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1.
Nucleic Acids Res ; 2024 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-38842933

RESUMO

The ParABS system, composed of ParA (an ATPase), ParB (a DNA binding protein), and parS (a centromere-like DNA), regulates bacterial chromosome partition. The ParB-parS partition complex interacts with the nucleoid-bound ParA to form the nucleoid-adaptor complex (NAC). In Helicobacter pylori, ParA and ParB homologs are encoded as HpSoj and HpSpo0J (HpParA and HpParB), respectively. We determined the crystal structures of the ATP hydrolysis deficient mutant, HpParAD41A, and the HpParAD41A-DNA complex. We assayed the CTPase activity of HpParB and identified two potential DNA binding modes of HpParB regulated by CTP, one is the specific DNA binding by the DNA binding domain and the other is the non-specific DNA binding through the C-terminal domain under the regulation of CTP. We observed an interaction between HpParAD41A and the N-terminus fragment of HpParB (residue 1-10, HpParBN10) and determined the crystal structure of the ternary complex, HpParAD41A-DNA-HpParBN10 complex which mimics the NAC formation. HpParBN10 binds near the HpParAD41A dimer interface and is clamped by flexible loops, L23 and L34, through a specific cation-π interaction between Arg9 of HpParBN10 and Phe52 of HpParAD41A. We propose a molecular mechanism model of the ParABS system providing insight into chromosome partition in bacteria.

2.
FEBS J ; 290(18): 4513-4532, 2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-37243454

RESUMO

Leptospirosis is a commonly overlooked zoonotic disease that occurs in tropical and subtropical regions. Recent studies have divided the Leptospira spp. into three groups based on virulence, including pathogenic, intermediate, and saprophytic species. Pathogenic species express a protein family with leucine-rich repeat (LRR) domains, which are less expressed or absent in nonpathogenic species, highlighting the importance of this protein family in leptospirosis. However, the role of LRR domain proteins in the pathogenesis of leptospirosis is still unknown and requires further investigation. In this study, the 3D structure of LSS_01692 (rLRR38) was obtained using X-ray crystallography at a resolution of 3.2 Å. The results showed that rLRR38 forms a typical horseshoe structure with 11 α-helices and 11 ß-sheets and an antiparallel dimeric structure. The interactions of rLRR38 with extracellular matrix and cell surface receptors were evaluated using ELISA and single-molecule atomic force microscopy. The results showed that rLRR38 interacted with fibronectin, collagen IV, and Toll-like receptor 2 (TLR2). Incubating HK2 cells with rLRR38 induced two downstream inflammation responses (IL-6 and MCP-1) in the TLR2 signal transduction pathway. The TLR2-TLR1 complex showed the most significant upregulation effects under rLRR38 treatment. Inhibitors also significantly inhibited nuclear factor κB and mitogen-activated protein kinases signals transduction under rLRR38 stimulation. In conclusion, rLRR38 was determined to be a novel LRR domain protein in 3D structure and demonstrated as a TLR2-binding protein that induces inflammatory responses. These structural and functional studies provide a deeper understanding of the pathogenesis of leptospirosis.


Assuntos
Leptospira , Leptospirose , Humanos , Leptospira/genética , Leptospira/química , Leptospira/metabolismo , NF-kappa B/genética , NF-kappa B/metabolismo , Receptor 2 Toll-Like/genética , Receptor 2 Toll-Like/metabolismo , Transdução de Sinais , Leptospirose/genética , Leptospirose/metabolismo
3.
Nucleic Acids Res ; 49(22): 13150-13164, 2021 12 16.
Artigo em Inglês | MEDLINE | ID: mdl-34850144

RESUMO

Genome segregation is a vital process in all organisms. Chromosome partitioning remains obscure in Archaea, the third domain of life. Here, we investigated the SegAB system from Sulfolobus solfataricus. SegA is a ParA Walker-type ATPase and SegB is a site-specific DNA-binding protein. We determined the structures of both proteins and those of SegA-DNA and SegB-DNA complexes. The SegA structure revealed an atypical, novel non-sandwich dimer that binds DNA either in the presence or in the absence of ATP. The SegB structure disclosed a ribbon-helix-helix motif through which the protein binds DNA site specifically. The association of multiple interacting SegB dimers with the DNA results in a higher order chromatin-like structure. The unstructured SegB N-terminus plays an essential catalytic role in stimulating SegA ATPase activity and an architectural regulatory role in segrosome (SegA-SegB-DNA) formation. Electron microscopy results also provide a compact ring-like segrosome structure related to chromosome organization. These findings contribute a novel mechanistic perspective on archaeal chromosome segregation.


