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Nature Communications May 2023Association of single nucleotide polymorphisms in the IL-23 receptor with several auto-inflammatory diseases, led to the heterodimeric receptor and its cytokine-ligand...
Association of single nucleotide polymorphisms in the IL-23 receptor with several auto-inflammatory diseases, led to the heterodimeric receptor and its cytokine-ligand IL-23, becoming important drug targets. Successful antibody-based therapies directed against the cytokine have been licenced and a class of small peptide antagonists of the receptor have entered clinical trials. These peptide antagonists may offer therapeutic advantages over existing anti-IL-23 therapies, but little is known about their molecular pharmacology. In this study, we use a fluorescent version of IL-23 to characterise antagonists of the full-length receptor expressed by living cells using a NanoBRET competition assay. We then develop a cyclic peptide fluorescent probe, specific to the IL23p19:IL23R interface and use this molecule to characterise further receptor antagonists. Finally, we use the assays to study the immunocompromising C115Y IL23R mutation, demonstrating that the mechanism of action is a disruption of the binding epitope for IL23p19.
Topics: HEK293 Cells; Humans; Receptors, Interleukin; Fluorescent Dyes; Mutation; Protein Binding; Small Molecule Libraries; Polymorphism, Single Nucleotide; Peptides, Cyclic
PubMed: 37208328
DOI: 10.1038/s41467-023-38541-2 -
International Journal of Molecular... Jul 2021Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part... (Review)
Review
Membrane proteins have evolved to work optimally within the complex environment of the biological membrane. Consequently, interactions with surrounding lipids are part of their molecular mechanism. Yet, the identification of lipid-protein interactions and the assessment of their molecular role is an experimental challenge. Recently, biophysical approaches have emerged that are compatible with the study of membrane proteins in an environment closer to the biological membrane. These novel approaches revealed specific mechanisms of regulation of membrane protein function. Lipids have been shown to play a role in oligomerization, conformational transitions or allosteric coupling. In this review, we summarize the recent biophysical approaches, or combination thereof, that allow to decipher the role of lipid-protein interactions in the mechanism of membrane proteins.
Topics: Animals; Cell Membrane; Humans; Membrane Lipids; Membrane Proteins; Protein Binding
PubMed: 34298884
DOI: 10.3390/ijms22147267 -
Protein Science : a Publication of the... Dec 2014A minimal model of protein-protein binding affinity that takes into account only two structural features of the complex, the size of its interface, and the amplitude of...
A minimal model of protein-protein binding affinity that takes into account only two structural features of the complex, the size of its interface, and the amplitude of the conformation change between the free and bound subunits, is tested on the 144 complexes of a structure-affinity benchmark. It yields Kd values that are within two orders of magnitude of the experiment for 67% of the complexes, within three orders for 88%, and fails on 12%, which display either large conformation changes, or a very high or a low affinity. The minimal model lacks the specificity and accuracy needed to make useful affinity predictions, but it should help in assessing the added value of parameters used by more elaborate models, and set a baseline for evaluating their performances.
Topics: Models, Molecular; Protein Binding; Protein Conformation; Proteins; Thermodynamics
PubMed: 25270898
DOI: 10.1002/pro.2560 -
Protein Science : a Publication of the... Jan 2006Engineered antibodies and their fragments are invaluable tools for a vast range of biotechnological and pharmaceutical applications. However, they are facing increasing... (Review)
Review
Engineered antibodies and their fragments are invaluable tools for a vast range of biotechnological and pharmaceutical applications. However, they are facing increasing competition from a new generation of protein display scaffolds, specifically selected for binding virtually any target. Some of them have already entered clinical trials. Most of these nonimmunoglobulin proteins are involved in natural binding events and have amazingly diverse origins, frameworks, and functions, including even intrinsic enzyme activity. In many respects, they are superior over antibody-derived affinity molecules and offer an ever-extending arsenal of tools for, e.g., affinity purification, protein microarray technology, bioimaging, enzyme inhibition, and potential drug delivery. As excellent supporting frameworks for the presentation of polypeptide libraries, they can be subjected to powerful in vitro or in vivo selection and evolution strategies, enabling the isolation of high-affinity binding reagents. This article reviews the generation of these novel binding reagents, describing validated and advanced alternative scaffolds as well as the most recent nonimmunoglobulin libraries. Characteristics of these protein scaffolds in terms of structural stability, tolerance to multiple substitutions, ease of expression, and subsequent applications as specific targeting molecules are discussed. Furthermore, this review shows the close linkage between these novel protein tools and the constantly developing display, selection, and evolution strategies using phage display, ribosome display, mRNA display, cell surface display, or IVC (in vitro compartmentalization). Here, we predict the important role of these novel binding reagents as a toolkit for biotechnological and biomedical applications.
