A glutamine-based single ¿-helix scaffold to target globular proteins.

The binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. These interactions offer opportunities for therapeutic intervention but their modulation with small molecules is challenging because they bury large surfaces. Linear peptides that display the residues that are key for binding can be targeted to globular proteins when they form stable helices, which in most cases requires their chemical modification. Here we present rules to design peptides that fold into single α-helices by instead concatenating glutamine side chain to main chain hydrogen bonds recently discovered in polyglutamine helices. The resulting peptides are uncharged, contain only natural amino acids, and their sequences can be optimized to interact with specific targets. Our results provide design rules to obtain single α-helices for a wide range of applications in protein engineering and drug design.We thank Luis Serrano for help with the Agadir predictions and helpful discussions, Ben Lehner and Ernest Giralt for helpful discussions and the ICTS NMR facility, managed by the scientific and technological centers of the University of Barcelona (CCiT UB), for their help in NMR. B.M. acknowledges funding from the Asociación Española contra el Cáncer (FCAECC project #POSTD211371MATE). C.G. acknowledges a graduate fellowship from MINECO (PRE2018-084684). M.S.-N. acknowledges funding from MINECO (PID2020-119810RB-I00). M.S.-N. holds a Ramón y Cajal contract (RYC2018-024759-I) from the Spanish Ministry of Science, Innovation, and Universities. X.S. acknowledges funding from AGAUR (2017 SGR 324), MINECO (BIO2015-70092-R and PID2019-110198RB-I00), and the European Research Council (CONCERT, contract number 648201). B.B.K acknowledges funding from the Novo Nordisk Foundation (#NNF18OC0033926). M.O. acknowledges funding from the Instituto Nacional de Bioinformática, The EU BioExcel Centre of Excellence for HPC and the Spanish Ministry of Science (PID2021-122478NB-I00) and the Instituto de Salud Carlos III–Instituto Nacional de Bioinformatica (ISCIII PT 17/0009/0007 co-funded by the Fondo Europeo de Desarrollo Regional). M.O. is an ICREA Academy scholar and J.A. is a Juan de la Cierva fellow. M.C. was supported by institutional funds of the Max Planck Society. This project has been carried out using the resources of CSUC. IRB Barcelona is the recipient of a Severo Ochoa Award of Excellence from MINECO (Government of Spain)

A glutamine-based single α-helix scaffold to target globular proteins

The binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. These interactions offer opportunities for therapeutic intervention but their modulation with small molecules is challenging because they bury large surfaces. Linear peptides that display the residues that are key for binding can be targeted to globular proteins when they form stable helices, which in most cases requires their chemical modification. Here we present rules to design peptides that fold into single α-helices by instead concatenating glutamine side chain to main chain hydrogen bonds recently discovered in polyglutamine helices. The resulting peptides are uncharged, contain only natural amino acids, and their sequences can be optimized to interact with specific targets. Our results provide design rules to obtain single α-helices for a wide range of applications in protein engineering and drug design.We thank Luis Serrano for help with the Agadir predictions and helpful discussions, Ben Lehner and Ernest Giralt for helpful discussions and the ICTS NMR facility, managed by the scientific and technological centers of the University of Barcelona (CCiT UB), for their help in NMR. B.M. acknowledges funding from the Asociación Española contra el Cáncer (FCAECC project #POSTD211371MATE). C.G. acknowledges a graduate fellowship from MINECO (PRE2018-084684). M.S.-N. acknowledges funding from MINECO (PID2020-119810RB-I00). M.S.-N. holds a Ramón y Cajal contract (RYC2018-024759-I) from the Spanish Ministry of Science, Innovation, and Universities. X.S. acknowledges funding from AGAUR (2017 SGR 324), MINECO (BIO2015-70092-R and PID2019-110198RB-I00), and the European Research Council (CONCERT, contract number 648201). B.B.K acknowledges funding from the Novo Nordisk Foundation (#NNF18OC0033926). M.O. acknowledges funding from the Instituto Nacional de Bioinformática, The EU BioExcel Centre of Excellence for HPC and the Spanish Ministry of Science (PID2021-122478NB-I00) and the Instituto de Salud Carlos III–Instituto Nacional de Bioinformatica (ISCIII PT 17/0009/0007 co-funded by the Fondo Europeo de Desarrollo Regional). M.O. is an ICREA Academy scholar and J.A. is a Juan de la Cierva fellow. M.C. was supported by institutional funds of the Max Planck Society. This project has been carried out using the resources of CSUC. IRB Barcelona is the recipient of a Severo Ochoa Award of Excellence from MINECO (Government of Spain).Peer reviewe

