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1.
Biochemistry ; 62(7): 1321-1329, 2023 04 04.
Artículo en Inglés | MEDLINE | ID: mdl-36883372

RESUMEN

The Myb transcription factor is involved in the proliferation of hematopoietic cells, and deregulation of its expression can lead to cancers such as leukemia. Myb interacts with various proteins, including the histone acetyltransferases p300 and CBP. Myb binds to a small domain of p300, the KIX domain (p300KIX), and inhibiting this interaction is a potential new drug discovery strategy in oncology. The available structures show that Myb binds to a very shallow pocket of the KIX domain, indicating that it might be challenging to identify inhibitors of this interaction. Here, we report the design of Myb-derived peptides which interact with p300KIX. We show that by mutating only two Myb residues that bind in or near a hotspot at the surface of p300KIX, it is possible to obtain single-digit nanomolar peptidic inhibitors of the Myb/p300KIX interaction that bind 400-fold tighter to p300KIX than wildtype Myb. These findings suggest that it might also be possible to design potent low molecular-weight compounds to disrupt the Myb/p300KIX interaction.


Asunto(s)
Proteína p300 Asociada a E1A , Péptidos , Proteínas Proto-Oncogénicas c-myb , Péptidos/farmacología , Unión Proteica , Proteínas Proto-Oncogénicas c-myb/antagonistas & inhibidores , Proteínas Proto-Oncogénicas c-myb/química , Proteína p300 Asociada a E1A/antagonistas & inhibidores , Proteína p300 Asociada a E1A/química
2.
Sci Rep ; 11(1): 24206, 2021 12 17.
Artículo en Inglés | MEDLINE | ID: mdl-34921182

RESUMEN

MYB proteins are highly conserved DNA-binding domains (DBD) and mutations in MYB oncoproteins have been reported to cause aberrant and augmented cancer progression. Identification of MYB molecular biomarkers predictive of cancer progression can be used for improving cancer management. To address this, a biomarker discovery pipeline was employed in investigating deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in predicting damaging and potential alterations on the properties of proteins. The nsSNP of the MYB family; MYB, MYBL1, and MYBL2 was extracted from the NCBI database. Five in silico tools (PROVEAN, SIFT, PolyPhen-2, SNPs&GO and PhD-SNP) were utilized to investigate the outcomes of nsSNPs. A total of 45 nsSNPs were predicted as high-risk and damaging, and were subjected to PMut and I-Mutant 2.0 for protein stability analysis. This resulted in 32 nsSNPs with decreased stability with a DDG score lower than - 0.5, indicating damaging effect. G111S, N183S, G122S, and S178C located within the helix-turn-helix (HTH) domain were predicted to be conserved, further posttranslational modifications and 3-D protein analysis indicated these nsSNPs to shift DNA-binding specificity of the protein thus altering the protein function. Findings from this study would help in the field of pharmacogenomic and cancer therapy towards better intervention and management of cancer.


Asunto(s)
Modelos Moleculares , Neoplasias , Proteínas Proto-Oncogénicas c-myb , Simulación por Computador , Humanos , Neoplasias/genética , Neoplasias/metabolismo , Polimorfismo de Nucleótido Simple , Conformación Proteica , Estabilidad Proteica , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/genética
3.
Phys Chem Chem Phys ; 22(47): 27903-27911, 2020 Dec 16.
Artículo en Inglés | MEDLINE | ID: mdl-33284914

RESUMEN

A common feature of intrinsically disordered proteins (IDPs) is a disorder-to-order transition upon binding to other proteins, which has been tied to multiple benefits, including accelerated association rates or binding with low affinity, yet high specificity. Given the balanced equilibrium concentrations of folded and unfolded state of an IDP we asked the question if changes in the chemical environment, such as the presence of osmolytes or crowding agents, have a strong influence on the interaction of an IDP. Here, we demonstrate the impact of cosolutes on the interaction of the intrinsically disordered transcription factor c-Myb and its binding partner, the kinase-inducible interaction domain (KIX) of the CREB-binding protein. Temperature jump relaxation kinetics and microscale thermophoresis were employed in order to quantify the rate constants and the binding affinity of the c-Myb/KIX complex, respectively, in the presence of various cosolutes. We find the binding free energy of the c-Myb/KIX complex only marginally modulated by cosolutes, whereas the enthalpy and entropy of the interaction are very sensitive to the respective solvent conditions. For different cosolutes we observe substantial changes in enthalpy, both favorable and unfavorable, which are going with entropy changes largely compensating the enthalpy effects in each case. These characteristics might reflect a potential mechanism by which c-Myb offsets changes in the physico-chemical environment to maintain a roughly unaltered binding affinity.


