Effector Binding Research Articles

A wheat resistosome defines common principles of immune receptor channels

Plant intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) detect pathogen effectors to trigger immune responses1. Indirect recognition of a pathogen effector by the dicotyledonous Arabidopsis thaliana coiled-coil domain containing NLR (CNL) ZAR1 induces the formation of a large hetero-oligomeric protein complex, termed the ZAR1 resistosome, which functions as a calcium channel required for ZAR1-mediated immunity2–4. Whether the resistosome and channel activities are conserved among plant CNLs remains unknown. Here we report the cryo-electron microscopy structure of the wheat CNL Sr355 in complex with the effector AvrSr356 of the wheat stem rust pathogen. Direct effector binding to the leucine-rich repeats of Sr35 results in the formation of a pentameric Sr35–AvrSr35 complex, which we term the Sr35 resistosome. Wheat Sr35 and Arabidopsis ZAR1 resistosomes bear striking structural similarities, including an arginine cluster in the leucine-rich repeats domain not previously recognized as conserved, which co-occurs and forms intramolecular interactions with the 'EDVID' motif in the coiled-coil domain. Electrophysiological measurements show that the Sr35 resistosome exhibits non-selective cation channel activity. These structural insights allowed us to generate new variants of closely related wheat and barley orphan NLRs that recognize AvrSr35. Our data support the evolutionary conservation of CNL resistosomes in plants and demonstrate proof of principle for structure-based engineering of NLRs for crop improvement.

MliR, a novel MerR-like regulator of iron homeostasis, impacts metabolism, membrane remodeling, and cell adhesion in the marine Bacteroidetes Bizionia argentinensis.

The MerR family is a group of transcriptional activators with conserved N-terminal helix-turn-helix DNA binding domains and variable C-terminal effector binding regions. In most MerR proteins the effector binding domain (EBD) contains a cysteine center suited for metal binding and mediates the response to environmental stimuli, such as oxidative stress, heavy metals or antibiotics. We here present a novel transcriptional regulator classified in the MerR superfamily that lacks an EBD domain and has neither conserved metal binding sites nor cysteine residues. This regulator from the psychrotolerant bacteria Bizionia argentinensis JUB59 is involved in iron homeostasis and was named MliR (MerR-like iron responsive Regulator). In silico analysis revealed that homologs of the MliR protein are widely distributed among different bacterial species. Deletion of the mliR gene led to decreased cell growth, increased cell adhesion and filamentation. Genome-wide transcriptomic analysis showed that genes associated with iron homeostasis were downregulated in mliR-deletion mutant. Through nuclear magnetic resonance-based metabolomics, ICP-MS, fluorescence microscopy and biochemical analysis we evaluated metabolic and phenotypic changes associated with mliR deletion. This work provides the first evidence of a MerR-family regulator involved in iron homeostasis and contributes to expanding our current knowledge on relevant metabolic pathways and cell remodeling mechanisms underlying in the adaptive response to iron availability in bacteria.

Ral GTPases are critical regulators of spinal cord myelination and homeostasis.

Efficient myelination supports nerve conduction and axonal health throughout life. In the central nervous system, oligodendrocytes (OLs) carry out this demanding anabolic duty in part through biosynthetic pathways controlled by mTOR. We identify Ral GTPases as critical regulators of mouse spinal cord myelination and myelin maintenance. Ablation of Ral GTPases (RalA, RalB) in OL-lineage cells impairs timely onset and radial growth of developmental myelination, accompanied by increased endosomal/lysosomal abundance. Further examinations, including transcriptomic analyses of Ral-deficient OLs, were consistent with mTORC1-related deficits. However, deletion of the mTOR signaling-repressor Pten in Ral-deficient OL-lineage cells is unable to rescue mTORC1 activation or developmental myelination deficiencies. Induced deletion of Ral GTPases in OLs of adult mice results in late-onset myelination defects and tissue degeneration. Together, our data indicate critical roles for Ral GTPases to promote developmental spinal cord myelination, to ensure accurate mTORC1 signaling, and to protect the healthy state of myelin-axon units over time.

