Allosteric Coupling of Drug Binding and Intracellular Signaling in the A2A Adenosine Receptor.

Signaling across cellular membranes, the 826 human G protein-coupled receptors (GPCRs) govern a wide range of vital physiological processes, making GPCRs prominent drug targets. X-ray crystallography provided GPCR molecular architectures, which also revealed the need for additional structural dynamics data to support drug development. Here, nuclear magnetic resonance (NMR) spectroscopy with the wild-type-like A2A adenosine receptor (A2AAR) in solution provides a comprehensive characterization of signaling-related structural dynamics. All six tryptophan indole and eight glycine backbone 15N-1H NMR signals in A2AAR were individually assigned. These NMR probes provided insight into the role of Asp522.50 as an allosteric link between the orthosteric drug binding site and the intracellular signaling surface, revealing strong interactions with the toggle switch Trp 2466.48, and delineated the structural response to variable efficacy of bound drugs across A2AAR. The present data support GPCR signaling based on dynamic interactions between two semi-independent subdomains connected by an allosteric switch at Asp522.50.

Solvent-Controlled, Site-Selective N-Alkylation Reactions of Azolo-Fused Ring Heterocycles at N1-, N2-, and N3-Positions, Including Pyrazolo[3,4- d]pyrimidines, Purines, [1,2,3]Triazolo[4,5]pyridines, and Related Deaza-Compounds.

Alkylation of 4-methoxy-1 H-pyrazolo[3,4- d]pyrimidine (1b) with iodomethane in THF using NaHMDS as base selectively provided N2-methyl product 4-methoxy-2-methyl-2 H-pyrazolo[3,4- d]pyrimidine (3b) in an 8/1 ratio over N1-methyl product (2b). Interestingly, conducting the reaction in DMSO reversed selectivity to provide a 4/1 ratio of N1/N2 methylated products. Crystal structures of product 3b with N1 and N7 coordinated to sodium indicated a potential role for the latter reinforcing the N2-selectivity. Limits of selectivity were tested with 26 heterocycles which revealed that N7 was a controlling element directing alkylations to favor N2 for pyrazolo- and N3 for imidazo- and triazolo-fused ring heterocycles when conducted in THF. Use of 1H-detected pulsed field gradient-stimulated echo (PFG-STE) NMR defined the molecular weights of ionic reactive complexes. This data and DFT charge distribution calculations suggest close ion pairs (CIPs) or tight ion pairs (TIPs) control alkylation selectivity in THF and solvent-separated ion pairs (SIPs) are the reactive species in DMSO.

Method for rapid optimization of recombinant GPCR protein expression and stability using virus-like particles.

Recent innovative approaches to stabilize and crystallize GPCRs have resulted in an unprecedented breakthrough in GPCR crystal structures as well as application of the purified receptor protein in biophysical and biochemical ligand binding assays. However, the protein optimization process to enable these technologies is lengthy and requires iterative overexpression, solubilization, purification and functional analysis of tens to hundreds of protein variants. Here, we report a new and versatile method to screen in parallel hundreds of GPCR variants in HEK293 produced virus-like particles (VLPs) for protein yield, stability, functionality and ligand binding. This approach reduces the time and resources during GPCR construct optimization by eliminating lengthy protein solubilization and purification steps and by its adaptability to many binding assay formats (label or label-free detection). We exemplified the robustness of our VLP method by screening 210 GALR3-VLP variants in a radiometric agonist-based binding assay and a subset of 88 variants in a label-free antagonist-based assay. The resulting GALR3 agonist or antagonist stabilizing variants were then further used for recombinant protein expression in transfected insect cells. The final purified protein variants were successfully immobilized on a biosensor chip and used in a surface plasmon resonance binding assay.

ß2-Adrenergic receptor solutions for structural biology analyzed with microscale NMR diffusion measurements.

Microcoil NMR measurements were performed to determine the final composition of solutions of the ß(2)-adrenergic receptor (ß(2)AR) reconstituted with a detergent and to study the hydrodynamic properties of the detergent micelles containing ß(2)AR. Standards are established for the reproducible preparation of G-protein-coupled receptor solutions for crystallization trials and solution NMR studies.

Micro-coil NMR to monitor optimization of the reconstitution conditions for the integral membrane protein OmpW in detergent micelles.

Optimization of aqueous solutions of the integral membrane protein (IMP) OmpW for NMR structure determination has been monitored with micro-coil NMR, which enables the acquisition of NMR spectra using only micrograms of protein and detergent. The detergent 30-Fos (2-undecylphosphocholine) was found to yield the best 2D [(15)N, (1)H]-TROSY correlation NMR spectra of [(2)H, (15)N]-labeled OmpW. For the OmpW structure determination we then optimized the 30-Fos concentration, the sample temperature and long-time stability, and the deuteration level of the protein. Some emerging guidelines for reconstitution of ß-barrel integral membrane proteins in structural biology are discussed.

