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1.
PLoS One ; 19(2): e0297281, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38359031

RESUMO

Multiple studies report that melanomas are innervated tumors with sensory and sympathetic fibers where these neural fibers play crucial functional roles in tumor growth and metastasis with branch specificity. Yet there is no study which reports the direct neural recording and its pattern during in-vivo progression of the cancer. We performed daily neural recordings from male and female mice bearing orthotopic metastasizing- melanomas and melanomas with low metastatic poential, derived from B16-F10 and B16-F1 cells, respectively. Further, to explore the origins of neural activity, 6-Hydroxidopamine mediated chemical sympathectomy was performed followed by daily microneurographic recordings. We also performed the daily bioluminescent imaging to track in vivo growth of primary tumors and distant metastasis to the cranial area. Our results show that metastasizing tumors display high levels of neural activity while tumors with low metastatic potential lack it indicating that the presence of neural activity is linked to the metastasizing potential of the tumors. Moreover, the neural activity is not continuous over the tumor progression and has a sex-specific temporal patterns where males have two peaks of high neural activity while females show a single peak. The neural peak activity originated in peripheral sympathetic nerves as sympathectomy completely eliminated the peak activity in both sexes. Peak activities were highly correlated with the distant metastasis in both sexes. These results show that sympathetic neural activity is crucially involved in tumor metastasis and has sex-specific role in malignancy initiation.


Assuntos
Melanoma , Masculino , Feminino , Animais , Camundongos , Melanoma/patologia , Metástase Neoplásica
2.
Nat Commun ; 14(1): 7431, 2023 11 16.
Artigo em Inglês | MEDLINE | ID: mdl-37973928

RESUMO

Bacterial AB toxins are secreted key virulence factors that are internalized by target cells through receptor-mediated endocytosis, translocating their enzymatic domain to the cytosol from endosomes (short-trip) or the endoplasmic reticulum (long-trip). To accomplish this, bacterial AB toxins evolved a multidomain structure organized into either a single polypeptide chain or non-covalently associated polypeptide chains. The prototypical short-trip single-chain toxin is characterized by a receptor-binding domain that confers cellular specificity and a translocation domain responsible for pore formation whereby the catalytic domain translocates to the cytosol in an endosomal acidification-dependent way. In this work, the determination of the three-dimensional structure of AIP56 shows that, instead of a two-domain organization suggested by previous studies, AIP56 has three-domains: a non-LEE encoded effector C (NleC)-like catalytic domain associated with a small middle domain that contains the linker-peptide, followed by the receptor-binding domain. In contrast to prototypical single-chain AB toxins, AIP56 does not comprise a typical structurally complex translocation domain; instead, the elements involved in translocation are scattered across its domains. Thus, the catalytic domain contains a helical hairpin that serves as a molecular switch for triggering the conformational changes necessary for membrane insertion only upon endosomal acidification, whereas the middle and receptor-binding domains are required for pore formation.


Assuntos
Toxinas Bacterianas , NF-kappa B , NF-kappa B/metabolismo , Toxinas Bacterianas/metabolismo , Endocitose , Endossomos/metabolismo , Peptídeos/metabolismo , Transporte Proteico
3.
Adv Sci (Weinh) ; 8(9): 2003630, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33977052

RESUMO

The molecular mechanisms and forces involved in the translocation of bacterial toxins into host cells are still a matter of intense research. The adenylate cyclase (CyaA) toxin from Bordetella pertussis displays a unique intoxication pathway in which its catalytic domain is directly translocated across target cell membranes. The CyaA translocation region contains a segment, P454 (residues 454-484), which exhibits membrane-active properties related to antimicrobial peptides. Herein, the results show that this peptide is able to translocate across membranes and to interact with calmodulin (CaM). Structural and biophysical analyses reveal the key residues of P454 involved in membrane destabilization and calmodulin binding. Mutational analysis demonstrates that these residues play a crucial role in CyaA translocation into target cells. In addition, calmidazolium, a calmodulin inhibitor, efficiently blocks CyaA internalization. It is proposed that after CyaA binding to target cells, the P454 segment destabilizes the plasma membrane, translocates across the lipid bilayer and binds calmodulin. Trapping of CyaA by the CaM:P454 interaction in the cytosol may assist the entry of the N-terminal catalytic domain by converting the stochastic motion of the polypeptide chain through the membrane into an efficient vectorial chain translocation into host cells.