In-silico Analysis and Functional Characterization of Rhizoctonia solani Effector Proteins

Sheath blight is considered the second most prevalent disease in rice with no proper resistance genes identified for its resistance. Out of the 14 anastomosis groups in R. solani (AG1 to AG13 and AGBI), the AG1 group is mostly responsible for the infection in the rice. There are many effector proteins under this group, function as transcription factors. Many bioinformatics tools are available to determine the interaction between the promoter region and effector proteins. But in an attempt to use these effector proteins for molecular docking and simulation studies, criteria like In-silico analysis and validation of the proteins are to be analyzed. The reactivity and stability of these proteins were evaluated physicochemically, domain prediction, and secondary structure prediction using bioinformatics methods such as Protparam, Pfam, and SOPMA, respectively. These bioinformatics techniques were found to be remarkably suitable for characterizing the protein's function. Robetta an abinitio approach was used to predict the 3D structure, and the models were validated using the SAVESv6.0 (PROCHECK) server. The effector protein functional analysis and 3D structure predictions made using empirical data can shed light on the interaction studies for locating effector binding elements in the promoter regions of host genes.

Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness

The family of coarse-grained models for protein dynamics known as Elastic Network Models (ENMs) require careful choice of parameters to represent well experimental measurements or fully-atomistic simulations. The most basic ENM that represents each protein residue by a node at the position of its C-alpha atom, all connected by springs of equal stiffness, up to a cut-off in distance. Even at this level a choice is required of the optimum cut-off distance and the upper limit of elastic normal modes taken in any sum for physical properties, such as dynamic correlation or allosteric effects on binding. Additionally, backbone-enhanced ENM (BENM) may improve the model by allocating a higher stiffness to springs that connect along the protein backbone. This work reports on the effect of varying these three parameters (distance and mode cutoffs, backbone stiffness) on the dynamical structure of three proteins, Catabolite Activator Protein (CAP), Glutathione S-transferase (GST), and the SARS-CoV-2 Main Protease (M pro ). Our main results are: (1) balancing B-factor and dispersion-relation predictions, a near-universal optimal value of 8.5 Å is advisable for ENMs; (2) inhomogeneity in elasticity brings the first mode containing spatial structure not well-resolved by the ENM typically within the first 20; (3) the BENM only affects modes in the upper third of the distribution, and, additionally to the ENM, is only able to model the dispersion curve better in this vicinity; (4) BENM does not typically affect fluctuation-allostery, which also requires careful treatment of the effector binding to the host protein to capture.

The activity of the RGA5 sensor NLR from rice requires binding of its integrated HMA domain to effectors but not HMA domain self-interaction.

The rice nucleotide‐binding (NB) and leucine‐rich repeat (LRR) domain immune receptors (NLRs) RGA4 and RGA5 form a helper NLR/sensor NLR (hNLR/sNLR) pair that specifically recognizes the effectors AVR‐Pia and AVR1‐CO39 from the blast fungus Magnaporthe oryzae. While RGA4 contains only canonical NLR domains, RGA5 has an additional unconventional heavy metal‐associated (HMA) domain integrated after its LRR domain. This RGA5HMA domain binds the effectors and is crucial for their recognition. Investigation of the three‐dimensional structure of the AVR1‐CO39/RGA5HMA complex by X‐ray crystallography identified a candidate surface for effector binding in the HMA domain and showed that the HMA domain self‐interacts in the absence of effector through the same surface. Here, we investigated the relevance of this HMA homodimerization for RGA5 function and the role of the RGA5HMA effector‐binding and self‐interaction surface in effector recognition. By analysing structure‐informed point mutations in the RGA5HMA‐binding surface in protein interaction studies and in Nicotiana benthamiana cell death assays, we found that HMA self‐interaction does not contribute to RGA5 function. However, the effector‐binding surface of RGA5HMA identified by X‐ray crystallography is crucial for both in vitro and in vivo effector binding as well as effector recognition. These results support the current hypothesis that noncanonical integrated domains of NLRs act primarily as effector traps and deepen our understanding of the sNLRs' function within NLR pairs.

Chemoproteomic identification of CO2-dependent lysine carboxylation in proteins.

Carbon dioxide is an omnipresent gas that drives adaptive responses within organisms from all domains of life. The molecular mechanisms by which proteins serve as sensors of CO2 are, accordingly, of great interest. Because CO2 is electrophilic, one way it can modulate protein biochemistry is by carboxylation of the amine group of lysine residues. However, the resulting CO2-carboxylated lysines spontaneously decompose, giving off CO2, which makes studying this modification difficult. Here we describe a method to stably mimic CO2-carboxylated lysine residues in proteins. We leverage this method to develop a quantitative approach to identify CO2-carboxylated lysines of proteins and explore the lysine 'carboxylome' of the CO2-responsive cyanobacterium Synechocystis sp. We uncover one CO2-carboxylated lysine within the effector binding pocket of the metabolic signaling protein PII. CO2-carboxylatation of this lysine markedly lowers the affinity of PII for its regulatory effector ligand ATP, illuminating a negative molecular control mechanism mediated by CO2.

