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1.
Cell ; 171(1): 163-178.e19, 2017 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-28844694

RESUMO

Alterations in transcriptional regulators can orchestrate oncogenic gene expression programs in cancer. Here, we show that the BRG1/BRM-associated factor (BAF) chromatin remodeling complex, which is mutated in over 20% of human tumors, interacts with EWSR1, a member of a family of proteins with prion-like domains (PrLD) that are frequent partners in oncogenic fusions with transcription factors. In Ewing sarcoma, we find that the BAF complex is recruited by the EWS-FLI1 fusion protein to tumor-specific enhancers and contributes to target gene activation. This process is a neomorphic property of EWS-FLI1 compared to wild-type FLI1 and depends on tyrosine residues that are necessary for phase transitions of the EWSR1 prion-like domain. Furthermore, fusion of short fragments of EWSR1 to FLI1 is sufficient to recapitulate BAF complex retargeting and EWS-FLI1 activities. Our studies thus demonstrate that the physical properties of prion-like domains can retarget critical chromatin regulatory complexes to establish and maintain oncogenic gene expression programs.


Assuntos
Proteínas de Ligação a Calmodulina/química , Proteínas de Ligação a Calmodulina/metabolismo , Proteínas de Fusão Oncogênica/metabolismo , Proteína Proto-Oncogênica c-fli-1/metabolismo , Proteína EWS de Ligação a RNA/metabolismo , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/metabolismo , Sarcoma de Ewing/genética , Linhagem Celular Tumoral , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Humanos , Células-Tronco Mesenquimais/metabolismo , Repetições de Microssatélites , Complexos Multiproteicos/química , Complexos Multiproteicos/metabolismo , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Proteínas Priônicas/metabolismo , Domínios Proteicos , Sarcoma de Ewing/patologia
2.
Trends Biochem Sci ; 41(11): 894-897, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-27283512

RESUMO

Low-complexity (LC) domains regulate the aggregation and phase transition of proteins in a modification-dependent manner. The study of LC domain modifications has now become feasible, as shown by genetic variants of the carboxy-terminal domain (CTD) of RNA Polymerase II (Pol II) that provide access to the type and position of modifications of a LC domain by mass spectrometry (MS).


Assuntos
Substituição de Aminoácidos , Proteínas de Ligação a Calmodulina/química , RNA Polimerase II/química , Proteína FUS de Ligação a RNA/química , Proteínas de Ligação a RNA/química , Fatores Associados à Proteína de Ligação a TATA/química , Sequência de Aminoácidos , Animais , Proteínas de Ligação a Calmodulina/genética , Galinhas , Expressão Gênica , Humanos , Camundongos , Mutação , Domínios Proteicos , RNA Polimerase II/genética , Proteína EWS de Ligação a RNA , Proteína FUS de Ligação a RNA/genética , Proteínas de Ligação a RNA/genética , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Fatores Associados à Proteína de Ligação a TATA/genética , Transcrição Gênica
3.
Int J Mol Sci ; 22(1)2020 Dec 30.
Artigo em Inglês | MEDLINE | ID: mdl-33396740

RESUMO

Calmodulin (CaM) is an important intracellular protein that binds Ca2+ and functions as a critical second messenger involved in numerous biological activities through extensive interactions with proteins and peptides. CaM's ability to adapt to binding targets with different structures is related to the flexible central helix separating the N- and C-terminal lobes, which allows for conformational changes between extended and collapsed forms of the protein. CaM-binding targets are most often identified using prediction algorithms that utilize sequence and structural data to predict regions of peptides and proteins that can interact with CaM. In this review, we provide an overview of different CaM-binding proteins, the motifs through which they interact with CaM, and shared properties that make them good binding partners for CaM. Additionally, we discuss the historical and current methods for predicting CaM binding, and the similarities and differences between these methods and their relative success at prediction. As new CaM-binding proteins are identified and classified, we will gain a broader understanding of the biological processes regulated through changes in Ca2+ concentration through interactions with CaM.


Assuntos
Proteínas de Ligação a Calmodulina/química , Proteínas de Ligação a Calmodulina/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Sítios de Ligação , Cálcio/química , Calmodulina/química , Análise por Conglomerados , Análise Discriminante , Humanos , Aprendizado de Máquina , Cadeias de Markov , Modelos Moleculares , Ligação Proteica , Conformação Proteica , Relação Estrutura-Atividade , Máquina de Vetores de Suporte
4.
Int J Mol Sci ; 21(4)2020 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-32054133

RESUMO

Dictyostelium discoideum is gaining increasing attention as a model organism for the study of calcium binding and calmodulin function in basic biological events as well as human diseases. After a short overview of calcium-binding proteins, the structure of Dictyostelium calmodulin and the conformational changes effected by calcium ion binding to its four EF hands are compared to its human counterpart, emphasizing the highly conserved nature of this central regulatory protein. The calcium-dependent and -independent motifs involved in calmodulin binding to target proteins are discussed with examples of the diversity of calmodulin binding proteins that have been studied in this amoebozoan. The methods used to identify and characterize calmodulin binding proteins is covered followed by the ways Dictyostelium is currently being used as a system to study several neurodegenerative diseases and how it could serve as a model for studying calmodulinopathies such as those associated with specific types of heart arrythmia. Because of its rapid developmental cycles, its genetic tractability, and a richly endowed stock center, Dictyostelium is in a position to become a leader in the field of calmodulin research.


