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1.
Nucleic Acids Res ; 52(1): 370-384, 2024 Jan 11.
Artículo en Inglés | MEDLINE | ID: mdl-37994783

RESUMEN

The phospholipase D (PLD) family is comprised of enzymes bearing phospholipase activity towards lipids or endo- and exonuclease activity towards nucleic acids. PLD3 is synthesized as a type II transmembrane protein and proteolytically cleaved in lysosomes, yielding a soluble active form. The deficiency of PLD3 leads to the slowed degradation of nucleic acids in lysosomes and chronic activation of nucleic acid-specific intracellular toll-like receptors. While the mechanism of PLD phospholipase activity has been extensively characterized, not much is known about how PLDs bind and hydrolyze nucleic acids. Here, we determined the high-resolution crystal structure of the luminal N-glycosylated domain of human PLD3 in its apo- and single-stranded DNA-bound forms. PLD3 has a typical phospholipase fold and forms homodimers with two independent catalytic centers via a newly identified dimerization interface. The structure of PLD3 in complex with an ssDNA-derived thymidine product in the catalytic center provides insights into the substrate binding mode of nucleic acids in the PLD family. Our structural data suggest a mechanism for substrate binding and nuclease activity in the PLD family and provide the structural basis to design immunomodulatory drugs targeting PLD3.


Asunto(s)
Exodesoxirribonucleasas , Fosfolipasa D , Humanos , Lisosomas/metabolismo , Fosfolipasa D/química , Fosfolipasas , Exodesoxirribonucleasas/química
2.
Proc Natl Acad Sci U S A ; 120(4): e2208941120, 2023 01 24.
Artículo en Inglés | MEDLINE | ID: mdl-36656859

RESUMEN

p97 is an essential AAA+ ATPase that extracts and unfolds substrate proteins from membranes and protein complexes. Through its mode of action, p97 contributes to various cellular processes, such as membrane fusion, ER-associated protein degradation, DNA repair, and many others. Diverse p97 functions and protein interactions are regulated by a large number of adaptor proteins. Alveolar soft part sarcoma locus (ASPL) is a unique adaptor protein that regulates p97 by disassembling functional p97 hexamers to smaller entities. An alternative mechanism to regulate the activity and interactions of p97 is by posttranslational modifications (PTMs). Although more than 140 PTMs have been identified in p97, only a handful of those have been described in detail. Here we present structural and biochemical data to explain how the p97-remodeling adaptor protein ASPL enables the metastasis promoting methyltransferase METTL21D to bind and trimethylate p97 at a single lysine side chain, which is deeply buried inside functional p97 hexamers. The crystal structure of a heterotrimeric p97:ASPL:METTL21D complex in the presence of cofactors ATP and S-adenosyl homocysteine reveals how structural remodeling by ASPL exposes the crucial lysine residue of p97 to facilitate its trimethylation by METTL21D. The structure also uncovers a role of the second region of homology (SRH) present in the first ATPase domain of p97 in binding of a modifying enzyme to the AAA+ ATPase. Investigation of this interaction in the human, fish, and plant reveals fine details on the mechanism and significance of p97 trimethylation by METTL21D across different organisms.


Asunto(s)
ATPasas Asociadas con Actividades Celulares Diversas , Adenosina Trifosfatasas , Metiltransferasas , Animales , Humanos , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Adenosina Trifosfatasas/metabolismo , ATPasas Asociadas con Actividades Celulares Diversas/metabolismo , Lisina/metabolismo , Metilación , Unión Proteica , Procesamiento Proteico-Postraduccional , Factores de Transcripción/metabolismo , Proteína que Contiene Valosina/metabolismo , Metiltransferasas/metabolismo
3.
Proc Natl Acad Sci U S A ; 120(17): e2217070120, 2023 04 25.
Artículo en Inglés | MEDLINE | ID: mdl-37068239

