The Predicted Binding Site and Dynamics of Peptide Inhibitors to the Methuselah GPCR from Drosophila melanogaster

Peptide inhibitors of Methuselah (Mth), a G protein-coupled receptor (GPCR), were reported that can extend the life span of Drosophila melanogaster. Mth is a class B GPCR, which is characterized by a large, N-terminal ectodomain that is often involved with ligand recognition. The crystal structure of the Mth ectodomain, which binds to the peptide inhibitors with high affinity, was previously determined. Here we report the predicted structures for RWR motif peptides in complex with the Mth ectodomain. We studied representatives of both Pro-class and Arg-class RWR motif peptides and identified ectodomain residues Asp139, Phe130, Asp127, and Asp78 as critical in ligand binding. To validate these structures, we predicted the effects of various ligand mutations on the structure and binding to Mth. The binding of five mutant peptides to Mth was characterized experimentally by surface plasmon resonance, revealing measured affinities that are consistent with predictions. The electron density map calculated from our MD structure compares well with the experimental map of a previously determined peptide/Mth crystal structure and could be useful in refining the current low-resolution data. The elucidation of the ligand binding site may be useful in analyzing likely binding sites in other class B GPCRs

Predicted Structures and Dynamics for Agonists and Antagonists Bound to Serotonin 5-HT2B and 5-HT2C Receptors

Subtype 2 serotonin (5-hydroxytryptamine, 5-HT) receptors are major drug targets for schizophrenia, feeding disorders, perception, depression, migraines, hypertension, anxiety, hallucinogens, and gastrointestinal dysfunctions.' We report here the predicted structure of 5-HT2B and 5-HT2C receptors bound to highly potent and selective 5-HT2B antagonist PRX-08066 3, (pKi: 30 nM), including the key binding residues [V103 (2.53), L132 (3.29), V190 (4.60), and L347 (6.58)] determining the selectivity of binding to 5-HT2B over 5-HT2A. We also report structures of the endogenous agonist (5 HT) and a HT2B selective antagonist 2 (1-methyl-1-1,6,7,8-tetrahydro-pyrrolo [2,3-g]quinoline-5-carboxylic acid pyridine-3-ylamide). We examine the dynamics for the agonist-and antagonist-bound HT2B receptors in explicit membrane and water finding dramatically different patterns of water migration into the NPxxY motif and the binding site that correlates with the stability of ionic locks in the D(E)RY region

DFT Study on the Nucleophilic Addition Reaction of Water and Ammonia to the Thymine Radical Cation

The nucleophilic addition reactions of water and ammonia molecules toward the C5−C6 double bond of thymine radical cations were investigated using density functional theory. We predicted that the nucleophilic addition favored the C5-site of thymine radical cations, in contrast to the previous experimental observations in bulk solution where the addition product to the C6-site was dominant. Considering the molecular orbital factors, we estimated the relative reactivity of the C5- and C6-sites of thymine radical cations for the nucleophilic addition of ammonia. We found that the C5 was more reactive than the C6 for the small-size clusters of Thy_1(NH_3)_n+, n = 0−2, in the gas phase and even in aqueous solution, though the difference in the reactivity between the two sites became smaller as the number of ammonia molecules increased. This variation of the reactivity was attributed to the electron density redistribution within the thymine radical cations induced by the ammonia molecules as a nucleophile. We suggest that the dominance of the C6-addition product in bulk solution is mainly due to the higher stability of the C6-addition product by solvation, rather than to the higher reactivity of the C6-site for the nucleophilic addition

Prediction of the 3-D structure of rat MrgA G protein-coupled receptor and identification of its binding site

