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1.
Microb Cell Fact ; 23(1): 52, 2024 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-38360657

RESUMO

BACKGROUND: Among the polyhydroxyalkanoate (PHA), poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)] is reported to closely resemble polypropylene and low-density polyethylene. Studies have shown that PHA synthase (PhaC) from mangrove soil (PhaCBP-M-CPF4) is an efficient PhaC for P(3HB-co-3HHx) production and N-termini of PhaCs influence its substrate specificity, dimerization, granule morphology, and molecular weights of PHA produced. This study aims to further improve PhaCBP-M-CPF4 through N-terminal truncation. RESULTS: The N-terminal truncated mutants of PhaCBP-M-CPF4 were constructed based on the information of the predicted secondary and tertiary structures using PSIPRED server and AlphaFold2 program, respectively. The N-terminal truncated PhaCBP-M-CPF4 mutants were evaluated in C. necator mutant PHB-4 based on the cell dry weight, PHA content, 3HHx molar composition, molecular weights, and granule morphology of the PHA granules. The results showed that most transformants harbouring the N-terminal truncated PhaCBP-M-CPF4 showed a reduction in PHA content and cell dry weight except for PhaCBP-M-CPF4 G8. PhaCBP-M-CPF4 G8 and A27 showed an improved weight-average molecular weight (Mw) of PHA produced due to lower expression of the truncated PhaCBP-M-CPF4. Transformants harbouring PhaCBP-M-CPF4 G8, A27, and T74 showed a reduction in the number of granules. PhaCBP-M-CPF4 G8 produced higher Mw PHA in mostly single larger PHA granules with comparable production as the full-length PhaCBP-M-CPF4. CONCLUSION: This research showed that N-terminal truncation had effects on PHA accumulation, substrate specificity, Mw, and granule morphology. This study also showed that N-terminal truncation of the amino acids that did not adopt any secondary structure can be an alternative to improve PhaCs for the production of PHA with higher Mw in mostly single larger granules.


Assuntos
Cupriavidus necator , Poli-Hidroxialcanoatos , Poli-Hidroxialcanoatos/metabolismo , Ácido 3-Hidroxibutírico , Caproatos/metabolismo , Hidroxibutiratos/metabolismo , Aciltransferases/genética , Aciltransferases/metabolismo , Grânulos Citoplasmáticos , Cupriavidus necator/genética , Cupriavidus necator/metabolismo
2.
Proc Natl Acad Sci U S A ; 115(11): 2764-2769, 2018 03 13.
Artigo em Inglês | MEDLINE | ID: mdl-29483251

RESUMO

Chemical cues presented on the adhesive substrate direct cell migration, a process termed haptotaxis. To migrate, cells must generate traction forces upon the substrate. However, how cells probe substrate-bound cues and generate directional forces for migration remains unclear. Here, we show that the cell adhesion molecule (CAM) L1-CAM is involved in laminin-induced haptotaxis of axonal growth cones. L1-CAM underwent grip and slip on the substrate. The ratio of the grip state was higher on laminin than on the control substrate polylysine; this was accompanied by an increase in the traction force upon laminin. Our data suggest that the directional force for laminin-induced growth cone haptotaxis is generated by the grip and slip of L1-CAM on the substrates, which occur asymmetrically under the growth cone. This mechanism is distinct from the conventional cell signaling models for directional cell migration. We further show that this mechanism is disrupted in a human patient with L1-CAM syndrome, suffering corpus callosum agenesis and corticospinal tract hypoplasia.


Assuntos
Quimiotaxia , Doenças Genéticas Ligadas ao Cromossomo X/metabolismo , Cones de Crescimento/metabolismo , Deficiência Intelectual/metabolismo , Molécula L1 de Adesão de Célula Nervosa/química , Molécula L1 de Adesão de Célula Nervosa/metabolismo , Paraplegia Espástica Hereditária/metabolismo , Actinas/metabolismo , Axônios/química , Axônios/metabolismo , Movimento Celular , Doenças Genéticas Ligadas ao Cromossomo X/genética , Cones de Crescimento/química , Humanos , Deficiência Intelectual/genética , Laminina/química , Laminina/metabolismo , Molécula L1 de Adesão de Célula Nervosa/genética , Paraplegia Espástica Hereditária/genética
3.
Genes Cells ; 23(5): 370-385, 2018 May.
Artigo em Inglês | MEDLINE | ID: mdl-29542234