Assuntos
Proteínas de Ligação a Calmodulina/metabolismo , Calmodulina/metabolismo , Dictyostelium/metabolismo , Proteínas de Protozoários/metabolismo , Sítios de Ligação , Cálcio/metabolismo , Sinalização do Cálcio , Calmodulina/química , Proteínas de Ligação a Calmodulina/química , Dictyostelium/química , Motivos EF Hand , Humanos , Modelos Moleculares , Ligação Proteica , Infecções por Protozoários/parasitologia , Proteínas de Protozoários/química
5.
BMC Bioinformatics ; 19(Suppl 14): 410, 2018 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-30453876

RESUMO

BACKGROUND: The prediction of calmodulin-binding (CaM-binding) proteins plays a very important role in the fields of biology and biochemistry, because the calmodulin protein binds and regulates a multitude of protein targets affecting different cellular processes. Computational methods that can accurately identify CaM-binding proteins and CaM-binding domains would accelerate research in calcium signaling and calmodulin function. Short-linear motifs (SLiMs), on the other hand, have been effectively used as features for analyzing protein-protein interactions, though their properties have not been utilized in the prediction of CaM-binding proteins. RESULTS: We propose a new method for the prediction of CaM-binding proteins based on both the total and average scores of known and new SLiMs in protein sequences using a new scoring method called sliding window scoring (SWS) as features for the prediction module. A dataset of 194 manually curated human CaM-binding proteins and 193 mitochondrial proteins have been obtained and used for testing the proposed model. The motif generation tool, Multiple EM for Motif Elucidation (MEME), has been used to obtain new motifs from each of the positive and negative datasets individually (the SM approach) and from the combined negative and positive datasets (the CM approach). Moreover, the wrapper criterion with random forest for feature selection (FS) has been applied followed by classification using different algorithms such as k-nearest neighbors (k-NN), support vector machines (SVM), naive Bayes (NB) and random forest (RF). CONCLUSIONS: Our proposed method shows very good prediction results and demonstrates how information contained in SLiMs is highly relevant in predicting CaM-binding proteins. Further, three new CaM-binding motifs have been computationally selected and biologically validated in this study, and which can be used for predicting CaM-binding proteins.


Assuntos
Proteínas de Ligação a Calmodulina/química , Biologia Computacional/métodos , Motivos de Aminoácidos , Sequência de Aminoácidos , Teorema de Bayes , Cálcio/metabolismo , Humanos , Probabilidade , Estrutura Quaternária de Proteína , Reprodutibilidade dos Testes , Máquina de Vetores de Suporte
6.
Biochem J ; 474(8): 1417-1438, 2017 04 07.
Artigo em Inglês | MEDLINE | ID: mdl-28389532

RESUMO

Approximately 70 human RNA-binding proteins (RBPs) contain a prion-like domain (PrLD). PrLDs are low-complexity domains that possess a similar amino acid composition to prion domains in yeast, which enable several proteins, including Sup35 and Rnq1, to form infectious conformers, termed prions. In humans, PrLDs contribute to RBP function and enable RBPs to undergo liquid-liquid phase transitions that underlie the biogenesis of various membraneless organelles. However, this activity appears to render RBPs prone to misfolding and aggregation connected to neurodegenerative disease. Indeed, numerous RBPs with PrLDs, including TDP-43 (transactivation response element DNA-binding protein 43), FUS (fused in sarcoma), TAF15 (TATA-binding protein-associated factor 15), EWSR1 (Ewing sarcoma breakpoint region 1), and heterogeneous nuclear ribonucleoproteins A1 and A2 (hnRNPA1 and hnRNPA2), have now been connected via pathology and genetics to the etiology of several neurodegenerative diseases, including amyotrophic lateral sclerosis, frontotemporal dementia, and multisystem proteinopathy. Here, we review the physiological and pathological roles of the most prominent RBPs with PrLDs. We also highlight the potential of protein disaggregases, including Hsp104, as a therapeutic strategy to combat the aberrant phase transitions of RBPs with PrLDs that likely underpin neurodegeneration.