Asunto(s)
Proteína de Unión a CREB/metabolismo , Proteínas Intrínsecamente Desordenadas/metabolismo , Proteínas Proto-Oncogénicas c-myb/metabolismo , Betaína/química , Proteína de Unión a CREB/química , Entropía , Glicina/química , Humanos , Proteínas Intrínsecamente Desordenadas/química , Cinética , Metilaminas/química , Unión Proteica , Dominios Proteicos , Proteínas Proto-Oncogénicas c-myb/química , Temperatura , Urea/química
4.
FEBS Open Bio ; 10(11): 2329-2342, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-32937031

RESUMEN

Transcription factors use a DNA-binding domain to localize their action and a transactivation domain (tAD) to stimulate activation of the associated gene. Recent work has renewed interest in how tADs activate genes, which remains poorly understood. Key features in the new models are exposure of short linear motifs (SLMs) and liquid-liquid phase separation (LLPS). Inspired by the new models for tAD function, we decided to revisit the tAD of the haematopoietic transcription factor c-Myb by performing a mutational analysis to see how these new models fit and potentially explain the tAD behaviour of this master regulator. We know that c-Myb has an acidic tAD, which contains a well-characterized SLM in the form of a LxxLL motif. By testing 12 alanine-scanning mutants and three mutants with major reorganization of its tAD in two mammalian reporter systems, we found a pattern of effects very close to what would be expected from the SLM-exposure model, with strong effects exerted by both acidic replacements and SLM mutation. When the same mutants were tested in a yeast system, the pattern of effects was dramatically different, with the SLM mutation exerting no effect, and tAD behaviour was much less affected by small alterations, as would be expected from a LLPS model. These observations are discussed in the light of the two new tAD models, and a two-step hypothesis for transactivation, combining both models, is proposed.


Asunto(s)
Modelos Biológicos , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/metabolismo , Activación Transcripcional , Secuencia de Aminoácidos , Animales , Cromatina/metabolismo , Análisis Mutacional de ADN , Células HEK293 , Humanos , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Dominios Proteicos , Proteínas Proto-Oncogénicas c-myb/genética , Saccharomyces cerevisiae/metabolismo
5.
J Chem Theory Comput ; 16(6): 3856-3868, 2020 Jun 09.
Artículo en Inglés | MEDLINE | ID: mdl-32325001

RESUMEN

Disordered proteins play important roles in cell signaling and are frequently involved in protein-protein interactions. They also have a larger proportion of charged and polar residues than their folded counterparts. Here, we developed a structure-based model and applied molecular dynamics simulations to examine the presence and importance of electrostatic interactions in the binding processes of two differently charged intrinsically disordered ligands of the KIX domain of CBP. We observed non-native opposite-charged contacts in the encounter complexes for both ligands with KIX, and this may be a general feature of coupled folding and binding reactions. The ensemble of successful encounter complexes is a diverse set of structures, and in the case of the highly charged ligand, this ensemble was found to be malleable with respect to ionic strength. There are only minor differences between encounter complex ensembles for successful and unsuccessful collisions with no key interactions that appear to make the process far more productive. The energy landscape at this early stage in the process does not appear highly funneled. Strikingly we observed many native interactions that appear to reduce chances of an encounter complex being productive. Instead it appears that collectively non-native electrostatic interactions in the encounter complex increase the likelihood of productivity by holding the proteins together long enough for folding to take place. This mechanism is more effective for the more highly charged ligand.


Asunto(s)
Proteínas Intrínsecamente Desordenadas/química , Secuencia de Aminoácidos , Proteína de Unión a CREB/química , N-Metiltransferasa de Histona-Lisina/química , Cinética , Ligandos , Modelos Moleculares , Simulación de Dinámica Molecular , Dominios Proteicos , Pliegue de Proteína , Proteínas Proto-Oncogénicas c-myb/química , Electricidad Estática
6.
Biol Open ; 9(5)2020 05 07.
Artículo en Inglés | MEDLINE | ID: mdl-32295830