RESUMO

Mechanotransduction by α-catenin facilitates the force-dependent development of adherens junctions (AJs) by recruiting vinculin to reinforce actin anchoring of AJs. The α-catenin mechanotransducing action is facilitated by its force-sensing device region that autoinhibits the vinculin-binding site 1 (VBS1). Here, we report the high-resolution structure of the force-sensing device region of α-catenin, which shows the autoinhibited form comprised of helix bundles E, F and G. The cryptic VBS1 is embedded into helix bundle E stabilized by direct interactions with the autoinhibitory region forming helix bundles F and G. Our molecular dissection study showed that helix bundles F and G are stable in solution in each isolated form, whereas helix bundle E that contains VBS1 is unstable and intrinsically disordered in solution in the isolated form. We successfully identified key residues mediating the autoinhibition and produced mutated α-catenins that display variable force sensitivity and autoinhibition. Using these mutants, we demonstrate both in vitro and in vivo that, in the absence of this stabilization, the helix bundle containing VBS1 would adopt an unfolded form, thus exposing VBS for vinculin binding. We provide evidence for importance of mechanotransduction with the intrinsic force sensitivity for vinculin recruitment to adherens junctions of epithelial cell sheets with mutated α-catenins.


Assuntos
Actinas/metabolismo , Junções Aderentes/fisiologia , Mecanotransdução Celular , Vinculina/metabolismo , alfa Catenina/química , alfa Catenina/metabolismo , Animais , Sítios de Ligação , Cristalografia por Raios X , Camundongos , Modelos Moleculares , Mutação , Ligação Proteica , Conformação Proteica , Dobramento de Proteína , Vinculina/química , Vinculina/genética , alfa Catenina/genética
4.
Appl Microbiol Biotechnol ; 103(3): 1131-1141, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30511262

RESUMO

Polyhydroxyalkanoates (PHAs) are biopolymers synthesized by a wide range of bacteria, which serve as a promising candidate in replacing some conventional petrochemical-based plastics. PHA synthase (PhaC) is the key enzyme in the polymerization of PHA, and the crystal structures were successfully determined using the catalytic domain of PhaC from Cupriavidus necator (PhaCCn-CAT) and Chromobacterium sp. USM2 (PhaCCs-CAT). Here, we review the beneficial mutations discovered in PhaCs from a structural perspective. The structural comparison of the residues involved in beneficial mutation reveals that the residues are near to the catalytic triad, but not inside the catalytic pocket. For instance, Ala510 of PhaCCn is near catalytic His508 and may be involved in the open-close regulation, which presumably play an important role in substrate specificity and activity. In the class II PhaC1 from Pseudomonas sp. 61-3 (PhaC1Ps), Ser325 stabilizes the catalytic cysteine through hydrogen bonding. Another residue, Gln508 of PhaC1Ps is located in a conserved hydrophobic pocket which is next to the catalytic Asp and His. A class I, II-conserved Phe420 of PhaCCn is one of the residues involved in dimerization and its mutation to serine greatly reduced the lag phase. The current structural analysis shows that the Phe362 and Phe518 of PhaC from Aeromonas caviae (PhaCAc) are assisting the dimer formation and maintaining the integrity of the core beta-sheet, respectively. The structure-function relationship of PhaCs discussed in this review will serve as valuable reference for future protein engineering works to enhance the performance of PhaCs and to produce novel biopolymers.


Assuntos
Aciltransferases/metabolismo , Aeromonas caviae/enzimologia , Chromobacterium/enzimologia , Cupriavidus necator/enzimologia , Poli-Hidroxialcanoatos/metabolismo , Pseudomonas/enzimologia , Aciltransferases/genética , Aeromonas caviae/genética , Aeromonas caviae/metabolismo , Sequência de Aminoácidos , Domínio Catalítico/genética , Chromobacterium/genética , Chromobacterium/metabolismo , Cristalografia por Raios X , Cupriavidus necator/genética , Cupriavidus necator/metabolismo , Engenharia de Proteínas , Estrutura Terciária de Proteína , Pseudomonas/genética , Pseudomonas/metabolismo , Relação Estrutura-Atividade , Especificidade por Substrato
5.
Protein Expr Purif ; 131: 70-75, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-26390940

RESUMO

S-locus protein kinase (SRK) is a receptor kinase that plays a critical role in self-recognition in the Brassicaceae self-incompatibility (SI) response. SRK is activated by binding of its ligand S-locus protein 11 (SP11) and subsequently induced phosphorylation of the intracellular kinase domain. However, a detailed activation mechanism of SRK is still largely unknown because of the difficulty in stably expressing SRK recombinant proteins. Here, we performed modeling-based protein engineering of the SRK kinase domain for stable expression in Escherichia coli. The engineered SRK intracellular domain was expressed about 54-fold higher production than wild type SRK, without loss of the kinase activity, suggesting it could be useful for further biochemical and structural studies.