Assuntos
Proteínas Arqueais/genética , Segregação de Cromossomos , Cromossomos de Archaea/genética , DNA Arqueal/genética , Sulfolobus solfataricus/genética , Difosfato de Adenosina/metabolismo , Adenosina Trifosfatases/química , Adenosina Trifosfatases/genética , Adenosina Trifosfatases/metabolismo , Trifosfato de Adenosina/metabolismo , Proteínas Arqueais/química , Proteínas Arqueais/metabolismo , Cromatina/genética , Cromatina/metabolismo , Cromatina/ultraestrutura , Cristalografia por Raios X , DNA Arqueal/química , DNA Arqueal/metabolismo , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Microscopia Eletrônica , Modelos Moleculares , Complexos Multiproteicos/química , Complexos Multiproteicos/metabolismo , Complexos Multiproteicos/ultraestrutura , Mutação , Conformação de Ácido Nucleico , Ligação Proteica , Conformação Proteica , Sulfolobus solfataricus/metabolismo
4.
Biochem J ; 477(21): 4313-4326, 2020 11 13.
Artigo em Inglês | MEDLINE | ID: mdl-33094809

RESUMO

Leptospirosis is the most common zoonotic disease caused by pathogenic Leptospira, which is classified into three groups according to virulence. Its pathogenic and intermediate species contain leucine-rich repeat (LRR) proteins that are rarely expressed in non-pathogenic strains. In this study, we presented the crystal structure of LSS_11580 (rLRR20) from pathogenic L. santarosai serovar Shermani. X-ray diffraction at a resolution of 1.99 Šrevealed a horseshoe-shaped structure containing seven α-helices and five ß-sheets. Affinity assays indicated that rLRR20 interacts with E-cadherin on the cell surface. Interestingly, its binds to the extracellular (EC) 1 domain in human epithelial (E)-cadherin, which is responsible for binding to another E-cadherin molecule in neighboring cells. Several charged residues on the concave face of LRR20 were predicted to interact with EC1 domain. In the affinity assays, these charged residues were replaced by alanine, and their affinities to E-cadherin were measured. Three vital residues and mutation variants of LRR20, namely D56A, E59A, and E123A, demonstrated significantly reduced affinity to E-cadherin compared with the control. Besides, we also demonstrated that rLRR20 induced the expression of neutrophil gelatinase-associated lipocalin (NGAL) in HK2 cells. The low ability of the three mutation variants to induce NGAL expression further demonstrates this induction. The present findings indicate that LRR20 from pathogenic Leptospira binds to E-cadherin and interacts with its EC1 domain. In addition, its induction of NGAL expression in HK2 cells is associated with acute kidney injury in human.


Assuntos
Caderinas/metabolismo , Cristalografia por Raios X/métodos , Leptospira/metabolismo , Proteínas/química , Proteínas/metabolismo , Proteínas de Transporte/metabolismo , Linhagem Celular , Humanos , Leptospirose/metabolismo , Proteínas de Repetições Ricas em Leucina
5.
Sci Adv ; 6(32): eabb4024, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32821837

RESUMO

Inorganic phosphate (Pi) is a fundamental and essential element for nucleotide biosynthesis, energy supply, and cellular signaling in living organisms. Human phosphate transporter (hPiT) dysfunction causes numerous diseases, but the molecular mechanism underlying transporters remains elusive. We report the structure of the sodium-dependent phosphate transporter from Thermotoga maritima (TmPiT) in complex with sodium and phosphate (TmPiT-Na/Pi) at 2.3-angstrom resolution. We reveal that one phosphate and two sodium ions (Pi-2Na) are located at the core of TmPiT and that the third sodium ion (Nafore) is located near the inner membrane boundary. We propose an elevator-like mechanism for sodium and phosphate transport by TmPiT, with the TmPiT-Na/Pi complex adopting an inward occluded conformation. We found that disease-related hPiT variants carry mutations in the corresponding sodium- and phosphate-binding residues identified in TmPiT. Our three-dimensional structure of TmPiT provides a framework for understanding PiT dysfunction and for future structure-based drug design.

