The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain.

Mutations in the tyrosine phosphatase Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2) are associated with a variety of human diseases. Most mutations in SHP2 increase its basal catalytic activity by disrupting autoinhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, some disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, and molecular dynamics simulations. We show that while some of these mutations alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also substantially alters ligand-binding specificity, despite being 8 to 10 Å from the specificity-determining region of the SH2 domain. This mutation exerts its effect on sequence specificity by remodeling the phosphotyrosine-binding pocket, altering the mode of engagement of both the phosphotyrosine and surrounding residues on the ligand. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands and enhances downstream signaling. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.

Use of phosphotyrosine-containing peptides to target SH2 domains: Antagonist peptides of the Crk/CrkL-p130Cas axis.

Protein-protein interactions between SH2 domains and segments of proteins that include a post-translationally phosphorylated tyrosine residue (pY) underpin numerous signal transduction cascades that allow cells to respond to their environment. Dysregulation of the writing, erasing, and reading of these posttranslational modifications is a hallmark of human disease, notably cancer. Elucidating the precise role of the SH2 domain-containing adaptor proteins Crk and CrkL in tumor cell migration and invasion is challenging because there are no specific and potent antagonists available. Crk and CrkL SH2s interact with a region of the docking protein p130Cas containing 15 potential pY-containing tetrapeptide motifs. This chapter summarizes recent efforts toward peptide antagonists for this Crk/CrkL-p130Cas interaction. We describe our protocol for recombinant expression and purification of Crk and CrkL SH2s for functional assays and our procedure to determine the consensus binding motif from the p130Cas sequence. To develop a more potent antagonist, we employ methods often associated with structure-based drug design. Computational docking using Rosetta FlexPepDock, which accounts for peptides having a greater number of conformational degrees of freedom than small organic molecules that typically constitute libraries, provides quantitative docking metrics to prioritize candidate peptides for experimental testing. A battery of biophysical assays, including fluorescence polarization, differential scanning fluorimetry and saturation transfer difference nuclear magnetic resonance spectroscopy, were employed to assess the candidates. In parallel, GST pulldown competition assays characterized protein-protein binding in vitro. Taken together, our methodology yields peptide antagonists of the Crk/CrkL-p130Cas axis that will be used to validate targets, assess druggability, foster in vitro assay development, and potentially serve as lead compounds for therapeutic intervention.

Integrated Platform for Large-Scale Quantitative Profiling of Phosphotyrosine Signaling Complexes Based on Cofractionation/Mass Spectrometry and Complex-Centric Algorithm.

The scarcity and dynamic nature of phosphotyrosine (pTyr)-modified proteins pose a challenge for researching protein complexes with pTyr modification, which are assembled through multiple protein-protein interactions. We developed an integrated complex-centric platform for large-scale quantitative profiling of pTyr signaling complexes based on cofractionation/mass spectrometry (CoFrac-MS) and a complex-centric algorithm. We initially constructed a trifunctional probe based on pTyr superbinder (SH2-S) for specifically binding and isolation of intact pTyr protein complexes. Then, the CoFrac-MS strategy was employed for the identification of pTyr protein complexes by integrating ion exchange chromatography in conjunction with data independent acquisition mass spectrometry. Furthermore, we developed a novel complex-centric algorithm for quantifying protein complexes based on the protein complex elution curve. Utilizing this algorithm, we effectively quantified 216 putative protein complexes. We further screened 21 regulated pTyr protein complexes related to the epidermal growth factor signal. Our study engenders a comprehensive framework for the intricate examination of pTyr protein complexes and presents, for the foremost occasion, a quantitative landscape delineating the composition of pTyr protein complexes in HeLa cells.

The intrinsic substrate specificity of the human tyrosine kinome.