Assuntos
Arabidopsis/genética , Expressão Gênica , Modelos Moleculares , Proteínas de Plantas , Engenharia de Proteínas , Proteínas Quinases , Proteínas de Plantas/biossíntese , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/isolamento & purificação , Domínios Proteicos , Proteínas Quinases/biossíntese , Proteínas Quinases/química , Proteínas Quinases/genética , Proteínas Quinases/isolamento & purificação , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação
6.
Genes Cells ; 20(10): 847-59, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26289026

RESUMO

Membrane type 1-matrix metalloproteinase (MT1-MMP) is a key enzyme involved in tumor cell invasion by shedding their cell-surface receptor CD44 anchored with F-actin through ezrin/radixin/moesin (ERM) proteins. We found the cytoplasmic tail of MT1-MMP directly binds the FERM domain of radixin, suggesting F-actin-based recruitment of MT1-MMP to CD44 for invasion. Our crystal structure shows that the central region of the MT1-MMP cytoplasmic tail binds subdomain A of the FERM domain, and makes an antiparallel ß-ß interaction with ß2A-strand. This binding mode is distinct from the previously determined binding mode of CD44 to subdomain C. We showed that radixin simultaneously binds both MT1-MMP and CD44, indicating ERM protein-mediated colocalization of MT1-MMP and its substrate CD44 and anchoring to F-actin. Our study implies that ERM proteins contribute toward accelerated CD44 shedding by MT1-MMP through ERM protein-mediated interactions between their cytoplasmic tails.


Assuntos
Micropartículas Derivadas de Células/metabolismo , Proteínas de Ligação a DNA/metabolismo , Receptores de Hialuronatos/metabolismo , Metaloproteinase 14 da Matriz/metabolismo , Fatores de Transcrição/metabolismo , Actinas/metabolismo , Sítios de Ligação , Proteínas do Citoesqueleto/química , Proteínas do Citoesqueleto/metabolismo , Humanos , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo , Ligação Proteica , Estrutura Terciária de Proteína
7.
Proc Natl Acad Sci U S A ; 110(29): 11821-6, 2013 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-23818613

RESUMO

Mpr1 (sigma1278b gene for proline-analog resistance 1), which was originally isolated as N-acetyltransferase detoxifying the proline analog L-azetidine-2-carboxylate, protects yeast cells from various oxidative stresses. Mpr1 mediates the L-proline and L-arginine metabolism by acetylating L-Δ(1)-pyrroline-5-carboxylate, leading to the L-arginine-dependent production of nitric oxide, which confers oxidative stress tolerance. Mpr1 belongs to the Gcn5-related N-acetyltransferase (GNAT) superfamily, but exhibits poor sequence homology with the GNAT enzymes and unique substrate specificity. Here, we present the X-ray crystal structure of Mpr1 and its complex with the substrate cis-4-hydroxy-L-proline at 1.9 and 2.3 Å resolution, respectively. Mpr1 is folded into α/ß-structure with eight-stranded mixed ß-sheets and six α-helices. The substrate binds to Asn135 and the backbone amide of Asn172 and Leu173, and the predicted acetyl-CoA-binding site is located near the backbone amide of Phe138 and the side chain of Asn178. Alanine substitution of Asn178, which can interact with the sulfur of acetyl-CoA, caused a large reduction in the apparent kcat value. The replacement of Asn135 led to a remarkable increase in the apparent Km value. These results indicate that Asn178 and Asn135 play an important role in catalysis and substrate recognition, respectively. Such a catalytic mechanism has not been reported in the GNAT proteins. Importantly, the amino acid substitutions in these residues increased the L-Δ(1)-pyrroline-5-carboxylate level in yeast cells exposed to heat stress, indicating that these residues are also crucial for its physiological functions. These studies provide some benefits of Mpr1 applications, such as the breeding of industrial yeasts and the development of antifungal drugs.


Assuntos
Acetiltransferases/química , Acetiltransferases/genética , Hidroxiprolina/química , Modelos Moleculares , Estresse Oxidativo/genética , Prolina/metabolismo , Conformação Proteica , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Acetilação , Acetiltransferases/metabolismo , Sequência de Aminoácidos , Sequência de Bases , Sítios de Ligação/genética , Cristalografia por Raios X , Hidroxiprolina/metabolismo , Cinética , Dados de Sequência Molecular , Estrutura Molecular , Dobramento de Proteína , Proteínas de Saccharomyces cerevisiae/metabolismo , Análise de Sequência de DNA , Especificidade por Substrato
8.
EMBO J ; 30(13): 2734-47, 2011 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-21642953