Aberrant phase separation and nucleolar dysfunction in rare genetic diseases

Thousands of genetic variants in protein-coding genes have been linked to disease. However, the functional impact of most variants is unknown as they occur within intrinsically disordered protein regions that have poorly defined functions1-3. Intrinsically disordered regions can mediate phase separation and the formation of biomolecular condensates, such as the nucleolus4,5. This suggests that mutations in disordered proteins may alter condensate properties and function6-8. Here we show that a subset of disease-associated variants in disordered regions alter phase separation, cause mispartitioning into the nucleolus and disrupt nucleolar function. We discover de novo frameshift variants in HMGB1 that cause brachyphalangy, polydactyly and tibial aplasia syndrome, a rare complex malformation syndrome. The frameshifts replace the intrinsically disordered acidic tail of HMGB1 with an arginine-rich basic tail. The mutant tail alters HMGB1 phase separation, enhances its partitioning into the nucleolus and causes nucleolar dysfunction. We built a catalogue of more than 200,000 variants in disordered carboxy-terminal tails and identified more than 600 frameshifts that create arginine-rich basic tails in transcription factors and other proteins. For 12 out of the 13 disease-associated variants tested, the mutation enhanced partitioning into the nucleolus, and several variants altered rRNA biogenesis. These data identify the cause of a rare complex syndrome and suggest that a large number of genetic variants may dysregulate nucleoli and other biomolecular condensates in humans.© 2023. The Author(s)

Liquid-liquid phase separation in gene regulation and disease

[eng] Intrinsically disordered (ID) proteins or regions are protein sequences that lack stable secondary and tertiary structures. ID proteins are particularly prone to undergo liquid- liquid phase separation (LLPS). The structures arising from this physical process are usually termed liquid droplets in vitro or biomolecular condensates in cells. The importance of LLPS in biological processes has been recognized in the last years, as the formation of biomolecular condensates allows for the efficient regulation of key cellular processes such as transcription or translation regulation. Additionally, mis- regulation of LLPS has been proposed as a disease mechanism. Generally, disease mutations can also cause liquid-to-solid phase transitions, a process named maturation. The general aim of this thesis was to characterize from a physicochemical point of view the LLPS of different protein systems involved in highly relevant biological processes: in transcription and translation regulation as well as in protein sorting. Additionally, we also assessed the effect of disease-related point mutations or alternative splicing on the LLPS process of proteins related to muscular dystrophy and autism spectrum disorder. We used a wide set of physical techniques such as nuclear magnetic resonance spectroscopy and apparent absorbance measurements, as well as optical and fluorescence microscopy experiments. We determined that the androgen and progesterone nuclear hormone receptors undergo LLPS, but the resulting liquid droplets are stabilized by different types of intermolecular interactions. Also, a protein that carries out its translational regulator function through LLPS, CPEB4, forms liquid droplets cooperatively which are stabilized by π-π and cation-π interactions. LLPS is also a possible mechanism for protein sorting at the Golgi apparatus, through the formation of biomolecular condensates by the TGN46 transmembrane protein. Disease mutations of ANXA11 increase the aggregation propensity of the protein leading to the formation of protein inclusions. Finally, CPEB4 mis-splicing related to autism spectrum disorder decreases the reversibility of the liquid droplets by promoting a liquid-to-solid phase transition. In summary, LLPS is a highly relevant phenomenon in biology because of its involvement in key processes such as transcription or translation regulation and protein sorting, and defects on LLPS can lead to disease, generally due to a liquid-to-solid maturation process. Understanding of the intermolecular interactions stabilizing the phase separated states can be used to design potential drugs to target ID proteins in their biomolecular condensates for treatment of diseases.[cat] Les proteïnes o regions intrínsecament desordenades (ID) són seqüències de proteïnes que manquen una estructura secundària i terciària estables. Les proteïnes ID són especialment propenses a experimentar separació de fases líquid-líquid (LLPS). Les estructures que es formen degut a aquest procés físic s’anomenen normalment gotes líquides in vitro o condensats biomoleculars en cèl·lules. La importància de la LLPS en processos biològics s’ha reconegut ens els últims anys, ja que s’ha vist que la formació de condensats biomoleculars permet l’eficient regulació de processos cel·lulars clau. En aquesta tesi s’ha caracteritzat des d’un punt de vista fisicoquímic la LLPS de diferents sistemes proteics involucrats en processos de gran rellevància biològica: en la regulació de la transcripció i traducció, així com en classificació i secreció de proteïnes. A més a més, també s’ha estudiat l’efecte de mutacions relacionades amb malalties i del splicing alternatiu sobre el procés de LLPS de proteïnes involucrades en malalties, que en general promouen una maduració de les gotes líquides, és a dir, una transició de líquid a sòlid. S’han utilitzat un ampli espectre de tècniques físiques per caracteritzar les interaccions intermoleculars i les propietats de les gotes líquides, incloent per exemple espectroscòpia de ressonància magnètica nuclear, mesures d’absorbància aparent i experiments de microscòpia òptica i de fluorescència. Poder entendre les interaccions intermoleculars que tenen lloc entre proteïnes per estabilitzar l’estat de separació de fases permet dissenyar fàrmacs dirigits a proteïnes ID en els condensats biomoleculars que formen per tractar malalties