Mrg receptors are orphan G protein-coupled receptors (GPCRs) located mainly at the specific set of sensory neurons in the dorsal root ganglia, suggesting a role in nociception. We report here the 3-D structure of rat MrgA (rMrgA) receptor [obtained from homology modeling to the recently validated predicted structures of mouse MrgA1 and MrgC11] and the structure of adenine (a known agonist, Ki = 18 nM) bound to rMrgA. This predicted binding site is located within transmembrane helical domains (TMs) 3, 4, 5 and 6, with Asn residues in TM3 and TM4 identified as the key residues for adenine binding. Here the side chain of Asn88 (TM3) forms two pairs of hydrogen bonds with N3 and N9 of adenine while Asn146 (TM4) makes two pairs of hydrogen bonds with N1 and N6 of adenine. These interactions lock adenine tightly in the binding pocket. We also predict the binding site of guanine (not an agonist) and seven other derivatives. Guanine cannot make the hydrogen bond to Asn146 (TM4), leading to binding too weak to be observed experimentally. The predicted binding affinity for other adenine derivatives correlates with the availability of the hydrogen bonds to these two Asn residues. These results validate the predicted structure for rat MrgA and suggest mutation experiments that could further validate the structure. Moreover, the predicted structure and binding site should be useful for seeking other small molecule agonists and antagonists

Panoramic Image-to-Image Translation

In this paper, we tackle the challenging task of Panoramic Image-to-Image translation (Pano-I2I) for the first time. This task is difficult due to the geometric distortion of panoramic images and the lack of a panoramic image dataset with diverse conditions, like weather or time. To address these challenges, we propose a panoramic distortion-aware I2I model that preserves the structure of the panoramic images while consistently translating their global style referenced from a pinhole image. To mitigate the distortion issue in naive 360 panorama translation, we adopt spherical positional embedding to our transformer encoders, introduce a distortion-free discriminator, and apply sphere-based rotation for augmentation and its ensemble. We also design a content encoder and a style encoder to be deformation-aware to deal with a large domain gap between panoramas and pinhole images, enabling us to work on diverse conditions of pinhole images. In addition, considering the large discrepancy between panoramas and pinhole images, our framework decouples the learning procedure of the panoramic reconstruction stage from the translation stage. We show distinct improvements over existing I2I models in translating the StreetLearn dataset in the daytime into diverse conditions. The code will be publicly available online for our community

Computational Studies of Orphan G Protein-Coupled Receptors

G protein-coupled receptors (GPCRs) play an essential role in cell communications and sensory functions. Consequently, they are involved in wide variety of diseases and are targets for many drug therapies. Particularly important is the large number of orphan GPCRs, which may play important, albeit unknown, functions in various cells. To understand their respective physiological roles, it is important to identify their endogenous ligands, and to find small molecule ligands that would serve as selective agonists or antagonists. The mas-related gene G protein-coupled receptors (Mrg receptors) belong to the orphan GPCR family, which is expressed in a specific subset of sensory neurons known to detect painful stimuli, suggesting that they could be involved in pain sensation or modulation. The primary focus of this thesis is to predict the 3D structure and binding site of Mrg receptors and to identify novel ligands that would be potential agonists or antagonists. We predict the 3D structure for the mouse MrgC11 (mMrgC11) and the binding site for five chiral FMRF-NH2 ligands. We correctly predict the relative binding observed for these five ligands. We find that Tyr110 (TM3), Asp161 (TM4), and Asp179 (TM5) are particularly important to binding the ligands. Subsequently, we carry out mutagenesis experiments followed by intracellular calcium release assays that demonstrate the dramatic decrease in activity for the Y110A, D161A, and D179A mutants predicted by our model. The all-atom molecular dynamics simulation of the mMrgC11/F-(D)M-R-F-NH2 complex structure in explicit water and infinite lipid membrane system shows that some conformational fluctuations are present, but no significant instability is detected, thus validating our structure prediction method. The virtual screening with the combination of QSPR and docking methods is carried out for the predicted mMrgC11 receptor. The compounds showing the antagonistic effect are identified by competitive functional assays. These hit compounds are certainly good staring points in designing better agonists or antagonists. The binding site of rat MrgA receptor that shows differential binding between adenine and guanine is also predicted. The predicted binding affinity correlates with the availability of the hydrogen bonds to two Asn residues, which would be primary mutation candidates to validate the structure.</p