RESUMO

Myosin-X is an important unconventional myosin that is critical for cargo transportation to filopodia tips and is also utilized in spindle assembly by interacting with microtubules. We present a series of structural and biochemical studies of the myosin-X tail domain cassette, consisting of myosin tail homology 4 (MyTH4) and FERM domains in complex with its specific cargo, a netrin receptor DCC (deleted in colorectal cancer). The MyTH4 domain is folded into a helical VHS-like structure and is associated with the FERM domain. We found an unexpected binding mode of the DCC peptide to the subdomain C groove of the FERM domain, which is distinct from previously reported ß-ß associations found in radixin-adhesion molecule complexes. We also revealed direct interactions between the MyTH4-FERM cassette and tubulin C-terminal acidic tails, and identified a positively charged patch of the MyTH4 domain, which is involved in tubulin binding. We demonstrated that both DCC and integrin bindings interfere with microtubule binding and that DCC binding interferes with integrin binding. Our results provide the molecular basis by which myosin-X facilitates alternative dual binding to cargos and microtubules.


Assuntos
Miosinas/química , Miosinas/metabolismo , Domínios e Motivos de Interação entre Proteínas , Sequência de Aminoácidos , Células Cultivadas , Receptor DCC , Humanos , Cadeias beta de Integrinas/genética , Cadeias beta de Integrinas/metabolismo , Microtúbulos/metabolismo , Modelos Biológicos , Modelos Moleculares , Dados de Sequência Molecular , Miosinas/genética , Ligação Proteica/genética , Ligação Proteica/fisiologia , Domínios e Motivos de Interação entre Proteínas/genética , Domínios e Motivos de Interação entre Proteínas/fisiologia , Estrutura Quaternária de Proteína , Estrutura Secundária de Proteína/fisiologia , Transporte Proteico/genética , Transporte Proteico/fisiologia , Receptores de Superfície Celular/química , Receptores de Superfície Celular/genética , Receptores de Superfície Celular/metabolismo , Homologia de Sequência de Aminoácidos , Proteínas Supressoras de Tumor/química , Proteínas Supressoras de Tumor/genética , Proteínas Supressoras de Tumor/metabolismo
9.
Genes Cells ; 19(5): 386-404, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24645846

RESUMO

Arabidopsis receptors of abscisic acid (ABA), the key plant hormone for adaptation to water stress, comprise 14 PYR/PYLs/RCARs proteins classified into three subfamilies I, II, and III, which suggests functional differentiation. Although their monomer-dimer equilibria may be correlated with differences in their ABA-binding affinities, how the dimerization decreases the affinity is unclear. Comparative structural and binding studies between PYL9, which is a representative of high-affinity subfamily I, and low-affinity members of subfamily III reveals that the nonpolar triplet (Ile110, Val162, and Leu165) and Pro64 contribute to enhance ABA-binding affinity by inducing a shift of the ABA carboxyl group to form additional direct hydrogen bonds with conserved Asn169. Our mutation studies of PYL1 successfully produced a monomeric mutant PYL1 exhibiting low ABA affinity and also a dimeric mutant PYL1 exhibiting high ABA-binding affinity, suggesting that dimer formation of ABA receptors is not essential for their low ABA-binding affinity. Our study contributes toward establishing the structural basis for the higher ABA-binding affinity of the subfamily receptors and provides a clue for understanding the broad spectrum of hormone actions in plants manifested by the different hormone-binding affinity of multiple receptors.


Assuntos
Ácido Abscísico/metabolismo , Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Proteínas de Transporte/metabolismo , Sequência de Aminoácidos , Proteínas de Arabidopsis/genética , Proteínas de Transporte/genética , Peptídeos e Proteínas de Sinalização Intracelular , Dados de Sequência Molecular , Mutação , Ligação Proteica , Multimerização Proteica
10.
Genes Cells ; 19(8): 603-19, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24912773

RESUMO

Merlin, a tumor suppressor encoded by the neurofibromatosis type 2 gene, has been shown to suppress tumorigenesis by inhibiting the Cullin 4-RING E3 ubiquitin ligase CRL4(DCAF) (1) in the nucleus. This inhibition is mediated by direct binding of merlin to DDB1-and-Cullin 4-associated Factor 1 (DCAF1), yet the binding mode of merlin to DCAF1 is not well defined. Here, we report structural and biophysical studies of the merlin binding to DCAF1 and its interference with CD44 binding. The crystal structure of the merlin FERM domain bound to the DCAF1 C-terminal acidic tail reveals that the hydrophobic IILXLN motif located at the C-terminal end of DCAF1 binds subdomain C of the FERM domain by forming a ß-strand. The binding site and mode resemble that of merlin binding to the CD44 cytoplasmic tail. Competition binding assay showed that CD44 and DCAF1 compete for binding to the merlin FERM domain in solution. The CD44 cytoplasmic tail is known to be cleaved for nuclear translocation by regulated intra-membrane proteolysis (RIP). Our structure implies that, in the nucleus, the CD44 cytoplasmic tail cleaved by RIP could release DCAF1 from merlin by competing for binding to the merlin FERM domain, which results in the inhibition of merlin-mediated suppression of tumorigenesis.