Assuntos
Toxina Adenilato Ciclase/metabolismo , Calmodulina/metabolismo , Células Eucarióticas/metabolismo , Domínios Proteicos/fisiologia , Sítios de Ligação/fisiologia , Ligação Proteica/fisiologia , Transporte Proteico/fisiologia
4.
Biophys J ; 120(10): 1869-1882, 2021 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-33741354

RESUMO

ErbB2 (or HER2) is a receptor tyrosine kinase overexpressed in some breast cancers and associated with poor prognosis. Treatments targeting the receptor extracellular and kinase domains have greatly improved disease outcome in the last 20 years. In parallel, the structures of these domains have been described, enabling better mechanistic understanding of the receptor function and targeted inhibition. However, the ErbB2 disordered C-terminal cytoplasmic tail (CtErbB2) remains very poorly characterized in terms of structure, dynamics, and detailed functional mechanism. Yet, it is where signal transduction is triggered via phosphorylation of tyrosine residues and carried out via interaction with adaptor proteins. Here, we report the first description, to our knowledge, of the ErbB2 disordered tail at atomic resolution using NMR, complemented by small-angle x-ray scattering. We show that although no part of CtErbB2 has any fully populated secondary or tertiary structure, it contains several transient α-helices and numerous transient polyproline II helices, populated up to 20 and 40%, respectively, and low but significant compaction. The presence of some structural elements suggests, along the lines of the results obtained for EGFR (ErbB1), that they may have a functional role in ErbB2's autoregulation processes. In addition, the transient formation of polyproline II helices is compliant with previously suggested interactions with SH3 domains. All in all, our in-depth structural study opens perspectives in the mechanistic understanding of ErbB2.


Assuntos
Neoplasias da Mama , Receptor ErbB-2 , Proteínas Adaptadoras de Transdução de Sinal , Feminino , Humanos , Fosforilação , Receptor ErbB-2/metabolismo , Transdução de Sinais , Domínios de Homologia de src
5.
Sci Rep ; 10(1): 14824, 2020 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-32908180

RESUMO

Nerve fibers are known to reside within malignant tumors and the greater the neuronal density the worse prognosis for the patient. Recent discoveries using tumor bearing animal models have eluded to the autonomic nervous system having a direct effect on tumor growth and metastasis. We report the first direct and chronic in vivo measurements of neural activity within tumors. Using a triple-negative mammary cancer mouse model and chronic neural interface techniques, we have recorded neural activity directly within the tumor mass while the tumor grows and metastasizes. The results indicate that there is a strong connection between the autonomic nervous system and the tumor and could help uncover the mechanisms of tumor growth and metastasis.


Assuntos
Glândulas Mamárias Animais/inervação , Neoplasias Mamárias Experimentais/patologia , Neoplasias de Mama Triplo Negativas/patologia , Animais , Linhagem Celular Tumoral , Feminino , Camundongos , Camundongos Endogâmicos BALB C , Metástase Neoplásica
6.
Nat Commun ; 10(1): 3967, 2019 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-31481669

RESUMO

N6-threonyl-carbamoylation of adenosine 37 of ANN-type tRNAs (t6A) is a universal modification essential for translational accuracy and efficiency. The t6A pathway uses two sequentially acting enzymes, YRDC and OSGEP, the latter being a subunit of the multiprotein KEOPS complex. We recently identified mutations in genes encoding four out of the five KEOPS subunits in children with Galloway-Mowat syndrome (GAMOS), a clinically heterogeneous autosomal recessive disease characterized by early-onset steroid-resistant nephrotic syndrome and microcephaly. Here we show that mutations in YRDC cause an extremely severe form of GAMOS whereas mutations in GON7, encoding the fifth KEOPS subunit, lead to a milder form of the disease. The crystal structure of the GON7/LAGE3/OSGEP subcomplex shows that the intrinsically disordered GON7 protein becomes partially structured upon binding to LAGE3. The structure and cellular characterization of GON7 suggest its involvement in the cellular stability and quaternary arrangement of the KEOPS complex.