Assuntos
Doenças Neurodegenerativas/metabolismo , Proteínas Priônicas/metabolismo , Deficiências na Proteostase/metabolismo , Proteínas de Ligação a RNA/metabolismo , Esclerose Lateral Amiotrófica/genética , Esclerose Lateral Amiotrófica/metabolismo , Esclerose Lateral Amiotrófica/patologia , Proteínas de Ligação a Calmodulina/química , Proteínas de Ligação a Calmodulina/genética , Proteínas de Ligação a Calmodulina/metabolismo , Grânulos Citoplasmáticos , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Demência Frontotemporal/genética , Demência Frontotemporal/metabolismo , Demência Frontotemporal/patologia , Ribonucleoproteína Nuclear Heterogênea A1 , Ribonucleoproteínas Nucleares Heterogêneas Grupo A-B/química , Ribonucleoproteínas Nucleares Heterogêneas Grupo A-B/genética , Ribonucleoproteínas Nucleares Heterogêneas Grupo A-B/metabolismo , Humanos , Mutação , Doenças Neurodegenerativas/genética , Doenças Neurodegenerativas/patologia , Proteínas Priônicas/química , Proteínas Priônicas/genética , Domínios Proteicos , Deficiências na Proteostase/genética , Deficiências na Proteostase/patologia , Proteína EWS de Ligação a RNA , Proteína FUS de Ligação a RNA/química , Proteína FUS de Ligação a RNA/genética , Proteína FUS de Ligação a RNA/metabolismo , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/genética , Fatores Associados à Proteína de Ligação a TATA/química , Fatores Associados à Proteína de Ligação a TATA/genética , Fatores Associados à Proteína de Ligação a TATA/metabolismo , Proteinopatias TDP-43/genética , Proteinopatias TDP-43/metabolismo , Proteinopatias TDP-43/patologia
7.
Proteins ; 85(9): 1724-1740, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28598584

RESUMO

Due to Ca2+ -dependent binding and the sequence diversity of Calmodulin (CaM) binding proteins, identifying CaM interactions and binding sites in the wet-lab is tedious and costly. Therefore, computational methods for this purpose are crucial to the design of such wet-lab experiments. We present an algorithm suite called CaMELS (CalModulin intEraction Learning System) for predicting proteins that interact with CaM as well as their binding sites using sequence information alone. CaMELS offers state of the art accuracy for both CaM interaction and binding site prediction and can aid biologists in studying CaM binding proteins. For CaM interaction prediction, CaMELS uses protein sequence features coupled with a large-margin classifier. CaMELS models the binding site prediction problem using multiple instance machine learning with a custom optimization algorithm which allows more effective learning over imprecisely annotated CaM-binding sites during training. CaMELS has been extensively benchmarked using a variety of data sets, mutagenic studies, proteome-wide Gene Ontology enrichment analyses and protein structures. Our experiments indicate that CaMELS outperforms simple motif-based search and other existing methods for interaction and binding site prediction. We have also found that the whole sequence of a protein, rather than just its binding site, is important for predicting its interaction with CaM. Using the machine learning model in CaMELS, we have identified important features of protein sequences for CaM interaction prediction as well as characteristic amino acid sub-sequences and their relative position for identifying CaM binding sites. Python code for training and evaluating CaMELS together with a webserver implementation is available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#camels.


Assuntos
Proteínas de Ligação a Calmodulina/química , Calmodulina/química , Proteoma/genética , Software , Algoritmos , Sequência de Aminoácidos , Sítios de Ligação , Proteínas de Ligação a Calmodulina/genética , Simulação por Computador , Ligação Proteica , Proteoma/química
8.
Adv Exp Med Biol ; 1006: 37-47, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28865013

RESUMO

Drebrin is an actin-binding protein mainly expressed in developing neurons and dendritic spine in mature neurons. To understand the functions of drebrin in vivo, we must understand its molecular properties. In this chapter, I will focus on the purification and characterization of drebrin in vitro. Drebrin binds to F-actin with a stoichiometry of 1:5~6 with a K d of 1~3 × 10-7 M and strongly inhibits the binding of other actin-binding proteins such as tropomyosin, caldesmon, fascin, α-actinin, and cofilin. It also inhibits the activities of myosin-II and myosin-V. These results are discussed in terms of the possible roles of drebrin in the stability, dynamics, and organizations of actin structures in neuronal cells.


Assuntos
Citoesqueleto de Actina/química , Actinas/química , Neuropeptídeos/química , Citoesqueleto de Actina/metabolismo , Actinas/metabolismo , Animais , Proteínas de Ligação a Calmodulina/química , Proteínas de Ligação a Calmodulina/metabolismo , Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Humanos , Proteínas dos Microfilamentos/química , Proteínas dos Microfilamentos/metabolismo , Miosina Tipo II/metabolismo , Miosina Tipo V/metabolismo , Neuropeptídeos/metabolismo , Ratos
9.
Protein Expr Purif ; 122: 97-104, 2016 06.
Artigo em Inglês | MEDLINE | ID: mdl-26892535

RESUMO

We have enriched several native bacterial proteins from Escherichia coli by chromatography on the immobilized eukaryotic Ca(2+)-binding protein, calmodulin. These bacterial proteins bound in a Ca(2+)-dependent manner to calmodulin, and were released by the addition of the Ca(2+)-chelator, EGTA, similar to many eukaryotic calmodulin-binding proteins. One of the bacterial proteins, F factor-encoded TraC, was purified to apparent homogeneity by an additional chromatographic step, anion exchange chromatography on MonoQ. Experiments with four chemically distinct calmodulin antagonists (R24571, Compound 48/80, melittin, and W7) showed that all of these substances inhibited the binding of purified TraC to calmodulin at effective concentrations comparable to those required for inhibiting in vitro binding of eukaryotic calmodulin-binding proteins. Three further bacterial proteins were identified as calmodulin-binding proteins: SecA, GlpD, and GlpC. We suggest that also these native bacterial proteins might be isolated by the unusual purification procedure including affinity chromatography on calmodulin Sepharose. Whether the identified proteins bind to, and are regulated by, putative bacterial calmodulin-like proteins in Escherichia coli remains to be established.