Phosphorylation of proteins on tyrosine (Tyr) residues evolved in metazoan organisms as a mechanism of coordinating tissue growth1. Multicellular eukaryotes typically have more than 50 distinct protein Tyr kinases that catalyse the phosphorylation of thousands of Tyr residues throughout the proteome1-3. How a given Tyr kinase can phosphorylate a specific subset of proteins at unique Tyr sites is only partially understood4-7. Here we used combinatorial peptide arrays to profile the substrate sequence specificity of all human Tyr kinases. Globally, the Tyr kinases demonstrate considerable diversity in optimal patterns of residues surrounding the site of phosphorylation, revealing the functional organization of the human Tyr kinome by substrate motif preference. Using this information, Tyr kinases that are most compatible with phosphorylating any Tyr site can be identified. Analysis of mass spectrometry phosphoproteomic datasets using this compendium of kinase specificities accurately identifies specific Tyr kinases that are dysregulated in cells after stimulation with growth factors, treatment with anti-cancer drugs or expression of oncogenic variants. Furthermore, the topology of known Tyr signalling networks naturally emerged from a comparison of the sequence specificities of the Tyr kinases and the SH2 phosphotyrosine (pTyr)-binding domains. Finally we show that the intrinsic substrate specificity of Tyr kinases has remained fundamentally unchanged from worms to humans, suggesting that the fidelity between Tyr kinases and their protein substrate sequences has been maintained across hundreds of millions of years of evolution.

Development of Novel Phosphonodifluoromethyl-Containing Phosphotyrosine Mimetics and a First-In-Class, Potent, Selective, and Bioavailable Inhibitor of Human CDC14 Phosphatases.

Together with protein tyrosine kinases, protein tyrosine phosphatases (PTPs) control protein tyrosine phosphorylation and regulate numerous cellular functions. Dysregulated PTP activity is associated with the onset of multiple human diseases. Nevertheless, understanding of the physiological function and disease biology of most PTPs remains limited, largely due to the lack of PTP-specific chemical probes. In this study, starting from a well-known nonhydrolyzable phosphotyrosine (pTyr) mimetic, phosphonodifluoromethyl phenylalanine (F2Pmp), we synthesized 7 novel phosphonodifluoromethyl-containing bicyclic/tricyclic aryl derivatives with improved cell permeability and potency toward various PTPs. Furthermore, with fragment- and structure-based design strategies, we advanced compound 9 to compound 15, a first-in-class, potent, selective, and bioavailable inhibitor of human CDC14A and B phosphatases. This study demonstrates the applicability of the fragment-based design strategy in creating potent, selective, and bioavailable PTP inhibitors and provides a valuable probe for interrogating the biological roles of hCDC14 phosphatases and assessing their potential for therapeutic interventions.

Legionella effector LnaB is a phosphoryl-AMPylase that impairs phosphosignalling

AMPylation is a post-translational modification in which AMP is added to the amino acid side chains of proteins1,2. Here we show that, with ATP as the ligand and actin as the host activator, the effector protein LnaB of Legionella pneumophila exhibits AMPylase activity towards the phosphoryl group of phosphoribose on PRR42-Ub that is generated by the SidE family of effectors, and deubiquitinases DupA and DupB in an E1- and E2-independent ubiquitination process3-7. The product of LnaB is further hydrolysed by an ADP-ribosylhydrolase, MavL, to Ub, thereby preventing the accumulation of PRR42-Ub and ADPRR42-Ub and protecting canonical ubiquitination in host cells. LnaB represents a large family of AMPylases that adopt a common structural fold, distinct from those of the previously known AMPylases, and LnaB homologues are found in more than 20 species of bacterial pathogens. Moreover, LnaB also exhibits robust phosphoryl AMPylase activity towards phosphorylated residues and produces unique ADPylation modifications in proteins. During infection, LnaB AMPylates the conserved phosphorylated tyrosine residues in the activation loop of the Src family of kinases8,9, which dampens downstream phosphorylation signalling in the host. Structural studies reveal the actin-dependent activation and catalytic mechanisms of the LnaB family of AMPylases. This study identifies, to our knowledge, an unprecedented molecular regulation mechanism in bacterial pathogenesis and protein phosphorylation.