Assuntos
Adenosina/análogos & derivados , Proteínas de Ligação ao GTP/genética , Hérnia Hiatal/genética , Proteínas Intrinsicamente Desordenadas/genética , Microcefalia/genética , Nefrose/genética , Proteínas Nucleares/genética , RNA de Transferência/genética , Proteínas de Ligação a RNA/genética , Adenosina/genética , Criança , Feminino , Proteínas de Ligação ao GTP/química , Proteínas de Ligação ao GTP/metabolismo , Humanos , Proteínas Intrinsicamente Desordenadas/metabolismo , Masculino , Complexos Multiproteicos/química , Complexos Multiproteicos/genética , Complexos Multiproteicos/metabolismo , Mutação , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/metabolismo
7.
J Chem Inf Model ; 59(5): 1743-1758, 2019 05 28.
Artigo em Inglês | MEDLINE | ID: mdl-30840442

RESUMO

The concept of intrinsically disordered proteins (IDPs) has emerged relatively slowly, but over the past 20 years, it has become an intense research area in structural biology. Indeed, because of their considerable flexibility and structural heterogeneity, the determination of IDP conformational ensemble is particularly challenging and often requires a combination of experimental measurements and computational approaches. With the improved accuracy of all-atom force fields and the increasing computing performances, molecular dynamics (MD) simulations have become more and more reliable to generate realistic conformational ensembles. And the combination of MD simulations with experimental approaches, such as nuclear magnetic resonance (NMR) and/or small-angle X-ray scattering (SAXS) allows one to converge toward a more accurate and exhaustive description of IDP structures. In this Review, we discuss the state of the art of MD simulations of IDP conformational ensembles, with a special focus on studies that back-calculated and directly compared theoretical and experimental NMR or SAXS observables, such as chemical shifts (CS), 3J-couplings (3Jc), residual dipolar couplings (RDC), or SAXS intensities. We organize the review in three parts. In the first section, we discuss the studies which used NMR and/or SAXS data to test and validate the development of force fields or enhanced sampling techniques. In the second part, we explore different methods for the refinement of MD-derived structural ensembles, such as NMR or SAXS data-restrained MD simulations or ensemble reweighting to better fit experiments. Finally, we survey some recent studies combining MD simulations with NMR and/or SAXS measurements to investigate the relationship between IDP conformational ensemble and biological activity, as well as their implication in human diseases. From this review, we noticed that quite a few studies compared MD-generated conformational ensembles with both NMR and SAXS measurements to validate IDP structures at both local and global levels. Yet, beside the IDP propensity to form local secondary structures, their dynamic extension or compactness also appears important for their activity. Thus, we believe that a close synergy between MD simulations, NMR, and SAXS experiments would be greatly appropriate to address the challenges of characterizing the disordered structures of proteins and their complexes, relative to their biological functions.


Assuntos
Proteínas Intrinsicamente Desordenadas/química , Simulação de Dinâmica Molecular , Peptídeos/química , Proteínas Amiloidogênicas/química , Animais , Humanos , Ressonância Magnética Nuclear Biomolecular , Conformação Proteica , Espalhamento a Baixo Ângulo , Proteínas Virais/química , Difração de Raios X
8.
Pathog Dis ; 76(8)2018 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-30452651

RESUMO

The adenylate cyclase toxin (CyaA) is a multi-domain protein secreted by Bordetella pertussis, the causative agent of whooping cough. CyaA is involved in the early stages of respiratory tract colonization by Bordetella pertussis. CyaA is produced and acylated in the bacteria, and secreted via a dedicated secretion system. The cell intoxication process involves a unique mechanism of transport of the CyaA toxin catalytic domain (ACD) across the plasma membrane of eukaryotic cells. Once translocated, ACD binds to and is activated by calmodulin and produces high amounts of cAMP, subverting the physiology of eukaryotic cells. Here, we review our work on the identification and characterization of a critical region of CyaA, the translocation region, required to deliver ACD into the cytosol of target cells. The translocation region contains a segment that exhibits membrane-active properties, i.e. is able to fold upon membrane interaction and permeabilize lipid bilayers. We proposed that this region is required to locally destabilize the membrane, decreasing the energy required for ACD translocation. To further study the translocation process, we developed a tethered bilayer lipid membrane (tBLM) design that recapitulate the ACD transport across a membrane separating two hermetic compartments. We showed that ACD translocation is critically dependent on calcium, membrane potential, CyaA acylation and on the presence of calmodulin in the trans compartment. Finally, we describe how calmodulin-binding triggers key conformational changes in ACD, leading to its activation and production of supraphysiological concentrations of cAMP.