NMR characterization of membrane protein-detergent micelle solutions by use of microcoil equipment.

Using microcoil NMR technology, the uniformly (2)H,(15)N-labeled integral membrane protein OmpX, and the phosphocholine derivative detergent Fos-10 (n-decylphosphocholine), we investigated solutions of mixed protein-detergent micelles to determine the influence of the detergent concentration on the NMR spectra of the protein. In a first step, we identified key parameters that influence the composition of the micelle solutions, which resulted in a new protocol for the preparation of well-defined concentrated protein solutions. This led to the observation that high-quality 2D [(15)N,(1)H]-transverse relaxation-optimized spectroscopy (TROSY) spectra of OmpX reconstituted in mixed micelles with Fos-10 were obtained only in a limited range of detergent concentrations. Outside of this range from about 90-180 mM, we observed a significant decrease of the average peak intensity. Relaxation-optimized NMR measurements of the rotational and translational diffusion coefficients of the OmpX/Fos-10 mixed micelles, D(r) and D(t), respectively, then showed that the stoichiometry and the effective hydrodynamic radius of the protein-containing micelles are not significantly affected by high Fos-10 concentrations and that the deterioration of NMR spectra is due to the increased viscosity at high detergent concentrations. The paper thus provides a basis for refined guidelines on the preparation of integral membrane proteins for structural studies.

Structural characterization of the intra- and inter-repeat copper binding modes within the N-terminal region of "prion related protein" (PrP-rel-2) of zebrafish.

The unique biology of prion proteins (PrPs) allied with the public-health risks posed by prion zoonoses, such as various animal neurodegenerations, has focused much attention on the molecular basis of the controls cross-species and on the similarities between PrPs from different species. Given the common feature of PrPs as Cu(2+) binding proteins, it appears relevant to compare the impact of Cu(2+) on the stability constants and structures of "physiological" complexes. After having comprehensively delineated the interaction of Cu(2+) with mammalian and avian PrPs, the stabilities and molecular structures of species generated by Cu(2+) interacting with the irregular repeated domain derived from Danio rerio zebrafish PrP-rel-2 were investigated. Copper complexes with different zebrafish PrP-rel-2 fragments were analyzed by potentiometric and spectroscopic techniques. The data were interpreted as to provide evidence of all investigated repeat units selectively binding Cu(2+) via the His imidazole(s). The structural models obtained from paramagnetic NMR showed an intra- or inter-copper binding according to the number of the His in the sequence. In comparison to the mammalian and avian cases, the enzymatic function referred to SOD-like activity was shown to be rather faint in the fish PrPs cases.

The whole hexapeptide repeats domain from avian PrP displays untypical hallmarks in aspect of the Cu2+ complexes formation.

Prions, the infectious agents responsible for the transmissible spongiform encephalopathies (TSEs) have defied full characterization for decades. Although the interactions of Cu(2+) ions with PrP both in vivo and in vitro are well documented, there are still a lot of ambiguities concerning the biological and chemical nature of these effects. In this work, we have investigated the interactions of Cu(2+) ions with whole repeat region of the copper-binding domain (hexapeptide repeats) of chicken PrP. Our results provide explanations for the structural and chemical basis of the specific interactions of Cu(2+) ions with the hexapeptide repeat region. Furthermore, we show that SOD-like activity depends on Cu(2+) complexes.

Dataset on Galanin Receptor 3 mutants that improve recombinant receptor expression and stability in an agonist and antagonist bound form.

Galanin Receptor 3 (GALR3) is a G-protein-coupled receptor with a widespread distribution in the brain and plays a role in a variety of physiologic processes including cognition/memory, sensory/pain processing, hormone secretion, and feeding behavior. Therefore, GALR3 is considered an attractive CNS drug target (Freimann et al., 2015) [1]. This dataset contains GALR3 point mutants that improve recombinant protein expression and thermal stability of the receptor contained in virus-like particles (VLPs) or obtained by detergent-purification of baculovirus-infected insect cells. The mutations listed can be grouped in those that improve the stability of the agonist-bound and the antagonist-bound form of the receptor. Protein characteristics in terms of protein expression and thermal stability were comparable between GPCR-VLP and GPCR overexpressing Sf9 cultures. The further analysis and detailed results of these mutants as well as their impact on biophysical assay development for drug discovery can be found in "Method for Rapid Optimization of Recombinant GPCR Protein Expression and Stability using Virus-Like Particles" (Ho et al., 2017) [2].

Fine tuning the structure of the Cu2+ complex with the prion protein chicken repeat by proline isomerization.