Assuntos
Calmodulina/metabolismo , Cromatografia de Afinidade/métodos , Escherichia coli/genética , Proteínas de Fímbrias/isolamento & purificação , Plasmídeos/isolamento & purificação , Sequência de Aminoácidos , Proteínas de Ligação a Calmodulina/química , Proteínas de Ligação a Calmodulina/isolamento & purificação , Proteínas de Ligação a Calmodulina/metabolismo , Escherichia coli/química , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/isolamento & purificação , Proteínas de Escherichia coli/metabolismo , Proteínas de Fímbrias/química , Proteínas de Fímbrias/genética , Proteínas de Fímbrias/metabolismo , Plasmídeos/química , Plasmídeos/genética , Plasmídeos/metabolismo , Sefarose/análogos & derivados
10.
Eur Biophys J ; 45(8): 861-867, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-27678004

RESUMO

In early studies on smooth muscle, I described a crude myosin fraction (CMF) in which self-assembly of myosin filaments was observed. For the first time, the 14-nm periodicity stemming from regular arrangement of myosin heads on the filament surface was observed (Sobieszek in J Mol Biol 70:741-744, 1972). In this fraction, we also observed formation of long ribbon-shaped aggregates exhibiting a 5.6-nm periodicity, characteristic of tropomyosin (TM) paracrystals (Sobieszek and Small in Phil Trans R Soc Lond B 265:203-212, 1973). We therefore concluded that these ribbons were made of TM and they might be related to the myosin ribbons observed in electron micrographs (EM) of intact smooth muscle (Lowy and Small in Nature 227:46-51, 1970; Small and Squire in Mol Biol 67:117-149, 1972). Subsequently, Small (J Cell Sci 24:327-349, 1977) concluded that the ribbons observed in the EM sections were an artifact, but their observation in the CMF was not addressed. I have now revisited two aspects of the above studies. Firstly, based on my new multi-angle laser-scattering data and considering the length and stability of the building unit for the filament, a myosin trimer fit better to the previously proposed helical structure. Secondly, after two decades of systematic examinations of protein compositions in multiple smooth muscle extracts and isolated filaments, I concluded that the ribbons were made of caldesmon and not TM. Thirdly, actin-activated ATPase activity measurements indicated that modulation of this activity (by CaD and TM) was synergistic, cooperative and depended on myosin to actin ratio.


Assuntos
Proteínas de Ligação a Calmodulina/química , Proteínas de Ligação a Calmodulina/metabolismo , Modelos Moleculares , Miosinas de Músculo Liso/química , Miosinas de Músculo Liso/metabolismo , Actomiosina/metabolismo , Adenosina Trifosfatases/metabolismo , Regulação Alostérica , Músculo Liso/metabolismo , Músculo Liso/fisiologia , Estrutura Secundária de Proteína
11.
J Biol Chem ; 289(14): 9651-61, 2014 Apr 04.
Artigo em Inglês | MEDLINE | ID: mdl-24550388

RESUMO

The protein phosphatase 2A (PP2A) and kinases such as germinal center kinase III (GCKIII) can interact with striatins to form a supramolecular complex called striatin-interacting phosphatase and kinase (STRIPAK) complex. Despite the fact that the STRIPAK complex regulates multiple cellular events, it remains only partially understood how this complex itself is assembled and regulated for differential biological functions. Our recent work revealed the activation mechanism of GCKIIIs by MO25, as well as how GCKIIIs heterodimerize with CCM3, a molecular bridge between GCKIII and striatins. Here we dissect the structural features of the coiled coil domain of striatin 3, a novel type of PP2A regulatory subunit that functions as a scaffold for the assembly of the STRIPAK complex. We have determined the crystal structure of a selenomethionine-labeled striatin 3 coiled coil domain, which shows it to assume a parallel dimeric but asymmetric conformation containing a large bend. This result combined with a number of biophysical analyses provide evidence that the coiled coil domain of striatin 3 and the PP2A A subunit form a stable core complex with a 2:2 stoichiometry. Structure-based mutational studies reveal that homodimerization of striatin 3 is essential for its interaction with PP2A and therefore assembly of the STRIPAK complex. Wild-type striatin 3 but not the mutants defective in PP2A binding strongly suppresses apoptosis of Jurkat cells induced by the GCKIII kinase MST3, most likely through a mechanism in which striatin recruits PP2A to negatively regulate the activation of MST3. Collectively, our work provides structural insights into the organization of the STRIPAK complex and will facilitate further functional studies.