RESUMEN

The five-protein MuvB core complex is highly conserved in animals. This nuclear complex interacts with RB-family tumor suppressor proteins and E2F-DP transcription factors to form DREAM complexes that repress genes that regulate cell cycle progression and cell fate. The MuvB core complex also interacts with Myb family oncoproteins to form the Myb-MuvB complexes that activate many of the same genes. We show that animal-type Myb genes are present in Bilateria, Cnidaria and Placozoa, the latter including the simplest known animal species. However, bilaterian nematode worms lost their animal-type Myb genes hundreds of millions of years ago. Nevertheless, amino acids in the LIN9 and LIN52 proteins that directly interact with the MuvB-binding domains of human B-Myb and Drosophila Myb are conserved in Caenorhabditiselegans Here, we show that, despite greater than 500 million years since their last common ancestor, the Drosophila melanogaster Myb protein can bind to the nematode LIN9-LIN52 proteins in vitro and can cause a synthetic multivulval (synMuv) phenotype in vivo This phenotype is similar to that caused by loss-of-function mutations in C. elegans synMuvB-class genes including those that encode homologs of the MuvB core, RB, E2F and DP. Furthermore, amino acid substitutions in the MuvB-binding domain of Drosophila Myb that disrupt its functions in vitro and in vivo also disrupt these activities in C. elegans We speculate that nematodes and other animals may contain another protein that can bind to LIN9 and LIN52 in order to activate transcription of genes repressed by DREAM complexes.


Asunto(s)
Proteínas de Ciclo Celular/genética , Proteínas de Drosophila/genética , Drosophila/fisiología , Regulación de la Expresión Génica , Estudios de Asociación Genética , Fenotipo , Proteínas Proto-Oncogénicas c-myb/genética , Secuencia de Aminoácidos , Animales , Evolución Biológica , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/metabolismo , Proteínas de Drosophila/química , Proteínas de Drosophila/metabolismo , Evolución Molecular , Estudios de Asociación Genética/métodos , Humanos , Modelos Moleculares , Filogenia , Conformación Proteica , Subunidades de Proteína/química , Subunidades de Proteína/genética , Subunidades de Proteína/metabolismo , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/metabolismo , Relación Estructura-Actividad
7.
Cell Rep ; 30(10): 3218-3228.e5, 2020 03 10.
Artículo en Inglés | MEDLINE | ID: mdl-32160531

RESUMEN

Drosophila Myb (Dm-Myb) encodes a protein that plays a key role in regulation of mitotic phase genes. Here, we further refine its role in the context of a developing tissue as a potentiator of gene expression required for proper RNA polymerase II (RNA Pol II) function and efficient H3K4 methylation at promoters. In contrast to its role in gene activation, Myb is also required for repression of many genes, although no specific mechanism for this role has been proposed. We now reveal a critical role for Myb in contributing to insulator function, in part by promoting binding of insulator proteins BEAF-32 and CP190 and stabilizing H3K27me3 Polycomb-group (PcG) domains. In the absence of Myb, H3K27me3 is markedly reduced throughout the genome, leading to H3K4me3 spreading and gene derepression. Finally, Myb is enriched at boundaries that demarcate chromatin environments, including chromatin loop anchors. These results reveal functions of Myb that extend beyond transcriptional regulation.


Asunto(s)
Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/metabolismo , Proteínas de Drosophila/química , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/metabolismo , Histonas/metabolismo , Elementos Aisladores/genética , Lisina/metabolismo , Proteínas Oncogénicas/metabolismo , Proteínas del Grupo Polycomb/química , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/metabolismo , Animales , Metilación , Unión Proteica , Dominios Proteicos , Estabilidad Proteica , ARN Polimerasa II/metabolismo , Sitio de Iniciación de la Transcripción
8.
Biochem Biophys Res Commun ; 524(2): 446-452, 2020 04 02.
Artículo en Inglés | MEDLINE | ID: mdl-32007275

RESUMEN

The cMyb trans-activation domain is one of the model systems to understand the folding and binding mechanisms in intrinsically disordered proteins. cMyb (291-315) TAD (cMyb TAD) upon interaction with KIX plays a crucial role in transcriptional regulation. However, nothing is known regarding its aggregation behaviour on change of buffer conditions or stressed environment. Notably, most of the disease-associated amyloid-forming proteins such as Aß, Tau, α-synuclein, and amylin are natively unstructured. Nevertheless, to date, very fewer evidence on aggregation behaviours on TAD domains are available. Therefore, this is necessary to investigate the aggregation propensity of intrinsically disordered cMyb TAD domain in isolation. As an essential step in that direction, we have extensively studied the aggregation behaviour of cMyb TAD using the standard approaches for aggregation studies and systematically probed the amyloid conformations. These aggregates are ThT and ANS-positive whose amyloid nature was also confirmed by Far-UV CD spectroscopic studies suggesting that cMyb TAD fibrils are rich in ß-sheet secondary structure, transmission electron microscopy revealed the formation of characteristic long branched amyloid fibrils of 6-16 nm diameter, and MTT assay in SH-SY5Y neuroblastoma cells suggest that these aggregates are cytotoxic. This amyloid nature of cMyb TAD may affect its binding with KIX and alter cMyb function (transcriptional regulation) under acidic/stressed conditions.


