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

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

  • Steffen Lippold,
  • Arnoud H. de Ru,
  • Jan Nouta,
  • Peter A. van Veelen,
  • Magnus Palmblad,
  • Manfred Wuhrer and
  • Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

Graphical Abstract
  • separation of glycopeptides in RPLC is mainly driven by the peptide portions. Thus, information on different proteins and glycosylation sites appears in the form of glycopeptide clusters. Next to the peptide portion, glycosylation features, such as sialic acids, can strongly influence the retention time [8
  • this, a sample containing immunoglobulins G and A (IgG and IgA), simultaneously captured from human plasma, was chosen. This sample showed a considerable level of complexity due to the presence of multiple glycoproteins of interest and cocaptured (glyco)proteins from the plasma. The tools included
  • by Byonic The automated and score-based MS/MS glycopeptide identification using Byonic resulted in the confident assignment of ten IgG/IgA N-glycopeptide clusters of interest (Table 1 and Figures S1–S10, Supporting Information File 2). Assigned glycopeptides from copurified human plasma proteins
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Published 11 Dec 2020

Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities

  • Heiko T. Kiesewalter,
  • Carlos N. Lozano-Andrade,
  • Mikael L. Strube and
  • Ákos T. Kovács

Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248

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  • (“control”). The error bars represent the standard error. N ≥ 5 (control and surfactin-treated assays), N = 2 (MeOH-treated assays). Overview on the biosynthetic pathways of surfactin (A), plipastatin (B), and bacillaene (C) produced by B. subtilis. The lightning bolt indicates the proteins for which the
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Published 04 Dec 2020

Selected peptide-based fluorescent probes for biological applications

  • Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

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  • ). Fluorescence resonance energy transfer (FRET) relies on the distance-dependent transfer of energy from a donor fluorophore to an acceptor fluorophore. Genetically encoded fluorophores, such as green fluorescent protein (GFP) and related blue, cyan, yellow and red fluorescent proteins have provided the ability
  • important biomolecules including nucleotides, DNA, proteins, lipids etc. in aqueous media. Fluorescent peptides have also been used for specific organelles such as lysosomes tracking. In this review, it is summarized Schmuck group’s tremendous effort in developing fluorescent peptide-based probes for
  • insulin Schmuck and co-workers reported a supramolecular ensemble in combination of a pyrene-tagged amphiphilic peptide beacon (6) and a macrocyclic host (cucurbit[8]uril, CB[8]) for ratiometric fluorescent detection of amino acid derivatives, specific peptides, and proteins in aqueous media (Figure 6
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Published 03 Dec 2020

UV resonance Raman spectroscopy of the supramolecular ligand guanidiniocarbonyl indole (GCI) with 244 nm laser excitation

  • Tim Holtum,
  • Vikas Kumar,
  • Daniel Sebena,
  • Jens Voskuhl and
  • Sebastian Schlücker

Beilstein J. Org. Chem. 2020, 16, 2911–2919, doi:10.3762/bjoc.16.240

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  • , Universitätsstrasse 7, 45141 Essen, Germany 10.3762/bjoc.16.240 Abstract Ultraviolet resonance Raman (UVRR) spectroscopy is a powerful vibrational spectroscopic technique for the label-free monitoring of molecular recognition of peptides or proteins with supramolecular ligands such as guanidiniocarbonyl pyrroles
  • UVRR approach from peptides to proteins as binding partners for GCPs is the UV-excited autofluorescence from aromatic amino acids observed for laser excitation wavelengths >260 nm. These excitation wavelengths are in the electronic resonance with the GCP for achieving both a signal enhancement and the
  • the results from density functional theory (DFT) calculations. Keywords: GCI; GCP; guanidiniocarbonyl indole; guanidiniocarbonyl pyrrole; UVRR; Raman spectroscopy; resonance Raman; Introduction Supramolecular ligands are capable to selectively bind to peptides and proteins via reversible non
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Published 27 Nov 2020

Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

  • Marius H. Heddinga and
  • Jens Müller

Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236

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  • function opens new possibilities for applications of oligonucleotides. Keywords: aptamer; ATP; bioinorganic chemistry; DNA; imidazole; metal-mediated base pairs; Introduction Aptamers are oligonucleotides capable of recognizing and binding to specific molecules up to the size of proteins [1]. While
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Published 25 Nov 2020

Using multiple self-sorting for switching functions in discrete multicomponent systems

  • Amit Ghosh and
  • Michael Schmittel

Beilstein J. Org. Chem. 2020, 16, 2831–2853, doi:10.3762/bjoc.16.233

Graphical Abstract
  • cytosine (C) [2]. Similarly, proteins, like microtubules and actin filaments, are self-sorted on the molecular level in living cells [3]. Furthermore, the smaller molecules of life such as sugars [4], peptides, and fatty acids [5] undergo self-sorting in the construction of a cell [6][7]. The above
  • activity in a Knoevenagel addition reaction. At the same time, the click reaction remained shut down (ON-1, OFF-2). In sum, the three interdependent states SelfSORT-I to III regulated two different reaction outcomes and an OFF state. In biology, motor proteins carry out essential tasks by walking along
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Published 20 Nov 2020

3-Acetoxy-fatty acid isoprenyl esters from androconia of the ithomiine butterfly Ithomia salapia

  • Florian Mann,
  • Daiane Szczerbowski,
  • Lisa de Silva,
  • Melanie McClure,
  • Marianne Elias and
  • Stefan Schulz

Beilstein J. Org. Chem. 2020, 16, 2776–2787, doi:10.3762/bjoc.16.228

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  • -hydroxyoctadecanoic and stearic acids as well as (E)-2-octadecenoic acids are obtained similarly directly from palmitic acid. The proposed biosynthesis likely takes place in form of the conjugated acids, e.g., coenzyme A esters or acyl carrier proteins. Finally, the acids are converted into the isoprenyl esters and
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Published 16 Nov 2020

Encrypting messages with artificial bacterial receptors

  • Pragati Kishore Prasad,
  • Naama Lahav-Mankovski,
  • Leila Motiei and
  • David Margulies

Beilstein J. Org. Chem. 2020, 16, 2749–2756, doi:10.3762/bjoc.16.225

Graphical Abstract
  • of cell-surface receptors to extracellular signals, such as small molecules or proteins. In recent years, there has been considerable interest in modifying cells with artificial receptors, as a means to provide them with new properties [1]. We have recently reported a method for decorating His-tagged
  • cell surface proteins with self-assembled synthetic receptors based on modified DNA duplexes [2] (Figure 1A). One of the oligodeoxynucleotides (ODNs) constituting the artificial receptors (ODN-1) is appended with a trinitrilotriacetic acid group (tri-NTA) that was developed by our group [3] and can
  • approach can be used to fluorescently label the His-tagged proteins with different colors, simply by changing the dye (Y) on Y-ODN-2. An interesting difference between the synthetic and the natural cell surface receptors, which is in the focus of this study, is that the number of artificial receptors per
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Published 12 Nov 2020

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

  • Rakesh Biswas,
  • Surya Ghosh,
  • Shubhra Kanti Bhaumik and
  • Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

Graphical Abstract
  • [20][21]. A number of elegant examples of self-assembled multivalent systems targeting biological analytes such as DNA, heparin, proteins, carbohydrates, etc. have been reported in the literature [22][23][24][25][26][27]. ATP is an important bio-anion that is the energy currency in cells and is
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Published 10 Nov 2020

Enzyme-instructed morphological transition of the supramolecular assemblies of branched peptides