6.
J Mol Biol ; 432(4): 1143-1157, 2020 02 14.
Artigo em Inglês | MEDLINE | ID: mdl-31931012

RESUMO

CC-type chemokine ligand 5 (CCL5) is involved in the pathogenesis of many inflammatory conditions. Under physiological conditions, CCL5 oligomerization and aggregation are considered to be responsible for its inflammatory properties. The structural basis of CCL5 oligomerization remains controversial because the current oligomer models contain no consensus interactions. In this study, NMR and biophysical analyses proposed evidence that the CC-type CCL5 dimer acts as the basic unit to constitute the oligomer and that CCL5 oligomerizes alternatively through E66-K25 and E66-R44/K45 interactions. In addition, a newly determined trimer structure, constituted by CCL5 and the E66S mutant, reported an interfacial interaction through the N-terminal 12FAY14 sequence. The interaction contributes to CCL5 aggregation and precipitation but not to oligomerization. In accordance with the observations, an integrative model explains the CCL5 oligomerization and aggregation mechanism in which CCL5 assembly consists of two types of dimer-dimer interactions and one aggregation mechanism. For full-length CCL5, the molecular accumulation triggers oligomerization through the E66-K25 and E66-R44/K45 interactions, and the 12FAY14 interaction acts as a secondary effect to derive aggregation and precipitation. In contrast, the E66-R44/K45 interaction might dominate in CCL5 N-terminal truncations, and the interaction would lead to the filament-like formation in solution.


Assuntos
Quimiocina CCL5/metabolismo , Sequência de Aminoácidos , Animais , Quimiocina CCL5/química , Glicosaminoglicanos/química , Glicosaminoglicanos/metabolismo , Humanos , Inflamação/metabolismo , Espectroscopia de Ressonância Magnética , Camundongos , Mutação , Ligação Proteica , Estrutura Secundária de Proteína
7.
J Mol Biol ; 431(8): 1619-1632, 2019 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-30878480

RESUMO

Membrane-embedded pyrophosphatase (M-PPase) hydrolyzes pyrophosphate to drive ion (H+ and/or Na+) translocation. We determined crystal structures and functions of Vigna radiata M-PPase (VrH+-PPase), the VrH+-PPase-2Pi complex and mutants at hydrophobic gate (residue L555) and exit channel (residues T228 and E225). Ion pore diameters along the translocation pathway of three VrH+-PPases complexes (Pi-, 2Pi- and imidodiphosphate-bound states) present a unique wave-like profile, with different pore diameters at the hydrophobic gate and exit channel, indicating that the ligands induced pore size alterations. The 2Pi-bound state with the largest pore diameter might mimic the hydrophobic gate open. In mutant structures, ordered waters detected at the hydrophobic gate among VrH+-PPase imply the possibility of solvation, and numerous waters at the exit channel might signify an open channel. A salt-bridge, E225-R562 is at the way out of the exit channel of VrH+-PPase; E225A mutant makes the interaction eliminated and reveals a decreased pumping ability. E225-R562 might act as a latch to regulate proton release. A water wire from the ion gate (R-D-K-E) through the hydrophobic gate and into the exit channel may reflect the path of proton transfer.


Assuntos
Proteínas de Plantas/metabolismo , Pirofosfatases/metabolismo , Vigna/metabolismo , Sequência de Aminoácidos , Cristalografia por Raios X , Interações Hidrofóbicas e Hidrofílicas , Transporte de Íons , Modelos Moleculares , Proteínas de Plantas/química , Conformação Proteica , Bombas de Próton/química , Bombas de Próton/metabolismo , Prótons , Pirofosfatases/química , Vigna/química
8.
Nucleic Acids Res ; 47(4): 2113-2129, 2019 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-30544248

RESUMO

ParABS, an important DNA partitioning process in chromosome segregation, includes ParA (an ATPase), ParB (a parS binding protein) and parS (a centromere-like DNA). The homologous proteins of ParA and ParB in Helicobacter pylori are HpSoj and HpSpo0J, respectively. We analyzed the ATPase activity of HpSoj and found that it is enhanced by both DNA and HpSpo0J. Crystal structures of HpSoj and its DNA complexes revealed a typical ATPase fold and that it is dimeric. DNA binding by HpSoj is promoted by ATP. The HpSoj-ATP-DNA complex non-specifically binds DNA through a continuous basic binding patch formed by lysine residues, with a single DNA-binding site. This complex exhibits a DNA-binding adept state with an active ATP-bound conformation, whereas the HpSoj-ADP-DNA complex may represent a transient DNA-bound state. Based on structural comparisons, HpSoj exhibits a similar DNA binding surface to the bacterial ParA superfamily, but the archaeal ParA superfamily exhibits distinct non-specific DNA-binding via two DNA-binding sites. We detected the HpSpo0J-HpSoj-DNA complex by electron microscopy and show that this nucleoid-adaptor complex (NAC) is formed through HpSoj and HpSpo0J interaction and parS DNA binding. NAC formation is promoted by HpSoj participation and specific parS DNA facilitation.