Asunto(s)
Amiloide/metabolismo , Proteínas Intrínsecamente Desordenadas/metabolismo , Agregación Patológica de Proteínas/metabolismo , Proteínas Proto-Oncogénicas c-myb/metabolismo , Amiloide/química , Línea Celular , Humanos , Proteínas Intrínsecamente Desordenadas/química , Agregado de Proteínas , Conformación Proteica en Lámina beta , Dominios Proteicos , Pliegue de Proteína , Proteínas Proto-Oncogénicas c-myb/química
9.
Biophys Chem ; 258: 106319, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-31927158

RESUMEN

The minimum functional unit of c-Myb for specific DNA binding, c-Myb R2R3, fluctuates largely in solution which is critical for its DNA-binding function. The thermal stability of R2R3 increases with increasing NaCl concentrations and upon DNA binding as well. The DNA-binding affinity of R2R3 is stringently dependent on NaCl concentration, and decreases both with an increase or decrease in NaCl concentration from the physiological levels. The decreased DNA-binding affinity under low NaCl concentrations is because of the unfavorable entropy change, in contrast to the thermodynamic contribution under high NaCl concentrations. Together with the findings from thermal stability and structure analyses, the results indicate that R2R3 fluctuates more largely under low ionic strength than high ionic strength, resulting in its decreased stability and DNA-binding affinity. Under physiological conditions, R2R3 fluctuates properly to express its DNA-binding ability. The present results clearly show the naïve balance between structural stability and DNA binding.


Asunto(s)
ADN/química , Proteínas Proto-Oncogénicas c-myb/química , Sitios de Unión , Iones/química , Mutación , Resonancia Magnética Nuclear Biomolecular , Conformación Proteica , Proteínas Proto-Oncogénicas c-myb/genética
10.
J Biol Chem ; 294(45): 16604-16619, 2019 11 08.
Artículo en Inglés | MEDLINE | ID: mdl-31515273

RESUMEN

The mammalian CLOCK:BMAL1 transcription factor complex and its coactivators CREB-binding protein (CBP)/p300 and mixed-lineage leukemia 1 (MLL1) critically regulate circadian transcription and chromatin modification. Circadian oscillations are regulated by interactions of BMAL1's C-terminal transactivation domain (TAD) with the KIX domain of CBP/p300 (activating) and with the clock protein CRY1 (repressing) as well as by the BMAL1 G-region preceding the TAD. Circadian acetylation of Lys537 within the G-region enhances repressive BMAL1-TAD-CRY1 interactions. Here, we characterized the interaction of the CBP-KIX domain with BMAL1 proteins, including the BMAL1-TAD, parts of the G-region, and Lys537 Tethering the small compound 1-10 in the MLL-binding pocket of the CBP-KIX domain weakened BMAL1 binding, and MLL1-bound KIX did not form a ternary complex with BMAL1, indicating that the MLL-binding pocket is important for KIX-BMAL1 interactions. Small-angle X-ray scattering (SAXS) models of BMAL1 and BMAL1:KIX complexes revealed that the N-terminal BMAL1 G-region including Lys537 forms elongated extensions emerging from the bulkier BMAL1-TAD:KIX core complex. Fitting high-resolution KIX domain structures into the SAXS-derived envelopes suggested that the G-region emerges near the MLL-binding pocket, further supporting a role of this pocket in BMAL1 binding. Additionally, mutations in the second CREB-pKID/c-Myb-binding pocket of the KIX domain moderately impacted BMAL1 binding. The BMAL1(K537Q) mutation mimicking Lys537 acetylation, however, did not affect the KIX-binding affinity, in contrast to its enhancing effect on CRY1 binding. Our results significantly advance the mechanistic understanding of the protein interaction networks controlling CLOCK:BMAL1- and CBP-dependent gene regulation in the mammalian circadian clock.


Asunto(s)
Factores de Transcripción ARNTL/metabolismo , Proteína de Unión a CREB/metabolismo , Relojes Circadianos , Factores de Transcripción ARNTL/química , Factores de Transcripción ARNTL/genética , Secuencia de Aminoácidos , Animales , Sitios de Unión , Proteína de Unión a CREB/química , N-Metiltransferasa de Histona-Lisina/química , N-Metiltransferasa de Histona-Lisina/metabolismo , Ratones , Mutagénesis Sitio-Dirigida , Proteína de la Leucemia Mieloide-Linfoide/química , Proteína de la Leucemia Mieloide-Linfoide/metabolismo , Unión Proteica , Dominios Proteicos , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/metabolismo , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/aislamiento & purificación , Dispersión del Ángulo Pequeño , Resonancia por Plasmón de Superficie , Difracción de Rayos X
11.
Mol Cell ; 74(3): 436-451.e7, 2019 05 02.
Artículo en Inglés | MEDLINE | ID: mdl-30926242

