Conformational selection of vasopressin upon V1a receptor binding

Structural and energetic insights into the selective inhibition of PKMYT1 against WEE1

Protein kinase, membrane-associated tyrosine/threonine 1 (PKMYT1), a member of the WEE family and responsible for the regulation of CDK1 phosphorylation, has been considered a promising therapeutic target for cancer therapy. However, the highly structural conservation of the ATP-binding sites of the WEE family poses a challenge to the design of selective inhibitors for PKMYT1. Here, molecular docking, multiple microsecond-length molecular dynamics (MD) simulations and end-point free energy calculations were performed to uncover the molecular mechanism of the binding selectivity of RP-6306 toward PKMYT1 over its highly homologous kinase WEE1. The binding specificity of RP-6306 reported in previous experimental bioassays was clarified by MD simulations and binding free energy calculations. Further, the binding free energy prediction indicated that the binding selectivity of RP-6306 largely derived from the difference in the protein-ligand electrostatic interactions. The per-residue free energy decomposition suggested that the non-conserved gatekeeper residue in the hinge domain of PKMYT1/WEE1, Thr187/Asn376, is the critical factor responsible for the binding selectivity of RP-6306 toward PKMYT1. In addition, a water-mediated hydrogen bond was formed between RP-6306 and Gly191 at the hinge domain in the PKMYT1/RP-6306 complex, which was absent in the WEE1/RP-6306 complex. This study is expected to offer useful information for the design of more potent and selective PKMYT1 inhibitors.Communicated by Ramaswamy H. Sarma.

Oxytocin and vasopressin signaling in health and disease

Neurohypophysial peptides are ancient and evolutionarily highly conserved neuropeptides that regulate many crucial physiological functions in vertebrates and invertebrates. The human neurohypophysial oxytocin/vasopressin (OT/VP) signaling system with its four receptors has become an attractive drug target for a variety of diseases, including cancer, pain, cardiovascular indications, and neurological disorders. Despite its promise, drug development faces hurdles, including signaling complexity, selectivity and off-target concerns, translational interspecies differences, and inefficient drug delivery. In this review we dive into the complexity of the OT/VP signaling system in health and disease, provide an overview of relevant pharmacological probes, and discuss the latest trends in therapeutic lead discovery and drug development.

Understanding Self-Assembly of Silica-Precipitating Peptides to Control Silica Particle Morphology

The most advanced materials are those found in nature. These evolutionary optimized substances provide highest efficiencies, e.g., in harvesting solar energy or providing extreme stability, and are intrinsically biocompatible. However, the mimicry of biological materials is limited to a few successful applications since there is still a lack of the tools to recreate natural materials. Herein, such means are provided based on a peptide library derived from the silaffin protein R5 that enables rational biomimetic materials design. It is now evident that biomaterials do not form via mechanisms observed in vitro. Instead, the material's function and morphology are predetermined by precursors that self-assemble in solution, often from a combination of protein and salts. These assemblies act as templates for biomaterials. The RRIL peptides used here are a small part of the silica-precipitation machinery in diatoms. By connecting RRIL motifs via varying central bi- or trifunctional residues, a library of stereoisomers is generated, which allows characterization of different template structures in the presence of phosphate ions by combining residue-resolved real-time NMR spectroscopy and molecular dynamics (MD) simulations. Understanding these templates in atomistic detail, the morphology of silica particles is controlled via manipulation of the template precursors.

Delineating the conformational landscape and intrinsic properties of the angiotensin II type 2 receptor using a computational study

As a key regulator for the renin-angiotensin system, a class A G protein-coupled receptor (GPCR), AngII type 2 receptor (AT₂R), plays a pivotal role in the homeostasis of the cardiovascular system. Compared with other GPCRs, AT₂R has a unique antagonist-bound conformation and its mechanism is still an enigma. Here, we applied combined dynamic and evolutional approaches to investigate the conformational space and intrinsic properties of AT₂R. With molecular dynamic simulations, Markov State Models, and statistics coupled analysis, we captured the conformational landscape of AT₂R and identified its uniquity from both dynamical and evolutional viewpoints. A cryptic pocket was also discovered in the intermediate state during conformation transitions. These findings offer a deeper understanding of the AT₂R mechanism at an atomic level and provide hints for the design of novel AT₂R modulators.

Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor

Class B G protein-coupled receptors (GPCRs) are important targets in the treatment of metabolic syndrome and diabetes. Although multiple structures of class B GPCRs-G protein complexes have been elucidated, the detailed activation mechanism of the receptors remains unclear. Here, we combine Gaussian accelerated molecular dynamics simulations and Markov state models (MSM) to investigate the activation mechanism of a canonical class B GPCR, human glucagon receptor-GCGR, including the negative allosteric modulator-bound inactive state, the agonist glucagon-bound active state, and both glucagon- and Gs-bound fully active state. The free-energy landscapes of GCGR show the conformational ensemble consisting of three activation-associated states: inactive, active, and fully active. The structural analysis indicates the high dynamics of GCGR upon glucagon binding with both active and inactive conformations in the ensemble. Significantly, the H8 and TM6 exhibits distinct features from the inactive to the active states. The additional simulations demonstrate the role of H8 in the recruitment of Gs. Gs binding presents a crucial function of stabilizing the glucagon binding site and MSM highlights the absolute requirement of Gs to help the GCGR reach the fully active state. Together, our results reveal the detailed activation mechanism of GCGR from the view of conformational dynamics.