Assuntos
Adenosina Trifosfatases/química , Proteínas de Bactérias/química , Segregação de Cromossomos/genética , Helicobacter pylori/genética , Adenosina Trifosfatases/genética , Proteínas de Bactérias/genética , Sítios de Ligação , Centrômero/genética , Cromossomos Bacterianos/genética , Cristalografia por Raios X , DNA/química , DNA/genética , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Helicobacter pylori/química , Helicobacter pylori/patogenicidade
9.
Acta Crystallogr F Struct Biol Commun ; 74(Pt 2): 82-85, 2018 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-29400316

RESUMO

The chemokine CCL5 is considered to be a potential therapeutic target because of its ability to recruit immune cells to inflammatory sites. CCL5 aggregates under physiological conditions, and high-order oligomer formation is considered to be significant for cell migration, immune-cell activation and HIV cell entry. The structure of the high-order oligomer is unknown and the mechanism by which the oligomer is derived has yet to be established. Here, a CCL5 mutant (CCL5-E66S) which is deficient in oligomer formation was mixed with native CCL5 to prepare a protein trimer. At an optimized ratio the trimeric CCL5 crystallized, and the crystal belonged to the tetragonal space group P41212, with unit-cell parameters a = 56.6, b = 56.6, c = 154.1 Å. The Matthews coefficient (VM) of the crystal is 2.58 Å3 Da-1 (three molecules in the asymmetric unit), with a solvent content of 52.32%. Diffraction data were collected to a resolution of 1.87 Šand the statistics indicated satisfactory data quality. The new structure will reveal the interfaces in the CCL5 oligomer, therefore assisting in understanding the mechanism of CCL5 oligomerization.


Assuntos
Quimiocina CCL5/química , Quimiocina CCL5/genética , Multimerização Proteica/genética , Análise de Sequência de DNA/métodos , Cristalografia por Raios X/métodos , Expressão Gênica , Humanos
10.
Struct Dyn ; 4(3): 032105, 2017 May.
Artigo em Inglês | MEDLINE | ID: mdl-28345008

RESUMO

Membrane-integral pyrophosphatases (mPPases) couple the hydrolysis of pyrophosphate (PPi) to the pumping of Na+, H+, or both these ions across a membrane. Recently solved structures of the Na+-pumping Thermotoga maritima mPPase (TmPPase) and H+-pumping Vigna radiata mPPase revealed the basis of ion selectivity between these enzymes and provided evidence for the mechanisms of substrate hydrolysis and ion-pumping. Our atomistic molecular dynamics (MD) simulations of TmPPase demonstrate that loop 5-6 is mobile in the absence of the substrate or substrate-analogue bound to the active site, explaining the lack of electron density for this loop in resting state structures. Furthermore, creating an apo model of TmPPase by removing ligands from the TmPPase:IDP:Na structure in MD simulations resulted in increased dynamics in loop 5-6, which results in this loop moving to uncover the active site, suggesting that interactions between loop 5-6 and the imidodiphosphate and its associated Mg2+ are important for holding a loop-closed conformation. We also provide further evidence for the transport-before-hydrolysis mechanism by showing that the non-hydrolyzable substrate analogue, methylene diphosphonate, induces low levels of proton pumping by VrPPase.

11.
Nat Commun ; 7: 13596, 2016 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-27922000

RESUMO

Membrane-bound pyrophosphatases (M-PPases), which couple proton/sodium ion transport to pyrophosphate synthesis/hydrolysis, are important in abiotic stress resistance and in the infectivity of protozoan parasites. Here, three M-PPase structures in different catalytic states show that closure of the substrate-binding pocket by helices 5-6 affects helix 13 in the dimer interface and causes helix 12 to move down. This springs a 'molecular mousetrap', repositioning a conserved aspartate and activating the nucleophilic water. Corkscrew motion at helices 6 and 16 rearranges the key ionic gate residues and leads to ion pumping. The pumped ion is above the ion gate in one of the ion-bound structures, but below it in the other. Electrometric measurements show a single-turnover event with a non-hydrolysable inhibitor, supporting our model that ion pumping precedes hydrolysis. We propose a complete catalytic cycle for both proton and sodium-pumping M-PPases, and one that also explains the basis for ion specificity.