RESUMEN

The evolutionarily related deubiquitinating enzymes (DUBs) USP25 and USP28 comprise an identical overall domain architecture but are functionally non-redundant: USP28 stabilizes c-MYC and other nuclear proteins, and USP25 regulates inflammatory TRAF signaling. We here compare molecular features of USP25 and USP28. Active enzymes form distinctively shaped dimers, with a dimerizing insertion spatially separating independently active catalytic domains. In USP25, but not USP28, two dimers can form an autoinhibited tetramer, where a USP25-specific, conserved insertion sequence blocks ubiquitin binding. In full-length enzymes, a C-terminal domain with a previously unknown fold has no impact on oligomerization, but N-terminal regions affect the dimer-tetramer equilibrium in vitro. We confirm oligomeric states of USP25 and USP28 in cells and show that modulating oligomerization affects substrate stabilization in accordance with in vitro activity data. Our work highlights how regions outside of the catalytic domain enable a conceptually intriguing interplay of DUB oligomerization and activity.


Asunto(s)
Inflamación/genética , Conformación Proteica , Ubiquitina Tiolesterasa/genética , Secuencia de Aminoácidos/genética , Dominio Catalítico/genética , Enzimas Desubicuitinizantes/química , Enzimas Desubicuitinizantes/genética , Humanos , Inflamación/patología , Mutación/genética , Unión Proteica/genética , Dominios Proteicos/genética , Multimerización de Proteína/genética , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/genética , Transducción de Señal/genética , Especificidad por Sustrato , Péptidos y Proteínas Asociados a Receptores de Factores de Necrosis Tumoral/genética , Ubiquitina/genética , Ubiquitina Tiolesterasa/química
12.
Int J Mol Sci ; 20(5)2019 Feb 28.
Artículo en Inglés | MEDLINE | ID: mdl-30823465

RESUMEN

Flower color is a charming phenotype with very important ornamental and commercial values. Anthocyanins play a critical role in determining flower color pattern formation, and their biosynthesis is typically regulated by R2R3-MYB transcription factors (TFs). Paeonia suffruticosa is a famous ornamental plant with colorful flowers. However, little is known about the R2R3-MYB TFs that regulate anthocyanin accumulation in P. suffruticosa. In the present study, two R2R3-MYB TFs, namely, PsMYB114L and PsMYB12L, were isolated from the petals of P. suffruticosa 'Shima Nishiki' and functionally characterized. Sequence analysis suggested that PsMYB114L contained a bHLH-interaction motif, whereas PsMYB12L contained two flavonol-specific motifs (SG7 and SG7-2). Subsequently, the in vivo function of PsMYB114L and PsMYB12L was investigated by their heterologous expression in Arabidopsis thaliana and apple calli. In transgenic Arabidopsis plants, overexpression of PsMYB114L and of PsMYB12L caused a significantly higher accumulation of anthocyanins, resulting in purple-red leaves. Transgenic apple calli overexpressing PsMYB114L and PsMYB12L also significantly enhanced the anthocyanins content and resulted in a change in the callus color to red. Meanwhile, gene expression analysis in A. thaliana and apple calli suggested that the expression levels of the flavonol synthase (MdFLS) and anthocyanidin reductase (MdANR) genes were significantly downregulated and the dihydroflavonol 4-reductase (AtDFR) and anthocyanin synthase (AtANS) genes were significantly upregulated in transgenic lines of PsMYB114L. Moreover, the expression level of the FLS gene (MdFLS) was significantly downregulated and the DFR (AtDFR/MdDFR) and ANS (AtANS/MdANS) genes were all significantly upregulated in transgenic lines plants of PsMYB12L. These results indicate that PsMYB114L and PsMYB12L both enhance anthocyanin accumulation by specifically regulating the expression of some anthocyanin biosynthesis-related genes in different plant species. Together, these results provide a valuable resource with which to further study the regulatory mechanism of anthocyanin biosynthesis in P. suffruticosa and for the breeding of tree peony cultivars with novel and charming flower colors.