Assuntos
Toxina Adenilato Ciclase/metabolismo , Bordetella pertussis/metabolismo , Calmodulina/metabolismo , AMP Cíclico/metabolismo , Acilação , Toxina Adenilato Ciclase/química , Cálcio/metabolismo , Membrana Celular/metabolismo , Células Eucarióticas , Humanos , Potenciais da Membrana , Permeabilidade , Ligação Proteica , Conformação Proteica , Dobramento de Proteína , Processamento de Proteína Pós-Traducional , Transporte Proteico
9.
Nucleic Acids Res ; 46(11): 5850-5860, 2018 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-29741707

RESUMO

The universal N6-threonylcarbamoyladenosine (t6A) modification at position A37 of ANN-decoding tRNAs is essential for translational fidelity. In bacteria the TsaC enzyme first synthesizes an l-threonylcarbamoyladenylate (TC-AMP) intermediate. In cooperation with TsaB and TsaE, TsaD then transfers the l-threonylcarbamoyl-moiety from TC-AMP onto tRNA. We determined the crystal structure of the TsaB-TsaE-TsaD (TsaBDE) complex of Thermotoga maritima in presence of a non-hydrolysable AMPCPP. TsaE is positioned at the entrance of the active site pocket of TsaD, contacting both the TsaB and TsaD subunits and prohibiting simultaneous tRNA binding. AMPCPP occupies the ATP binding site of TsaE and is sandwiched between TsaE and TsaD. Unexpectedly, the binding of TsaE partially denatures the active site of TsaD causing loss of its essential metal binding sites. TsaE interferes in a pre- or post-catalytic step and its binding to TsaBD is regulated by ATP hydrolysis. This novel binding mode and activation mechanism of TsaE offers good opportunities for antimicrobial drug development.


Assuntos
Adenosina/análogos & derivados , Proteínas de Bactérias/química , RNA de Transferência/metabolismo , Thermotoga maritima/enzimologia , Adenosina/biossíntese , Trifosfato de Adenosina/análogos & derivados , Trifosfato de Adenosina/metabolismo , Proteínas Arqueais/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Domínio Catalítico , Enzimas/química , Enzimas/metabolismo , Modelos Moleculares , Conformação Proteica , Estrutura Quaternária de Proteína , RNA de Transferência/química
10.
Sci Rep ; 8(1): 1564, 2018 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-29367722

RESUMO

Fast and slow neural waves have been observed to propagate in the human brain during seizures. Yet the nature of these waves is difficult to study in a surgical setting. Here, we report an observation of two different traveling waves propagating in the in-vitro epileptic hippocampus at speeds similar to those in the human brain. A fast traveling spike and a slow moving wave were recorded simultaneously with a genetically encoded voltage sensitive fluorescent protein (VSFP Butterfly 1.2) and a high speed camera. The results of this study indicate that the fast traveling spike is NMDA-sensitive but the slow moving wave is not. Image analysis and model simulation demonstrate that the slow moving wave is moving slowly, generating the fast traveling spike and is, therefore, a moving source of the epileptiform activity. This slow moving wave is associated with a propagating neural calcium wave detected with calcium dye (OGB-1) but is independent of NMDA receptors, not related to ATP release, and much faster than those previously recorded potassium waves. Computer modeling suggests that the slow moving wave can propagate by the ephaptic effect like epileptiform activity. These findings provide an alternative explanation for slow propagation seizure wavefronts associated with fast propagating spikes.


Assuntos
Potenciais de Ação , Hipocampo/fisiopatologia , Convulsões/fisiopatologia , Trifosfato de Adenosina/metabolismo , Animais , Sinalização do Cálcio , Simulação por Computador , Agonistas de Aminoácidos Excitatórios/metabolismo , Camundongos Transgênicos , Modelos Neurológicos , N-Metilaspartato/metabolismo , Receptores de N-Metil-D-Aspartato/metabolismo
11.
Toxicon ; 149: 37-44, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-29337218