Assuntos
Autoantígenos , Proteínas de Ligação a Calmodulina , Complexos Multiproteicos , Proteína Fosfatase 2 , Autoantígenos/química , Autoantígenos/genética , Autoantígenos/metabolismo , Proteínas de Ligação a Calmodulina/química , Proteínas de Ligação a Calmodulina/genética , Proteínas de Ligação a Calmodulina/metabolismo , Cristalografia por Raios X , Quinases do Centro Germinativo , Humanos , Células Jurkat , Complexos Multiproteicos/química , Complexos Multiproteicos/genética , Complexos Multiproteicos/metabolismo , Proteínas do Tecido Nervoso/química , Proteínas do Tecido Nervoso/genética , Proteínas do Tecido Nervoso/metabolismo , Proteína Fosfatase 2/química , Proteína Fosfatase 2/genética , Proteína Fosfatase 2/metabolismo , Proteínas Serina-Treonina Quinases/química , Proteínas Serina-Treonina Quinases/genética , Proteínas Serina-Treonina Quinases/metabolismo , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína
12.
J Neurosci Res ; 93(9): 1462-70, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25981177

RESUMO

Neurons have well-developed membrane microdomains called "rafts" that are recovered as a detergent-resistant membrane microdomain fraction (DRM). Neuronal tissue-enriched acidic protein of 22 kDa (NAP-22) is one of the major protein components of neuronal DRM. To determine the cellular function of NAP-22, interacting proteins were screened with an immunoprecipitation assay, and calcineurin (CaN) was detected. Further studies with NAP-22 prepared from DRM and CaN expressed in bacteria showed the binding of these proteins and a dose-dependent inhibitory effect of the NAP-22 fraction on the phosphatase activity of CaN. On the other hand, NAP-22 expressed in bacteria showed low binding to CaN and a weak inhibitory effect on phosphatase activity. To solve this discrepancy, identification of a nonprotein component that modulates CaN activity in the DRM-derived NAP-22 fraction was attempted. After lyophilization, a lipid fraction was extracted with chloroform/methanol. The lipid fraction showed an inhibitory effect on CaN without NAP-22, and further fractionation of the extract with thin-layer chromatography showed the presence of several lipid bands having an inhibitory effect on CaN. The mobility of these bands coincided with that of authentic ganglioside (GM1a, GD1a, GD1b, and GT1b), and authentic ganglioside showed an inhibitory effect on CaN. Treatment of lipid with endoglycoceramidase, which degrades ganglioside to glycochain and ceramide, caused a diminution of the inhibitory effect. These results show that DRM-derived NAP-22 binds several lipids, including ganglioside, and that ganglioside inhibits the phosphatase activity of CaN.


Assuntos
Encéfalo/citologia , Calcineurina/metabolismo , Proteínas de Ligação a Calmodulina/metabolismo , Proteínas do Citoesqueleto/metabolismo , Gangliosídeos/metabolismo , Microdomínios da Membrana/metabolismo , Proteínas do Tecido Nervoso/metabolismo , Animais , Proteínas de Ligação a Calmodulina/química , Células Cultivadas , Cromatografia em Camada Fina , Proteínas do Citoesqueleto/química , Detergentes/farmacologia , Gangliosídeos/química , Glicosídeo Hidrolases/farmacologia , Imunoprecipitação , Metabolismo dos Lipídeos/efeitos dos fármacos , Microdomínios da Membrana/efeitos dos fármacos , Proteínas do Tecido Nervoso/química , Neurônios/metabolismo , Neurônios/ultraestrutura , Monoéster Fosfórico Hidrolases/metabolismo , Ratos , Ratos Wistar
13.
Proc Natl Acad Sci U S A ; 109(34): 13608-13, 2012 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-22869697

RESUMO

Titin-like kinases are an important class of cytoskeletal kinases that intervene in the response of muscle to mechanical stimulation, being central to myofibril homeostasis and development. These kinases exist in autoinhibited states and, allegedly, become activated during muscle activity by the elastic unfolding of a C-terminal regulatory segment (CRD). However, this mechano-activation model remains controversial. Here we explore the structural, catalytic, and tensile properties of the multidomain kinase region of Caenorhabditis elegans twitchin (Fn(31)-Nlinker-kinase-CRD-Ig(26)) using X-ray crystallography, small angle X-ray scattering, molecular dynamics simulations, and catalytic assays. This work uncovers the existence of an inhibitory segment that flanks the kinase N-terminally (N-linker) and that acts synergistically with the canonical CRD tail to silence catalysis. The N-linker region has high mechanical lability and acts as the primary stretch-sensor in twitchin kinase, while the CRD is poorly responsive to pulling forces. This poor response suggests that the CRD is not a generic mechanosensor in this kinase family. Instead, the CRD is shown here to be permissive to catalysis and might protect the kinase active site against mechanical damage. Thus, we put forward a regulatory model where kinase inhibition results from the combined action of both N- and C-terminal tails, but only the N-terminal extension undergoes mechanical removal, thereby affording partial activation. Further, we compare invertebrate and vertebrate titin-like kinases and identify variations in the regulatory segments that suggest a mechanical speciation of these kinase classes.