Asunto(s)
Antocianinas/biosíntesis , Paeonia/genética , Proteínas de Plantas/genética , Proteínas Proto-Oncogénicas c-myb/genética , Arabidopsis/genética , Arabidopsis/metabolismo , Regulación de la Expresión Génica de las Plantas , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Paeonia/metabolismo , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/metabolismo
13.
Proteins ; 87(4): 265-275, 2019 04.
Artículo en Inglés | MEDLINE | ID: mdl-30520528

RESUMEN

Intrinsically disordered proteins (IDPs) are extensively involved in dynamic signaling processes which require a high association rate and a high dissociation rate for rapid binding/unbinding events and at the same time a sufficient high affinity for specific recognition. Although the coupled folding-binding processes of IDPs have been extensively studied, it is still impossible to predict whether an unfolded protein is suitable for molecular signaling via coupled folding-binding. In this work, we studied the interplay between intrinsic folding mechanisms and coupled folding-binding process for unfolded proteins through molecular dynamics simulations. We first studied the folding process of three representative IDPs with different folded structures, that is, c-Myb, AF9, and E3 rRNase. We found the folding free energy landscapes of IDPs are downhill or show low barriers. To further study the influence of intrinsic folding mechanism on the binding process, we modulated the folding mechanism of barnase via circular permutation and simulated the coupled folding-binding process between unfolded barnase permutant and folded barstar. Although folding of barnase was coupled to target binding, the binding kinetics was significantly affected by the intrinsic folding free energy barrier, where reducing the folding free energy barrier enhances binding rate up to two orders of magnitude. This accelerating effect is different from previous results which reflect the effect of structure flexibility on binding kinetics. Our results suggest that coupling the folding of an unfolded protein with no/low folding free energy barrier with its target binding may provide a way to achieve high specificity and rapid binding/unbinding kinetics simultaneously.


Asunto(s)
Proteínas Intrínsecamente Desordenadas/metabolismo , Pliegue de Proteína , Animales , Bacillus amyloliquefaciens/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Humanos , Proteínas Intrínsecamente Desordenadas/química , Ratones , Modelos Moleculares , Unión Proteica , Desplegamiento Proteico , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/metabolismo , Ribonucleasas/química , Ribonucleasas/metabolismo , Termodinámica
14.
Proteins ; 87(4): 302-312, 2019 04.
Artículo en Inglés | MEDLINE | ID: mdl-30582223

RESUMEN

Here a differential geometry (DG) representation of protein backbone is explored on the analyses of protein conformational ensembles. The protein backbone is described by curvature, κ, and torsion, τ, values per residue and we propose 1) a new dissimilarity and protein flexibility measurement and 2) a local conformational clustering method. The methods were applied to Ubiquitin and c-Myb-KIX protein conformational ensembles and results show that κ\τ metric space allows to properly judge protein flexibility by avoiding the superposition problem. The dmax measurement presents equally good or superior results when compared to RMSF, especially for the intrinsically unstructured protein. The clustering method is unique as it relates protein global to local dynamics by providing a global clustering solutions per residue. The methods proposed can be especially useful to the analyses of highly flexible proteins. The software written for the analyses presented here is available at https://github.com/AMarinhoSN/FleXgeo for academic usage only.


Asunto(s)
Proteínas/química , Animales , Análisis por Conglomerados , Humanos , Modelos Moleculares , Análisis de Componente Principal , Conformación Proteica , Proteínas Proto-Oncogénicas c-myb/química , Programas Informáticos , Ubiquitina/química
15.
Methods Enzymol ; 611: 101-136, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-30471686

RESUMEN

Protein disorder is a pervasive phenomenon in biology and a natural consequence of polymer evolution that facilitates cell signaling by organizing sites for posttranslational modifications and protein-protein interactions into arrays of short linear motifs that can be rearranged by RNA splicing. Disordered proteins are missing the long-range nonpolar interactions that form tertiary structures, but they often contain regions with residual secondary structure that are stabilized by protein binding. NMR spectroscopy is uniquely suited to detect residual secondary structure in a disordered protein and it can provide atomic resolution data on the structure and dynamics of disordered protein interaction sites. Here we describe how backbone chemical shifts are used for assigning residual secondary structure in disordered proteins and discuss some of the tools available for estimating secondary structure populations with a focus on disordered proteins containing different levels of alpha helical secondary structure which are stabilized by protein binding.


Asunto(s)
Proteínas Intrínsecamente Desordenadas/química , Resonancia Magnética Nuclear Biomolecular/métodos , Secuencia de Aminoácidos , Animales , Humanos , Proteínas Intrínsecamente Desordenadas/metabolismo , Modelos Moleculares , Unión Proteica , Pliegue de Proteína , Estructura Secundaria de Proteína , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/metabolismo , Proteína p53 Supresora de Tumor/química , Proteína p53 Supresora de Tumor/metabolismo
16.
Proc Natl Acad Sci U S A ; 115(40): 10040-10045, 2018 10 02.
Artículo en Inglés | MEDLINE | ID: mdl-30232260