Abstract LB505: Design and discovery of MRTX0902, a potent, selective, and orally bioavailable SOS1 inhibitor

Abstract KRAS mutations are the most common activating mutations in human cancer that ultimately lead to hyperactivation of the MAPK pathway and uncontrolled growth. KRAS functions as a small GTPase that cycles through its GTP-loaded “on” state and its GDP-loaded “off” state, a highly regulated process that is crucial for normal cell proliferation and survival. The guanine nucleotide exchange factor (GEF) SOS1 plays a critical role in this process by regulating the “on/off” state of KRAS. The protein-protein interaction between SOS1 and KRAS facilitates turnover of KRAS from the GDP-loaded inactive state to its activated and GTP-loaded state, a critical step to enable productive KRAS effector binding and activation of downstream signaling. The KRASG12C inhibitor, adagrasib (MRTX849), irreversibly binds to the GDP-loaded inactive conformation of KRASG12C and has recently shown encouraging clinical activity across several cancer types. As adagrasib binds preferentially to the inactive state of KRAS, blockade of SOS1 is anticipated to shift KRASG12C into the adagrasib-susceptible GDP-loaded state. Furthermore, this combination strategy could be used to target other mutant-driven cancers within the MAPK pathway using the appropriate KRASmut inhibitors and/or inhibitors of other targets within the MAPK pathway including MEK or EGFR. MRTX0902 was identified using iterative structure-based design as a selective inhibitor of SOS1 that demonstrates an IC50 value of 2 nM in a SOS1 HTRF binding assay and 30 nM in an MKN1 cellular assay. In pharmacokinetic evaluation across species, MRTX0902 demonstrated low extraction ratios and moderate to high bioavailability in mice, rats, and dogs. In preclinical models, MRTX0902 augmented the antitumor activity of adagrasib and other selected therapies. The design, discovery, and preclinical characterization of the potential best-in-class candidate MRTX0902 will be described. Citation Format: John M. Ketcham, David M. Briere, Aaron C. Burns, James G. Christensen, Robin J. Gunn, Jacob Haling, Anthony Ivetac, Shilpi Khare, Jon Kuehler, Svitlana Kulyk, Jade Laguer, John D. Lawson, Krystal Moya, Natalie Nguyen, Peter Olson, Lisa Rahbaek, Christopher R. Smith, Niranjan Sudhakar, Nicole C. Thomas, Darin Vanderpool, Xiaolun Wang, Matthew A. Marx. Design and discovery of MRTX0902, a potent, selective, and orally bioavailable SOS1 inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB505.

Abstract 2918: Comprehensive survey of KRas4B membrane interaction and orientation

Abstract Three RAS genes encode four Ras proteins, HRas, NRas, and KRas splice variants, KRas4A and KRas4B. In human cancers, KRAS oncogene is highly expressed (85%) as compared to other RAS oncogenes, NRAS (11%) and HRAS (4%). Oncogenic Ras leads to aberrant cell proliferation signaling, primarily through the MAPK (Raf/MEK/ERK) pathway. At the plasma membrane, nanoclustered Ras proteins promote Raf activation, mediating the downstream signaling pathway. Among the Ras isoforms, KRas4B in the membrane has been studied extensively due to its higher level of mutations in cancer. Although a number of experimental studies have focused on KRas4B subcellular localization and their nanocluster formation at the signaling platform, the mechanistic details of the membrane anchorage and the membrane orientation of KRas4B at atomic resolution are still unknown. Here, comprehensive computational studies were performed for KRas4B at the anionic lipid bilayers, composed of the phospholipids, PS and PA, and the phosphoinositides, PIP2, PI4P, and PI5P. Wild-type and two oncogenic mutants, G12D and G12V KRas4B in the GTP- and GDP-bound states were considered. The lysine rich HVR was post-translationally modified with the farnesyl and methyl groups. Previous studies showed that wild-type KRas4B-GDP interacts weakly and nonspecifically with anionic phospholipids, while oncogenic mutations alter selective anionic lipid binding toward anionic lipids, PA, PI3P, PI4P, and PI5P. Our studies indicate that the membrane interaction of KRas4B is highly sensitive depending on the types of nucleotides, mutational states, and anionic lipids enriched the lipid bilayer. While the GTP-bound spontaneously inserts its prenyl group into the hydrophobic core of the bilayer, the occurrence of spontaneous insertion is reduced in the GDP-bound form. The distance of GTP-bound catalytic domain from the bilayer surface is longer than the GDP-bound form. The HVR is sequestered by the GDP-bound catalytic domain, which causes the catalytic domain to be occluded and increases the membrane interaction by the catalytic domain. In contrast, the GTP-bound catalytic domain releases its HVR and liberates from the membrane interaction. The occlusion of catalytic domain is less prevalent in the GTP-bound state. KRas4BG12D/G12V-GTP exhibits the active-state orientation, exposing its effector binding site for recruiting the effectors. While PA and PIP2 support the active-state orientation, the PIP4 enriched bilayer prevents the spontaneous prenyl insertion resulting in the occlusion of catalytic domain. Our results underscore the importance of detailed structural mechanisms of KRas4B membrane interaction and orientation, elucidating vital mechanistic role of KRas4B, a key membrane-anchored protein in cancer. Funded by Frederick National Laboratory for Cancer Research, National Institutes of Health, under contract HHSN261201500003I. Citation Format: Hyunbum Jang, Mingzhen Zhang, Vadim Gaponenko, Ruth Nussinov. Comprehensive survey of KRas4B membrane interaction and orientation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2918.