Assuntos
Proteínas de Caenorhabditis elegans/química , Proteínas de Ligação a Calmodulina/química , Proteínas Musculares/química , Sequência de Aminoácidos , Animais , Caenorhabditis elegans , Catálise , Domínio Catalítico , Cristalografia por Raios X/métodos , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Estrutura Terciária de Proteína , Espalhamento de Radiação , Homologia de Sequência de Aminoácidos , Raios X
14.
Biochim Biophys Acta ; 1833(1): 11-20, 2013 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23063531

RESUMO

Cyclin-dependent kinase 5 (Cdk5) is a serine/threonine kinase that has been implicated in a number of cellular processes. In Dictyostelium, Cdk5 localizes to the nucleus and cytoplasm, interacts with puromycin-sensitive aminopeptidase A (PsaA), and regulates endocytosis, secretion, growth, and multicellular development. Here we show that Cdk5 is a calmodulin (CaM)-binding protein (CaMBP) in Dictyostelium. Cdk5, PsaA, and CaM were all present in isolated nuclei and Cdk5 and PsaA co-immunoprecipitated with nuclear CaM. Although nuclear CaMBPs have previously been identified in Dictyostelium, the detection of CaM in purified nuclear fractions had not previously been shown. Putative CaM-binding domains (CaMBDs) were identified in Cdk5 and PsaA. Deletion of one of the two putative CaMBDs in Cdk5 ((132)LLINRKGELKLADFGLARAFGIP(154)) prevented CaM-binding indicating that this region encompasses a functional CaMBD. This deletion also increased the nuclear distribution of Cdk5 suggesting that CaM regulates the nucleocytoplasmic transport of Cdk5. A direct binding between CaM and PsaA could not be determined since deletion of the one putative CaMBD in PsaA prevented the nuclear localization of the deletion protein. Together, this study provides the first direct evidence for nuclear CaM in Dictyostelium and the first evidence in any system for Cdk5 being a CaMBP.


Assuntos
Aminopeptidases/metabolismo , Proteínas de Ligação a Calmodulina , Núcleo Celular/metabolismo , Quinase 5 Dependente de Ciclina/metabolismo , Quinase 5 Dependente de Ciclina/fisiologia , Dictyostelium , Aminopeptidases/antagonistas & inibidores , Antígenos de Protozoários/metabolismo , Calmodulina/metabolismo , Proteínas de Ligação a Calmodulina/química , Proteínas de Ligação a Calmodulina/genética , Proteínas de Ligação a Calmodulina/metabolismo , Proteínas de Ligação a Calmodulina/fisiologia , Núcleo Celular/enzimologia , Quinase 5 Dependente de Ciclina/química , Quinase 5 Dependente de Ciclina/genética , Dictyostelium/enzimologia , Dictyostelium/crescimento & desenvolvimento , Dictyostelium/metabolismo , Dictyostelium/ultraestrutura , Resistência Microbiana a Medicamentos , Imunoprecipitação , Glicoproteínas de Membrana/metabolismo , Modelos Biológicos , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas/genética , Domínios e Motivos de Interação entre Proteínas/fisiologia , Proteínas de Protozoários/metabolismo , Puromicina/farmacologia , Deleção de Sequência , Tripanossomicidas/farmacologia
15.
Mol Microbiol ; 89(2): 264-75, 2013 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-23714328

RESUMO

The tubulin homologue FtsZ provides the cytoskeletal framework and constriction force for bacterial cell division. FtsZ has an 50-amino-acid (aa) linker between the protofilament-forming globular domain and the C-terminal (Ct) peptide that binds FtsA and ZipA, tethering FtsZ to the membrane. This Ct-linker is widely divergent across bacterial species and thought to be an intrinsically disordered peptide (IDP). We confirmed that the Ct-linkers from three bacterial species behaved as IDPs in vitro by circular dichroism and trypsin proteolysis. We made chimeras, swapping the Escherichia coli linker for Ct-linkers from other bacteria, and even for an unrelated IDP from human α-adducin. Most substitutions allowed for normal cell division, suggesting that sequence of the IDP did not matter. With few exceptions, almost any sequence appears to work. Length, however, was important: IDPs shorter than 43 or longer than 95 aa had compromised or no function. We conclude that the Ct-linker functions as a flexible tether between the globular domain of FtsZ in the protofilament, and its attachment to FtsA/ZipA at the membrane. Modelling the Ct-linker as a worm-like chain, we predict that it functions as a stiff entropic spring linking the bending protofilaments to the membrane.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Proteínas do Citoesqueleto/química , Proteínas do Citoesqueleto/metabolismo , Escherichia coli/metabolismo , Peptídeos/metabolismo , Proteínas de Bactérias/genética , Proteínas de Ligação a Calmodulina/química , Proteínas de Ligação a Calmodulina/genética , Proteínas de Ligação a Calmodulina/metabolismo , Divisão Celular , Proteínas do Citoesqueleto/genética , Escherichia coli/citologia , Escherichia coli/genética , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Humanos , Modelos Moleculares , Peptídeos/química , Peptídeos/genética , Ligação Proteica , Conformação Proteica
16.
Plant Physiol ; 163(4): 1741-51, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24134885

