Molecular basis for GIGYF-TNRC6 complex assembly in miRNA-mediated translational repression

The GIGYF proteins associate with 4EHP and RNA-associated proteins to elicit transcript-specific translational repression. However, the mechanism by which the GIGYF1/2-4EHP complex is recruited to its target transcripts remain unclear. Here we report the crystal structures of the GYF domains from GIGYF1 and GIGYF2 in complex with proline-rich sequences from miRISC-binding proteins TNRC6C and TNRC6A, respectively. The TNRC6 proline-rich motifs bind to a conserved array of aromatic residues on the surface of the GIGYF1/2 GYF domain, bridging 4EHP to Argonaute-miRNA mRNA targets. Our structures also reveal a phenylalanine residue conserved from yeast to human GYF domains that contributes to GIGYF2 thermostability. The molecular details we outline here are likely to be conserved between GIGYF1/2 and other RNA-binding proteins to elicit 4EHP-mediated repression in different biological contexts.

Structures of Bdellovibrio bacteriovorus phosphoglucose isomerase reveal novel rigidity in the active site of a selected subset of enzymes upon substrate binding.

Glycolysis and gluconeogenesis are central pathways of metabolism across all domains of life. A prominent enzyme in these pathways is phosphoglucose isomerase (PGI) which mediates the interconversion of glucose-6-phosphate and fructose-6-phosphate (F6P). The predatory bacterium Bdellovibrio bacteriovorus leads a complex lifecycle, switching between intraperiplasmic replicative and extracellular hunter attack-phase stages. Passage through this complex lifecycle involves different metabolic states. Here we present the unliganded and substrate bound structures of the Bdellovibrio bacteriovorus PGI, solved to 1.74 Å and 1.67 Å, respectively. These structures reveal that an induced-fit conformational change within the active site is not a pre-requisite for the binding of substrates in some PGIs. Crucially, we suggest a phenylalanine residue, conserved across most PGI enzymes but substituted for a glycine in Bdellovibrio and other select organisms, is central to the induced-fit mode of substrate recognition for PGIs. This enzyme also represents the smallest conventional PGI characterised to date and likely represents the minimal requirements for a functional PGI.

Production of CFTR-ΔF508 Rabbits

Cystic Fibrosis (CF) is a lethal autosomal recessive disease caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). The most common mutation is the deletion of phenylalanine residue at position 508 (ΔF508). Here we report the production of CFTR-ΔF508 rabbits by CRISPR/Cas9-mediated gene editing. After microinjection and embryo transfer, 77 kits were born, of which five carried the ΔF508 mutation. To confirm the germline transmission, one male ΔF508 founder was bred with two wild-type females and produced 16 F1 generation kits, of which six are heterozygous ΔF508/WT animals. Our work adds CFTR-ΔF508 rabbits to the toolbox of CF animal models for biomedical research.

PROPOSAL FOR A COMPUTATIONAL MODEL TO STUDY THE SELECTIVITY BETWEEN PTP1B AND ITS ALLOSTERIC INHIBITORS

Diabetes mellitus type II has spread as a problematic pandemia for countries all over the world. Despite of the current available treatments, approved drugs still show undesirable side effects, loss of efficacy or they target symptoms instead of causes. Since its discovery, protein tyrosine phosphatase 1B has emerged as a very promising target against this disease. Despite of the information about the enzyme, there is no knowledge regarding the selectivity between this enzyme and its closest homologue, lymphocyte T tyrosine phosphatase, responsible of complicate side effects. In this study different computational approaches have let us to highlight the importance of a phenylalanine residue located in protein tyrosine phosphatase 1B, but no in its homologue, as a crucial hotspot that causes selectivity. These results let to explain the observed selectivity and they can be used as a guide for the design of new inhibitors.