Assuntos
Membrana Celular/enzimologia , Pirofosfatases/metabolismo , Thermotoga maritima/enzimologia , Vigna/enzimologia , Biocatálise , Cristalografia por Raios X , Ligação de Hidrogênio , Hidrólise , Íons , Cinética , Modelos Moleculares , Estrutura Secundária de Proteína , Bombas de Próton/metabolismo , Pirofosfatases/química , Sódio/metabolismo
12.
Sci Rep ; 6: 27838, 2016 06 09.
Artigo em Inglês | MEDLINE | ID: mdl-27278903

RESUMO

Leptospirosis is an often overlooked cause of acute kidney injury that can lead to multiple organ failure and even death. The principle protein that conserved in many pathogenic leptospires is the outer membrane protein LipL32. However, the role of LipL32 in the pathogenesis of renal injury in leptospirosis is not entirely clear. Here we studied the effects of LipL32 on the developing kidney in zebrafish larvae. Incubation of zebrafish larvae with Leptospira santarosai serovar Shermani induced acute tubular injury predominantly in the proximal pronephric ducts. Furthermore, microinjection of lipl32 mRNA or recombinant LipL32 protein into zebrafish larvae increased macrophage accumulation and disrupted the basolateral location of NA-K-ATPase in pronephric ducts. These changes led to substantial impairment of the pronephric kidney structure. We further demonstrated that morpholino knockdown of tlr2, but not tlr4, reduced the LipL32-induced leukocyte infiltration and kidney injury. These data demonstrate that LipL32 contributes to the renal pathology in leptospirosis and gives some clues to the potential virulence of LipL32. Our results support the use of zebrafish as a model organism for studying the disease mechanism of leptospiral infection. This model might permit the future exploration of the virulence and molecular pathways of different leptospiral outer membrane proteins.


Assuntos
Proteínas da Membrana Bacteriana Externa/metabolismo , Nefropatias , Rim , Leptospira/metabolismo , Lipoproteínas/metabolismo , Pronefro , Peixe-Zebra , Animais , Proteínas da Membrana Bacteriana Externa/genética , Inflamação/embriologia , Inflamação/genética , Inflamação/microbiologia , Rim/embriologia , Rim/microbiologia , Nefropatias/embriologia , Nefropatias/genética , Nefropatias/microbiologia , Leptospira/genética , Lipoproteínas/genética , Pronefro/embriologia , Pronefro/microbiologia , Peixe-Zebra/embriologia , Peixe-Zebra/microbiologia
13.
J Struct Biol ; 194(1): 90-101, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26850168

RESUMO

Helicobacter pylori cell binding factor 2 (HpCBF2) is an antigenic virulence factor belonging to the SurA-like peptidyl-prolyl cis-trans isomerase family with implications for pathogenicity in the human gastrointestinal tract. HpCBF2 possesses PPIase activity and could act as a periplasmic chaperone to regulate outer membrane protein assembly. Here, we measured the isomerization and chaperone activity of HpCBF2, and determined the crystal structure of HpCBF2 in complex with an inhibitor, indole-2-carboxylic acid (I2CA), at 2.4Å resolution. HpCBF2-I2CA forms a homodimer encasing a large central hydrophobic cavity with a basket-like structure, and each monomer contains a PPIase and a chaperone domain. In the HpCBF2-I2CA dimer, the two PPIase domains separate by a distance of 22.8Å, while the two chaperone domains arrange in a domain-swap manner. The PPIase domains bound with I2CA ligand face towards the chaperone domains and are shielded by surrounding hydrophobic residues. With the aid of SAXS experiments, we also revealed domain motion between the apo- and I2CA-bound states of HpCBF2. The domain motion in HpCBF2 might be necessary for the isomerization activity of PPIase and the accommodation of the unfolded and partially folded peptides to refold by chaperone domain.