RESUMEN

Studying mechanisms of bacterial biofilm generation is of vital importance to understanding bacterial cell-cell communication, multicellular cohabitation principles, and the higher resilience of microorganisms in a biofilm against antibiotics. Biofilms of the nonpathogenic, gram-positive soil bacterium Bacillus subtilis serve as a model system with biotechnological potential toward plant protection. Its major extracellular matrix protein components are TasA and TapA. The nature of TasA filaments has been of debate, and several forms, amyloidic and non-Thioflavin T-stainable have been observed. Here, we present the three-dimensional structure of TapA and uncover the mechanism of TapA-supported growth of nonamyloidic TasA filaments. By analytical ultracentrifugation and NMR, we demonstrate TapA-dependent acceleration of filament formation from solutions of folded TasA. Solid-state NMR revealed intercalation of the N-terminal TasA peptide segment into subsequent protomers to form a filament composed of ß-sandwich subunits. The secondary structure around the intercalated N-terminal strand ß0 is conserved between filamentous TasA and the Fim and Pap proteins, which form bacterial type I pili, demonstrating such construction principles in a gram-positive organism. Analogous to the chaperones of the chaperone-usher pathway, the role of TapA is in donating its N terminus to serve for TasA folding into an Ig domain-similar filament structure by donor-strand complementation. According to NMR and since the V-set Ig fold of TapA is already complete, its participation within a filament beyond initiation is unlikely. Intriguingly, the most conserved residues in TasA-like proteins (camelysines) of Bacillaceae are located within the protomer interface.


Asunto(s)
Bacillus subtilis , Proteínas Bacterianas , Proteínas Bacterianas/metabolismo , Bacillus subtilis/metabolismo , Espectroscopía de Resonancia Magnética , Estructura Secundaria de Proteína , Chaperonas Moleculares/metabolismo , Biopelículas
4.
Nat Chem Biol ; 19(10): 1196-1204, 2023 10.
Artículo en Inglés | MEDLINE | ID: mdl-37142807

RESUMEN

Presentation of antigenic peptides by major histocompatibility complex class II (MHC-II) proteins determines T helper cell reactivity. The MHC-II genetic locus displays a large degree of allelic polymorphism influencing the peptide repertoire presented by the resulting MHC-II protein allotypes. During antigen processing, the human leukocyte antigen (HLA) molecule HLA-DM (DM) encounters these distinct allotypes and catalyzes exchange of the placeholder peptide CLIP by exploiting dynamic features of MHC-II. Here, we investigate 12 highly abundant CLIP-bound HLA-DRB1 allotypes and correlate dynamics to catalysis by DM. Despite large differences in thermodynamic stability, peptide exchange rates fall into a target range that maintains DM responsiveness. A DM-susceptible conformation is conserved in MHC-II molecules, and allosteric coupling between polymorphic sites affects dynamic states that influence DM catalysis. As exemplified for rheumatoid arthritis, we postulate that intrinsic dynamic features of peptide-MHC-II complexes contribute to the association of individual MHC-II allotypes with autoimmune disease.


Asunto(s)
Antígenos HLA-D , Antígenos HLA-DR , Humanos , Antígenos HLA-D/metabolismo , Antígenos HLA-DR/metabolismo , Péptidos/química , Presentación de Antígeno , Catálisis , Unión Proteica
5.
Nat Chem Biol ; 19(1): 18-27, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-36109648

RESUMEN

Phosphatidylinositol 3-kinase type 2α (PI3KC2α) and related class II PI3K isoforms are of increasing biomedical interest because of their crucial roles in endocytic membrane dynamics, cell division and signaling, angiogenesis, and platelet morphology and function. Herein we report the development and characterization of PhosphatidylInositol Three-kinase Class twO INhibitors (PITCOINs), potent and highly selective small-molecule inhibitors of PI3KC2α catalytic activity. PITCOIN compounds exhibit strong selectivity toward PI3KC2α due to their unique mode of interaction with the ATP-binding site of the enzyme. We demonstrate that acute inhibition of PI3KC2α-mediated synthesis of phosphatidylinositol 3-phosphates by PITCOINs impairs endocytic membrane dynamics and membrane remodeling during platelet-dependent thrombus formation. PITCOINs are potent and selective cell-permeable inhibitors of PI3KC2α function with potential biomedical applications ranging from thrombosis to diabetes and cancer.


Asunto(s)
Fosfatidilinositol 3-Quinasa , Fosfatidilinositol 3-Quinasas , Fosfatidilinositol 3-Quinasas/metabolismo , Fosfatidilinositoles , Fosfatos de Fosfatidilinositol/metabolismo
6.
Nucleic Acids Res ; 49(9): 5369-5381, 2021 05 21.
Artículo en Inglés | MEDLINE | ID: mdl-33950203