Identification and Optimization of Protein Tyrosine Phosphatase Inhibitors Via Fragment Ligation.

Phosphotyrosine biomimetics are starting points for potent inhibitors of protein tyrosine phosphatases (PTPs) and, thus, crucial for drug development. Their identification, however, has been heavily driven by rational design, limiting the discovery of diverse, novel, and improved mimetics. In this chapter, we describe two screening approaches utilizing fragment ligation methods: one to identify new mimetics and the other to optimize existing mimetics into more potent and selective inhibitors.

Mimosine increases the expressions of tyrosine phosphorylated protein in mouse seminal vesicles / La mimosina aumenta la expresión de la proteína tirosina fosforilada en las vesículas seminales del ratón

Acute effect of purified mimosine (MiMo) extracted from Leucaena leucocephala on testicular histopathology has been documented with seminal vesicle (SV) atrophy. Since protein phosphorylation and seminal secretions play important roles in sperm physiology, this study aimed to study the alteration of substances including tyrosine phosphorylated (TyrPho) proteins in seminal vesicle treated with MiMo. Male mice were divided into a control and experimental groups treated with purified MiMo at 3 doses of 15, 30, and 60 mg/KgBW, respectively for 35 consecutive days. The morphology and weights of SV were compared among groups. The levels of magnesium and fructosamine in SV fluid were assayed. The profiles of equally SV total proteins were compared using SDS-PAGE. The expression of seminal TyrPho proteins was detected by western blotting. Recent results showed the decreased weights of SV in MiMo treated mice compared to control. However MiMo in all doses did not affect the levels of magnesium and fructosamine in SV fluid. The SV protein expression of 130 and 55 kDas was obviously decreased in a high dose MiMo. In dose-dependent response, the expressions of 72 and 55 kDas TyrPho proteins of SV were increased. In conclusion, MiMo could affect SV morphological size and protein secretions especially TyrPho proteins.

El efecto agudo de la mimosina purificada (MiMo) extraída de Leucaena leucocephala en la histopatología testicular se ha documentado con atrofia de vesícula seminal (VS). Debido a que la fosforilación de proteínas y las secreciones seminales tienen un papel importante en la fisiología de los espermatozoides, este estudio tuvo como objetivo estudiar la alteración de sustancias como la proteína tirosina fosforilada (TyrPho) en vesículas seminales tratadas con MiMo. Los ratones se dividieron en un grupo control y un grupo experimental y se trataron con MiMo purificado en 3 dosis de 15, 30 y 60 mg / KgBW, respectivamente, durante 35 días seguidos. La morfología y los pesos de VS se compararon entre los grupos. Fueron analizados los niveles de magnesio y fructosamina en el fluido VS. Los perfiles de las proteínas totales de VS se compararon utilizando SDS-PAGE. La expresión de la proteína TyrPho en las vesículas seminales se detectó mediante transferencia de Western blot. Los resultados recientes muestran la disminución del peso de las VS en ratones tratados con MiMo, en comparación con el grupo control. Sin embargo, en ninguna de las dosis se vieron afectados por mimosina purificada los niveles de magnesio y fructosamina en el líquido de las VS. La expresión de la proteína en VS de 130 y 55 kDas disminuyó notablemente en una dosis alta de MiMo. En la respuesta dependiente de la dosis, aumentaron las expresiones de 72 y 55 kDas de las proteínas TyrPho en las VS. En conclusión, la mimosina purificada podría afectar el tamaño morfológico de las VS y la expresión de proteínas, especialmente las proteínas TyrPho.