Assuntos
Proteínas de Bactérias/química , Chaperonas Moleculares/química , Peptidilprolil Isomerase/química , Domínios Proteicos , Multimerização Proteica , Estrutura Secundária de Proteína , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Cristalografia por Raios X , Eletroforese em Gel de Poliacrilamida , Helicobacter pylori/genética , Helicobacter pylori/metabolismo , Modelos Moleculares , Chaperonas Moleculares/genética , Chaperonas Moleculares/metabolismo , Peptidilprolil Isomerase/genética , Peptidilprolil Isomerase/metabolismo , Ligação Proteica , Espalhamento a Baixo Ângulo , Homologia de Sequência de Aminoácidos , Difração de Raios X
14.
Proc Natl Acad Sci U S A ; 112(21): 6613-8, 2015 May 26.
Artigo em Inglês | MEDLINE | ID: mdl-25964325

RESUMO

Spo0J (stage 0 sporulation protein J, a member of the ParB superfamily) is an essential component of the ParABS (partition system of ParA, ParB, and parS)-related bacterial chromosome segregation system. ParB (partition protein B) and its regulatory protein, ParA, act cooperatively through parS (partition S) DNA to facilitate chromosome segregation. ParB binds to chromosomal DNA at specific parS sites as well as the neighboring nonspecific DNA sites. Various ParB molecules can associate together and spread along the chromosomal DNA. ParB oligomer and parS DNA interact together to form a high-order nucleoprotein that is required for the loading of the structural maintenance of chromosomes proteins onto the chromosome for chromosomal DNA condensation. In this report, we characterized the binding of parS and Spo0J from Helicobacter pylori (HpSpo0J) and solved the crystal structure of the C-terminal domain truncated protein (Ct-HpSpo0J)-parS complex. Ct-HpSpo0J folds into an elongated structure that includes a flexible N-terminal domain for protein-protein interaction and a conserved DNA-binding domain for parS binding. Two Ct-HpSpo0J molecules bind with one parS. Ct-HpSpo0J interacts vertically and horizontally with its neighbors through the N-terminal domain to form an oligomer. These adjacent and transverse interactions are accomplished via a highly conserved arginine patch: RRLR. These interactions might be needed for molecular assembly of a high-order nucleoprotein complex and for ParB spreading. A structural model for ParB spreading and chromosomal DNA condensation that lead to chromosome segregation is proposed.


Assuntos
Proteínas de Bactérias/química , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sequência de Bases , Segregação de Cromossomos/genética , Segregação de Cromossomos/fisiologia , Cristalografia por Raios X , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Helicobacter pylori/genética , Helicobacter pylori/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Estrutura Quaternária de Proteína , Espalhamento a Baixo Ângulo , Homologia de Sequência de Aminoácidos , Esporos Bacterianos/genética , Esporos Bacterianos/metabolismo , Difração de Raios X
15.
J Biol Chem ; 290(2): 1197-209, 2015 Jan 09.
Artigo em Inglês | MEDLINE | ID: mdl-25451931

RESUMO

Single molecule atomic force microscopy (smAFM) was employed to unfold transmembrane domain interactions of a unique vacuolar H(+)-pyrophosphatase (EC 3.6.1.1) from Vigna radiata. H(+)-Pyrophosphatase is a membrane-embedded homodimeric protein containing a single type of polypeptide and links PPi hydrolysis to proton translocation. Each subunit consists of 16 transmembrane domains with both ends facing the lumen side. In this investigation, H(+)-pyrophosphatase was reconstituted into the lipid bilayer in the same orientation for efficient fishing out of the membrane by smAFM. The reconstituted H(+)-pyrophosphatase in the lipid bilayer showed an authentically dimeric structure, and the size of each monomer was ∼4 nm in length, ∼2 nm in width, and ∼1 nm in protrusion height. Upon extracting the H(+)-pyrophosphatase out of the membrane, force-distance curves containing 10 peaks were obtained and assigned to distinct domains. In the presence of pyrophosphate, phosphate, and imidodiphosphate, the numbers of interaction curves were altered to 7, 8, and 10, respectively, concomitantly with significant modification in force strength. The substrate-binding residues were further replaced to verify these domain changes upon substrate binding. A working model is accordingly proposed to show the interactions between transmembrane domains of H(+)-pyrophosphatase in the presence and absence of substrate and its analog.


Assuntos
Pirofosfatase Inorgânica/química , Pirofosfatase Inorgânica/ultraestrutura , Transporte de Íons , Vacúolos/enzimologia , Fabaceae/química , Fabaceae/enzimologia , Hidrólise , Pirofosfatase Inorgânica/metabolismo , Cinética , Bicamadas Lipídicas/química , Microscopia de Força Atômica , Estrutura Terciária de Proteína , Prótons , Especificidade por Substrato
16.
PLoS One ; 9(8): e105821, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25157844