Abstract 3598: A first-in-class tri-complex KRASG13C(ON) inhibitor validates therapeutic targeting of KRASG13Cand drives tumor regressions in preclinical models

Abstract The clinical activity of KRASG12C(OFF) inhibitors has validated KRASG12C as an oncogenic driver in human cancers and demonstrated the power of targeting cysteine mutations with covalent inhibitors. A second oncogenic RAS cysteine mutation, KRASG13C, is found predominantly in non-small cell lung cancer (NSCLC), with > 2,700 new cases reported in the USA in 2020 but relatively little is known about the biochemical and cellular properties of KRASG13C. KRASG12C-selective inhibitors are not active against KRASG13C and currently there are no direct, targeted inhibitors available for patients with KRASG13C-driven cancers. We report the development of a potent, selective, orally bioavailable tri-complex inhibitor of KRASG13C. Using chemical and genetic approaches, we describe unique properties of KRASG13C and their influence on oncogenic signaling and the co-mutational landscape of KRASG13C mutant tumors. These insights provide the basis for targeting KRASG13C NSCLC in the clinic and shape future combination strategies. RM-041 is a potent and selective covalent inhibitor of KRASG13C(ON) with attractive drug-like properties. RM-041 forms a tri-complex between KRASG13C(ON) and cyclophilin A (CypA), a highly abundant intracellular chaperone protein. The assembled non-covalent tri-complex rapidly prevents KRASG13C(ON) signaling via steric blockade of RAS effector binding, and covalent engagement with Cys-13 converts the inactive assembly into an irreversibly inhibited complex. In cells, RM-041 covalently modifies KRASG13C(ON), drives deep suppression of RAS pathway signaling, and inhibits cell proliferation in KRASG13C mutant cancer cell lines. In KRASG13C xenograft tumor models, oral administration of RM-041 produces deep and durable suppression of RAS pathway activity and induces tumor regressions in vivo at well-tolerated doses. Compared to KRASG12C, KRASG13C exhibits a higher rate of spontaneous nucleotide exchange, reducing its dependence on GEF reloading and sensitivity to upstream inhibitors (e.g., SHP2 and SOS1) and underscoring the need for direct KRASG13C inhibition. In addition, KRASG13C is uniquely sensitive to select GAPs, including NF1. In line with this observation, an analysis of the co-mutational landscape of KRASG13C patient tumor samples revealed a high prevalence of NF1LOF mutation, likely resulting in enhanced wild-type RAS signaling. Our preclinical combination data support a therapeutic strategy of mutant selective KRASG13C inhibition with RM-041 and co-targeting an upstream node, such as SHP2, to attenuate cooperative wild-type RAS signaling. In summary, RM-041 is a first-in-class, mutant-selective, oral, tricomplex inhibitor of KRASG13C(ON) with the potential to address an unmet need in patients with KRASG13C mutant cancer, supporting the advancement of RM-041 towards clinical evaluation. Citation Format: Christopher J. Schulze, Jim Cregg, Kyle J. Seamon, Yu Chi Yang, Zhican Wang, Lindsay S. Garrenton, Alun Bermingham, John E. Knox, Aidan Tomlinson, Kang-Jye Chou, Shaoling Li, David P. Wildes, Mallika Singh, Elena S. Koltun, Adrian L. Gill, Robert J. Nichols, Jacqueline A. Smith. A first-in-class tri-complex KRASG13C(ON) inhibitor validates therapeutic targeting of KRASG13Cand drives tumor regressions in preclinical models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3598.

