Development of a receptor peptide antagonist to human gamma-interferon and characterization of its ligand-bound conformation using transferred nuclear Overhauser effect spectroscopy

Targeting PRMT3 impairs methylation and oligomerization of HSP60 to boost anti-tumor immunity by activating cGAS/STING signaling

Immune checkpoint blockade (ICB) has emerged as a promising therapeutic option for hepatocellular carcinoma (HCC), but resistance to ICB occurs and patient responses vary. Here, we uncover protein arginine methyltransferase 3 (PRMT3) as a driver for immunotherapy resistance in HCC. We show that PRMT3 expression is induced by ICB-activated T cells via an interferon-gamma (IFNγ)-STAT1 signaling pathway, and higher PRMT3 expression levels correlate with reduced numbers of tumor-infiltrating CD8+ T cells and poorer response to ICB. Genetic depletion or pharmacological inhibition of PRMT3 elicits an influx of T cells into tumors and reduces tumor size in HCC mouse models. Mechanistically, PRMT3 methylates HSP60 at R446 to induce HSP60 oligomerization and maintain mitochondrial homeostasis. Targeting PRMT3-dependent HSP60 methylation disrupts mitochondrial integrity and increases mitochondrial DNA (mtDNA) leakage, which results in cGAS/STING-mediated anti-tumor immunity. Lastly, blocking PRMT3 functions synergize with PD-1 blockade in HCC mouse models. Our study thus identifies PRMT3 as a potential biomarker and therapeutic target to overcome immunotherapy resistance in HCC.

A biaryl peptide crosslink in a MetJ peptide model confers cooperative, nonspecific binding to DNA that ablates both repressor binding and in vitro transcription

The MetJ repressor is the archetypal example of the beta-ribbon-helix-helix DNA binding motif. A model of the MetJ beta-ribbon (residues 22-28) was prepared by forming a dityrosine crosslinked dimer from the heptapeptide KKYTVSI. Using SPR, the peptide dimer 2 was shown to bind to dsDNA under physiologically relevant conditions, whereas the monomeric peptide did not. The peptide dimer appeared to inhibit binding of the MetJ repressor to natural met operators. Based on the stoichiometry of binding, the binding of peptide dimer 2 seems both highly co-operative and to lack sequence specificity. Peptide binding also appears to prevent transcription in vitro.

The conformations of a substrate and a product bound to the active site of S-adenosylmethionine synthetase

S-Adenosylmethionine (AdoMet) is the most widely used alkyl group donor in biological systems. The formation of AdoMet from ATP and L-methionine is catalyzed by S-adenosylmethionine synthetase (AdoMet synthetase). Elucidation of the conformations of enzyme-bound substrates, product, and inhibitors is important for the understanding of the catalytic mechanism of the enzyme and the design of new inhibitors. To obtain structural data for enzyme-bound substrates and product, we have used two-dimensional transferred nuclear Overhauser effect spectroscopy to determine the conformation of enzyme-bound AdoMet and 5'-adenylyl imidodiphosphate (AMPPNP). AMPPNP, an analogue of ATP, is resistant to the ATP hydrolysis activity of AdoMet synthetase because of the presence of a nonhydrolyzable NH-link between the beta- and gamma-phosphates but is a substrate for AdoMet formation during which tripolyphosphate is produced. AdoMet and AMPPNP both bind in an anti conformation about the glycosidic bond. The ribose rings are in C3'-exo and C4'-exo conformations in AdoMet and AMPPNP, respectively. The differences in ribose ring conformations presumably reflect the different steric requirements of the C5' substituents in AMPPNP and AdoMet. The NMR-determined conformations of AdoMet and AMPPNP were docked into the E. coli AdoMet synthetase active site taken from the enzyme.ADP. Pi crystal structure. Since there are no nonexchangeable protons either in the carboxy-terminal end of the methionine segment of AdoMet or in the tripolyphosphate segment of AMPPNP, these portions of the molecules were modeled into the enzyme active site. The interactions of AdoMet and AMPPNP with the enzyme predict the location of the methionine binding site and suggest how the positive charge formed on the sulfur during AdoMet synthesis is stabilized.