RESUMEN

The human T cell leukemia virus I basic leucine zipper protein (HTLV-1 HBZ) maintains chronic viral infection and promotes leukemogenesis through poorly understood mechanisms involving interactions with the KIX domain of the transcriptional coactivator CBP and its paralog p300. The KIX domain binds regulatory proteins at the distinct MLL and c-Myb/pKID sites to form binary or ternary complexes. The intrinsically disordered N-terminal activation domain of HBZ (HBZ AD) deregulates cellular signaling pathways by competing directly with cellular and viral transcription factors for binding to the MLL site and by allosterically perturbing binding of the transactivation domain of the hematopoietic transcription factor c-Myb. Crystal structures of the ternary KIX:c-Myb:HBZ complex show that the HBZ AD recruits two KIX:c-Myb entities through tandem amphipathic motifs (L/V)(V/L)DGLL and folds into a long α-helix upon binding. Isothermal titration calorimetry reveals strong cooperativity in binding of the c-Myb activation domain to the KIX:HBZ complex and in binding of HBZ to the KIX:c-Myb complex. In addition, binding of KIX to the two HBZ (V/L)DGLL motifs is cooperative; the structures suggest that this cooperativity is achieved through propagation of the HBZ α-helix beyond the first binding motif. Our study suggests that the unique structural flexibility and the multiple interaction motifs of the intrinsically disordered HBZ AD are responsible for its potency in hijacking KIX-mediated transcription pathways. The KIX:c-Myb:HBZ complex provides an example of cooperative stabilization in a transcription factor:coactivator network and gives insights into potential mechanisms through which HBZ dysregulates hematopoietic transcriptional programs and promotes T cell proliferation.


Asunto(s)
Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/química , Virus Linfotrópico T Tipo 1 Humano/química , Proteínas Proto-Oncogénicas c-myb/química , Proteínas de los Retroviridae/química , Transcripción Genética , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/metabolismo , Virus Linfotrópico T Tipo 1 Humano/metabolismo , Humanos , Dominios Proteicos , Estructura Cuaternaria de Proteína , Estructura Secundaria de Proteína , Proteínas Proto-Oncogénicas c-myb/metabolismo , Proteínas de los Retroviridae/metabolismo
17.
Biochem Biophys Res Commun ; 503(1): 338-343, 2018 09 03.
Artículo en Inglés | MEDLINE | ID: mdl-29885838

RESUMEN

Previous structural analyses have shown that R2R3, the minimum unit of the DNA-binding domain of the transcriptional factor c-Myb, is largely flexible in solution, and changes to a more rigid structure upon DNA binding. In this study, we evaluated the structural dynamics using the diffracted X-ray tracking method, in correlation with DNA-binding abilities under different salt conditions, and compared them with the previous results. The resultant curve of the mean square angular displacements (MSD) clearly showed that the flexibility of R2R3 was decreased upon DNA binding, and the DNA-binding energies determined using the angular diffusion coefficients were in good agreement with those determined using isothermal titration calorimetry. The results of the MSD curves also indicate that the translational length reduces by approximately half upon DNA binding.


Asunto(s)
ADN/metabolismo , Proteínas Proto-Oncogénicas c-myb/metabolismo , Sitios de Unión , Calorimetría , Mutación , Unión Proteica , Conformación Proteica , Dominios Proteicos , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Termodinámica , Difracción de Rayos X
18.
J Mol Biol ; 430(16): 2389-2402, 2018 08 03.
Artículo en Inglés | MEDLINE | ID: mdl-29890118

RESUMEN

The relationship between helical stability and binding affinity was examined for the intrinsically disordered transactivation domain of the myeloblastosis oncoprotein, c-Myb, and its ordered binding partner, KIX. A series of c-Myb mutants was designed to either increase or decrease helical stability without changing the binding interface with KIX. This included a complimentary series of A, G, P, and V mutants at three non-interacting sites. We were able to use the glycine mutants as a reference state and show a strong correlation between binding affinity and helical stability. The intrinsic helicity of c-Myb is 21%, and helicity values of the mutants ranged from 8% to 28%. The c-Myb helix is divided into two conformationally distinct segments. The N-terminal segment, from K291-L301, has an average helicity greater than 60% and the C-terminal segment, from S304-L315, has an average helicity less than 10%. We observed different effects on binding when these two segments were mutated. Mutants in the N-terminal segment that increased helicity had no effect on the binding affinity to KIX, while helix destabilizing glycine and proline mutants reduced binding affinity by more than 1 kcal/mol. Mutants that either increased or decreased helical stability in the C-terminal segment had almost no effect on binding. However, several of the mutants reveal the presence of multiple conformations accessible in the bound state based on changes in enthalpy and linkage analysis of binding free energies. These results may explain the high level of sequence identity (>90%), even at non-interacting sites, for c-Myb homologues.