RESUMO

Two members of the eight-member CALMODULIN-BINDING PROTEIN60 (CBP60) gene family, CBP60g and SYSTEMIC ACQUIRED RESISTANCE DEFICIENT1 (SARD1), encode positive regulators of plant immunity that promote the production of salicylic acid (SA) and affect the expression of SA-dependent and SA-independent defense genes. Here, we investigated the other six family members in Arabidopsis (Arabidopsis thaliana). Only cbp60a mutations affected growth of the bacterial pathogen Pseudomonas syringae pv maculicola ES4326. In contrast to cbp60g and sard1 mutations, cbp60a mutations reduced pathogen growth, indicating that CBP60a is a negative regulator of immunity. Bacterial growth was increased by cbp60g only in the presence of CBP60a, while the increase in growth due to sard1 was independent of CBP60a, suggesting that the primary function of CBP60g may be to counter the repressive effect of CBP60a. In the absence of pathogen, levels of SA as well as of several SA-dependent and SA-independent pathogen-inducible genes were higher in cbp60a plants than in the wild type, suggesting that the enhanced resistance of cbp60a plants may result from the activation of immune responses prior to pathogen attack. CBP60a bound calmodulin, and the calmodulin-binding domain was defined at the C-terminal end of the protein. Transgenes encoding mutant versions of CBP60a lacking the ability to bind calmodulin failed to complement null cbp60a mutations, indicating that calmodulin-binding ability is required for the immunity-repressing function of CBP60a. Regulation at the CBP60 node involves negative regulation by CBP60a as well as positive regulation by CBP60g and SARD1, providing multiple levels of control over the activation of immune responses.


Assuntos
Arabidopsis/imunologia , Proteínas de Ligação a Calmodulina/metabolismo , Família Multigênica , Imunidade Vegetal , Arabidopsis/genética , Arabidopsis/microbiologia , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Calmodulina/metabolismo , Proteínas de Ligação a Calmodulina/química , Proteínas de Ligação a Calmodulina/genética , Epistasia Genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas/genética , Teste de Complementação Genética , Modelos Biológicos , Mutação/genética , Imunidade Vegetal/genética , Plantas Geneticamente Modificadas , Ligação Proteica , Estrutura Terciária de Proteína , Pseudomonas syringae/crescimento & desenvolvimento , Ácido Salicílico/metabolismo , Transgenes
17.
FASEB J ; 27(12): 4965-74, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23975937

RESUMO

The three FET (FUS, EWSR1, and TAF15) family RNA binding proteins are expressed in all tissues and almost all cell types. The disordered N-terminal parts are always present in FET fusion oncoproteins of sarcomas and leukemia. Mutations in FUS and TAF15 cause aggregation of FET proteins in neurological disorders. Here we used recombinant proteins in pulldown experiments and mass spectrometry to identify major interaction partners of the FET N-terminal parts. We report that FUS, EWSR1, and TAF15 form homo- and heterocomplexes as major binding partners and identify an evolutionarily conserved N-terminal motif (FETBM1) that is required for this interaction. The binding is RNA and DNA independent and robust up to 1 M of NaCl. The localization of FETBM1 and its target sequences supports a simple model for FET protein aggregation as reported in neurological disorders such as amyotrophic lateral sclerosis, frontotemporal dementia, and essential tremor. The FETBM1 localization also explains the binding of normal full-length FET proteins to their oncogenic fusion proteins.


Assuntos
Proteínas de Ligação a Calmodulina/química , Proteínas de Fusão Oncogênica/química , Proteína FUS de Ligação a RNA/química , Proteínas de Ligação a RNA/química , Fatores Associados à Proteína de Ligação a TATA/química , Motivos de Aminoácidos , Sequência de Aminoácidos , Sítios de Ligação , Proteínas de Ligação a Calmodulina/metabolismo , Linhagem Celular Tumoral , Humanos , Dados de Sequência Molecular , Proteínas de Fusão Oncogênica/metabolismo , Ligação Proteica , Estrutura Terciária de Proteína , Proteína EWS de Ligação a RNA , Proteína FUS de Ligação a RNA/metabolismo , Proteínas de Ligação a RNA/metabolismo , Fatores Associados à Proteína de Ligação a TATA/metabolismo
18.
Nat Genet ; 37(3): 282-8, 2005 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-15723066