The interaction between the single hexarepeat unit of chicken prion protein [ChPrP(54-59)] and Cu(II) was investigated by NMR, finding different coordination modes for the trans/trans and cis/trans isomers.

NMR polypeptide backbone conformation of the E. coli outer membrane protein W.

The outer membrane proteins (Omps) are key factors for bacterial survival and virulence. Among the Omps that have been structurally characterized either by X-ray crystallography or by NMR in solution, the crystal structure of OmpW stands out because three of its four extracellular loops are well defined, whereas long extracellular loops in other E. coli Omps are disordered in the crystals as well as in NMR structures. OmpW thus presented an opportunity for a detailed comparison of the extracellular loops in a ß-barrel membrane protein structure in crystals and in noncrystalline milieus. Here, the polypeptide backbone conformation of OmpW in 30-Fos micelles was determined. Complete backbone NMR assignments were obtained and the loops were structurally characterized. In combination with the OmpW crystal structure, NMR line shape analyses, and (15)N{(1)H}-NOE data, these results showed that intact regular secondary structures in the loops undergo slow hinge motions at the detergent-solvent interface.

Translational diffusion measurements by microcoil NMR in aqueous solutions of the Fos-10 detergent-solubilized membrane protein OmpX.

Aqueous solutions of the detergent Fos-10 (n-decylphosphocholine) without and with addition of the integral membrane protein (IMP) OmpX (outer membrane protein X) have been characterized using pulsed field gradient-stimulated echo (PFG-STE) NMR experiments for measurements of translational diffusion coefficients. Effective diffusion coefficients for Fos-10 micelles in the absence of OmpX were obtained by observation of NMR signals from 10-bromodecan-1-ol that had been inserted into the micelles, and in the presence of OmpX by NMR observation of the protein. It is thus shown that solutions of Fos-10-reconstituted OmpX can be quantitatively described as a mixture of Fos-10 monomers, uniform Fos-10 micelles, and uniform OmpX-containing Fos-10 micelles, with Fos-10 monomers in fast exchange between the pools of these three species. This result establishes an avenue for efficient determination of the effective translational diffusion coefficients of IMP-containing detergent micelles based on observation of the intense detergent NMR signals, which is also applicable with unlabeled IMPs. This monitoring of the species present in a given IMP solution contributes to improved guidelines for rational selection of detergent and buffer conditions in structural studies of integral membrane proteins.

Mutations in mammalian tolloid-like 1 gene detected in adult patients with ASD.

Atrial septal defect (ASD) is an incomplete septation of atria in human heart causing circulatory problems. Its frequency is estimated at one per 10 000. Actions of numerous genes have been linked to heart development. However, no single gene defect causing ASD has yet been identified. Incomplete heart septation similar to ASD was reported in transgenic mice with both inactive alleles of gene encoding mammalian zinc metalloprotease a mammalian tolloid-like 1 (tll1). Here, we have screened 19 ASD patients and 15 healthy age-matched individuals for mutations in TLL1 gene. All 22 exons were analyzed exon by exon for heteroduplex formation. Subsequently, DNA fragments forming heteroduplexes were sequenced. In four nonrelated patients, three missense mutations in coding sequence, and one single base change in the 5'UTR have been detected. Two mutations (Met182Leu, and Ala238Val) were detected in ASD patients with the same clinical phenotype. As the second mutation locates immediately upstream of the catalytic zinc-binding signature, it might change the enzyme substrate specificity. The third change, Leu627Val in the CUB3 domain, has been found in an ASD patient with interatrial septum aneurysm in addition to ASD. The CUB3 domain is important for substrate-specific recognition. In the remaining 15 patients as well as in 15 reference samples numerous base substitutions, deletions, and insertions have been detected, but no mutations changing the coding sequence have been found. Lack of mutations in relation to ASD of these patients could possibly be because of genetic heterogeneity of the syndrome.

Can chicken and human PrPs possess SOD-like activity after beta-cleavage?

The prion protein is a membrane attached glycoprotein that is involved in binding of divalent copper ions. In vivo human and chicken PrPs exhibit SOD-like activity associated with octarepeat and hexarepeat regions, respectively, when bind Cu(II) ions. However, the species of Cu(II)-PrP involved in the Cu(II) center which determines the highest SOD-like activity is still unknown. The data presented here clearly show that the single Cu(II) ion bound to PrP octapeptide repeat region of mammalian prion and hexapeptide repeat region of avian prion via 4 His side-chain imidazoles reveals the highest SOD activity.

ASD--lessons on genetic background from transgenic mice with inactive gene encoding metalloprotease, Tolloid-like 1 (TLL1).