RESUMO

The multi S1/P1 nuclease AtBFN2 (EC 3.1.30.1) encoded by the Arabidopsis thaliana At1g68290 gene is a glycoprotein that digests RNA, ssDNA, and dsDNA. AtBFN2 depends on three zinc ions for cleaving DNA and RNA at 3'-OH to yield 5'-nucleotides. In addition, AtBFN2's enzymatic activity is strongly glycan dependent. Plant Zn(2+)-dependent endonucleases present a unique fold, and belong to the Phospholipase C (PLC)/P1 nuclease superfamily. In this work, we present the first complete, ligand-free, AtBFN2 crystal structure, along with sulfate, phosphate and ssDNA co-crystal structures. With these, we were able to provide better insight into the glycan structure and possible enzymatic mechanism. In comparison with other nucleases, the AtBFN2/ligand-free and AtBFN2/PO4 models suggest a similar, previously proposed, catalytic mechanism. Our data also confirm that the phosphate and vanadate can inhibit the enzyme activity by occupying the active site. More importantly, the AtBFN2/A5T structure reveals a novel and conserved secondary binding site, which seems to be important for plant Zn(2+)-dependent endonucleases. Based on these findings, we propose a rational ssDNA binding model, in which the ssDNA wraps itself around the protein and the attached surface glycan, in turn, reinforces the binding complex.


Assuntos
Proteínas de Arabidopsis/química , Arabidopsis/enzimologia , DNA de Cadeia Simples/química , Endonucleases/química , Sequência de Aminoácidos , Domínio Catalítico , Complexos de Coordenação/química , Cristalografia por Raios X , Modelos Moleculares , Dados de Sequência Molecular , Fosfatos/química , Sulfatos/química , Zinco/química
17.
Curr Opin Struct Biol ; 27: 38-47, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24768824

RESUMO

Membrane-bound pyrophosphatases (M-PPases) are homodimeric enzymes that couple the generation and utilization of membrane potentials to pyrophosphate (PPi) hydrolysis and synthesis. Since the discovery of the link between PPi use and proton transport in purple, non-sulphur bacteria in the 1960s, M-PPases have been found in all three domains of life and have been shown to have a crucial role in stress tolerance and in plant maturation. The discovery of sodium-pumping and sodium/proton-pumping M-PPases showed that the pumping specificity of these enzymes is not limited to protons, further suggesting that M-PPases are evolutionarily very ancient. The recent structures of two M-PPases, the Vigna radiata H(+)-pumping M-PPase and Thermotoga maritima Na(+)-pumping M-PPase, provide the basis for understanding the functional data. They show that M-PPases have a novel fold and pumping mechanism, different to the other primary pumps. This review discusses the current structural understanding of M-PPases and of ion selection among various M-PPases.


Assuntos
Prótons , Pirofosfatases/metabolismo , Sódio/metabolismo , Sequência de Aminoácidos , Transporte Biológico , Humanos , Dados de Sequência Molecular , Pirofosfatases/química
18.
Mol Cell Biol ; 34(6): 1003-19, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24396070

RESUMO

Neurite outgrowth is an essential process during neuronal differentiation as well as neuroregeneration. Thus, understanding the molecular and cellular control of neurite outgrowth will benefit patients with neurological diseases. We have previously shown that overexpression of the signaling adaptor protein SH2B1ß promotes fibroblast growth factor 1 (FGF1)-induced neurite outgrowth (W. F. Lin, C. J. Chen, Y. J. Chang, S. L. Chen, I. M. Chiu, and L. Chen, Cell. Signal. 21:1060-1072, 2009). SH2B1ß also undergoes nucleocytoplasmic shuttling and regulates a subset of neurotrophin-induced genes. Although these findings suggest that SH2B1ß regulates gene expression, the nuclear role of SH2B1ß was not known. In this study, we show that SH2B1ß interacts with the transcription factor, signal transducer, and activator of transcription 3 (STAT3) in neuronal PC12 cells, cortical neurons, and COS7 fibroblasts. By affecting the subcellular distribution of STAT3, SH2B1ß increased serine phosphorylation and the concomitant transcriptional activity of STAT3. As a result, overexpressing SH2B1ß enhanced FGF1-induced expression of STAT3 target genes Egr1 and Cdh2. Chromatin immunoprecipitation assays further reveal that, in response to FGF1, overexpression of SH2B1ß promotes the in vivo occupancy of STAT3-Sp1 heterodimers at the promoter of Egr1 and Cdh2. These findings establish a central role of SH2B1ß in orchestrating signaling events to transcriptional activation through interacting and regulating STAT3-containing complexes during neuronal differentiation.


