Binding residues
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Ebook "Heterologous gene expression in E. coli: Methods and protocols" herein describe methods, for example, to successfully express proteins in E. coli that would otherwise form aggregates in this host, to add post-translational modifications, to incorporate non-standard amino acid residues or moieties into E. coli expressed proteins, to identify binding partners, and to express membrane proteins.
312p dongmelo 27-05-2024 6 2 Download
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ERAP1 is a major aminopeptidase that serves as an editor of the peptide repertoire by trimming N-terminal residues of antigenic peptides, creating a pool of peptides with the optimal length for MHC-I binding.
11p vischultz 20-10-2023 4 1 Download
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The thesis is structured as follows: In Chapter 1, the scientific literature is summarized within the scope of this study. Chapter 2 provides a comprehensive overview of the principles of the applied computational approaches in this study. Chapter 3 identifies the important residues of the LsIA/α7 nAChR complex that affect the interactions between the toxin and the membrane protein due to C-terminal carboxylation of LsIA. The effects of C-terminal modification of LsIA on interactions with α3β2 nAChR, involved in cardiovascular diseases, were also investigated in Chapter 4.
234p runthenight04 02-02-2023 6 2 Download
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Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding
The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown.
15p vialfrednobel 29-01-2022 7 0 Download
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Sugammadex, a γ-cyclodextrin derivative, belongs to a new class of selective relaxant binding agents. Sugammadex was approved 10-years ago by the European medicines agency and today is used in clinical anesthesia and emergency medicine globally. In this review, indications for neuromuscular block, the challenge of neuromuscular monitoring and the practice of under-dosing of sugammadex as a potential cost-saving strategy are discussed.
5p vampires36 30-12-2021 13 2 Download
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The system reached equilibrium at around 0.1 µs. The overall 3-dimensional structure was well preserved throughout the simulation. Local residue-based fluctuations were in good agreement with fully atomistic MD simulations. Four distinct snapshots were selected and reverse-mapped to all-atom representations with around 65,000 atoms. Each reverse-mapped system was later subjected to 100 ns of MD simulation for equilibration.
15p langthannam 29-12-2021 16 0 Download
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Residual neuromuscular block at the end of surgery may compromise the patient’s safety. The risk of airway complications can be minimized through monitoring of neuromuscular function and reversal of neuromuscular block if needed. Effective reversal can be achieved with selective relaxant binding agents, however, sugammadex is the only clinically approved drug in this group.
9p vidietmarhopp 28-12-2021 7 0 Download
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Mutations in the transcription factor, KLF1, are common within certain populations of the world. Heterozygous missense mutations in KLF1 mostly lead to benign phenotypes, but a heterozygous mutation in a DNA-binding residue (E325K in human) results in severe Congenital Dyserythropoietic Anemia type IV (CDA IV); i.e. an autosomal-dominant disorder characterized by neonatal hemolysis.
12p visilicon2711 20-08-2021 7 1 Download
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CD4+ T-cell epitopes play a crucial role in eliciting vigorous protective immune responses during peptide (epitope)-based vaccination. The prediction of these epitopes focuses on the peptide binding process by MHC class II proteins. The ability to account for MHC class II polymorphism is critical for epitope-based vaccine design tools, as different allelic variants can have different peptide repertoires.
11p viwyoming2711 16-12-2020 20 1 Download
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The vitamins are important cofactors in various enzymatic-reactions. In past, many inhibitors have been designed against vitamin binding pockets in order to inhibit vitamin-protein interactions. Thus, it is important to identify vitamin interacting residues in a protein.
14p viwyoming2711 16-12-2020 8 0 Download
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Binding free energy and binding hot spots at protein-protein interfaces are two important research areas for understanding protein interactions. Computational methods have been developed previously for accurate prediction of binding free energy change upon mutation for interfacial residues.
10p vikentucky2711 26-11-2020 8 1 Download
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Protein–protein interactions can be seen as a hierarchical process occurring at three related levels: Proteins bind by means of specific domains, which in turn form interfaces through patches of residues.
18p vikentucky2711 26-11-2020 6 0 Download
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Vitamins are typical ligands that play critical roles in various metabolic processes. The accurate identification of the vitamin-binding residues solely based on a protein sequence is of significant importance for the functional annotation of proteins, especially in the post-genomic era, when large volumes of protein sequences are accumulating quickly without being functionally annotated.
14p vikentucky2711 26-11-2020 7 1 Download
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RNA-protein complexes play an essential role in many biological processes. To explore potential functions of RNA-protein complexes, it’s important to identify RNA-binding residues in proteins.
10p vikentucky2711 26-11-2020 10 1 Download
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Protein families participating in protein-protein interactions may contain sub-families that have different binding characteristics, ranging from right binding to showing no interaction at all. Composition differences at the sequence level in these sub-families are often decisive to their differential functional interaction.
12p vikentucky2711 24-11-2020 7 1 Download
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RNA-binding proteins participate in many important biological processes concerning RNA-mediated gene regulation, and several computational methods have been recently developed to predict the protein-RNA interactions of RNA-binding proteins.
14p vioklahoma2711 19-11-2020 11 1 Download
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Prediction of ligand binding sites is important to elucidate protein functions and is helpful for drug design. Although much progress has been made, many challenges still need to be addressed. Prediction methods need to be carefully developed to account for chemical and structural differences between ligands
12p vioklahoma2711 19-11-2020 11 0 Download
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Prediction of DNA-binding residue is important for understanding the protein-DNA recognition mechanism. Many computational methods have been proposed for the prediction, but most of them do not consider the relationships of evolutionary information between residues.
16p viflorida2711 30-10-2020 11 2 Download
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RNA binding proteins play important roles in post-transcriptional RNA processing and transcriptional regulation. Distinguishing the RNA-binding residues in proteins is crucial for understanding how protein and RNA recognize each other and function together as a complex.
12p viconnecticut2711 29-10-2020 7 2 Download
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Hot spots are interface residues that contribute most binding affinity to protein-protein interaction. A compact and relevant feature subset is important for building machine learning methods to predict hot spots on protein-protein interfaces.
16p viconnecticut2711 29-10-2020 12 4 Download