Low amounts of heavy water increase the phase separation propensity of a fragment of the androgen receptor activation domain

The phase equilibria of intrinsically disordered proteins are exquisitely sensitive to changes in solution conditions and this can be used to investigate the driving forces of phase separation in vitro as well as the biological roles of phase transitions in live cells. Here we investigate how using D2O as co-solvent in an aqueous buffer changes the phase equilibrium of a fragment of the activation domain of the androgen receptor, a transcription factor that plays a role in the development of the male phenotype and is a therapeutic target for castration resistant prostate cancer. We show how replacing even small fractions of H2O with D2O increases the propensity of this fragment to undergo liquid-liquid phase separation, likely reflecting a stabilization of the hydrophobic interactions that drive condensation. Our results indicate that it is necessary to take this effect into consideration when studying phase separation phenomena with biophysical methods that require using D2O as a co-solvent. In addition, they suggest that additions of D2O may be used to enhance phase separation phenomena in cells, facilitating their observation

Low amounts of heavy water increase the phase separation propensity of a fragment of the androgen receptor activation domain

The phase equilibria of intrinsically disordered proteins are exquisitely sensitive to changes in solution conditions and this can be used to investigate the driving forces of phase separation in vitro as well as the biological roles of phase transitions in live cells. Here we investigate how using D2O as co-solvent in an aqueous buffer changes the phase equilibrium of a fragment of the activation domain of the androgen receptor, a transcription factor that plays a role in the development of the male phenotype and is a therapeutic target for castration resistant prostate cancer. We show how replacing even small fractions of H2O with D2O increases the propensity of this fragment to undergo liquid-liquid phase separation, likely reflecting a stabilization of the hydrophobic interactions that drive condensation. Our results indicate that it is necessary to take this effect into consideration when studying phase separation phenomena with biophysical methods that require using D2O as a co-solvent. In addition, they suggest that additions of D2O may be used to enhance phase separation phenomena in cells, facilitating their observation