Assuntos
Carcinogênese/patologia , Proteínas de Transporte/química , Receptores de Hialuronatos/química , Neurofibromina 2/química , Sequência de Aminoácidos , Animais , Carcinogênese/metabolismo , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Cristalografia por Raios X , Proteínas do Citoesqueleto/química , Proteínas do Citoesqueleto/metabolismo , Humanos , Receptores de Hialuronatos/metabolismo , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo , Camundongos , Modelos Moleculares , Dados de Sequência Molecular , Neurofibromina 2/genética , Neurofibromina 2/metabolismo , Proteínas Serina-Treonina Quinases , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Ubiquitina-Proteína Ligases
11.
Biochim Biophys Acta ; 1834(2): 499-507, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23128140

RESUMO

End-binding protein 1 (EB1) is one of the best studied plus-end tracking proteins. It is known that EB1 specifically binds the plus ends of microtubules (MTs) and promotes MT growth. EB1 activity is thought to be autoinhibited by an intramolecular interaction. Recent cryo-EM analyses showed that the CH domain of Mal3p (Schizosaccharomyces pombe EB1 homolog) binds to GMPCPP-MT (Sandblad, L. Cell 127 (2006) 1415-24), and strongly binds GTPγS-MT which is proposed to mimic MT plus ends better than GMPCPP-MT (Maurer S.P. et al. Cell 149 (2012) 371-82). Here, we report on the MT binding sites of the CH domain of EB1 as revealed by NMR using the transferred cross-saturation method. In this study, we used GMPCPP-MT and found that the MT binding sites are very similar to the binding site for GTPγS-MT as suggested by cryo-EM (Maurer S.P. et al. Cell 149 (2012) 371-82). Notably, the N-terminal tip of helix α6 of the CH domain did not make contact with GMPCPP-MT, in contrast to the cryo-EM study which showed that it is closely located to a putative switch region of ß-tubulin in GTPγS-MT (Maurer S.P. et al. Cell 149 (2012) 371-82). Further, we found that the intramolecular interaction site of EB1 overlaps the MT binding sites, indicating that the MT binding sites are masked by interaction with the C-terminal domain. We propose a structural view of autoinhibition and its release mechanism through competition binding with binding partners such as adenomatous polyposis coli protein.


Assuntos
Proteínas Associadas aos Microtúbulos/química , Modelos Moleculares , Proteína da Polipose Adenomatosa do Colo/química , Proteína da Polipose Adenomatosa do Colo/genética , Proteína da Polipose Adenomatosa do Colo/metabolismo , Sítios de Ligação , Microscopia Crioeletrônica , Guanosina Trifosfato/análogos & derivados , Guanosina Trifosfato/química , Guanosina Trifosfato/metabolismo , Células HeLa , Humanos , Proteínas Associadas aos Microtúbulos/genética , Proteínas Associadas aos Microtúbulos/metabolismo , Ressonância Magnética Nuclear Biomolecular , Estrutura Terciária de Proteína , Relação Estrutura-Atividade , Tubulina (Proteína)/química , Tubulina (Proteína)/genética , Tubulina (Proteína)/metabolismo
12.
EMBO J ; 29(1): 236-50, 2010 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-19893486

RESUMO

Tiam1 and Tiam2 (Tiam1/2) are guanine nucleotide-exchange factors that possess the PH-CC-Ex (pleckstrin homology, coiled coil and extra) region that mediates binding to plasma membranes and signalling proteins in the activation of Rac GTPases. Crystal structures of the PH-CC-Ex regions revealed a single globular domain, PHCCEx domain, comprising a conventional PH subdomain associated with an antiparallel coiled coil of CC subdomain and a novel three-helical globular Ex subdomain. The PH subdomain resembles the beta-spectrin PH domain, suggesting non-canonical phosphatidylinositol binding. Mutational and binding studies indicated that CC and Ex subdomains form a positively charged surface for protein binding. We identified two unique acidic sequence motifs in Tiam1/2-interacting proteins for binding to PHCCEx domain, Motif-I in CD44 and ephrinB's and the NMDA receptor, and Motif-II in Par3 and JIP2. Our results suggest the molecular basis by which the Tiam1/2 PHCCEx domain facilitates dual binding to membranes and signalling proteins.