  • Dongsik Yang,
  • Hongjian He and
  • Bing Xu

Beilstein J. Org. Chem. 2020, 16, 2709–2718, doi:10.3762/bjoc.16.221

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  • of the N-terminal of the branch increased the stability of the branched peptides. Moreover, these branched peptides facilitate the delivery of the proteins into cells. This work contributes insights for the development of peptide supramolecular assemblies via enzymatic noncovalent synthesis in
  • serendipitously found that an enzyme-responsive branched peptide was able to deliver small molecules or proteins to mitochondria efficiently in a cell-specific manner [33]. The branched peptide, which bears FLAG-tag as the branch [32], forms micelles. Certain proteases on the mitochondria of certain cells cleave
  • . Both 1 and 2, being synthesized for the first time, are able to facilitate the delivery of the proteins into cells. This work, illustrating enzymatic debranching to control the morphology of peptide assemblies, contributes to the development of peptide supramolecular assemblies via enzymatic
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Published 04 Nov 2020

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

  • Lena Reinke,
  • Julia Bartl,
  • Marcus Koch and
  • Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

Graphical Abstract
  • described for analytes ranging from inorganic ions over low-molecular-weight neutral and charged organic compounds, such as carboxylic acids, amino acids, and nucleotides, to larger biomolecules such as peptides and proteins [1][2][3][4][5][6][13]. All of these systems have specific areas of application
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Published 02 Nov 2020

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

  • Haroldas Bagdonas,
  • Daniel Ungar and
  • Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

Graphical Abstract
  • convey significantly more information than what is available through protein synthesis and the expression of the genetic code alone. For example, glycosylation is used as a switch to modulate protein activity [1]; glycosylation plays a crucial part in folding/unfolding pathways of some proteins in cells
  • high concentrations are required to produce well-diffracting crystals [26]. Samples containing glycoprotein molecules do not usually fulfill this criterion. More often than not, MX falls short at elucidating carbohydrate features in glycoproteins due to glycosylated proteins being inherently mobile and
  • atomic model will be expected as the final result of the study. Modelling of carbohydrates into 3D maps can be more complex than modelling proteins [33], although recent advances in software are closing the gap [34][35][36]. However, to date it remains true that most model building software is protein
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Published 09 Oct 2020

NMR Spectroscopy of supramolecular chemistry on protein surfaces

  • Peter Bayer,
  • Anja Matena and
  • Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

Graphical Abstract
  • interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to
  • shapes and chemical properties. In contrast, the interaction between two proteins often involves docking of larger patches on the protein surface, which are complementary in shape and charge. The specific recognition of these patches by synthetic molecules poses challenges because these areas on the
  • protein surface are shallow and a similar composition of hydrophilic and charged residues is often found on multiple proteins. To specifically address such an area on a protein without risking non-specific binding to many others, the topology of the surface - including shape, surface accessibility as well
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Published 09 Oct 2020

Computational tools for drawing, building and displaying carbohydrates: a visual guide

  • Kanhaya Lal,
  • Rafael Bermeo and
  • Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

Graphical Abstract
  • together either linearly or branched); (ii) polysaccharides (for glycan chains composed of more than ten monosaccharides); (iii) glycoconjugates (where the glycan chains are covalently linked to proteins (glycoproteins), lipids (glycolipids). The complexity of glycans is a consequence of their branched
  • various force fields dedicated for carbohydrates. The accurately predicted oligosaccharide conformations are good starting points for further investigations. Of particular interest are the evaluations of the dynamics of glycans and their interactions with proteins which is a most significant concern in
  • assembles data resources ranging from glycoscience standard ontologies to pathologies associated with glycans. GlyCosmos is recognized as the official portal of the Japanese Society for Carbohydrate Research and provides information about genes, proteins, lipids, pathways and diseases. GlyTouCan (Figure 5
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Published 02 Oct 2020

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

  • Patrizia Andreozzi,
  • Lorenza Tamberi,
  • Elisamaria Tasca,
  • Gina Elena Giacomazzo,
  • Marta Martinez,
  • Mirko Severi,
  • Marco Marradi,
  • Stefano Cicchi,
  • Sergio Moya,
  • Giacomo Biagiotti and
  • Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