RESUMO

The adenylate cyclase toxin (CyaA) plays an essential role in the early stages of respiratory tract colonization by Bordetella pertussis, the causative agent of whooping cough. Once secreted, CyaA invades eukaryotic cells, leading to cell death. The cell intoxication process involves a unique mechanism of translocation of the CyaA catalytic domain directly across the plasma membrane of the target cell. Herein, we review our recent results describing how calcium is involved in several steps of this intoxication process. In conditions mimicking the low calcium environment of the crowded bacterial cytosol, we show that the C-terminal, calcium-binding Repeat-in-ToXin (RTX) domain of CyaA, RD, is an extended, intrinsically disordered polypeptide chain with a significant level of local, secondary structure elements, appropriately sized for transport through the narrow channel of the secretion system. Upon secretion, the high calcium concentration in the extracellular milieu induces the refolding of RD, which likely acts as a scaffold to favor the refolding of the upstream domains of the full-length protein. Due to the presence of hydrophobic regions, CyaA is prone to aggregate into multimeric forms in vitro, in the absence of a chaotropic agent. We have recently defined the experimental conditions required for CyaA folding, comprising both calcium binding and molecular confinement. These parameters are critical for CyaA folding into a stable, monomeric and functional form. The monomeric, calcium-loaded (holo) toxin exhibits efficient liposome permeabilization and hemolytic activities in vitro, even in a fully calcium-free environment. By contrast, the toxin requires sub-millimolar calcium concentrations in solution to translocate its catalytic domain across the plasma membrane, indicating that free calcium in solution is actively involved in the CyaA toxin translocation process. Overall, this data demonstrates the remarkable adaptation of bacterial RTX toxins to the diversity of calcium concentrations it is exposed to in the successive environments encountered in the course of the intoxication process.


Assuntos
Toxina Adenilato Ciclase/química , Cálcio/química , Modelos Biológicos , Coqueluche/microbiologia , Toxina Adenilato Ciclase/metabolismo , Bordetella pertussis , Células Eucarióticas/microbiologia , Domínios Proteicos , Dobramento de Proteína , Sistemas de Translocação de Proteínas , Transporte Proteico
12.
PLoS Biol ; 15(12): e2004486, 2017 12.
Artigo em Inglês | MEDLINE | ID: mdl-29287065

RESUMO

Once translocated into the cytosol of target cells, the catalytic domain (AC) of the adenylate cyclase toxin (CyaA), a major virulence factor of Bordetella pertussis, is potently activated by binding calmodulin (CaM) to produce supraphysiological levels of cAMP, inducing cell death. Using a combination of small-angle X-ray scattering (SAXS), hydrogen/deuterium exchange mass spectrometry (HDX-MS), and synchrotron radiation circular dichroism (SR-CD), we show that, in the absence of CaM, AC exhibits significant structural disorder, and a 75-residue-long stretch within AC undergoes a disorder-to-order transition upon CaM binding. Beyond this local folding, CaM binding induces long-range allosteric effects that stabilize the distant catalytic site, whilst preserving catalytic loop flexibility. We propose that the high enzymatic activity of AC is due to a tight balance between the CaM-induced decrease of structural flexibility around the catalytic site and the preservation of catalytic loop flexibility, allowing for fast substrate binding and product release. The CaM-induced dampening of AC conformational disorder is likely relevant to other CaM-activated enzymes.


Assuntos
Toxina Adenilato Ciclase/química , Bordetella pertussis/química , Calmodulina/química , Toxina Adenilato Ciclase/metabolismo , Toxina Adenilato Ciclase/fisiologia , Bordetella pertussis/patogenicidade , Sinalização do Cálcio , Calmodulina/metabolismo , Calmodulina/fisiologia , Catálise , Domínio Catalítico , Dicroísmo Circular , AMP Cíclico/metabolismo , Medição da Troca de Deutério , Espectrometria de Massas , Modelos Moleculares , Ligação Proteica , Conformação Proteica , Espalhamento a Baixo Ângulo , Síncrotrons
13.
Nucleic Acids Res ; 45(10): 6209-6216, 2017 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-28379452

