Search results
Search for "proteins" in Full Text gives 525 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response
Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223
- [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
Enzyme-instructed morphological transition of the supramolecular assemblies of branched peptides
Beilstein J. Org. Chem. 2020, 16, 2709–2718, doi:10.3762/bjoc.16.221
- 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
Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes
Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219
- 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
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer
Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204
- 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
NMR Spectroscopy of supramolecular chemistry on protein surfaces
Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203
- 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
Computational tools for drawing, building and displaying carbohydrates: a visual guide
Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199
- 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
The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY
Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188
- 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
Tools for generating and analyzing glycan microarray data
Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187
- 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
GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis
Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180
- 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
How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates
Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171
- 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
Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA
Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170
- ; 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
Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides
Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167
- 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
Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions
Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160
- 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
Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines
Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151
- 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
Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies
Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145
- 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
Models of necessity
Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137
- -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
A dynamic combinatorial library for biomimetic recognition of dipeptides in water
Beilstein J. Org. Chem. 2020, 16, 1588–1595, doi:10.3762/bjoc.16.131
- 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
Heterogeneous photocatalysis in flow chemical reactors
Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125
Synthesis of new fluorescent molecules having an aggregation-induced emission property derived from 4-fluoroisoxazoles
Beilstein J. Org. Chem. 2020, 16, 1411–1417, doi:10.3762/bjoc.16.117
- be visualized using fluorescent probes, the use of AIE fluorescent probes is being investigated as a tool for analyzing the causal relationship between prion diseases and prion proteins. The importance of fluorinated heterocyclic derivatives in the pharmaceutical and agrochemical industries continues
Photocatalytic trifluoromethoxylation of arenes and heteroarenes in continuous-flow
Beilstein J. Org. Chem. 2020, 16, 1305–1312, doi:10.3762/bjoc.16.111
- (Scheme 1A). This property might be responsible for stronger binding affinities of trifluoromethoxylated compounds with the active sites in enzymes, proteins, or other biomolecules [8][9]. Several procedures for the synthesis of trifluoromethyl aryl ethers were reported from the mid-1900s, mostly based on
Anthelmintic drug discovery: target identification, screening methods and the role of open science
Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105
- basis for finding compounds that are anthelmintic in vivo but do not cause paralysis, perhaps involving aspects of the interaction with the host, interfering with the secretion of proteins, or other ways of damaging the worm [146]. They are also useful for understanding in more detail the mechanism of
A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA
Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100
- . Petersburg, 197101, Russian Federation 10.3762/bjoc.16.100 Abstract Nowadays a variety of biosensors are widely used in different fields, including biomedical diagnostics and self-testing. Nucleic acid-based biosensors are typically applied to detect another nucleic acid, proteins, ions, and several other
- different levels, including DNA, RNA, proteins, and small molecule metabolites. Today, along with other methods in clinical diagnosis biosensors are ubiquitously used in the biomedical field. The first prototype of a biosensor was invented by Leland Clark and Champ Lyons in 1962 as an amperometric Clark
- . Reproducibility and linearity are also very important as well as costs and ease of manufacturing each component of the biosensor. Unlike proteins or antibodies the nucleic acid-based biosensors (NAs) can be easily commercially synthesized, they are smaller, more stable, and can be repeatedly used without losing
Synthesis of esters of diaminotruxillic bis-amino acids by Pd-mediated photocycloaddition of analogs of the Kaede protein chromophore
Beilstein J. Org. Chem. 2020, 16, 1111–1123, doi:10.3762/bjoc.16.98
- in the last few years due to the discovery that truxillic acid derivatives are inhibitors of FABP (fatty acid binding proteins), which are responsible for the cellular reuptake of anandamide, an endocannabinoid neurotransmitter, and that they can be involved in a very efficient treatment for chronic
Fluorinated phenylalanines: synthesis and pharmaceutical applications
Beilstein J. Org. Chem. 2020, 16, 1022–1050, doi:10.3762/bjoc.16.91
- . Incorporation of fluorinated aromatic amino acids into proteins increases their catabolic stability especially in therapeutic proteins and peptide-based vaccines. This review seeks to summarize the different synthetic approaches in the literature to prepare ᴅ- or ʟ-fluorinated phenylalanines and their
- the properties of peptides and proteins [5][6][7], influencing aspects such as protein folding, protein–protein interactions, ribosomal translation, lipophilicity, acidity/basicity, optimal pH, stability, thermal stability, and therapeutic properties [8][9][10]. This extends to metabolic properties of
- membrane permeability and reactivity [11][12][13][14]. The effect of peptide structure and stability has been found to depend on the position and number of fluorine atoms within the amino acid chains [15][16][17]. Incorporation of fluorinated aromatic amino acids into proteins can increase their shelf life
Synthesis of new asparagine-based glycopeptides for future scanning tunneling microscopy investigations
Beilstein J. Org. Chem. 2020, 16, 888–894, doi:10.3762/bjoc.16.80
- Glycopeptides are generally found on virtually every eukaryotic and prokaryotic cell surface. So far, the study of glycopeptide interactions with other proteins gave some insight into important biological functions, for instance, intracellular communication, cell–cell recognition, immune response, and
- pathogenesis [1][2][3][4]. Glycosylation is also considered to be one of the most important post-translational modification (PTM) since more than half of all human proteins are glycopeptides or glycoproteins [5]. Therefore, understanding how glycopeptides interact on an intra- and intermolecular level is
Other Beilstein-Institut Open Science Activities