Topics: Animals; Combinatorial Chemistry Techniques; Humans; Peptide Library; Protein Binding; Protein Interaction Mapping; Proteins
PubMed: 16373474
DOI: 10.1110/ps.051817606 -
The Journal of General Physiology Apr 2014ATP-binding cassette (ABC) transporters form a large superfamily of ATP-dependent protein complexes that mediate transport of a vast array of substrates across... (Review)
Review
ATP-binding cassette (ABC) transporters form a large superfamily of ATP-dependent protein complexes that mediate transport of a vast array of substrates across membranes. The 14 currently available structures of ABC transporters have greatly advanced insight into the transport mechanism and revealed a tremendous structural diversity. Whereas the domains that hydrolyze ATP are structurally related in all ABC transporters, the membrane-embedded domains, where the substrates are translocated, adopt four different unrelated folds. Here, we review the structural characteristics of ABC transporters and discuss the implications of this structural diversity for mechanistic diversity.
Topics: ATP-Binding Cassette Transporters; Animals; Crystallization; Humans; Protein Binding; Protein Structure, Secondary; Protein Structure, Tertiary
PubMed: 24638992
DOI: 10.1085/jgp.201411164 -
ACS Chemical Biology Jan 2011Small-molecule target identification is a vital and daunting task for the chemical biology community as well as for researchers interested in applying the power of... (Review)
Review
Small-molecule target identification is a vital and daunting task for the chemical biology community as well as for researchers interested in applying the power of chemical genetics to impact biology and medicine. To overcome this "target ID" bottleneck, new technologies are being developed that analyze protein-drug interactions, such as drug affinity responsive target stability (DARTS), which aims to discover the direct binding targets (and off targets) of small molecules on a proteome scale without requiring chemical modification of the compound. Here, we review the DARTS method, discuss why it works, and provide new perspectives for future development in this area.
Topics: Chromatography, Affinity; Drug Delivery Systems; Drug Design; Molecular Targeted Therapy; Pharmaceutical Preparations; Protein Binding; Proteome; Proteomics; Small Molecule Libraries
PubMed: 21077692
DOI: 10.1021/cb100294v -
Journal of Medicinal Chemistry Feb 2022Development of inhibitors for histone methyllysine reader proteins is an active area of research due to the importance of reader protein-methyllysine interactions in...
Development of inhibitors for histone methyllysine reader proteins is an active area of research due to the importance of reader protein-methyllysine interactions in transcriptional regulation and disease. Optimized peptide-based chemical probes targeting methyllysine readers favor larger alkyllysine residues in place of methyllysine. However, the mechanism by which these larger substituents drive tighter binding is not well understood. This study describes the development of a two-pronged approach combining genetic code expansion (GCE) and structure-activity relationships (SAR) through systematic variation of both the aromatic binding pocket in the protein and the alkyllysine residues in the peptide to probe inhibitor recognition in the CBX5 chromodomain. We demonstrate a novel change in driving force for larger alkyllysines, which weaken cation-π interactions but increases dispersion forces, resulting in tighter binding. This GCE-SAR approach establishes discrete energetic contributions to binding from both ligand and protein, providing a powerful tool to gain mechanistic understanding of SAR trends.