RESUMO

tRNAs are synthesized as precursor RNAs that have to undergo processing steps to become functional. Yeast Trz1 is a key endoribonuclease involved in the 3΄ maturation of tRNAs in all domains of life. It is a member of the ß-lactamase family of RNases, characterized by an HxHxDH sequence motif involved in coordination of catalytic Zn-ions. The RNase Z family consists of two subfamilies: the short (250-400 residues) and the long forms (about double in size). Short form RNase Z enzymes act as homodimers: one subunit embraces tRNA with a protruding arm, while the other provides the catalytic site. The long form is thought to contain two fused ß-lactamase domains within a single polypeptide. Only structures of short form RNase Z enzymes are known. Here we present the 3.1 Å crystal structure of the long-form Trz1 from Saccharomyces cerevisiae. Trz1 is organized into two ß-lactamase domains connected by a long linker. The N-terminal domain has lost its catalytic residues, but retains the long flexible arm that is important for tRNA binding, while it is the other way around in the C-terminal domain. Trz1 likely evolved from a duplication and fusion of the gene encoding the monomeric short form RNase Z.


Assuntos
Endorribonucleases/química , Proteínas de Saccharomyces cerevisiae/química , Sequência de Aminoácidos , Domínio Catalítico , Sequência Conservada , Cristalografia por Raios X , Evolução Molecular , Modelos Moleculares , Fases de Leitura Aberta , Conformação Proteica , Domínios Proteicos , RNA de Transferência/metabolismo , Proteínas Recombinantes de Fusão/química , Saccharomyces cerevisiae/enzimologia , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos
14.
Nucleic Acids Res ; 43(6): 3358-72, 2015 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-25735745

RESUMO

The yeast KEOPS protein complex comprising Kae1, Bud32, Cgi121, Pcc1 and Gon7 is responsible for the essential tRNA threonylcarbamoyladenosine (t(6)A) modification. Deletion of genes coding for the KEOPS subunits also affects telomere elongation and transcriptional regulation. In the present work, the crystal structure of Bud32/Cgi121 in complex with ADP revealed that ADP is bound in the catalytic site of Bud32 in a canonical manner characteristic of Protein Kinase A (PKA) family proteins. We found that Gon7 forms a stable heterodimer with Pcc1 and report the crystal structure of the Pcc1-Gon7 heterodimer. Gon7 interacts with the same Pcc1 region engaged in the archaeal Pcc1 homodimer. We further show that yeast KEOPS, unlike its archaeal counterpart, exists as a heteropentamer in which Gon7, Pcc1, Kae1, Bud32 and Cgi121 also adopt a linear arrangement. We constructed a model of yeast KEOPS that provides structural insight into the role of Gon7. The model also revealed the presence of a highly positively charged crater surrounding the entrance of Kae1 that likely binds tRNA.


Assuntos
Proteínas Serina-Treonina Quinases/química , Proteínas de Saccharomyces cerevisiae/química , Fatores de Transcrição/química , Difosfato de Adenosina/química , Sequência de Aminoácidos , Proteínas Arqueais/química , Cristalografia por Raios X , Modelos Moleculares , Dados de Sequência Molecular , Complexos Multiproteicos/química , Domínios e Motivos de Interação entre Proteínas , Proteínas Serina-Treonina Quinases/genética , Estrutura Quaternária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Espalhamento a Baixo Ângulo , Homologia de Sequência de Aminoácidos , Fatores de Transcrição/genética , Difração de Raios X
15.
Nucleic Acids Res ; 43(3): 1804-17, 2015 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-25578970

RESUMO

The essential and universal N(6)-threonylcarbamoyladenosine (t(6)A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon-anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (TsaB), YjeE (TsaE) and YrdC (TsaC) proteins are necessary and sufficient for the in vitro biosynthesis of t(6)A, using tRNA, ATP, L-threonine and bicarbonate as substrates. YrdC synthesizes the short-lived L-threonylcarbamoyladenylate (TCA), and YgjD, YeaZ and YjeE cooperate to transfer the L-threonylcarbamoyl-moiety from TCA onto adenosine at position 37 of substrate tRNA. We determined the crystal structure of the heterodimer YgjD-YeaZ at 2.3 Å, revealing the presence of an unexpected molecule of ADP bound at an atypical site situated at the YgjD-YeaZ interface. We further showed that the ATPase activity of YjeE is strongly activated by the YgjD-YeaZ heterodimer. We established by binding experiments and SAXS data analysis that YgjD-YeaZ and YjeE form a compact ternary complex only in presence of ATP. The formation of the ternary YgjD-YeaZ-YjeE complex is required for the in vitro biosynthesis of t(6)A but not its ATPase activity.