Localization and changes of tyrosine phosphorylated proteins and ß actin in epididymis of rats treated with valproic acid / Localización y cambios de las proteínas tirosina fosforiladas y la ß actina en epidídimos de ratas tratadas con ácido valproico

Tyrosine phosphorylated proteins have been localized and identified in male reproductive tissues such as testis and capacitated/ acrosome reacted sperm except epididymis. The changes of such proteins are associated with decreased sperm quality of valproic acid treatment. This study aimed to investigate the presence and alterations of protein phosphorylation in epididymal epithelium and fluid of rats treated VPA. Sixteen adult male rats were divided into control and VPA-treated groups (n=8/ each). Treated rats were injected with VPA (500 mg/ kgBW, intraperitoneally) for 10 consecutive days. At the end of experiment, the monoclonal antiphosphotyrosine (clone 4G10) was used for immunohistochemistry to probe tyrosine phosphorylated proteins and also to examine the expression of such proteins using immuno-Western blotting in epididymal tissue and fluid. The result showed that positive reactivity of phosphorylated proteins was clearly observed in cytoplasmic principle cells, nuclei of apical & basal cells and sperm mass surrounded with epididymal fluids. The profiles of phosphorylated proteins in epididymal fluid were 182, 127, 80, 70, 57, 45, 34, and 31 kDas, respectively. Interestingly, VPA affected the changes of phosphorylated proteins and β actin in head, body, and tail epididymal fluids. We conclude that tyrosine phosphorylated proteins were detected in epididymal epithelium and fluid. The expressions of those proteins and actin were altered under VPA treating.

Las proteínas tirosina fosforiladas han sido localizadas e identificadas en tejidos reproductores masculinos tales como testículos y espermatozoides, capacitados a nivel acrosómico, excepto en el epidídimo. Los cambios de estas proteínas están asociadas con una disminución de la calidad del esperma en el tratamiento con ácido valproico (AVP). Este estudio tuvo como objetivo investigar la presencia y las alteraciones de la fosforilación de proteínas en el epitelio epididimal y en el fluido espermático de ratas tratadas con AVP. Dieciséis ratas macho adultas se dividieron en dos grupos: control y tratadas con AVP (n = 8 / cada uno). A las ratas tratadas se les inyectó AVP por vía intraperitoneal (500 mg / kg de peso corporal) durante 10 días consecutivos. Al final del experimento, se realizó inmunohistoquímica con la anti-fosfotirosina monoclonal (clon 4G10) para sondear las proteínas tirosina fosforiladas y también para examinar la expresión de tales proteínas usando inmunotransferencia Western, en tejido y fluido epididimarios. El resultado mostró reactividad positiva de proteínas fosforiladas en células citoplásmicas principales, en los núcleos de las células apicales y basales y en la masa de esperma rodeada por fluidos epididimarios. Los perfiles de proteínas fosforiladas en el fluido epididimal fueron 182, 127, 80, 70, 57, 45, 34 y 31 kDas, respectivamente. El AVP provocó cambios en las proteínas fosforiladas y en la β actina de los fluidos epididimarios de cabeza, cuerpo y cola del epidídimo. Concluimos que las proteínas tirosina fosforiladas se detectaron en el epitelio y el fluido epididimarios. Las expresiones de esas proteínas y de la β actina se alteraron bajo tratamiento con AVP.

Methotrexate changes the testicular tyrosine phosphorylated protein expression and seminal vesicle epithelia of adult rats / El metotrexato cambia la expresión de la proteína testicular-tirosina fosforilada y el epitelio vesicular seminal en ratas adultas

Methotrexate (MTX) is commonly used as a chemotherapy agent and immune system suppressant but its adverse effect on male reproductive system is still limited. This study aimed to investigate the effect of MTX on structure and functional proteins of testis and seminal vesicle. Adult male rats were divided into control and MTX groups (n =12). In 30 experimental days, the treated animals were injected with MTX (tail i.v., 75 mg/KgBW) at days 8 and 15. Then, the reproductive parameters and histology of both groups were examined. Thickness of seminal seminal vesicle epithelia was analyzed. Also, the expressions of testicular tyrosine phosphorylated proteins and steroidogenic acute regulatory (StAR) protein were investigated. The results showed that MTX could significantly decrease epididymal sperm concentration. In addition, the germ cell degeneration, increased spaces of interstitial tissues, and low epididymal sperm mass density were observed in MTX group. The thickness of seminal vesicle epithelia in MTX group was significantly lower than that of control group. Moreover, the intensity of testicular phosphorylated proteins of 31, 32, 72, and 85 kDas was significantly increased while of 42 and 47 kDas in MTX group was decreased as compared to control. The expression of testicular StAR protein in MTX group was also significantly decreased as compared to the control. In conclusion, MTX affects testicular and seminal tissues and changes testicular functional proteins in adult rats.