Congenital heart defects still constitute serious medical problems. The background of such defects, however, is poorly understood. Little is also known about their pattern of inheritance. Lack of atrial and ventricular septum closures counts for a significant percentage of all congenital heart defects. Individuals harboring such defects always suffer poor quality of life. The only way to help those patients is cardiac surgery. Several genes have been implicated in the process of controlling heart development. Recent studies on transgenic mice null for tolloid-like 1 (tll1) gene revealed factors possibly involved in signaling pathways that, when absent, might affect heart development and cause problems mimicking those observed in atrial septal defects (ASDs). Lack of activity of this metalloprotease caused incomplete closure of the septum in murine fetal hearts and led to death in mid-gestation due to severe circulation problems. tll1 gene is located on the long arm of chromosome 4 (4q32-q33). The gene comprises of 6654 nucleotides and it encodes a protein 1013 amino acids long. Its human homologue tll1 is poorly investigated and until now no particular disorders have been linked to mutations in this gene.

Tandem repeat-like domain of "similar to prion protein" (StPrP) of Japanese pufferfish binds Cu(II) as effectively as the mammalian protein.

The main structural domains of prion proteins, in particular the N-terminal region containing characteristic amino acid repeats, are well conserved among different species, despite divergence in primary sequence. The repeat region seems to play an important role, as verified by pathogenicity only observed in organisms having repeats composed of eight residues. In this work three different peptides belonging to the tandem repeat region of StPrP-2 from the Japanese pufferfish Takifugu rubripes have been considered; the coordination modes and conformations of their complexes with Cu(II) have been investigated by using potentiometric titrations, spectroscopic data, and restrained molecular dynamics simulations. In all cases the histidine imidazole(s) provide the anchoring site for copper, with the further involvement of amide nitrogens depending on the peptide sequence and on pH. An increase in copper binding affinity has been observed going from the shortest peptide, corresponding to a single repeat and containing two histidines, to the longest one, encompassing three repeats with six histidines.

[Postinfarction left ventricular pseudoaneurysm]. / Pozawalowy tetniak rzekomy lewej komory serca.

Left ventricular pseudoaneurysm is a rare complication of heart rupture as a result of acute myocardial infarction, tumour infiltration or infective pericarditis. This pathology is often diagnosed accidentally because of non-specific clinical manifestations such as congestive heart failure or no symptoms at all. Diagnosis of pseudoaneurysm should result in an urgent surgical treatment as the risk of sudden death due to aneurysm rupture is high. In this report we present a patient who underwent successful surgical treatment of left ventricular pseudoaneurysm as a complication of myocardial infarction.

Structure and stability of the CuII complexes with tandem repeats of the chicken prion.

Prion protein (PrP) misfolding is one of the pivotal issues in understanding the rudiments of neurodegenerative disorders. The conformational change of mammalian cellular PrP to scrapie PrP is caused by an unknown agent, but there is reasonable evidence supporting the key role of copper ions in this process. The structure of the avian PrP was found to be very similar to the mammalian protein, although there is only 30% homology in the secondary structure. This work shows that copper ions are very effectively bound by hexarepeat fragments of chicken prion protein, although not as effectively as it was found in the case of mammalian protein. By means of potentiometric and spectroscopic techniques (nuclear magnetic resonance, circular dichroism, UV-vis, and electronic paramagnetic resonance), it was shown that Cu(II) ions coordinate to the chicken PrP hexapeptide domain in physiological pH via imidazole nitrogen donors of His residue(s). The binding pattern changes the structure of peptide involved, indicating a possible impact of Cu(II) ions in the biology and pathology of nonmammalian PrP, which could be similar to that found for mammalian PrP. The present study shows that, similar to the human prion octapeptide repeats, chicken prion hexapeptide repeats might bind copper ions in two different ways, depending on the number of repeats and metal/ligand molar ratio: (i) an intra-repeat coordination mode in which copper ion is chelated by His imidazole and deprotonated amide nitrogen in monomeric peptide and (ii) an inter-repeat coordination mode in which a polymeric peptide ligand (dimer and trimer) forms polyimidazole complexes that are very stable at physiological pH. Two proline residues inserted into the hexapeptide unit have a critical impact on the metal-binding ability.

Interactions of Cu2+ ions with chicken prion tandem repeats.

The potentiometric and spectroscopic (EPR, UV-Vis, CD) data have shown that the chicken prion hexa-repeat (Ac-His-Asn-Pro-Gly-Tyr-Pro-NH(2)) is a very specific ligand for Cu(2+) ions. The His imidazole is an anchoring binding site, then the adjacent amide nitrogen coordinates as a second donor. The presence of Pro at position 3 induces binding of phenolate oxygen as a third donor atom. The tridentate coordination dominates around physiological pH. Similar to human octapeptide fragments, chicken tandem repeats exhibit a cooperative effect in binding Cu(2+) ions, although chicken peptides are much less effective in metal ion coordination.