Abstract 3595: RMC-6291, a next-generation tri-complex KRASG12C(ON) inhibitor, outperforms KRASG12C(OFF) inhibitors in preclinical models of KRASG12C cancers

Abstract The KRASG12C mutation is found in 11% of non-small cell lung cancers, 4% of colorectal cancers, and 2% of pancreatic cancers in the U.S., and drives these cancers by shifting the cellular equilibrium of KRAS towards the GTP-bound, active state, KRASG12C(ON). The resulting increased levels of KRASG12C(ON) in turn increase signaling output to initiate and support the oncogenic state. In recent years, a class of KRASG12C(OFF) inhibitors has transformed the treatment landscape for patients with cancers bearing KRASG12C. These inhibitors work via sequestration of the GDP-bound, inactive state, KRASG12C(OFF), starving cancer cells of their oncogenic driver, KRASG12C(ON). Recent reports on the nature of resistance to KRASG12C(OFF) inhibitors suggest this class of drugs can be overcome through reactivation of KRASG12C to the ON form. Direct inhibition of KRASG12C(ON) with a first in class, potent, orally bioavailable, selective, tri-complex inhibitor RMC-6291, represents a more robust approach and presents the possibility that RMC-6291 will be a ‘best-in-class’ inhibitor of tumors harboring KRASG12C. RMC-6291 is a potent covalent inhibitor of KRASG12C(ON) that forms a tri-complex within tumor cells between KRASG12C(ON) and cyclophilin A (CypA), a highly abundant immunophilin. The assembled tri-complex prevents KRASG12C(ON) from signaling via steric blockade of RAS effector binding. In cells, kinetic analyses demonstrate near-immediate disruption of RAS effector binding and extinction of KRASG12C(ON) signaling. Oral administration of RMC-6291 produces deep and durable suppression of RAS pathway activity in KRASG12C tumor models and drives profound tumor regressions in vivo at well-tolerated doses. In a mouse clinical trial consisting of multiple patient- and cell line-derived xenograft models of KRASG12C NSCLC, RMC-6291 outperformed adagrasib, a KRASG12C(OFF) inhibitor, by increasing the number of responses, the depth of tumor regressions, and the durability of responses. Combination treatment with RMC-6291 and SHP2 or SOS1 inhibitors was well tolerated in preclinical models and further increased anti-tumor activity, likely by preventing reactivation of wild-type RAS proteins that cooperate with KRASG12C to fuel cancer growth. RMC-6291 also combined well with immune checkpoint inhibitors, sensitizing KRASG12C-bearing cancer models to anti-tumor immunity. RMC-6291 is a next-generation, mutant-selective inhibitor of KRASG12C(ON) that overcomes limitations of first-generation KRASG12C(OFF) inhibitors in preclinical models by directly targeting the active form of this important oncogenic driver. Citation Format: Robert J. Nichols, Y.C. Yang, Jim Cregg, Chris J. Schulze, Zhican Wang, Richa Dua, Jingjing Jiang, Lindsay S. Garrenton, Nicole Nasholm, Alun Bermingham, John E. Knox, Kyle Seamon, Michael Longhi, Kang-Jye Chou, Shaoling Li, David P. Wildes, Mallika Singh, Elena S. Koltun, Adrian L. Gill, Jacqueline A.M. Smith. RMC-6291, a next-generation tri-complex KRASG12C(ON) inhibitor, outperforms KRASG12C(OFF) inhibitors in preclinical models of KRASG12C cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3595.

Binding of the transcription activator-like effector augments transcriptional regulation by another transcription factor.

DNA transcription is regulated by a range of diverse mechanisms and primarily by transcription factors that recruit the RNA polymerase complex to the promoter region on the DNA. Protein binding to DNA at nearby or distant sites can synergistically affect this process in a variety of ways, but mainly through direct interactions between DNA-binding proteins. Here we show that a Transcription Activator-Like Effector (TALE), which lacks an activation domain, can enhance transcription in mammalian cells when it binds in the vicinity of and without direct interaction with several different dimeric or monomeric transcription factors. This effect was observed for several TALEs regardless of the recognition sequences and their DNA-bound orientation. TALEs can exert an effect over the distance of tens of nucleotides and it also potentiated KRAB-mediated repression. The augmentation of transcriptional regulation of another transcription factor is characteristic of TALEs, as it was not observed for dCas9/gRNA, zinc finger, or Gal4 DNA-binding domains. We propose that this mechanism involves an allosteric effect exerted on DNA structure or dynamics. This mechanism could be used to modulate transcription but may also play a role in the natural context of TALEs.