RESUMEN

The CCCH-type zinc finger (ZnF) containing ZC3H12 ribonucleases are crucial in post-transcriptional immune homoeostasis with ZC3H12A being the only structurally studied member of the family. In this study, we present a structural-biochemical characterization of ZC3H12C, which is linked with chronic immune disorders like psoriasis. We established that the RNA substrate is cooperatively recognized by the PIN and ZnF domains of ZC3H12C and analyzed the crystal structure of ZC3H12C bound to a single-stranded RNA substrate. The RNA engages in hydrogen-bonded contacts and stacking interactions with the PIN and ZnF domains simultaneously. The ZC3H12 ZnF shows unprecedented structural features not previously observed in any member of the CCCH-ZnF family and utilizes stacking interactions via a unique combination of spatially conserved aromatic residues to align the target transcript in a bent conformation onto the ZnF scaffold. Further comparative structural analysis of ZC3H12 CCCH-ZnF suggests that a trinucleotide sequence is recognized by ZC3H12 ZnF in target RNA. Our work not only describes the initial structure-biochemical study on ZC3H12C, but also provides the first molecular insight into RNA recognition by a ZC3H12 family member. Finally, our work points to an evolutionary code for RNA recognition adopted by CCCH-type ZnF proteins.


Asunto(s)
ARN/química , Ribonucleasas/química , Regiones no Traducidas 3' , Animales , Cristalografía por Rayos X , Células HEK293 , Humanos , Interleucina-6/genética , Interleucina-6/metabolismo , Magnesio , Ratones , Modelos Moleculares , Unión Proteica , Dominios Proteicos , ARN/metabolismo , Ribonucleasas/metabolismo , Dedos de Zinc
7.
Proc Natl Acad Sci U S A ; 117(47): 29684-29690, 2020 11 24.
Artículo en Inglés | MEDLINE | ID: mdl-33184177

RESUMEN

Battling metastasis through inhibition of cell motility is considered a promising approach to support cancer therapies. In this context, Ena/VASP-depending signaling pathways, in particular interactions with their EVH1 domains, are promising targets for pharmaceutical intervention. However, protein-protein interactions involving proline-rich segments are notoriously difficult to address by small molecules. Hence, structure-based design efforts in combination with the chemical synthesis of additional molecular entities are required. Building on a previously developed nonpeptidic micromolar inhibitor, we determined 22 crystal structures of ENAH EVH1 in complex with inhibitors and rationally extended our library of conformationally defined proline-derived modules (ProMs) to succeed in developing a nanomolar inhibitor ([Formula: see text] Da). In contrast to the previous inhibitor, the optimized compounds reduced extravasation of invasive breast cancer cells in a zebrafish model. This study represents an example of successful, structure-guided development of low molecular weight inhibitors specifically and selectively addressing a proline-rich sequence-recognizing domain that is characterized by a shallow epitope lacking defined binding pockets. The evolved high-affinity inhibitor may now serve as a tool in validating the basic therapeutic concept, i.e., the suppression of cancer metastasis by inhibiting a crucial protein-protein interaction involved in actin filament processing and cell migration.


Asunto(s)
Neoplasias de la Mama/tratamiento farmacológico , Moléculas de Adhesión Celular/metabolismo , Proteínas de Unión al ADN/metabolismo , Proteínas de Microfilamentos/metabolismo , Fosfoproteínas/metabolismo , Dominios y Motivos de Interacción de Proteínas/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/farmacología , Animales , Neoplasias de la Mama/metabolismo , Línea Celular Tumoral , Movimiento Celular/efectos de los fármacos , Femenino , Humanos , Células Jurkat , Prolina/metabolismo , Unión Proteica/efectos de los fármacos , Pez Cebra
8.
J Biol Chem ; 296: 100286, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33450228

RESUMEN

Pathogenic microorganisms often reside in glycan-based biofilms. Concentration and chain length distribution of these mostly anionic exopolysaccharides (EPS) determine the overall biophysical properties of a biofilm and result in a highly viscous environment. Bacterial communities regulate this biofilm state via intracellular small-molecule signaling to initiate EPS synthesis. Reorganization or degradation of this glycan matrix, however, requires the action of extracellular glycosidases. So far, these were mainly described for bacteriophages that must degrade biofilms for gaining access to host bacteria. The plant pathogen Pantoea stewartii (P. stewartii) encodes the protein WceF within its EPS synthesis cluster. WceF has homologs in various biofilm forming plant pathogens of the Erwinia family. In this work, we show that WceF is a glycosidase active on stewartan, the main P. stewartii EPS biofilm component. WceF has remarkable structural similarity with bacteriophage tailspike proteins (TSPs). Crystal structure analysis showed a native trimer of right-handed parallel ß-helices. Despite its similar fold, WceF lacks the high stability found in bacteriophage TSPs. WceF is a stewartan hydrolase and produces oligosaccharides, corresponding to single stewartan repeat units. However, compared with a stewartan-specific glycan hydrolase of bacteriophage origin, WceF showed lectin-like autoagglutination with stewartan, resulting in notably slower EPS cleavage velocities. This emphasizes that the bacterial enzyme WceF has a role in P. stewartii biofilm glycan matrix reorganization clearly different from that of a bacteriophage exopolysaccharide depolymerase.