The conformation of NADH bound to inosine 5'-monophosphate dehydrogenase determined by transferred nuclear Overhauser effect spectroscopy

Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the oxidation of inosine 5-monophosphate (IMP) to xanthosine 5'-monophosphate (XMP). The reaction proceeds with concomitant conversion of NAD+ to NADH and is the rate-limiting step in the de novo biosynthesis of guanosine nucleotides. IMPDH is a target for numerous chemotherapeutic agents. The conformations of enzyme-bound substrates, enzyme-bound products and enzyme-bound ligands in general, are of interest for the understanding of the catalytic mechanism of the enzyme and the design of new inhibitors. Although several of the chemotherapeutic inhibitors of IMPDH are NAD+ or NADH analogues, no structural data for IMPDH-bound NAD+ (or NADH) are available. In the present work, we have used transferred nuclear Overhauser effect spectroscopy (TRNOESY) to determine the conformation of NADH bound to the active site of human type II IMPDH (IMPDH-h2). The inter-proton distances determined from TRNOESY data indicate that NADH binds to the enzyme active site in an overall extended conformation. The adenosine moiety and the nicotinamide riboside moiety are both in the anti conformation about the glycosidic bond, and both ribose rings are in approximately C4'-exo conformations. The nicotinamide amide group was found to be in a cis conformation. The anti conformation of the nicotinamide riboside moiety is in accord with the preferred conformations of several potent and selective dinucleotide inhibitors and is consistent with that implied by the stereospecificity of hydride transfer in the enzymatic reaction. The implications of this conformation for the catalytic mechanism of IMPDH-h2 are discussed.

Does a peptide bound to a monoclonal antibody always adopt a unique conformation?

The conformation of a synthetic undecapeptide derived from the Escherichia coli tryptophan synthase beta2 subunit was studied by NMR spectroscopy when bound to a monoclonal antibody (mAb 164-2) Fab' fragment directed against the native protein. The peptide 1(H-G-R-V-G-I-Y-F-G-M-K)11, peptide 11, was recognized by the antibody and its corresponding Fab' fragments with high affinity (K(D) = 1.1+/-0.2* 10(-8) M). Peptide 11 was labelled with 15N and its structure at the binding site of the Fab' 164-2 fragment was studied by isotope-editing techniques. 1H-15N heteronuclear spectra indicated the presence of two Fab'-peptide 11 complexes with two different conformations in slow chemical exchange on the chemical shift time scale.

Binding of immunoglobulin G from patients with autoimmune thyroid disease to rat sodium-iodide symporter peptides: evidence for the iodide transporter as an autoantigen

The recent cloning of the rat sodium-iodide symporter (rNIS) from FRTL-5 cells makes possible studies of the role of this thyroid-specific protein as an antigen in autoimmune diseases of the thyroid (AITD). We generated 21 synthetic peptides replicating the entire sequence of the extramembranous domains (ExMD) of rNIS. Each was synthesized by automated chemistry, purified by high-pressure liquid chromatography (HPLC), and characterized by mass spectroscopy. Immunoglobulins were purified using protein A from serum of 27 patients with Graves' disease (GD), 27 patients with autoimmune hypothyroidism (HT), and 20 normal controls. Binding of IgG from patients and controls to each of the rNIS peptides was measured by enzyme-linked immunosorbent assay (ELISA). Binding of patient IgG significantly greater than control was observed with six peptides: peptide 262-280 (representing ExMD 8 between transmembrane [TM] domains VII and VIII), peptide 437-444 (ExMD 11), peptides 468-487, 483-602, and 498-517 from ExMD 12, and peptides 560-579 from the proximal portion of the carboxyl terminus (ExMD 13). 63% of GD patients and 26% of HT patients immunoglobulin G (IgG) bound peptide 498-517 compared to zero controls. Similarly, 59% of GD were positive against peptide 468-487 versus zero controls. Peptide 262-280 bound IgG from 44% of GD patients, 15% of HT patients, and none of the controls. The remaining peptides showed little or no binding of patient IgG. These data indicate that patients with GD and HT possess antibodies that recognize rNIS significantly greater than do normal individuals, suggesting that the iodide transporter represents an important autoantigen in AITD. They further suggest that the incidence of the antibodies is higher in GD than HT, and that the antigenic epitopes involve ExMD 8, 11, 12, and 13.

The conformation of inosine 5'-monophosphate (IMP) bound to IMP dehydrogenase determined by transferred nuclear overhauser effect spectroscopy

IMP dehydrogenase (IMPDH) catalyzes the NAD-dependent synthesis of xanthosine 5'-monophosphate which is the rate-limiting step in guanine nucleotide biosynthesis. Although IMPDH is the target of numerous chemotherapeutic agents, nothing has been known about the conformation of the enzyme-bound substrates. The conformation of IMP bound to human type II IMP dehydrogenase has been determined by two-dimensional transferred nuclear Overhauser effect NMR spectroscopy at 600 MHz. NOE buildup rates were determined by recording NOESY spectra at numerous mixing times. The cross-relaxation rates determined from the initial NOE build-up rates were used to calculate inter-proton distances of bound IMP. The conformation of the enzyme-bound IMP was obtained by molecular modeling with energy minimization using the experimentally determined inter-proton distance constraints. The glycosidic torsion angle of the bound nucleotide is anti and the sugar is in the C2-endo-conformation. This conformation places H2 of IMP, which is transferred to NAD in the reaction, in a position clear of the rest of the molecule in order to facilitate the reaction.