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Search for "protein recognition" in Full Text gives 9 result(s) in Beilstein Journal of Organic Chemistry.
Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling
Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144
- GAG properties, especially protein recognition specificity and multipose binding. We found that the binding free energy landscape in the proximity of the GAG native binding pose is complex and implies the co-existence of several binding poses. The sliding of a GAG chain along a protein surface could
- whether the application of the US approach is able to reproduce experimentally obtained structures, and how useful it is for understanding GAG properties as protein recognition specificity and multipose binding. We also check for any trace of transition from the 3C9E to the 4N8W structure by pulling the
- study, the US approach was used to pull away a GAG ligand from the binding site and then to pull it back in to the binding site. The goal was to analyze if US is able to reproduce experimentally obtained structures, and if it can contribute to a deeper understanding of GAG properties as protein
Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups
Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137
- an ideal candidate to be used for protein recognition. In a previous study, GCP containing polycationic ligands for 14-3-3 proteins had a significant effect on PPIs [12][13]. Furthermore, a simple GCP derivative, GCP-Lys-OMe, was identified as the first binder for the specific binding area of the 14
GlycoBioinformatics
Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184
- one of the authors of this article, Fadda, used glyco-adapted molecular dynamics to explain in a separate publication [4] how the COVID-19 spike protein recognition element requires N-linked glycosylation to be exposed. Another approach to understanding glyco-interactions is described in a review
Lectins of Mycobacterium tuberculosis – rarely studied proteins
Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1
- '-dimycolate (TDM) and its precursor trehalose 6-monomycolate (TMM) [55]. Mycobacteria therefore possess α-D-mannopyranosides, α-D-arabinofuranosides, α-D-glucopyranosides, α-D-galactofuranosides, and their associated oligomeric forms as surface-exposed carbohydrates accessible to extracellular protein
- recognition. While manno- and glucopyranosides are also present in the eukaryotic glycocalyx, galactofuranosides, arabinofuranosides, and the (1→1)-linked glucose disaccharide trehalose are unique to the mycobacterial cell wall. The occurrence of galactose in the furanose form is restricted to bacteria [56
Novel solid-phase strategy for the synthesis of ligand-targeted fluorescent-labelled chelating peptide conjugates as a theranostic tool for cancer
Beilstein J. Org. Chem. 2018, 14, 2665–2679, doi:10.3762/bjoc.14.244
- of the intermediates. The various components that are assembled include the cell surface protein recognition ligand, a peptide spacer for enhanced solubility and binding affinity, a fluorescent tag for tissue staining and a chelating core to tether therapeutic cargos. This goal is smoothly achieved
- folate protein from the interference of fluorescent cargo attached to lysine and the chelating core as described for 13. Thus our newly designed bioconstructs 13 and 17 have the following four components, (i) a cell surface protein recognition ligand, (ii) a peptidic spacer which enhances the binding
Smart molecules for imaging, sensing and health (SMITH)
Beilstein J. Org. Chem. 2015, 11, 2540–2548, doi:10.3762/bjoc.11.274
- , it contains a mixture of polar and non-polar functional groups. In water, the non-polar groups drive affinity due to hydrophobic effects, and the polar groups produce selectivity due to directional interactions, such as hydrogen bonding. It is insightful to consider the protein–protein recognition
Similarity analysis, synthesis, and bioassay of antibacterial cyclic peptidomimetics
Beilstein J. Org. Chem. 2012, 8, 1146–1160, doi:10.3762/bjoc.8.128
- ]. Many reports describe the successful use of heterocycles as peptide-bond surrogates or as potential protein-recognition motifs to achieve superior potency in biological assays [10][11][12][13][14]. Pyridines are well-established as important heterocycles in medicinally and biologically active compounds
RAFT polymers for protein recognition
Beilstein J. Org. Chem. 2010, 6, No. 66, doi:10.3762/bjoc.6.66
- : electrostatic interactions; hydrophobic effect; isothermal calorimetry; protein recognition; RAFT polymers; Introduction The ability of biological receptors to bind strongly and specifically to a particular molecular target is an essential part of biological machinery. The best example is the immune system
- ]. Rotello and Thayumanavan have described amphiphilic polymer scaffolds, which nonspecifically bound to chymotrypsin, inhibited its peptidase activity and modulated substrate specificity; very high ionic strengths again released the protein from the polymer [6][7]. Protein recognition by multifunctional
- substantially by 1–2 orders of magnitude (see Table 1: T20 vs T20CH15). In other words, the random incorporation of cyclohexyl comonomers into the polymer was beneficial for the protein recognition event. Close inspection of thermodynamic data revealed that the entropy term was responsible for this increased
Synthesis and binding studies of two new macrocyclic receptors for the stereoselective recognition of dipeptides
Beilstein J. Org. Chem. 2010, 6, No. 5, doi:10.3762/bjoc.6.5
- enantioselectivities exhibited by the complex protein–protein recognition processes that occur in biology. Moreover, short oligopeptides are themselves worthwhile targets for recognition and their conformational flexibility represents an added challenge to achieve selective binding. The preparation of synthetic
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