Graphical Abstract
  • range of biomolecules: amino acids [8], peptides [9], glycosides [10], nucleosides/nucleotides [11], and lipids [12]. Also, protein-based nano-bio-conjugates [13] have been prepared by ball milling, retaining the native properties of the proteins after mechanochemical synthesis. Boronic acids and their
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Published 11 Sep 2020

Tools for generating and analyzing glycan microarray data

  • Akul Y. Mehta,
  • Jamie Heimburg-Molinaro and
  • Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

Graphical Abstract
  • structural informatics tools. Keywords: data analysis; glycan binding; glycan microarray; glycomics; informatics; Introduction Glycans represent a major type of biomolecule in all living things, along with DNA, RNA, lipids and proteins [1]. In mammals, glycans commonly occur as post-translational
  • modifications of proteins (glycoproteins), but they are also linked to lipids (glycolipids) and occur as free molecules. Such glycomolecules have vital roles in a wide range of physiological functions and also participate in many pathologic conditions [2]. Some classic examples of important glycans include the
  • , and could possibly promote cancer [4], and the O-glycan of PSGL-1 which is recognized by P- and L-selectin, which is critical for leukocyte recruitment [5][6]. Other roles of glycans (including glycosaminoglycans/proteoglycans) and glycan binding proteins (GBPs) (including lectins and antibodies) in
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Published 10 Sep 2020

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

  • Toan K. Phung,
  • Cassandra L. Pegg and
  • Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

Graphical Abstract
  • proteomic sample preparation and protease digestion, coupled with depletion of abundant proteins or enrichment of glycopeptides to enable their measurement. There have also been several advances in glycopeptide quantification strategies including chemical labelling, label-free and data-independent
  • ]. Our analysis revealed differences in occupancy and glycan compositions of several proteins as potential HCC tumor biomarkers. Results and Discussion GlypNirO Byonic is powerful software that allows identification of glycopeptides and peptides from complex glyco/proteomic LC–MS/MS datasets but does not
  • depleted of six abundant proteins from liver cancer (hepatocellular carcinoma (HCC)) patients and healthy controls. We identified glycopeptides and peptides in the datafiles from these samples using Byonic, searching separately for O- and N-glycopeptides (Supporting Information File 1, Tables S1–S24), and
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Published 01 Sep 2020

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

  • Carl A. Fogarty,
  • Aoife M. Harbison,
  • Amy R. Dugdale and
  • Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

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  • Carl A. Fogarty Aoife M. Harbison Amy R. Dugdale Elisa Fadda Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland 10.3762/bjoc.16.171 Abstract The N-glycosylation is one of the most abundant and diverse post-translational modifications of proteins
  • implicated in the cell’s interactions with its environment, facilitating communication and infection [1][2]. These processes are often initiated by molecular recognition involving carbohydrate-binding proteins (lectins) or by glycan–glycan interactions [1][3][4][5], all events that hinge on specific
  • the links between glycans’ sequence and the 3D structure. This direct relationship is a well-recognized and broadly accepted concept in proteins’ structural biology, according to which the amino acid sequence dictates the functional 3D fold and its stability. However, the same notion is not generally
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Published 21 Aug 2020

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

  • Annike Weißenstein,
  • Myroslav O. Vysotsky,
  • Ivo Piantanida and
  • Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

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  • ; Introduction The interplay of non-covalent interactions between nucleic acids and proteins or peptides is the basis of life and is also often used for the design of artificial small molecules, aiming for sensing or control of biorelevant processes. Many naturally occurring bioactive molecules contain a short
  • several decades, consequently becoming increasingly complex [5][6][7]. This includes examples incorporating several types of non-covalent interaction with DNA/RNA (intercalation, groove binding, positive–negative charge interaction [5][8]) in one molecule or even modified biomacromolecules (e.g., proteins
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Published 19 Aug 2020

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

  • Rémi Martinent,
  • Javier López-Andarias,
  • Dimitri Moreau,
  • Yangyang Cheng,
  • Naomi Sakai and
  • Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