Assuntos
Fatores de Troca do Nucleotídeo Guanina/química , Fatores de Troca do Nucleotídeo Guanina/metabolismo , Sequência de Aminoácidos , Animais , Sítios de Ligação , Cristalografia por Raios X , Fatores de Troca do Nucleotídeo Guanina/genética , Humanos , Receptores de Hialuronatos/química , Receptores de Hialuronatos/genética , Receptores de Hialuronatos/metabolismo , Técnicas In Vitro , Camundongos , Modelos Moleculares , Dados de Sequência Molecular , Dobramento de Proteína , Domínios e Motivos de Interação entre Proteínas , Estrutura Terciária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Homologia de Sequência de Aminoácidos , Eletricidade Estática , Proteína 1 Indutora de Invasão e Metástase de Linfoma de Células T
13.
Genes Cells ; 18(2): 147-60, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23301669

RESUMO

Strigolactones (SLs) are plant hormones that inhibit shoot branching. DWARF14 (D14) inhibits rice tillering and is an SL receptor candidate in the branching inhibition pathway, whereas the close homologue DWARF14-LIKE (D14L) participates in the signaling pathway of karrikins (KARs), which are derived from burnt vegetation as smoke stimulants of seed germination. We provide the first evidence for direct binding of the bioactive SL analogue GR24 to D14. Isothermal titration calorimetry measurements show a D14-GR24 binding affinity in the sub-micromolar range. Similarly, bioactive KAR1 directly binds D14L in the micromolar range. The crystal structure of rice D14 shows a compact α-/ß-fold hydrolase domain forming a deep ligand-binding pocket capable of accommodating GR24. Insertion of four α-helices between ß6 strand and αD helix forms the helical cap of the pocket, although the pocket is open to the solvent. The pocket contains the conserved catalytic triad Ser-His-Asp aligned with the oxyanion hole, suggesting hydrolase activity. Although these structural characteristics are conserved in D14L, the D14L pocket is smaller than that of D14. The KAR-insensitive mutation kai2-1 is located at the prominent long ß6-αD1 loop, which is characteristic in D14 and D14L, but not in related α-/ß-fold hydrolases.


Assuntos
Furanos/metabolismo , Oryza/metabolismo , Reguladores de Crescimento de Plantas/metabolismo , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Piranos/metabolismo , Transdução de Sinais , Sequência de Aminoácidos , Domínio Catalítico , Modelos Moleculares , Dados de Sequência Molecular , Mutação , Oryza/genética , Reguladores de Crescimento de Plantas/química , Ligação Proteica , Conformação Proteica , Estabilidade Proteica , Alinhamento de Sequência
14.
Nature ; 456(7221): 459-63, 2008 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-19037309

RESUMO

Gibberellins control a range of growth and developmental processes in higher plants and have been widely used in the agricultural industry. By binding to a nuclear receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), gibberellins regulate gene expression by promoting degradation of the transcriptional regulator DELLA proteins, including GIBBERELLIN INSENSITIVE (GAI). The precise manner in which GID1 discriminates and becomes activated by bioactive gibberellins for specific binding to DELLA proteins remains unclear. Here we present the crystal structure of a ternary complex of Arabidopsis thaliana GID1A, a bioactive gibberellin and the amino-terminal DELLA domain of GAI. In this complex, GID1A occludes gibberellin in a deep binding pocket covered by its N-terminal helical switch region, which in turn interacts with the DELLA domain containing DELLA, VHYNP and LExLE motifs. Our results establish a structural model of a plant hormone receptor that is distinct from the mechanism of the hormone perception and effector recognition of the known auxin receptors.


Assuntos
Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Arabidopsis/química , Giberelinas/farmacologia , Reguladores de Crescimento de Plantas/farmacologia , Receptores de Superfície Celular/química , Receptores de Superfície Celular/metabolismo , Motivos de Aminoácidos , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Dicroísmo Circular , Cristalografia por Raios X , Giberelinas/metabolismo , Modelos Biológicos , Modelos Moleculares , Reguladores de Crescimento de Plantas/metabolismo , Ligação Proteica , Estrutura Terciária de Proteína/efeitos dos fármacos , Receptores de Superfície Celular/genética , Especificidade por Substrato
15.
Proc Natl Acad Sci U S A ; 107(31): 13666-71, 2010 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-20639466

RESUMO

Heterotrimeric GTP-binding proteins (G proteins) transmit extracellular stimuli perceived by G protein-coupled receptors (GPCRs) to intracellular signaling cascades. Hundreds of GPCRs exist in humans and are the targets of a large percentage of the pharmaceutical drugs used today. Because G proteins are regulated by GPCRs, small molecules that directly modulate G proteins have the potential to become therapeutic agents. However, strategies to develop modulators have been hampered by a lack of structural knowledge of targeting sites for specific modulator binding. Here we present the mechanism of action of the cyclic depsipeptide YM-254890, which is a recently discovered Gq-selective inhibitor. YM-254890 specifically inhibits the GDP/GTP exchange reaction of alpha subunit of Gq protein (Galphaq) by inhibiting the GDP release from Galphaq. X-ray crystal structure analysis of the Galphaqbetagamma-YM-254890 complex shows that YM-254890 binds the hydrophobic cleft between two interdomain linkers connecting the GTPase and helical domains of the Galphaq. The binding stabilizes an inactive GDP-bound form through direct interactions with switch I and impairs the linker flexibility. Our studies provide a novel targeting site for the development of small molecules that selectively inhibit each Galpha subunit and an insight into the molecular mechanism of G protein activation.