Assuntos
Trifosfato de Adenosina/fisiologia , Proteínas de Escherichia coli/metabolismo , Escherichia coli/genética , RNA Bacteriano/biossíntese , RNA de Transferência/biossíntese , Difosfato de Adenosina/metabolismo , Trifosfato de Adenosina/metabolismo , Sítios de Ligação , Dimerização , Eletroforese em Gel de Ágar , Proteínas de Escherichia coli/química , Modelos Moleculares , Conformação Proteica , RNA Bacteriano/metabolismo
16.
Biochemistry ; 50(29): 6409-22, 2011 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-21714500

RESUMO

Cdc31, the Saccharomyces cerevisiae centrin, is an EF-hand calcium-binding protein essential for the cell division and mRNA nuclear export. We used biophysical techniques to investigate its calcium, magnesium, and protein target binding properties as well as their conformations in solution. We show here that Cdc31 displays one Ca(2+)/Mg(2+) mixed site in the N-terminal domain and two low-affinity Ca(2+) sites in the C-terminal domain. The affinity of Cdc31 for different natural target peptides (from Kar1, Sfi1, Sac3) that we obtained by isothermal titration calorimetry shows weakly Ca(2+), but also Mg(2+) dependence. The characteristics of target surface binding were shown to be similar; we highlight that the 1-4 hydrophobic amino acid motif, in a stable amphipathic α-helix, is critical for binding. Ca(2+) and Mg(2+) binding increase the α-helix content and stabilize the structure. Analysis of small-angle X-ray scattering experiments revealed that N- and C-terminal domains are not individualized in apo-Cdc31; in contrast, they are separated in the Mg(2+) state, creating a groove in the middle of the molecule that is occupied by the target peptide in the liganded form. Consequently, Mg(2+) seems to have consequences on Cdc31's function and could be important to stimulate interactions in resting cells.


Assuntos
Proteínas de Ligação ao Cálcio/metabolismo , Cálcio/metabolismo , Proteínas de Ciclo Celular/metabolismo , Magnésio/metabolismo , Peptídeos/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Sequência de Aminoácidos , Proteínas de Ligação ao Cálcio/química , Calorimetria , Proteínas de Ciclo Celular/química , Dicroísmo Circular , Cristalografia por Raios X , Humanos , Interações Hidrofóbicas e Hidrofílicas , Cinética , Modelos Moleculares , Dados de Sequência Molecular , Peptídeos/química , Ligação Proteica , Conformação Proteica , Proteínas de Saccharomyces cerevisiae/química , Alinhamento de Sequência , Termodinâmica
17.
Epilepsy Behav ; 21(3): 267-70, 2011 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-21576037

RESUMO

Longitudinal hippocampal pathways are needed for seizure synchronization, and there is evidence that their transection may abolish seizures. However, the effect of such transection on memory is unknown. In this study, we investigated the effect of transverse CA3 transections on memory function in Sprague-Dawley rats. With a stereotactic knife, a single CA3 transection was made unilaterally (n=5) or bilaterally (n=5). Sham surgery was done in another group (n=4). Morris water maze and novel object recognition tests were started 18 days later and revealed no significant differences between transected animals and controls. Cresyl-violet brain staining confirmed the locations of transections in the CA3 region. We conclude that normal performances in Morris water maze and novel object recognition tests do not appear to require intact transmission throughout the whole length of CA3, supporting the hypothesis that CA3 transections may be used in temporal lobe epilepsy to interrupt seizure circuitry while preserving memory.


Assuntos
Região CA3 Hipocampal/lesões , Região CA3 Hipocampal/fisiologia , Memória/fisiologia , Análise de Variância , Animais , Comportamento Exploratório , Lateralidade Funcional/fisiologia , Masculino , Aprendizagem em Labirinto/fisiologia , Ratos , Ratos Sprague-Dawley
18.
Biophys J ; 99(2): 656-65, 2010 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-20643086