Asunto(s)
Proteínas Bacterianas/química , Biopelículas/crecimiento & desarrollo , Glicósido Hidrolasas/química , Pantoea/enzimología , Polisacáridos Bacterianos/química , Proteínas de la Cola de los Virus/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Bacteriófagos/química , Bacteriófagos/enzimología , Sitios de Unión , Secuencia de Carbohidratos , Clonación Molecular , Cristalografía por Rayos X , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Glicósido Hidrolasas/genética , Glicósido Hidrolasas/metabolismo , Modelos Moleculares , Oligosacáridos/química , Oligosacáridos/metabolismo , Pantoea/genética , Plantas/microbiología , Polisacáridos Bacterianos/metabolismo , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Multimerización de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Homología Estructural de Proteína , Proteínas de la Cola de los Virus/genética , Proteínas de la Cola de los Virus/metabolismo
9.
Proc Natl Acad Sci U S A ; 115(13): 3237-3242, 2018 03 27.
Artículo en Inglés | MEDLINE | ID: mdl-29531041

RESUMEN

Microorganisms form surface-attached communities, termed biofilms, which can serve as protection against host immune reactions or antibiotics. Bacillus subtilis biofilms contain TasA as major proteinaceous component in addition to exopolysaccharides. In stark contrast to the initially unfolded biofilm proteins of other bacteria, TasA is a soluble, stably folded monomer, whose structure we have determined by X-ray crystallography. Subsequently, we characterized in vitro different oligomeric forms of TasA by NMR, EM, X-ray diffraction, and analytical ultracentrifugation (AUC) experiments. However, by magic-angle spinning (MAS) NMR on live biofilms, a swift structural change toward only one of these forms, consisting of homogeneous and protease-resistant, ß-sheet-rich fibrils, was observed in vivo. Thereby, we characterize a structural change from a globular state to a fibrillar form in a functional prokaryotic system on the molecular level.


Asunto(s)
Bacillus subtilis/fisiología , Proteínas Bacterianas/química , Biopelículas/crecimiento & desarrollo , Bacillus subtilis/química , Proteínas Bacterianas/metabolismo , Calorimetría , Cristalografía por Rayos X , Concentración de Iones de Hidrógeno , Espectroscopía de Resonancia Magnética , Metaloendopeptidasas/química , Microscopía Electrónica , Modelos Moleculares , Peso Molecular , Conformación Proteica , Homología Estructural de Proteína , Ultracentrifugación
10.
J Struct Biol ; 211(2): 107536, 2020 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-32473201

RESUMEN

Complete genome sequencing of the kinetoplastid protozoans Trypanosoma cruzi, Trypanosoma brucei and Leishmania major (Tritryp), published in 2005, opened up new perspectives for drug development targeting Chagas disease, African sleeping sickness and Leishmaniasis, neglected diseases affecting millions of most economically disadvantaged people. Still, half of the Tritryp genes code for proteins of unknown function. Moreover, almost 50% of conserved eukaryotic protein domains are missing in the Tritryp genomes. This suggests that functional and structural characterization of proteins of unknown function could reveal novel protein folds used by the trypanosomes for common cellular processes. Furthermore, proteins without homologous counterparts in humans may provide potential targets for therapeutic intervention. Here we describe the crystal structure of the T. cruzi protein Q4D6Q6, a conserved and kinetoplastid-specific protein essential for cell viability. Q4D6Q6 is a representative of a family of 20 orthologs, all annotated as proteins of unknown function. Q4D6Q6 monomers adopt a ßßαßßαßß topology and form a propeller-like tetramer. Oligomerization was verified in solution using NMR, SAXS, analytical ultra-centrifugation and gel filtration chromatography. A rigorous search for similar structures using the DALI server revealed similarities with propeller-like structures of several different functions. Although a Q4D6Q6 function could not be inferred from such structural comparisons, the presence of an oxidized cysteine at position 69, part of a cluster with phosphorylated serines and hydrophobic residues, identifies a highly reactive site and suggests a role of this cysteine as a nucleophile in a post-translational modification reaction.


