GPCRs undergo large conformational changes during their activation. Starting from existing X-ray structures, we used Normal Modes Analyses to study the collective motions of the agonist-bound β2-adrenergic receptor both in its isolated "uncoupled" and G-protein "coupled" conformations. We interestingly observed that the receptor was able to adopt only one major motion in the protein:protein complex. This motion corresponded to an anti-symmetric rotation of both its extra- and intra-cellular parts, with a key role of previously identified highly conserved proline residues. Because this motion was also retrieved when performing NMA on 7 other GPCRs which structures were available, it is strongly suspected to possess a significant biological role, possibly being the "activation mode" of a GPCR when coupled to G-proteins.
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http://dx.doi.org/10.1016/j.febslet.2013.06.052 | DOI Listing |
Phys Chem Chem Phys
January 2025
Department of Applied Physics, Hebrew University, Jerusalem, Israel.
In an era of interdisciplinary scientific research, new methodologies are necessary to simultaneously advance several fields of study. One such case involves the measurement of electron spin effects on biological systems. While magnetic effects are well known in biology, recent years have shown a surge in published evidence isolating the dependence on spin, rather than magnetic field, in biological contexts.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.
The inherent antigen cross-reactivity of the T cell receptor (TCR) is balanced by high specificity. Surprisingly, TCR specificity often manifests in ways not easily interpreted from static structures. Here we show that TCR discrimination between an HLA-A*03:01 (HLA-A3)-restricted public neoantigen and its wild-type (WT) counterpart emerges from distinct motions within the HLA-A3 peptide binding groove that vary with the identity of the peptide's first primary anchor.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Department of Peptide Therapeutics, Genentech, South San Francisco, CA 94080, USA.
mRNA display is an effective tool to identify high-affinity macrocyclic binders for challenging protein targets. The success of an mRNA display selection is dependent on generating highly diverse libraries with trillions of peptides. While translation elongation can canonically accommodate the 61 proteinogenic triplet codons, translation initiation is restricted to the native start codon AUG.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland.
Designing RNA sequences that form a specific structure remains a challenge. Current computational methods often struggle with the complexity of RNA structures, especially when considering pseudoknots or restrictions related to RNA function. We developed DesiRNA, a computational tool for the design of RNA sequences based on the Replica Exchange Monte Carlo approach.
View Article and Find Full Text PDFIntegrins are a large family of heterodimeric receptors important for cell adhesion and signaling. Integrin α5β1, also known as the fibronectin receptor, is a key mediator of angiogenesis and its dysregulation is associated with tumor proliferation, progression, and metastasis. Despite numerous efforts, α5β1-targeting therapeutics have been unsuccessful in large part due to efficacy and off-target effects.
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