RESUMO

Three basic proline-rich salivary proteins have been produced through the recombinant route. IB5 is a small basic proline-rich protein that is involved in the binding of plant tannins in the oral cavity. II-1 is a larger protein with a closely related backbone; it is glycosylated, and it is also able to bind plant tannins. II-1 ng has the same polypeptidic backbone as II-1, but it is not glycosylated. Small angle x-ray scattering experiments on dilute solutions of these proteins confirm that they are intrinsically disordered. IB5 and II-1 ng can be described through a chain model including a persistence length and cross section. The measured radii of gyration (Rg=27.9 and 41.0+/-1 A respectively) and largest distances (rmax=110 and 155+/-10 A respectively) show that their average conformations are rather extended. The length of the statistical segment (twice the persistence length) is b=30 A, which is larger than the usual value (18 A-20 A) for unstructured polypeptide chains. These characteristics are presumably related to the presence of polyproline helices within the polypeptidic backbones. For both proteins, the radius of gyration of the chain cross-section is Rc=2.7+/-0.2A. The glycosylated protein II-1 has similar conformations but the presence of large polyoside sidegroups yields the structure of a branched macromolecule with the same hydrophobic backbone and hydrophilic branches. It is proposed that the unusually extended conformations of these proteins in solution facilitate the capture of plant tannins in the oral cavity.


Assuntos
Proteínas Salivares Ricas em Prolina/química , Sequência de Aminoácidos , Biologia Computacional , Eletroforese em Gel de Poliacrilamida , Glicosilação , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Proteínas Recombinantes/química , Espalhamento a Baixo Ângulo , Difração de Raios X
19.
Recent Adv Res Updat ; 11(2): 211-225, 2010 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-21866209

RESUMO

An algorithm is presented to predict the intensity and timing of a singular single stimulus required to switch the state of a bistable system from repetitive activity to a stable point. The algorithm is first tested on a modified Hodgkin-Huxley model to predict the parameters of a stimulus capable of annihilating the spontaneously occurring repetitive action potentials. Elevation of the potassium equilibrium potential causes oscillations in the V, m, h and n parameters and generates periodic activity. Equations describing the time-varying behavior of these parameters can be used to predict the pulse width, coupling interval and intensity of a single anodic pulse applied between two consecutive action potentials to suppress the activity. The algorithm was then applied to predict the singular parameters of quasi-periodic epileptiform activity generated in the hippocampus slice preparation exposed to high-potassium concentrations. The results indicate that a stimulus with the estimated parameters was able to either completely annihilate the action potentials in the HH model or predict the region of unpredictable latencies. Therefore this algorithm is capable a predicting singular parameters accurately when the model is known. In the case of an experimental system where the equations of the system are not known, the algorithm predicted parameters in the range of those observed experimentally. Therefore, the algorithm could reduce significantly the amount of time required to find the singular parameters of experimental bistable systems normally obtained by a systematic exploration of the parameter space. In particular, this algorithm could be useful to predict the singular parameters of quasi periodic epileptiform activity leading to the suppression of this activity if the system is bistable.

20.
Artigo em Inglês | MEDLINE | ID: mdl-19963753

RESUMO

It has been shown that oscillations can be generated by additive Gaussian white noise in a recurrent Hodgkin-Huxley neuron model. Type 1 oscillation was induced with Stochastic Resonance (SR) by additive Gaussian noise at lower amplitudes, while Type 2 oscillation was observed at higher amplitudes. However, the mechanism of Type 2 oscillation is not clear. In this article, we test the hypothesis through computer simulations that the period of the Type 2 oscillation can be affected by temperature in a recurrent neural network in which the recurrent model is constructed by four Hodgkin-Huxley (HH) neuron models. Each HH neuron model is driven by Gaussian noise and sub-threshold excitatory synaptic currents with an alpha function from another HH neuron model, and the action potentials (spike firings) of each HH neuron model are transferred to the other HH neuron model via sub-threshold synaptic currents. From spike firing times recorded, the inter spike interval (ISI) histogram was generated, and the periodicity of spike firings was detected from the ISI histogram at each HH neuron model. The results show that the probability of spike firings in the Type1 oscillation is maximized at a specific standard deviation (S.D.) of the Gaussian white noise with SR at 6.3, 15.0 and 25.0 degrees C, while the period of the Type 2 oscillation depends on temperature. It is concluded that the Type1 oscillation can be induced by additive Gaussian white noise on the basis of a synaptic delay in the recurrent HH neuron model, whereas ISIs of the Type 2 oscillation may be determined by refractory periods of HH neuron models.


Assuntos
Redes Neurais de Computação , Ruído
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