Graphical Abstract
  • challenge is most pronounced with large substrates, such as proteins, oligonucleotides, or nanoparticles, due to the permeability barriers formed by the lipophilic core of the cell membrane [18][19]. In recent decades, the use of arginine-rich cell-penetrating peptides (CPPs) as carriers has emerged as an
  • generally decreases with the size [18], this similarity is particularly impressive, considering that the COC carrying a 52 kDa protein is compared to a small undecapeptide. The compatibility of the assay with other fusion proteins and more adverse conditions, such as transient transfection, has never been
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Published 14 Aug 2020

Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions

  • Clément Q. Fontenelle,
  • Thibault Thierry,
  • Romain Laporte,
  • Emmanuel Pfund and
  • Thierry Lequeux

Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160

Graphical Abstract
  • hydrogen-bond accepting capacity with proteins or enzymes would be restored [14]. The synthesis of fluoroalkene precursors of modified acyclonucleosides (VIII) has been explored by Choi, and more recently by us [15][16][17]. Nevertheless, it was reported that no antiviral activity for compounds of series
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Published 07 Aug 2020

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

  • Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

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  • Vladimir Kubyshkin University of Manitoba, Dysart Rd. 144, Winnipeg, R3T 2N2, Canada 10.3762/bjoc.16.151 Abstract Fluorine-containing analogues of proline are valuable tools in engineering and NMR spectroscopic studies of peptides and proteins. Their use relies on the fundamental understanding of
  • complex structures: peptides and proteins. Results and Discussion Model compounds The study was originally set up following an assumption that a peptide containing a proline analogue would form a system of three dipoles. The peptide bond itself creates a strong dipole, with a direction that roughly aligns
  • protein chemistry. The peptide bond can exist in two discrete states, commonly designated as trans- and cis-rotamers (ω = 180 and 0°, respectively). The cis-peptide bond is very rare in natural proteins [79], except for the cases when it precedes a proline residue. The secondary amino group of proline
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Published 23 Jul 2020

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

  • Giovanni Picca,
  • Markus Probst,
  • Simon M. Langenegger,
  • Oleg Khorev,
  • Peter Bütikofer,
  • Anant K. Menon and
  • Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

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  • Bern, Switzerland Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, 10065 New York, United States of America 10.3762/bjoc.16.145 Abstract The chemical synthesis of molecular probes to identify and study membrane proteins involved in the biological pathway of protein
  • the use of photoreactive, clickable MPD mimics. As such, an attempt already showed great promise in a previous report by Rush et al. from 2015 [10]. Similarly, we envisioned that these analogs could be used to capture MPD-recognizing proteins, including the scramblase, from a crude mixture of ER
  • membrane proteins [11][12]. The captured proteins would be subsequently identified by mass spectrometry, and their function in MPD scrambling validated by biochemical and genetic approaches. A suitable molecular probe and mimic of MPD (Figure 1) can be subdivided into three essential components: a β-ᴅ
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Published 20 Jul 2020

Models of necessity

  • Timothy Clark and
  • Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

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  • -atomic representation [73]. These force fields have attained a remarkable level of accuracy for proteins, so that force-field based simulations have become predictive in many fields of biology, medicinal chemistry and biophysics [74]. Models, approximations and paradigms Despite the many advances made
  • molecular aggregation via weak interactions. Paradoxically, exactly such interactions between drug molecules and proteins form much of the basis of classical cheminformatics. These are, however, very specific in nature and have generally been defined in detail for, for instance, scoring functions. Current
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Published 13 Jul 2020

A dynamic combinatorial library for biomimetic recognition of dipeptides in water

  • Florian Klepel and
  • Bart Jan Ravoo

Beilstein J. Org. Chem. 2020, 16, 1588–1595, doi:10.3762/bjoc.16.131

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  • the parallel dimer of CHC (p(CHC)2), which binds two molecules of the neurotransmitter N-acetylneuraminic acid (NANA) in a cooperative fashion (K1 = 143, K2 = 5.1 × 103 M−1). Recently we rationalized that since our peptide building blocks consist of the same binding motifs as binding proteins (amines
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Published 02 Jul 2020
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