Structural basis of transcription activation by Rob, a pleiotropic AraC/XylS family regulator.

Rob, which serves as a paradigm of the large AraC/XylS family transcription activators, regulates diverse subsets of genes involved in multidrug resistance and stress response. However, the underlying mechanism of how it engages bacterial RNA polymerase and promoter DNA to finely respond to environmental stimuli is still elusive. Here, we present two cryo-EM structures of Rob-dependent transcription activation complex (Rob-TAC) comprising of Escherichia coli RNA polymerase (RNAP), Rob-regulated promoter and Rob in alternative conformations. The structures show that a single Rob engages RNAP by interacting with RNAP αCTD and σ70R4, revealing their generally important regulatory roles. Notably, by occluding σ70R4 from binding to -35 element, Rob specifically binds to the conserved Rob binding box through its consensus HTH motifs, and retains DNA bending by aid of the accessory acidic loop. More strikingly, our ligand docking and biochemical analysis demonstrate that the large Rob C-terminal domain (Rob CTD) shares great structural similarity with the global Gyrl-like domains in effector binding and allosteric regulation, and coordinately promotes formation of competent Rob-TAC. Altogether, our structural and biochemical data highlight the detailed molecular mechanism of Rob-dependent transcription activation, and provide favorable evidences for understanding the physiological roles of the other AraC/XylS-family transcription factors.

The Rice ILI2 Locus Is a Bidirectional Target of the African Xanthomonas oryzae pv. oryzae Major Transcription Activator-like Effector TalC but Does Not Contribute to Disease Susceptibility.

Xanthomonas oryzae pv. oryzae (Xoo) strains that cause bacterial leaf blight (BLB) limit rice (Oryza sativa) production and require breeding more resistant varieties. Transcription activator-like effectors (TALEs) activate transcription to promote leaf colonization by binding to specific plant host DNA sequences termed effector binding elements (EBEs). Xoo major TALEs universally target susceptibility genes of the SWEET transporter family. TALE-unresponsive alleles of clade III OsSWEET susceptibility gene promoter created with genome editing confer broad resistance on Asian Xoo strains. African Xoo strains rely primarily on the major TALE TalC, which targets OsSWEET14. Although the virulence of a talC mutant strain is severely impaired, abrogating OsSWEET14 induction with genome editing does not confer equivalent resistance on African Xoo. To address this contradiction, we postulated the existence of a TalC target susceptibility gene redundant with OsSWEET14. Bioinformatics analysis identified a rice locus named ATAC composed of the INCREASED LEAF INCLINATION 2 (ILI2) gene and a putative lncRNA that are shown to be bidirectionally upregulated in a TalC-dependent fashion. Gain-of-function approaches with designer TALEs inducing ATAC sequences did not complement the virulence of a Xoo strain defective for SWEET gene activation. While editing the TalC EBE at the ATAC loci compromised TalC-mediated induction, multiplex edited lines with mutations at the OsSWEET14 and ATAC loci remained essentially susceptible to African Xoo strains. Overall, this work indicates that ATAC is a probable TalC off-target locus but nonetheless documents the first example of divergent transcription activation by a native TALE during infection.

Quantitative Analysis of Dynamic Allostery.

Dynamic allostery refers to one important class of allosteric regulation that does not involve noticeable conformational changes upon effector binding. In recent years, many "quasi"-dynamic allosteric proteins have been found to only experience subtle conformational changes during allosteric regulation. However, as enthalpic and entropic contributions are coupled to each other and even tiny conformational changes could bring in noticeable free energy changes, a quantitative description is essential to understand the contribution of pure dynamic allostery. Here, by developing a unified anisotropic elastic network model (uANM) considering both side-chain information and ligand heavy atoms, we quantitatively estimated the contribution of pure dynamic allostery in a dataset of known allosteric proteins by excluding the conformational changes upon ligand binding. We found that the contribution of pure dynamic allostery is generally small (much weaker than previously expected) and robustly exhibits an allosteric activation effect, which exponentially decays with the distance between the substrate and the allosteric ligand. We further constructed toy models to study the determinant factors of dynamic allostery in monomeric and oligomeric proteins using the uANM. Analysis of the toy models revealed that a short distance, a small angle between the two ligands, strong protein-ligand interactions, and weak protein internal interactions lead to strong dynamic allostery. Our study provides a quantitative estimation of pure dynamic allostery and facilitates the understanding of dynamic-allostery-controlled biological processes and the design of allosteric drugs and proteins.