Asunto(s)
Proteínas Protozoarias/ultraestructura , Trypanosoma cruzi/ultraestructura , Animales , Humanos , Leishmania major/ultraestructura , Modelos Moleculares , Proteínas Protozoarias/genética , Dispersión del Ángulo Pequeño , Trypanosoma brucei brucei/ultraestructura , Trypanosoma cruzi/genética , Difracción de Rayos X
11.
J Biol Chem ; 294(31): 11751-11761, 2019 08 02.
Artículo en Inglés | MEDLINE | ID: mdl-31189652

RESUMEN

Myoviruses, bacteriophages with T4-like architecture, must contract their tails prior to DNA release. However, quantitative kinetic data on myovirus particle opening are lacking, although they are promising tools in bacteriophage-based antimicrobial strategies directed against Gram-negative hosts. For the first time, we show time-resolved DNA ejection from a bacteriophage with a contractile tail, the multi-O-antigen-specific Salmonella myovirus Det7. DNA release from Det7 was triggered by lipopolysaccharide (LPS) O-antigen receptors and notably slower than in noncontractile-tailed siphoviruses. Det7 showed two individual kinetic steps for tail contraction and particle opening. Our in vitro studies showed that highly specialized tailspike proteins (TSPs) are necessary to attach the particle to LPS. A P22-like TSP confers specificity for the Salmonella Typhimurium O-antigen. Moreover, crystal structure analysis at 1.63 Šresolution confirmed that Det7 recognized the Salmonella Anatum O-antigen via an ϵ15-like TSP, DettilonTSP. DNA ejection triggered by LPS from either host showed similar velocities, so particle opening is thus a process independent of O-antigen composition and the recognizing TSP. In Det7, at permissive temperatures TSPs mediate O-antigen cleavage and couple cell surface binding with DNA ejection, but no irreversible adsorption occurred at low temperatures. This finding was in contrast to short-tailed Salmonella podoviruses, illustrating that tailed phages use common particle-opening mechanisms but have specialized into different infection niches.


Asunto(s)
ADN Viral/metabolismo , Fagos de Salmonella/metabolismo , Salmonella typhimurium/virología , Cristalografía por Rayos X , Glicósido Hidrolasas , Lipopolisacáridos/farmacología , Antígenos O/metabolismo , Estructura Terciaria de Proteína , Fagos de Salmonella/efectos de los fármacos , Salmonella typhimurium/metabolismo , Proteínas de la Cola de los Virus/química , Proteínas de la Cola de los Virus/metabolismo
12.
Biochem Biophys Res Commun ; 523(2): 287-292, 2020 03 05.
Artículo en Inglés | MEDLINE | ID: mdl-31862141

RESUMEN

Cyclic-di-GMP (c-di-GMP) synthesized by diguanylate cyclases has been an important and ubiquitous secondary messenger in almost all bacterial systems. In Vibrio cholerae, c-di-GMP plays an intricate role in the production of the exopolysaccharide matrix, and thereby, in biofilm formation. The formation of the surface biofilm enables the bacteria to survive in aquatic bodies, when not infecting a human host. Diguanylate cyclases are the class of enzymes which synthesize c-di-GMP from two molecules of GTP and are endowed with a GGDEF or, a GGEEF signature domain. The VC0395_0300 protein from V. cholerae, has been established as a diguanylate cyclase with a necessary role in biofilm formation. Here we present the structure of an N-terminally truncated form of VC0395_0300, which retains the active GGEEF domain for diguanylate cyclase activity but lacks 160 residues from the poorly organized N-terminal domain. X-ray diffraction data was collected from a crystal of VC0395_0300(161-321) to a resolution of 1.9 Å. The structure displays remarkable topological similarity with diguanylate cyclases from other bacterial systems, but lacks the binding site for c-di-GMP present in its homologues. Finally, we demonstrate the ability of the truncated diguanylate cyclase VC0395_0300(161-321) to produce c-di-GMP, and its role in biofilm formation for the bacteria.