Topics: Chromobox Protein Homolog 5; Genetic Code; Humans; Ligands; Lysine; Molecular Structure; Mutagenesis, Site-Directed; Peptidomimetics; Protein Binding; Static Electricity; Structure-Activity Relationship
PubMed: 35014255
DOI: 10.1021/acs.jmedchem.1c02049 -
Trends in Biochemical Sciences Dec 2009How can a single hub protein bind so many different partners? Numerous studies have sought differences between hubs and non-hubs to explain what makes a protein a hub... (Review)
Review
How can a single hub protein bind so many different partners? Numerous studies have sought differences between hubs and non-hubs to explain what makes a protein a hub and how a shared hub-binding site can be promiscuous, yet at the same time be specific. Here, we suggest that the problem is largely non-existent and resides in the popular representation of protein interaction networks: protein products derived from a single gene, even if different, are clustered in maps into a single node. This leads to the impression that a single protein binds to a very large number of partners. In reality, it does not; rather, protein networks reflect the combination of multiple proteins, each with a distinct conformation.
Topics: Models, Biological; Protein Binding; Proteins
PubMed: 19837592
DOI: 10.1016/j.tibs.2009.07.007 -
Mathematical Biosciences and... Jan 2024DNA-protein binding is crucial for the normal development and function of organisms. The significance of accurately identifying DNA-protein binding sites lies in its...
DNA-protein binding is crucial for the normal development and function of organisms. The significance of accurately identifying DNA-protein binding sites lies in its role in disease prevention and the development of innovative approaches to disease treatment. In the present study, we introduce a precise and robust identifier for DNA-protein binding residues. In the context of protein representation, we combine the evolutionary information of the protein, represented by its position-specific scoring matrix, with the spatial information of the protein's secondary structure, enriching the overall informational content. This approach initially employs a combination of Bi-directional Long Short-Term Memory and Transformer encoder to jointly extract the interdependencies among residues within the protein sequence. Subsequently, convolutional operations are applied to the resulting feature matrix to capture local features of the residues. Experimental results on the benchmark dataset demonstrate that our method exhibits a higher level of competitiveness when compared to contemporary classifiers. Specifically, our method achieved an MCC of 0.349, SP of 96.50%, SN of 44.03% and ACC of 94.59% on the PDNA-41 dataset.
Topics: Protein Binding; Memory, Short-Term; Proteins; Binding Sites; DNA
PubMed: 38303418
DOI: 10.3934/mbe.2024008 -
Bioconjugate Chemistry Jul 2018Developing strategies to interfere with allosteric interactions in proteins not only promises to deepen our understanding of vital cellular processes but also allows...
Developing strategies to interfere with allosteric interactions in proteins not only promises to deepen our understanding of vital cellular processes but also allows their regulation using external triggers. Light is particularly attractive as a trigger being spatiotemporally selective and compatible with the physiological environment. Here, we engineered a hybrid protein in which irradiation with light opens a new allosteric communication route that is not inherent to the natural system. We select human serum albumin, a promiscuous protein responsible for transporting a variety of ligands in plasma, and show that by covalently incorporating a synthetic photoswitch to subdomain IA we achieve optical control of the ligand binding in subdomain IB. Molecular dynamics simulations confirm the allosteric nature of the interactions between IA and IB in the engineered protein. Specifically, upon illumination, photoconversion of the switch is found to correlate with a less-coordinated motion of the two subdomains and an increased flexibility of the binding pocket in subdomain IB, whose fluctuations are cooperatively enhanced by the presence of ligands, ultimately facilitating their release. Our combined experimental and computational work demonstrates how harnessing artificial molecular switches enables photoprogramming the allosteric regulation of binding activities in such a prominent protein.
Topics: Allosteric Regulation; Binding Sites; Humans; Ligands; Light; Molecular Dynamics Simulation; Protein Binding; Protein Engineering; Serum Albumin, Human
PubMed: 29975051
DOI: 10.1021/acs.bioconjchem.8b00184