Alternative GTPase‐deficient mutants of Gα12/13 show differences in signaling potency and effector binding

Heterotrimeric G proteins are implicated in tumorigenic signaling in a variety of cancer types. Although G protein α subunits of the Gs, Gi, and Gq subfamilies have been found in tumors as mutationally activated, GTPase‐deficient variants, the G12/13 subfamily has the unusual property of participating in cancer progression as an overexpressed, wildtype form. Recent work by Maziarz et al. (2020) identified two “hotspot” mutations at the Arg200 position of Gα13 in bladder tumor samples, demonstrating that mutational activation of G12/13 subfamily proteins may also play a role in cancer progression. Although corresponding mutations at this Arg residue in Gα12 have not been located in tumors, the recent findings for Gα13 suggest that such Gα12 mutants may be identified in future work. Most in vitro signaling studies employing constitutively active Gα12 and/or Gα13 have utilized a Gln‐to‐Leu (QL) substitution in the switch II region to eliminate GTPase activity. Therefore, we sought to compare these QL variants of Gα12 and Gα13 to the recently reported Arg mutants in several G12/13‐specific signaling readouts. We engineered the previously identified hotspot Gα13 mutants (R200K and R200G) along with corresponding mutants of Gα12 (R203K and R203G). Our preliminary findings from reporter gene assays in HEK293 cells suggest that Gα12.R203K and Gα12.R203G are more potent than the Gα12.QL variant in driving two pathways implicated in Gα12‐mediated tumor progression: serum response factor (SRF) and YAP/TAZ. Gα13.R200K and Gα13.R200G appear to stimulate SRF and TEAD reporters at a similar strength to Gα13.QL, consistent with the findings of Maziarz et al. In addition, we investigated binding of these mutants to the RGS‐homology RhoGEFs LARG, p115RhoGEF, and PDZ‐RhoGEF. Unexpectedly, Gα13.R200G showed a RhoGEF binding profile that was different from Gα13.QL, suggesting these GTPase‐deficient mutants differ in their affinity for specific effector proteins. We currently are examining the comparative binding of these mutants to other targets such as epithelial cadherin (E‐cadherin) and radixin. Further, we found these activated Gα12/13 mutants to cause a decrease in cellular levels of E‐cadherin. Interestingly, these mutants appear to have differential effects on E‐cadherin levels compared to QL variants of Gα12/13. We have found this difference to be most pronounced between Gα12 Arg and QL mutants, in comparison to the Gα13 mutants. Due to our recent finding that Gα12 and Gα13 cause an increase in levels of calreticulin, a protein reported to down‐regulate E‐cadherin gene expression, we are using RNA interference to test the hypothesis that Gα12 and/or Gα13 modulate E‐cadherin levels in a calreticulin‐dependent manner.

Identification of Peptide Inhibitors of Gαs that Block its Effector Binding Site

Heterotrimeric G proteins (Gαβγ) are molecular switches that alternate between “on” (GTP‐bound) and “off” (GDP‐bound) states to control the flow of signals from the extracellular milieu to the cytoplasm. Gαs is a prototypical Gα subunit of heterotrimeric G proteins. When bound to GTP, Gαs promotes the synthesis of cAMP in the cytosol through stimulation of the enzymatic activity of adenylyl cyclases. Dysregulation of this mechanism leads to human diseases. For example, naturally occurring mutations like R201C lock Gαs in an active conformation that leads to signaling hyperactivity in cancer. Despite the critical role of Gαs in signaling and its involvement in disease, there are currently no chemical or peptide tools to specifically inhibit its signaling activity. We reasoned that peptides that bind to active Gαs and block the effector binding site would inhibit its ability to signal through adenylyl cyclases. For this, we screened peptides from a phage display library and identified two unrelated peptides that bound to active Gαs. These peptides bound efficiently to GTP‐bound Gαs or to the constitutively active Gαs R201C mutant, but not to inactive GDP‐bound Gαs. Fluorescence polarization experiments revealed an equilibrium dissociation constant (KD) of approximately 1 μM for the binding of these peptides to Gαs‐GTP. Mutations in the adenylyl cyclase binding region of Gαs greatly reduced binding of these two peptides, indicating that they may work as competitive inhibitors of adenylyl cyclase stimulation. Consistently, both peptides blocked Gas‐mediated stimulation of adenylyl cyclase activity in vitrowith μM potency, but had no effect on Gαs‐independent stimulation of adenylyl cyclase activity by forskolin. Protein‐protein binding experiments revealed that one of the two peptides bound to Gαs but not to Gα subunits of other G protein families, whereas the second peptide bound to Gαi‐GTP in addition to Gαs‐GTP. In summary, we have identified a peptide inhibitor specific for Gαs‐GTP that acts by binding to its effector binding site and precluding adenylyl cyclase stimulation. The peptide identified here could be leveraged as a genetically‐encoded probe or derivatized as a cell‐penetrating peptide to inhibit Gαs‐mediated cell signaling.

Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase.

Deciphering the molecular mechanisms of enzymatic allosteric regulation requires the structural characterization of functional states and also their time evolution toward the formation of the allosterically activated ternary complex. The transient nature and usually slow millisecond time scale interconversion between these functional states hamper their experimental and computational characterization. Here, we combine extensive molecular dynamics simulations, enhanced sampling techniques, and dynamical networks to describe the allosteric activation of imidazole glycerol phosphate synthase (IGPS) from the substrate-free form to the active ternary complex. IGPS is a heterodimeric bienzyme complex whose HisH subunit is responsible for hydrolyzing glutamine and delivering ammonia for the cyclase activity in HisF. Despite significant advances in understanding the underlying allosteric mechanism, essential molecular details of the long-range millisecond allosteric activation of IGPS remain hidden. Without using a priori information of the active state, our simulations uncover how IGPS, with the allosteric effector bound in HisF, spontaneously captures glutamine in a catalytically inactive HisH conformation, subsequently attains a closed HisF:HisH interface, and finally forms the oxyanion hole in HisH for efficient glutamine hydrolysis. We show that the combined effector and substrate binding dramatically decreases the conformational barrier associated with oxyanion hole formation, in line with the experimentally observed 4500-fold activity increase in glutamine hydrolysis. The allosteric activation is controlled by correlated time-evolving dynamic networks connecting the effector and substrate binding sites. This computational strategy tailored to describe millisecond events can be used to rationalize the effect of mutations on the allosteric regulation and guide IGPS engineering efforts.

Conservation and Diversity in Allosteric Fingerprints of Proteins for Evolutionary-inspired Engineering and Design

Hand-in-hand work of physics and evolution delivered protein universe with diversity of forms, sizes, and functions. Pervasiveness and advantageous traits of allostery made it an important component of the protein function regulation, calling for thorough investigation of its structural determinants and evolution. Learning directly from nature, we explored here allosteric communication in several major folds and repeat proteins, including α/β and β-barrels, β-propellers, Ig-like fold, ankyrin and α/β leucine-rich repeat proteins, which provide structural platforms for many different enzymatic and signalling functions. We obtained a picture of conserved allosteric communication characteristic in different fold types, modifications of the structure-driven signalling patterns via sequence-determined divergence to specific functions, as well as emergence and potential diversification of allosteric regulation in multi-domain proteins and oligomeric assemblies. Our observations will be instrumental in facilitating the engineering and de novo design of proteins with allosterically regulated functions, including development of therapeutic biologics. In particular, results described here may guide the identification of the optimal structural platforms (e.g. fold type, size, and oligomerization states) and the types of diversifications/perturbations, such as mutations, effector binding, and order–disorder transition. The tunable allosteric linkage across distant regions can be used as a pivotal component in the design/engineering of modular biological systems beyond the traditional scaffolding function.

Predicting the binding of small molecules to nuclear receptors using machine learning.

Nuclear receptors (NRs) are important biological targets of endocrine-disrupting chemicals (EDCs). Identifying chemicals that can act as EDCs and modulate the function of NRs is difficult because of the time and cost of in vitro and in vivo screening to determine the potential hazards of the 100000s of chemicals that humans are exposed to. Hence, there is a need for computational approaches to prioritize chemicals for biological testing. Machine learning (ML) techniques are alternative methods that can quickly screen millions of chemicals and identify those that may be an EDC. Computational models of chemical binding to multiple NRs have begun to emerge. Recently, a Nuclear Receptor Activity (NuRA) dataset, describing experimentally derived small-molecule activity against various NRs has been created. We have used the NuRA dataset to develop an ensemble of ML-based models to predict the agonism, antagonism, binding and effector binding of small molecules to nine different human NRs. We defined the applicability domain of the ML models as a measure of Tanimoto similarity to the molecules in the training set, which enhanced the performance of the developed classifiers. We further developed a user-friendly web server named 'NR-ToxPred' to predict the binding of chemicals to the nine NRs using the best-performing models for each receptor. This web server is freely accessible at http://nr-toxpred.cchem.berkeley.edu. Users can upload individual chemicals using Simplified Molecular-Input Line-Entry System, CAS numbers or sketch the molecule in the provided space to predict the compound's activity against the different NRs and predict the binding mode for each.