Asunto(s)
Proteínas Bacterianas/química , Proteínas de Escherichia coli/química , Liasas de Fósforo-Oxígeno/química , Vibrio cholerae/enzimología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Biopelículas/crecimiento & desarrollo , Dominio Catalítico , Cristalografía por Rayos X , GMP Cíclico/análogos & derivados , GMP Cíclico/biosíntesis , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Humanos , Modelos Moleculares , Liasas de Fósforo-Oxígeno/genética , Liasas de Fósforo-Oxígeno/metabolismo , Dominios Proteicos , Sistemas de Mensajero Secundario , Solubilidad , Electricidad Estática , Vibrio cholerae/genética , Vibrio cholerae/fisiología
13.
Nucleic Acids Res ; 46(4): 2082-2095, 2018 02 28.
Artículo en Inglés | MEDLINE | ID: mdl-29309642

RESUMEN

Grainyhead (Grh)/CP2 transcription factors are highly conserved in multicellular organisms as key regulators of epithelial differentiation, organ development and skin barrier formation. In addition, they have been implicated as being tumor suppressors in a variety of human cancers. Despite their physiological importance, little is known about their structure and DNA binding mode. Here, we report the first structural study of mammalian Grh/CP2 factors. Crystal structures of the DNA-binding domains of grainyhead-like (Grhl) 1 and Grhl2 reveal a closely similar conformation with immunoglobulin-like core. Both share a common fold with the tumor suppressor p53, but differ in important structural features. The Grhl1 DNA-binding domain binds duplex DNA containing the consensus recognition element in a dimeric arrangement, supporting parsimonious target-sequence selection through two conserved arginine residues. We elucidate the molecular basis of a cancer-related mutation in Grhl1 involving one of these arginines, which completely abrogates DNA binding in biochemical assays and transcriptional activation of a reporter gene in a human cell line. Thus, our studies establish the structural basis of DNA target-site recognition by Grh transcription factors and reveal how tumor-associated mutations inactivate Grhl proteins. They may serve as points of departure for the structure-based development of Grh/CP2 inhibitors for therapeutic applications.


Asunto(s)
ADN/química , Proteínas Represoras/química , Activación Transcripcional , Animales , Arginina/química , Línea Celular , Claudina-4/genética , ADN/metabolismo , Proteínas de Unión al ADN/química , Humanos , Ratones , Modelos Moleculares , Mutación , Regiones Promotoras Genéticas , Unión Proteica , Dominios Proteicos , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Factores de Transcripción/química
14.
J Am Chem Soc ; 140(33): 10447-10455, 2018 08 22.
Artículo en Inglés | MEDLINE | ID: mdl-30044908

RESUMEN

The principles of protein-glycan binding are still not well understood on a molecular level. Attempts to link affinity and specificity of glycan recognition to structure suffer from the general lack of model systems for experimental studies and the difficulty to describe the influence of solvent. We have experimentally and computationally addressed energetic contributions of solvent in protein-glycan complex formation in the tailspike protein (TSP) of E. coli bacteriophage HK620. HK620TSP is a 230 kDa native trimer of right-handed, parallel beta-helices that provide extended, rigid binding sites for bacterial cell surface O-antigen polysaccharides. A set of high-affinity mutants bound hexa- or pentasaccharide O-antigen fragments with very similar affinities even though hexasaccharides introduce an additional glucose branch into an occluded protein surface cavity. Remarkably different thermodynamic binding signatures were found for different mutants; however, crystal structure analyses indicated that no major oligosaccharide or protein topology changes had occurred upon complex formation. This pointed to a solvent effect. Molecular dynamics simulations using a mobility-based approach revealed an extended network of solvent positions distributed over the entire oligosaccharide binding site. However, free energy calculations showed that a small water network inside the glucose-binding cavity had the most notable influence on the thermodynamic signature. The energy needed to displace water from the glucose binding pocket depended on the amino acid at the entrance, in agreement with the different amounts of enthalpy-entropy compensation found for introducing glucose into the pocket in the different mutants. Studies with small molecule drugs have shown before that a few active water molecules can control protein complex formation. HK620TSP oligosaccharide binding shows that similar fundamental principles also apply for glycans, where a small number of water molecules can dominate the thermodynamic signature in an extended binding site.


Asunto(s)
Oligosacáridos/química , Proteínas/química , Solventes/química , Termodinámica , Sitios de Unión , Colifagos/química , Cristalografía por Rayos X , Glicósido Hidrolasas , Simulación de Dinámica Molecular , Conformación Proteica , Proteínas de la Cola de los Virus/química
15.
Proc Natl Acad Sci U S A ; 112(16): 5011-6, 2015 Apr 21.
Artículo en Inglés | MEDLINE | ID: mdl-25848013