CEBPA phase separation links transcriptional activity and 3D chromatin hubs

We thank the Graf lab members for helpful discussions, and the CRG Genomics, Flow Cytometry and Advanced Light Microscopy core facilities; M.C.-K. was supported by an EMBO postdoctoral fellowship (ALTF 1057-2019) and PCIN-MSCA-fellowship (Ministerio de Ciencia e Innovación PCI2021-122032-2B). S.C. is supported by a "La Caixa" Junior Leader fellowship, by the Jérôme Lejeune Foundation (JLF#1902) and the Spanish Ministry of Science and Innovation (PID2020-117950RA-I00). G.S. was supported by the "Fundación Científica de la Asociación Española Contra el Cáncer. " M.V.N. was supported by People Program (Marie Curie Actions) FP7/2007-2013 under REA grant 6089 and Juan de la Cierva-Incorporación 2017. C.G.-C. acknowledges a graduate fellowship from MINECO (PRE2018-084684). X.S. acknowledges funding from AGAUR (2017 SGR 324), MINECO (BIO2015-70092-R and PID2019-110198RB-I00), and the European Research Council (CONCERT, contract number 648201). This work was funded by the Max Planck Society and partially supported by grants from the Deutsche Forschungsgemeinschaft (DFG) SPP2202 Priority Program Grant HN 4/1-1 (to D.H.) and by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) Plan Estatal 2015, SAF.2015-68740-P (to T.G.). We acknowledge support by the Spanish Ministry of Science and Innovation, to the EMBL partnership, the Centro de Excelencia Severo Ochoa, the Josep Carreras Foundation, and the CERCA Programme / Generalitat de Catalunya.Cell identity is orchestrated through an interplay between transcription factor (TF) action and genome architecture. The mechanisms used by TFs to shape three-dimensional (3D) genome organization remain incompletely understood. Here we present evidence that the lineage-instructive TF CEBPA drives extensive chromatin compartment switching and promotes the formation of long-range chromatin hubs during induced B cell-to-macrophage transdifferentiation. Mechanistically, we find that the intrinsically disordered region (IDR) of CEBPA undergoes in vitro phase separation (PS) dependent on aromatic residues. Both overexpressing B cells and native CEBPA-expressing cell types such as primary granulocyte-macrophage progenitors, liver cells, and trophectoderm cells reveal nuclear CEBPA foci and long-range 3D chromatin hubs at CEBPA-bound regions. In short, we show that CEBPA can undergo PS through its IDR, which may underlie in vivo foci formation and suggest a potential role of PS in regulating CEBPA function

Common pathophysiology for ANXA11 disorders caused by aspartate 40 variants

Abstract Objective Mutations in ANXA11 cause amyotrophic lateral sclerosis (ALS) and have recently been identified as a cause of multisystem proteinopathy and adult‐onset muscular dystrophy. These conditions are adult‐onset diseases and result from the substitution of Aspartate 40 (Asp40) for an apolar residue in the intrinsically disordered domain (IDD) of ANXA11. Some ALS‐related variants are known to affect ANXA11 IDD; however, the mechanism by which the myopathy occurs is unknown. Methods Genetic analysis was performed using WES‐trio. For the study of variant pathogenicity, we used recombinant proteins, muscle biopsy, and fibroblasts. Results Here we describe an individual with severe and rapidly progressive childhood‐onset oculopharyngeal muscular dystrophy who carries a new ANXA11 variant at position Asp40 (p.Asp40Ile; c.118_119delGAinsAT). p.Asp40Ile is predicted to enhance the aggregation propensity of ANXA11 to a greater extent than other changes affecting this residue. In vitro studies using recombinant ANXA11p.Asp40Ile showed abnormal phase separation and confirmed this variant is more aggregation‐prone than the ALS‐associated variant ANXA11p.Asp40Gly. The study of the patient's fibroblasts revealed defects in stress granules dynamics and clearance, and muscle histopathology showed a myopathic pattern with ANXA11 protein aggregates. Super‐resolution imaging showed aggregates expressed as pearl strips or large complex structures in the sarcoplasm, and as layered subsarcolemmal chains probably reflecting ANXA11 multifunctionality. Interpretation We demonstrate common pathophysiology for disorders associated with ANXA11 Asp40 allelic variants. Clinical phenotypes may result from different deleterious impacts of variants upon ANXA11 stability against aggregation, and differential muscle or motor neuron dysfunction expressed as a temporal and tissue‐specific continuum

CEBPA phase separation links transcriptional activity and 3D chromatin hubs

Summary: Cell identity is orchestrated through an interplay between transcription factor (TF) action and genome architecture. The mechanisms used by TFs to shape three-dimensional (3D) genome organization remain incompletely understood. Here we present evidence that the lineage-instructive TF CEBPA drives extensive chromatin compartment switching and promotes the formation of long-range chromatin hubs during induced B cell-to-macrophage transdifferentiation. Mechanistically, we find that the intrinsically disordered region (IDR) of CEBPA undergoes in vitro phase separation (PS) dependent on aromatic residues. Both overexpressing B cells and native CEBPA-expressing cell types such as primary granulocyte-macrophage progenitors, liver cells, and trophectoderm cells reveal nuclear CEBPA foci and long-range 3D chromatin hubs at CEBPA-bound regions. In short, we show that CEBPA can undergo PS through its IDR, which may underlie in vivo foci formation and suggest a potential role of PS in regulating CEBPA function