforce of the cell. Proteins relay some of their functionality via interactions between protein nodes called
  • protein–protein interactions (PPIs). Hedin characterised the first PPI with trypsin and antitrypsin in 1906 [1], which provided a landmark for the awareness of what role PPIs have in cellular physiology. In fact, even though individual proteins perform essential functions, their effectiveness in the cell
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Published 04 Jan 2021
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