Bias in FGFR1 signaling in response to FGF4, FGF8, and FGF9

FGFR1 signals differently in response to the FGF ligands FGF4, FGF8 and FGF9, but the mechanism behind the differential ligand recognition is poorly understood. Here, we use biophysical tools to quantify multiple aspects of FGFR1 signaling in response to the three FGFs: potency, efficacy, ligand-induced oligomerization and downregulation, and conformation of the active FGFR1 dimers. We show that FGF4, FGF8, and FGF9 are biased ligands, and that bias can explain differences in FGF8 and FGF9-mediated cellular responses. Our data suggest that ligand bias arises due to structural differences in the ligand-bound FGFR1 dimers, which impact the interactions of the FGFR1 transmembrane helices, leading to differential recruitment and activation of the downstream signaling adaptor FRS2. This study expands the mechanistic understanding of FGF signaling during development and brings the poorly understood concept of receptor tyrosine kinase ligand bias into the spotlight.

Activation and Evasion of RLR Signaling by DNA Virus Infection

Antiviral innate immune response triggered by nucleic acid recognition plays an extremely important role in controlling viral infections. The initiation of antiviral immune response against RNA viruses through ligand recognition of retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) was extensively studied. RLR’s role in DNA virus infection, which is less known, is increasing attention. Here, we review the research progress of the ligand recognition of RLRs during the DNA virus infection process and the viral evasion mechanism from host immune responses.

Plasticity in Ligand Recognition at Somatostatin Receptors

Somatostatin is a signaling peptide that plays a pivotal and wide-ranging role in physiologic processes relating to metabolism and growth through its actions at somatostatin receptors (SSTRs). Somatostatin receptors, particularly somatostatin receptor 2, are key drug targets for neuroendocrine neoplasms, with several synthetic peptide agonists currently in use. Here, we present the cryogenic electron microscopy structures of SSTR2 in the active G-protein complex with either the endogenous ligand SST14 or the FDA-approved drug octreotide. Complemented by biochemical assays and molecular dynamics simulations, these structures reveal key details of ligand recognition, receptor activation, and subtype-selectivity at somatostatin receptors. We find that SSTR ligand recognition is highly diverse, as demonstrated by ligand-induced conformational changes in ECL2, substantial sequence divergence across subtypes in extracellular regions, and loss of ligand binding upon several structurally homologous substitutions between subtypes. Despite this complexity, were are able to rationalize several discrete sources of SSTR subtype selectivity and identify an additional key interaction for SSTR2/3/5 specific binding. These results shed light on the basis of ligand recognition by somatostatin receptors and provide valuable insights for structure-based drug discovery at these important targets.

Interrogating RNA-small molecule interactions with structure probing and AI augmented-molecular simulations

While there is increasing interest in the study of RNA as a therapeutic target, efforts to understand RNA-ligand recognition at the molecular level lag far behind our understanding of protein-ligand recognition. This problem is complicated due to the more than ten orders of magnitude in timescales involved in RNA dynamics and ligand binding events, making it not straightforward to design experiments or simulations. Here we make use of artificial intelligence (AI)-augmented molecular dynamics simulations to directly observe ligand dissociation for cognate and synthetic ligands from a riboswitch system. The site-specific flexibility profiles from our simulations are in excellent agreement with in vitro measurements of flexibility using Selective 2' Hydroxyl Acylation analyzed by Primer Extension and Mutational Profiling (SHAPE-MaP). Our simulations reproduce known binding affinity profiles for the cognate and synthetic ligands, and pinpoint how both ligands make use of different aspects of riboswitch flexibility. On the basis of our dissociation trajectories, we also make and validate predictions of pairs of mutations for both the ligand systems that would show differing binding affinities. These mutations are distal to the binding site and could not have been predicted solely on the basis of structure. The methodology demonstrated here shows how molecular dynamics simulations with all-atom force-fields have now come of age in making predictions that complement existing experimental techniques and illuminate aspects of systems otherwise not trivial to understand.

Ligand recognition and G-protein coupling selectivity of cholecystokinin A receptor

Cholecystokinin A receptor (CCKAR) belongs to family A G-protein-coupled receptors and regulates nutrient homeostasis upon stimulation by cholecystokinin (CCK). It is an attractive drug target for gastrointestinal and metabolic diseases. One distinguishing feature of CCKAR is its ability to interact with a sulfated ligand and to couple with divergent G-protein subtypes, including Gs, Gi and Gq. However, the basis for G-protein coupling promiscuity and ligand recognition by CCKAR remains unknown. Here, we present three cryo-electron microscopy structures of sulfated CCK-8-activated CCKAR in complex with Gs, Gi and Gq heterotrimers, respectively. CCKAR presents a similar conformation in the three structures, whereas conformational differences in the ‘wavy hook’ of the Gα subunits and ICL3 of the receptor serve as determinants in G-protein coupling selectivity. Our findings provide a framework for understanding G-protein coupling promiscuity by CCKAR and uncover the mechanism of receptor recognition by sulfated CCK-8.