RESUMO

Nephronophthisis (NPHP) is the most frequent genetic cause of chronic renal failure in children. Identification of four genes mutated in NPHP subtypes 1-4 (refs. 4-9) has linked the pathogenesis of NPHP to ciliary functions. Ten percent of affected individuals have retinitis pigmentosa, constituting the renal-retinal Senior-Loken syndrome (SLSN). Here we identify, by positional cloning, mutations in an evolutionarily conserved gene, IQCB1 (also called NPHP5), as the most frequent cause of SLSN. IQCB1 encodes an IQ-domain protein, nephrocystin-5. All individuals with IQCB1 mutations have retinitis pigmentosa. Hence, we examined the interaction of nephrocystin-5 with RPGR (retinitis pigmentosa GTPase regulator), which is expressed in photoreceptor cilia and associated with 10-20% of retinitis pigmentosa. We show that nephrocystin-5, RPGR and calmodulin can be coimmunoprecipitated from retinal extracts, and that these proteins localize to connecting cilia of photoreceptors and to primary cilia of renal epithelial cells. Our studies emphasize the central role of ciliary dysfunction in the pathogenesis of SLSN.


Assuntos
Proteínas de Ligação a Calmodulina/genética , Proteínas de Ligação a Calmodulina/metabolismo , Calmodulina/metabolismo , Proteínas do Olho/metabolismo , Mutação , Sequência de Aminoácidos , Northern Blotting , Proteínas de Ligação a Calmodulina/química , Feminino , Humanos , Masculino , Dados de Sequência Molecular , Linhagem , Síndrome , Técnicas do Sistema de Duplo-Híbrido
19.
Nat Genet ; 37(3): 305-10, 2005 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-15731759

RESUMO

Several transient receptor potential channels were recently found to be activated by temperature stimuli in vitro. Their physiological and behavioral roles are largely unknown. From a temperature-preference behavior screen of 27,000 Drosophila melanogaster P-insertion mutants, we isolated a gene, named pyrexia (pyx), encoding a new transient receptor potential channel. Pyx was opened by temperatures above 40 degrees C in Xenopus laevis oocytes and HEK293T cells. It was ubiquitously expressed along the dendrites of a subset of peripheral nervous system neurons and was more permeable to K(+) than to Na(+). Although some pyx alleles resulted in abnormal temperature preferences, pyx null flies did not have significantly different temperature preferences than wild-type flies. But 60% of pyx null flies were paralyzed within 3 min of exposure to 40 degrees C, whereas only 9% of wild-type flies were paralyzed by the same stimulus. From these findings, we propose that the primary in vivo role of Pyx is to protect flies from high-temperature stress.


Assuntos
Proteínas de Ligação a Calmodulina/fisiologia , Proteínas de Drosophila/fisiologia , Drosophila melanogaster/fisiologia , Febre/fisiopatologia , Temperatura Alta , Proteínas de Membrana/fisiologia , Sequência de Aminoácidos , Animais , Proteínas de Ligação a Calmodulina/química , Linhagem Celular , Clonagem Molecular , DNA Complementar , Proteínas de Drosophila/química , Humanos , Imuno-Histoquímica , Proteínas de Membrana/química , Dados de Sequência Molecular , Homologia de Sequência de Aminoácidos , Canais de Potencial de Receptor Transitório , Xenopus laevis
20.
J Biol Chem ; 287(37): 31447-53, 2012 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-22791711

RESUMO

Actin is a highly ubiquitous protein in eukaryotic cells that plays a crucial role in cell mechanics and motility. Cell motility is driven by assembling actin as polymerizing actin drives cell protrusions in a process closely involving a host of other actin-binding proteins, notably the actin-related protein 2/3 (Arp2/3) complex, which nucleates actin and forms branched filamentous structures. The Arp2/3 complex preferentially binds specific actin networks at the cell leading edge and forms branched filamentous structures, which drive cell protrusions, but the exact regulatory mechanism behind this process is not well understood. Here we show using in vitro imaging and binding assays that a fragment of the actin-binding protein caldesmon added to polymerizing actin increases the Arp2/3-mediated branching activity, whereas it has no effect on branch formation when binding to aged actin filaments. Because this caldesmon effect is shown to be independent of nucleotide hydrolysis and phosphate release from actin, our results suggest a mechanism by which caldesmon maintains newly polymerized actin in a distinct state that has a higher affinity for the Arp2/3 complex. Our data show that this new state does not affect the level of cooperativity of binding by Arp2/3 complex or its distribution on actin. This presents a novel regulatory mechanism by which caldesmon, and potentially other actin-binding proteins, regulates the interactions of actin with its binding partners.


Assuntos
Citoesqueleto de Actina/química , Complexo 2-3 de Proteínas Relacionadas à Actina/química , Citoesqueleto de Actina/metabolismo , Complexo 2-3 de Proteínas Relacionadas à Actina/metabolismo , Animais , Proteínas de Ligação a Calmodulina/química , Proteínas de Ligação a Calmodulina/metabolismo , Bovinos , Humanos , Ligação Proteica
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