Assuntos
Subunidades alfa Gq-G11 de Proteínas de Ligação ao GTP/química , Peptídeos Cíclicos/química , Sequência de Aminoácidos , Cristalografia por Raios X , Subunidades alfa Gq-G11 de Proteínas de Ligação ao GTP/antagonistas & inibidores , Subunidades alfa Gq-G11 de Proteínas de Ligação ao GTP/genética , Subunidades alfa Gq-G11 de Proteínas de Ligação ao GTP/metabolismo , Interações Hidrofóbicas e Hidrofílicas , Modelos Moleculares , Dados de Sequência Molecular , Mutação , Peptídeos Cíclicos/metabolismo , Peptídeos Cíclicos/farmacologia , Ligação Proteica , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína , Alinhamento de Sequência
16.
J Biochem ; 175(1): 57-67, 2023 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-37812440

RESUMO

The Bin-Amphiphysin-Rvs (BAR) domain of endophilin binds to the cell membrane and shapes it into a tubular shape for endocytosis. Endophilin has a Src-homology 3 (SH3) domain at their C-terminal. The SH3 domain interacts with the proline-rich motif (PRM) that is found in proteins such as neural Wiskott-Aldrich syndrome protein (N-WASP). Here, we re-examined the binding sites of the SH3 domain of endophilin in N-WASP by machine learning-based prediction and identified the previously unrecognized binding site. In addition to the well-recognized PRM at the central proline-rich region, we found a PRM in front of the N-terminal WASP homology 1 (WH1) domain of N-WASP (NtPRM) as a binding site of the endophilin SH3 domain. Furthermore, the diameter of the membrane tubules in the presence of NtPRM mutant was narrower and wider than that in the presence of N-WASP and in its absence, respectively. Importantly, the NtPRM of N-WASP was involved in the membrane localization of endophilin A2 in cells. Therefore, the NtPRM contributes to the binding of endophilin to N-WASP in membrane remodeling.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal , Proteínas de Transporte , Proteínas de Transporte/metabolismo , Proteínas Adaptadoras de Transdução de Sinal/genética , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Sítios de Ligação , Domínios de Homologia de src , Fatores de Transcrição/metabolismo , Prolina/metabolismo , Ligação Proteica
17.
Sci Adv ; 9(17): eadf5143, 2023 04 28.
Artigo em Inglês | MEDLINE | ID: mdl-37126564

RESUMO

The higher-order assembly of Bin-amphiphysin-Rvs (BAR) domain proteins, including the FCH-BAR (F-BAR) domain proteins, into lattice on the membrane is essential for the formation of subcellular structures. However, the regulation of their ordered assembly has not been elucidated. Here, we show that the higher ordered assembly of growth-arrested specific 7 (GAS7), an F-BAR domain protein, is regulated by the multivalent scaffold proteins of Wiskott-Aldrich syndrome protein (WASP)/neural WASP, that commonly binds to the BAR domain superfamily proteins, together with WISH, Nck, the activated small guanosine triphosphatase Cdc42, and a membrane-anchored phagocytic receptor. The assembly kinetics by fluorescence resonance energy transfer monitoring indicated that the GAS7 assembly on liposomes started within seconds and was further increased by the presence of these proteins. The regulated GAS7 assembly was abolished by Wiskott-Aldrich syndrome mutations both in vitro and in cellular phagocytosis. Therefore, Cdc42 and the scaffold proteins that commonly bind to the BAR domain superfamily proteins promoted GAS7 assembly.