Assuntos
Proteínas de Transporte/metabolismo , Diferenciação Celular/genética , Fator 1 de Crescimento de Fibroblastos/metabolismo , Expressão Gênica/genética , Neurônios/metabolismo , Fator de Transcrição STAT3/metabolismo , Animais , Células COS , Caderinas/genética , Caderinas/metabolismo , Proteínas de Transporte/genética , Linhagem Celular Tumoral , Chlorocebus aethiops , Proteína 1 de Resposta de Crescimento Precoce/genética , Proteína 1 de Resposta de Crescimento Precoce/metabolismo , Fator 1 de Crescimento de Fibroblastos/genética , Células HEK293 , Humanos , Imunoglobulinas/genética , Imunoglobulinas/metabolismo , Peptídeos e Proteínas de Sinalização Intracelular , Proteínas do Tecido Nervoso/genética , Proteínas do Tecido Nervoso/metabolismo , Células PC12 , Fosforilação/genética , Regiões Promotoras Genéticas/genética , Ratos , Ratos Sprague-Dawley , Fator de Transcrição STAT3/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Transcrição Gênica/genética
19.
Proteins ; 82(6): 1079-85, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24108499

RESUMO

Glucoamylases are responsible for hydrolysis of starch and polysaccharides to yield ß-D-glucose. Rhizopus oryzae glucoamylase (RoGA) is composed of an N-terminal starch binding domain (SBD) and a C-terminal catalytic domain connected by an O-glycosylated linker. Two carbohydrate binding sites in RoSBD have been identified, site I is created by three highly conserved aromatic residues, Trp47, Tyr83, and Tyr94, and site II is built up by Tyr32 and Phe58. Here, the two crystal structures of RoSBD in complex with only α-(1,6)-linked isomaltotriose (RoSBD-isoG3) and isomaltotetraose (RoSBD-isoG4) have been determined at 1.2 and 1.3 Å, respectively. Interestingly, site II binding is observed in both complexes, while site I binding is only found in the RoSBD-isoG4 complex. Hence, site II acts as the recognition binding site for carbohydrate and site I accommodates site II to bind isoG4. Site I participates in sugar binding only when the number of glucosyl units of oligosaccharides is more than three. Taken together, two carbohydrate binding sites in RoSBD cooperate to reinforce binding mode of glucoamylase with polysaccharides as well as the starch.


Assuntos
Polissacarídeos Fúngicos/química , Proteínas Fúngicas/química , Glucana 1,4-alfa-Glucosidase/química , Oligossacarídeos/química , Rhizopus/enzimologia , Trissacarídeos/química , Configuração de Carboidratos , Sequência de Carboidratos , Cristalografia por Raios X , Ligação de Hidrogênio , Ligantes , Modelos Moleculares , Dados de Sequência Molecular , Ligação Proteica , Estrutura Secundária de Proteína
20.
PLoS One ; 8(12): e83246, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24349474

RESUMO

Leptospirosis is one of the most widespread zoonotic diseases in the world. It is caused by the pathogen Leptospira that results in multiple-organ failure, in particular of the kidney. Outer membrane lipoprotein is the suspected virulence factor of Leptospira. In Leptospira spp LipL41 is one major lipoprotein and is highly conserved. Previous study suggests that LipL41 bears hemin-binding ability and might play a possible role in iron regulation and storage. However, the characterization of hemin-binding ability of LipL41 is still unclear. Here the hemin-binding ability of LipL41 was examined, yielding a K d = 0.59 ± 0.14 µM. Two possible heme regulatory motifs (HRMs), C[P/S], were found in LipL41 at (140)Cys-Ser and (220)Cys-Pro. The mutation study indicates that Cys140 and Cys220 might be cooperatively involved in hemin binding. A supramolecular assembly of LipL41 was determined by transmission electron microscopy. The LipL41 oligomer consists of 36 molecules and folds as a double-layered particle. At the C-terminus of LipL41, there are two tetratricopeptide repeats (TPRs), which might be involved in the protein-protein interaction of the supramolecular assembly.


Assuntos
Proteínas de Bactérias/metabolismo , Proteínas de Transporte/metabolismo , Hemeproteínas/metabolismo , Hemina/metabolismo , Leptospira/metabolismo , Lipoproteínas/metabolismo , Multimerização Proteica/fisiologia , Proteínas de Bactérias/genética , Proteínas de Transporte/genética , Proteínas Ligantes de Grupo Heme , Hemeproteínas/genética , Hemina/genética , Leptospira/genética , Lipoproteínas/genética
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