RESUMEN

Small-molecule competitors of protein-protein interactions are urgently needed for functional analysis of large-scale genomics and proteomics data. Particularly abundant, yet so far undruggable, targets include domains specialized in recognizing proline-rich segments, including Src-homology 3 (SH3), WW, GYF, and Drosophila enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) homology 1 (EVH1) domains. Here, we present a modular strategy to obtain an extendable toolkit of chemical fragments (ProMs) designed to replace pairs of conserved prolines in recognition motifs. As proof-of-principle, we developed a small, selective, peptidomimetic inhibitor of Ena/VASP EVH1 domain interactions. Highly invasive MDA MB 231 breast-cancer cells treated with this ligand showed displacement of VASP from focal adhesions, as well as from the front of lamellipodia, and strongly reduced cell invasion. General applicability of our strategy is illustrated by the design of an ErbB4-derived ligand containing two ProM-1 fragments, targeting the yes-associated protein 1 (YAP1)-WW domain with a fivefold higher affinity.


Asunto(s)
Dominios Proteicos Ricos en Prolina , Mapeo de Interacción de Proteínas , Animales , Moléculas de Adhesión Celular/química , Línea Celular Tumoral , Permeabilidad de la Membrana Celular , Cristalografía por Rayos X , Drosophila melanogaster/metabolismo , Esterificación , Técnica del Anticuerpo Fluorescente , Humanos , Cinética , Ligandos , Proteínas de Microfilamentos/química , Modelos Moleculares , Peso Molecular , Péptidos/química , Fosfoproteínas/química , Unión Proteica , Estructura Terciaria de Proteína , Seudópodos , Fibras de Estrés/metabolismo , Zixina/química
16.
Nature ; 477(7366): 556-60, 2011 Sep 18.
Artículo en Inglés | MEDLINE | ID: mdl-21927000

RESUMEN

Dynamin is a mechanochemical GTPase that oligomerizes around the neck of clathrin-coated pits and catalyses vesicle scission in a GTP-hydrolysis-dependent manner. The molecular details of oligomerization and the mechanism of the mechanochemical coupling are currently unknown. Here we present the crystal structure of human dynamin 1 in the nucleotide-free state with a four-domain architecture comprising the GTPase domain, the bundle signalling element, the stalk and the pleckstrin homology domain. Dynamin 1 oligomerized in the crystals via the stalks, which assemble in a criss-cross fashion. The stalks further interact via conserved surfaces with the pleckstrin homology domain and the bundle signalling element of the neighbouring dynamin molecule. This intricate domain interaction rationalizes a number of disease-related mutations in dynamin 2 and suggests a structural model for the mechanochemical coupling that reconciles previous models of dynamin function.


Asunto(s)
Dinamina I/química , Nucleótidos , Cristalografía por Rayos X , Dinamina I/metabolismo , Dinamina II/genética , Dinamina II/metabolismo , GTP Fosfohidrolasas/química , GTP Fosfohidrolasas/metabolismo , Guanosina Trifosfato/metabolismo , Células HeLa , Humanos , Hidrólisis , Modelos Moleculares , Simulación de Dinámica Molecular , Unión Proteica , Estructura Terciaria de Proteína , Transducción de Señal , Transferrina/metabolismo
17.
Biochem J ; 473(13): 1881-94, 2016 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-27102985

RESUMEN

A-kinase anchoring proteins (AKAPs) interact with the dimerization/docking (D/D) domains of regulatory subunits of the ubiquitous protein kinase A (PKA). AKAPs tether PKA to defined cellular compartments establishing distinct pools to increase the specificity of PKA signalling. Here, we elucidated the structure of an extended PKA-binding domain of AKAP18ß bound to the D/D domain of the regulatory RIIα subunits of PKA. We identified three hydrophilic anchor points in AKAP18ß outside the core PKA-binding domain, which mediate contacts with the D/D domain. Such anchor points are conserved within AKAPs that bind regulatory RII subunits of PKA. We derived a different set of anchor points in AKAPs binding regulatory RI subunits of PKA. In vitro and cell-based experiments confirm the relevance of these sites for the interaction of RII subunits with AKAP18 and of RI subunits with the RI-specific smAKAP. Thus we report a novel mechanism governing interactions of AKAPs with PKA. The sequence specificity of each AKAP around the anchor points and the requirement of these points for the tight binding of PKA allow the development of selective inhibitors to unequivocally ascribe cellular functions to the AKAP18-PKA and other AKAP-PKA interactions.