3348 Structural Determinants of Neoantigen Immunogenicity for Cancer Therapy

OBJECTIVES/SPECIFIC AIMS: We are exploring the structure of the interaction between an immunogenic neoantigen and a T cell receptor (TCR) that recognizes the neoantigen while tolerating the counterpart self antigen. No structural example exists to date of how a TCR can discriminate between a neoantigen and the self antigen. We aim to determine the structural and biophysical features that underlie the immunogenicity for this neoantigen, and the features we determine are likely to be present in other immunogenic neoantigens. Algorithms to predict the immunogenicity of neoantigens are available, but do not incorporate structural or biophysical factors. We aim to improve these methods for immunogenic neoantigen prediction by determining structural and biophysical factors that result in recognition by the immune system. METHODS/STUDY POPULATION: Recombinant protein expression, production, and purification. Protein x-ray crystallography. Biophysical protein-protein binding experiments RESULTS/ANTICIPATED RESULTS: The T cell receptor (TCR) bound to the neoantigen with an affinity 15-fold higher than the self antigen. The leucine to phenylalanine mutation occurs at position 8 of a 9-amino acid long peptide antigen. This position is typically in the interface bound by the T cell receptor. The structures of the unbound neoantigen and self antigen showed that the mutated residue was in the TCR interface. Additionally we noted a change in the side chain position of a proximal tryptophan, potentially due to clashes with the larger phenylalanine residue. The structure of the TCR bound to the neoantigen showed that the TCR interacted with the tryptophan in the mutation-induced conformation and with the phenylalanine residue. Thus the mutation may be altering TCR binding affinity by interactions of the residue itself with the TCR, and by locking the proximal tryptophan residue in an optimal position to interact with the TCR. We are testing the contributions of each of these factors to the overall affinity change. Hydrophobicity has been linked to immunogenicity, so mutations that increase hydrophobicity compared to the self antigen are likely to be immunogenic. However, leucine and phenylalanine are similar on hydrophobicity scales. On the other hand, a side chain rotation is unlikely to represent a large energy barrier. Therefore, we hypothesize that another property of the phenylalanine, such as size or aromaticity, is driving the affinity difference. DISCUSSION/SIGNIFICANCE OF IMPACT: Traditional forms of cancer therapy do not specifically target cancer cells, and their toxicity to healthy cells limits their effectiveness. Immunotherapy, which involves orchestrating a specific anti-cancer immune response, is now an established cancer therapy. Several forms of immunotherapy target “neoantigens,” which are derived from mutated proteins in cancer, and are therefore are cancer-specific. Neoantigens represent a foothold that can allow the immune system to distinguish between cancer cells and healthy cells, and thus specifically target cancer cells for destruction while imparting no activity toward healthy cells that lack the neoantigen. Most cancer mutations that result in neoantigens arise from random passenger mutations in cancer and will be different among patients. Neoantigen-based cancer therapies are thus a precision medicine technique. The quality of neoantigens to induce an immune response (immunogenicity), which relates to how likely they are to be presented to the immune system and recognized as foreign, has been shown to be a critical factor in predicting the outcome of immunotherapy treatment. We are investigating, on a structural and biophysical level, features that may increase the likelihood of a neoantigen being recognized as foreign by the immune system. The structural insight we gain can be incorporated into algorithms that predict neoantigens from cancer exome sequencing for patient-specific identification of immunogenic neoantigens for immunotherapeutic intervention.

Gain-of-function screen of α-transducin identifies an essential phenylalanine residue necessary for full effector activation

Two regions on the α subunits of heterotrimeric GTP-binding proteins (G-proteins), the Switch II/α2 helix (which changes conformation upon GDP–GTP exchange) and the α3 helix, have been shown to contain the binding sites for their effector proteins. However, how the binding of Gα subunits to their effector proteins is translated into the stimulation of effector activity is still poorly understood. Here, we took advantage of a reconstituted rhodopsin-coupled phototransduction system to address this question and identified a distinct surface and an essential residue on the α subunit of the G-protein transducin (αT) that is necessary to fully activate its effector enzyme, the cGMP phosphodiesterase (PDE). We started with a chimeric G-protein α subunit (αT*) comprising residues mainly from αT and a short stretch of residues from the Gi1 α subunit (αi1), which only weakly stimulates PDE activity. We then reinstated the αT residues by systematically replacing the corresponding αi1 residues within αT* with the aim of fully restoring PDE stimulatory activity. These experiments revealed that the αG/α4 loop and a phenylalanine residue at position 283 are essential for conferring the αT* subunit with full PDE stimulatory capability. We further demonstrated that this same region and amino acid within the α subunit of the Gs protein (αs) are necessary for full adenylyl cyclase activation. These findings highlight the importance of the αG/α4 loop and of an essential phenylalanine residue within this region on Gα subunits αT and αs as being pivotal for their selective and optimal stimulation of effector activity.

A natural, single-residue substitution yields a less active peptaibiotic: the structure of bergofungin A at atomic resolution

Bergofungin is a peptide antibiotic that is produced by the ascomycetous fungusEmericellopsis donezkiiHKI 0059 and belongs to peptaibol subfamily 2. The crystal structure of bergofungin A has been determined and refined to 0.84 Å resolution. This is the second crystal structure of a natural 15-residue peptaibol, after that of samarosporin I. The amino-terminal phenylalanine residue in samarosporin I is exchanged to a valine residue in bergofungin A. According to agar diffusion tests, this results in a nearly inactive antibiotic peptide compared with the moderately active samarosporin I. Crystals were obtained from methanol solutions of purified bergofungin mixed with water. Although there are differences in the intramolecular hydrogen-bonding scheme of samarosporin I, the overall folding is very similar for both peptaibols, namely 310-helical at the termini and α-helical in the middle of the molecules. Bergofungin A and samarosporin I molecules are arranged in a similar way in both lattices. However, the packing of bergofungin A exhibits a second solvent channel along the twofold axis. This latter channel occurs in the vicinity of the N-terminus, where the natural substitution resides.