Asunto(s)
Proteína de Unión a CREB/química , Proteína de Unión a CREB/metabolismo , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/metabolismo , Sitios de Unión , Fenómenos Biofísicos , Humanos , Modelos Moleculares , Mutación , Unión Proteica , Conformación Proteica , Pliegue de Proteína , Proteínas Proto-Oncogénicas c-myb/genética , Termodinámica
19.
PLoS One ; 13(2): e0190934, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-29394256

RESUMEN

Myb is a key regulator of hematopoietic progenitor cell proliferation and differentiation and has emerged as a potential target for the treatment of acute leukemia. Using a myeloid cell line with a stably integrated Myb-inducible reporter gene as a screening tool we have previously identified Celastrol, a natural compound with anti-tumor activity, as a potent Myb inhibitor that disrupts the interaction of Myb with the co-activator p300. We showed that Celastrol inhibits the proliferation of acute myeloid leukemia (AML) cells and prolongs the survival of mice in an in vivo model of AML, demonstrating that targeting Myb with a small-molecule inhibitor is feasible and might have potential as a therapeutic approach against AML. Recently we became aware that the reporter system used for Myb inhibitor screening also responds to inhibition of C/EBPß, a transcription factor known to cooperate with Myb in myeloid cells. By re-investigating the inhibitory potential of Celastrol we have found that Celastrol also strongly inhibits the activity of C/EBPß by disrupting its interaction with the Taz2 domain of p300. Together with previous studies our work reveals that Celastrol independently targets Myb and C/EBPß by disrupting the interaction of both transcription factors with p300. Myb, C/EBPß and p300 cooperate in myeloid-specific gene expression and, as shown recently, are associated with so-called super-enhancers in AML cells that have been implicated in the maintenance of the leukemia. We hypothesize that the ability of Celastrol to disrupt the activity of a transcriptional Myb-C/EBPß-p300 module might explain its promising anti-leukemic activity.


Asunto(s)
Antineoplásicos Fitogénicos/farmacología , Proteínas Potenciadoras de Unión a CCAAT/antagonistas & inhibidores , Proteínas Proto-Oncogénicas c-myb/antagonistas & inhibidores , Triterpenos/farmacología , Factores de Transcripción p300-CBP/antagonistas & inhibidores , Células 3T3-L1 , Secuencia de Aminoácidos , Animales , Proteínas Potenciadoras de Unión a CCAAT/química , Proteínas Potenciadoras de Unión a CCAAT/genética , Línea Celular , Proliferación Celular/efectos de los fármacos , Pollos , Cisteína/química , Expresión Génica/efectos de los fármacos , Humanos , Leucemia Mieloide Aguda/tratamiento farmacológico , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/patología , Ratones , Células Mieloides/efectos de los fármacos , Células Mieloides/metabolismo , Triterpenos Pentacíclicos , Dominios y Motivos de Interacción de Proteínas , Proteínas Proto-Oncogénicas c-myb/química , Codorniz , Factores de Transcripción p300-CBP/química , Factores de Transcripción p300-CBP/genética
20.
Biosci Biotechnol Biochem ; 81(9): 1762-1767, 2017 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-28644769

RESUMEN

The CAPRICE (CPC) encodes an R3-type MYB transcription factor, which promotes root-hair differentiation. Previously, we showed that the CPC protein moves from the non-hair cell to the neighboring cell and induces root-hair differentiation in Arabidopsis. In addition, we proposed two cell-to-cell movement signal sequences, S1 and S2, in CPC. However, an S1:2xGFP:S2 chimera protein did not move between root epidermal cells. Here, we show that the S1 and S2 sequences do not confer cell-to-cell movement or nuclear localization ability to a GFP protein. The ENHANCER OF TRY AND CPC1 (ETC1) gene encodes the CPC homolog R3 MYB; this protein does not possess cell-to-cell movement ability or the S1 sequence. To elucidate whether the S1 sequence can induce cell-to-cell movement ability in ETC1, CPCp:S1:ETC1:2xGFP was constructed and introduced into Arabidopsis. Our results indicate that the addition of the S1 sequence was not sufficient for ETC1 to acquire cell-to-cell movement ability.


Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Proteínas de Unión al ADN/metabolismo , Epidermis de la Planta/metabolismo , Raíces de Plantas/metabolismo , Proteínas Proto-Oncogénicas c-myb/metabolismo , Proteínas Recombinantes de Fusión/metabolismo , Secuencia de Aminoácidos , Arabidopsis/citología , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/genética , Núcleo Celular/metabolismo , Proteínas de Unión al ADN/genética , Fenotipo , Transporte de Proteínas , Proteínas Proto-Oncogénicas c-myb/química , Proteínas Proto-Oncogénicas c-myb/genética , Proteínas Recombinantes de Fusión/genética , Tricomas/metabolismo
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