Asunto(s)
Proteínas de Anclaje a la Quinasa A/química , Proteínas de Anclaje a la Quinasa A/metabolismo , Proteínas Quinasas Dependientes de AMP Cíclico/química , Proteínas Quinasas Dependientes de AMP Cíclico/metabolismo , Secuencia de Aminoácidos , Sitios de Unión , Calorimetría , Células HEK293 , Humanos , Inmunoprecipitación , Datos de Secuencia Molecular , Unión Proteica , Conformación Proteica , Subunidades de Proteína/química , Subunidades de Proteína/metabolismo , Transducción de Señal , Resonancia por Plasmón de Superficie
18.
Sci Rep ; 14(1): 12685, 2024 06 03.
Artículo en Inglés | MEDLINE | ID: mdl-38830962

RESUMEN

White kidney bean (Phaseolus vulgaris L.) extracts can aid weight management by reducing calorie intake from complex carbohydrates through alpha-amylase inhibition. We examined the impact of a proprietary aqueous extract from whole dried white kidney beans standardized by its alpha-amylase inhibitor activity (Phase 2 white kidney bean extract (WKBE)) on weight management in subjects with overweight and moderate obesity. In a randomized, double-blind, placebo-controlled fashion, 81 participants completed the study and ingested either a high dose of Phase 2 (1000 mg, WKBE HIGH), a low dose (700 mg, WKBE LOW), or a matching placebo (microcrystalline cellulose, PLA) three times a day, 30 min before meals, for 12 weeks during a calorie restricted diet. In a dose-dependent manner, Phase 2 significantly reduced body weight, fat mass, BMI, waist, hip and in the WKBE HIGH group thigh circumference. Phase 2 is an effective and safe supplement aiding weight and fat loss. ClinicalTrials.gov identifier NCT02930668.


Asunto(s)
Phaseolus , Extractos Vegetales , Humanos , Masculino , Femenino , Método Doble Ciego , Phaseolus/química , Persona de Mediana Edad , Adulto , Extractos Vegetales/química , Extractos Vegetales/farmacología , Pérdida de Peso/efectos de los fármacos , Obesidad/tratamiento farmacológico , alfa-Amilasas/antagonistas & inhibidores , alfa-Amilasas/metabolismo , Sobrepeso/tratamiento farmacológico , Lectinas de Plantas
19.
Structure ; 2024 May 03.
Artículo en Inglés | MEDLINE | ID: mdl-38749445

RESUMEN

Orthomyxoviruses, such as influenza and thogotoviruses, are important human and animal pathogens. Their segmented viral RNA genomes are wrapped by viral nucleoproteins (NPs) into helical ribonucleoprotein complexes (RNPs). NP structures of several influenza viruses have been reported. However, there are still contradictory models of how orthomyxovirus RNPs are assembled. Here, we characterize the crystal structure of Thogoto virus (THOV) NP and found striking similarities to structures of influenza viral NPs, including a two-lobed domain architecture, a positively charged RNA-binding cleft, and a tail loop important for trimerization and viral transcription. A low-resolution cryo-electron tomography reconstruction of THOV RNPs elucidates a left-handed double helical assembly. By providing a model for RNP assembly of THOV, our study suggests conserved NP assembly and RNA encapsidation modes for thogoto- and influenza viruses.

20.
Nat Commun ; 15(1): 3146, 2024 Apr 11.
Artículo en Inglés | MEDLINE | ID: mdl-38605029

RESUMEN

Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be regulated by post-translational modifications like phosphorylation. 20% of pathogenic missense mutations are found in IDRs, and understanding how such mutations affect PPIs is essential for unraveling disease mechanisms. Here, we employ peptide-based interaction proteomics to investigate 36 disease-associated mutations affecting phosphorylation sites. Our results unveil significant differences in interactomes between phosphorylated and non-phosphorylated peptides, often due to disrupted phosphorylation-dependent SLiMs. We focused on a mutation of a serine phosphorylation site in the transcription factor GATAD1, which causes dilated cardiomyopathy. We find that this phosphorylation site mediates interaction with 14-3-3 family proteins. Follow-up experiments reveal the structural basis of this interaction and suggest that 14-3-3 binding affects GATAD1 nucleocytoplasmic transport by masking a nuclear localisation signal. Our results demonstrate that pathogenic mutations of human phosphorylation sites can significantly impact protein-protein interactions, offering insights into potential molecular mechanisms underlying pathogenesis.


Asunto(s)
Proteínas Intrínsecamente Desordenadas , Péptidos , Humanos , Fosforilación , Péptidos/metabolismo , Procesamiento Proteico-Postraduccional , Regulación de la Expresión Génica , Mutación , Proteínas Intrínsecamente Desordenadas/metabolismo , Unión Proteica , Sitios de Unión , Proteínas del Ojo/genética
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