Assuntos
Proteínas Monoméricas de Ligação ao GTP , Proteína da Síndrome de Wiskott-Aldrich , Proteína da Síndrome de Wiskott-Aldrich/metabolismo , Proteínas Monoméricas de Ligação ao GTP/metabolismo , Proteína Neuronal da Síndrome de Wiskott-Aldrich/genética , Proteína Neuronal da Síndrome de Wiskott-Aldrich/metabolismo , Proteínas do Tecido Nervoso/metabolismo , Actinas/metabolismo
18.
J Biosci Bioeng ; 134(4): 288-294, 2022 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-35953354

RESUMO

Poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)] has a high potential to serve as a commercial bioplastic due to its biodegradability, thermoplastic and mechanical properties. The properties of this copolymer are greatly affected by the composition of 3HHx monomer. One of the most efficient ways to modulate the composition of 3HHx monomer in P(3HB-co-3HHx) is by manipulating the (R)-3HHx-CoA monomer supply. In this study, a new (R)-specific enoyl-CoA hydratase originating from a non-PHA producer, Streptomyces sp. strain CFMR 7 (PhaJSs), was characterized and found to be effective in supplying 3HHx monomer during in vivo production of P(3HB-co-3HHx) copolymer. The P(3HB-co-3HHx) copolymer produced from the Cupriavidus necator transformant that harbors phaJSs, PHB-4/pBBR1-CBP-M-CPF4JSs, showed enhanced 3HHx incorporation of up to 11 mol% without affecting the P(3HB-co-3HHx) production when palm oil was used as the carbon source. In addition, both kcat and kcat/Km of PhaJSs were higher toward the C6 than the shorter C4 substrates, underscoring the preference for 3-hydroxyhexanoyl-CoA. These results suggest that PhaJSs has a significant ability to supply 3HHx monomers for PHA biosynthesis via ß-oxidation and can be applied for metabolic engineering of robust PHA-producing strains.


Assuntos
Cupriavidus necator , Streptomyces , Ácido 3-Hidroxibutírico/metabolismo , Caproatos/metabolismo , Carbono/metabolismo , Coenzima A/metabolismo , Cupriavidus necator/metabolismo , Enoil-CoA Hidratase/metabolismo , Óleo de Palmeira/metabolismo , Streptomyces/metabolismo
19.
Acta Crystallogr F Struct Biol Commun ; 77(Pt 11): 427-434, 2021 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-34726182

RESUMO

Glutamine synthetase (GS) is a decameric enzyme that plays a key role in nitrogen metabolism. Acetylation of the N-terminal degron (N-degron) of GS is essential for ubiquitylation and subsequent GS degradation. The full-length GS structure showed that the N-degron is buried inside the GS decamer and is inaccessible to the acetyltransferase. The structure of N-degron-truncated GS reported here reveals that the N-degron is not essential for GS decamer formation. It is also shown that the N-degron can be exposed to a solvent region through a series of conformational adjustments upon ligand binding. In summary, this study elucidated the dynamic movement of the N-degron and the possible effect of glutamine in enhancing the acetylation process.


Assuntos
Glutamato-Amônia Ligase , Glutamina , Cristalografia por Raios X , Glutamato-Amônia Ligase/química , Glutamato-Amônia Ligase/genética , Glutamato-Amônia Ligase/metabolismo , Glutamina/química , Humanos , Ubiquitinação
20.
Int J Biol Macromol ; 186: 414-423, 2021 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-34246679

RESUMO

Polyhydroxyalkanoates (PHAs) are biopolyesters synthesized by microorganisms as intracellular energy reservoirs under stressful environmental conditions. PHA synthase (PhaC) is the key enzyme responsible for PHA biosynthesis, but the importance of its N- and C-terminal ends still remains elusive. Six plasmid constructs expressing truncation variants of Aquitalea sp. USM4 PhaC (PhaC1As) were generated and heterologously expressed in Cupriavidus necator PHB-4. Removal of the first six residues at the N-terminus enabled the modulation of PHA composition without altering the PHA content in cells. Meanwhile, deletion of 13 amino acids from the C-terminus greatly affected the catalytic activity of PhaC1As, retaining only 1.1-7.4% of the total activity. Truncation(s) at the N- and/or C-terminus of PhaC1As gradually diminished the incorporation of comonomer units, and revealed that the N-terminal region is essential for PhaC1As dimerization whereas the C-terminal region is required for stabilization. Notably, transmission electron microscopy analysis showed that PhaC modification affected the morphology of intracellular PHA granules, which until now is only known to be regulated by phasins. This study provided substantial evidence and highlighted the significance of both the N- and C-termini of PhaC1As in regulating intracellular granule morphology, activity, substrate specificity, dimerization and stability of the synthase.


Assuntos
Aciltransferases/metabolismo , Betaproteobacteria/enzimologia , Corpos de Inclusão/enzimologia , Poli-Hidroxialcanoatos/metabolismo , Aciltransferases/química , Aciltransferases/genética , Betaproteobacteria/genética , Betaproteobacteria/ultraestrutura , Sítios de Ligação , Domínio Catalítico , Estabilidade Enzimática , Corpos de Inclusão/genética , Corpos de Inclusão/ultraestrutura , Domínios Proteicos , Multimerização Proteica , Relação Estrutura-Atividade , Especificidade por Substrato
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