An autopsy case of lung adenocarcinoma with immune checkpoint inhibitor-induced pneumonia and fulminant myocarditis following pembrolizumab administration: a case report.

Immune checkpoint inhibitors (ICIs) are the current standard of care for non-small-cell lung cancer (NSCLC). Myocarditis is a rare but serious immune-related adverse event (irAE) associated with ICI therapy. We present a patient who received a single dose of pembrolizumab for NSCLC and developed ICI-associated pneumonia.

Differential Regulation of Bilastine Affinity for Human Histamine H Receptors by Lys 179 and Lys 191 via Its Binding Enthalpy and Entropy.

Bilastine, a zwitterionic second-generation antihistamine containing a carboxyl group, has higher selectivity for H receptors than first-generation antihistamines. Ligand-receptor docking simulations have suggested that the electrostatic interaction between the carboxyl group of second-generation antihistamines and the amino group of Lys179 and Lys191 of human H receptors might contribute to increased affinity of these antihistamines to H receptors. In this study, we evaluated the roles of Lys179 and Lys191 in regulating the electrostatic and hydrophobic binding of bilastine to H receptors by thermodynamic analyses.

SEVENS: a database for comprehensive GPCR genes obtained from genomes: -Update to 68 eukaryotes.

We report the development of the SEVENS database, which contains information on G-protein coupled receptor (GPCR) genes that are identified with high confidence levels (A, B, C, and D) from various eukaryotic genomes, by using a pipeline comprising bioinformatics softwares, including a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor. SEVENS compiles detailed information on GPCR genes, such as chromosomal mapping position, phylogenetic tree, sequence similarity to known genes, and protein function described by motif/domain and transmembrane helices. They are presented in a user-friendly interface.

Dynamics of bovine opsin bound to G-protein fragments.

G protein-coupled receptors (GPCRs) are a large class of membrane proteins that mediate communication of the cell with the outer environment. Upon activation by an agonist, GPCRs undergo large-scale conformational changes that enable binding of the G protein to the receptor. A key open question concerns the mechanism of the long-distance coupling between the agonist-binding site and the cytoplasmic site where G protein binds.

Identification of a binding element for the cytoplasmic regulator FROUNT in the membrane-proximal C-terminal region of chemokine receptors CCR2 and CCR5.

Chemokine receptors mediate the migration of leucocytes during inflammation. The cytoplasmic protein FROUNT binds to chemokine receptors CCR2 [chemokine (C-C motif) receptor 2] and CCR5, and amplifies chemotactic signals in leucocytes. Although the interaction between FROUNT and chemokine receptors is important for accurate chemotaxis, the interaction mechanism has not been elucidated.

Structural elements of the signal propagation pathway in squid rhodopsin and bovine rhodopsin.

Squid and bovine rhodopsins are G-protein coupled receptors (GPCRs) that activate Gq- and Gt-type G-proteins, respectively. To understand the structural elements of the signal propagation pathway, we performed molecular dynamics (MD) simulations of squid and bovine rhodopsins plus a detailed sequence analysis of class A GPCRs. The computations indicate that although the geometry of the retinal is similar in bovine and squid rhodopsins, the important interhelical hydrogen bond networks are different.

9-Demethylrhodopsin: theoretical evidence for a relaxed batho intermediate.

The 9-methyl group of retinal is crucial for the photoreaction of rhodopsin. On the basis of the results of QM/MM simulations, we propose that the primary function of the methyl group is not to properly align the chromophore in the ground state, but that it is a prerequisite for the peculiarly twisted and strained chromophore observed in the batho state. With the methyl group firmly anchored in the protein binding pocket the protein, at the cost of the incipient photon energy, manages to increase the strain energy stored in the chromophore by 25%, which may be crucial for driving the subsequent transformations.

Origin and consequences of steric strain in the rhodopsin binding pocket.

To study the origin and the effects of steric strain on the chromophore conformation in rhodopsin, we have performed quantum-mechanical calculations on the wild-type retinal chromophore and four retinal derivatives, 13-demethyl-, 10-methyl-13-demethyl-, 10-methyl-, and 9-demethylretinal. For the dynamics of the whole protein, a combined quantum mechanics/molecular mechanics method (DFTB/CHARMM) was used and for the calculation of excited-state properties the nonempirical CASSCF/CASPT2 method. After relaxation inside the protein, all chromophores show significant nonplanar distortions from C10 to C13, most strongly for 10-methylretinal and least pronounced for 9-demethylretinal.

The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure.

A new high-resolution structure is reported for bovine rhodopsin, the visual pigment in rod photoreceptor cells. Substantial improvement of the resolution limit to 2.2 A has been achieved by new crystallization conditions, which also reduce significantly the probability of merohedral twinning in the crystals.

Monitoring and characterization of Magnaporthe grisea isolates with decreased sensitivity to scytalone dehydratase inhibitors.

Rice blast fungus isolates were collected in Kyushu to investigate resistance to scytalone dehydratase inhibitors of melanin biosynthesis (MBI-D). In 2001, failure of control of rice blast was reported in the Saga prefecture, where MBI-Ds have been used since 1998. At that time, the distribution of resistant isolates was mainly limited to that area.

Genomic organization of the S-locus region of Brassica.

To gain some insights into the structure of the S-locus and the mechanisms that have kept its diversity, a 75-kb genomic fragment containing the self-incompatibility (S) locus region was isolated from the S12-haplotype of Brassica rapa and compared with those of other S-haplotypes. The region around the S determinant genes was highly polymorphic and filled with S-haplotype-specific intergenic sequences. The diverse genomic structure must contribute to the suppression of recombination at the S-locus.

11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore.

Density functional theory (DFT) calculations based on the self-consistent-charge tight-binding approximation have been performed to study the influence of the protein pocket on the 3-dimensional structure of the 11-cis-retinal Schiff base (SB) chromophore. Starting with an effectively planar chromophore embedded in a protein pocket consisting of the 27 next-nearest amino acids, the relaxed chromophore geometry resulting from energy optimization and molecular dynamics (MD) simulations has yielded novel insights with respect to the following questions: (i) The conformation of the beta-ionone ring. The protein pocket tolerates both conformations, 6-s-cis and 6-s-trans, with a total energy difference of 0.