El metotrexato (MTX) se usa comúnmente como agente de quimioterapia y supresor del sistema inmunitario, pero su efecto adverso en el sistema reproductor masculino sigue siendo limitado. Este estudio tuvo como objetivo investigar el efecto del MTX sobre la estructura y las proteínas funcionales del testículo y la vesícula seminal. Ratas macho adultas se dividieron en grupos control y grupo con MTX (n = 12). En 30 días experimentales, a los animales tratados se les inyectó MTX (cola i.v., 75 mg / KgBW) los días 8 y 15. Luego, se examinaron los parámetros reproductivos y la histología de ambos grupos. Se analizó el espesor del epitelio de la vesícula seminal. Además, se investigaron las expresiones de la proteína tirosina testicular fosforilada y de la proteína reguladora aguda esteroidogénica (StAR). Los resultados mostraron que el MTX podría disminuir significativamente la concentración de espermatozoides epididimarios. Además, se observó la degeneración de las células germinales, el aumento de los espacios de los tejidos intersticiales y la baja densidad de masa del espermatozoide epididimal en el grupo de MTX. El grosor del epitelio de la vesícula seminal en el grupo MTX fue significativamente menor que el del grupo control. Además, la intensidad de las proteínas testiculares fosforiladas de 31, 32, 72 y 85 kDas aumentó significativamente, mientras que la de 42 y 47 kDas en el grupo MTX disminuyó en comparación con el control. La expresión de la proteína StAR testicular en el grupo MTX también se redujo significativamente en comparación con el control. En conclusión, el MTX afecta los tejidos testiculares y seminales y cambia las proteínas funcionales testiculares en ratas adultas.

Avaliação histológica e bioquímica da resposta celular ao enxerto de osso cortical bovino previamente submetido a altas temperaturas. Efeito da temperatura no preparo de enxerto xenógeno / Histological and biochemical analysis od cell responses to bovine cortical bone grafting previously submitted to high temperatures. Effect of the temperature on xenograft preparation

A despeito do sucesso no uso clínico de vários materiais para enxertos ósseos, os seus efeitos biológicos não são ainda completamente conhecidos. Este trabalho teve o propósito de avaliar a biocompatibilidade de dois materiais para enxerto ósseo, preparados a partir de osso cortical bovino, um desproteinizado a 100°C e outro a 1.000°C. Esses materiais em partículas com 1000-2000 mA,m foram implantados no tecido subcutâneo de 60 ratos. Os animais foram sacrificados após 10, 20, 30 e 60 dias, e as biópsias removidas para análise microscópica e perfil de fosfatases ácidas. A análise microscópica apresentou para ambos os materiais reação granulomatosa tipo corpo estranho de baixa renovação contendo macrófagos e células gigantes multinucleadas (presentes em maior número no osso tratado a 1000°C) em contato com o material, reação semelhante ao descrito na literatura para implantação subcutânea de osso alógeno mineralizado. Os níveis de fosfatase ácida lisossomal confirmaram um período de maior inflamação nos primeiros 10 dias pós-implantação, em resposta a cada um dos materiais. No tecido reacional ao osso desmineralizado a 1000°C notou-se fibrosamento maior e as células gigantes não exibiam indícios de atuarem na degradação do material. Por outro lado, a resposta celular ao osso 100°C indicou que ocorreu interação maior com as células gigantes e sinais de reabsorção. Os autores concluem que a temperatura de desproteinização modificou a respostá biológica, provavelmente devido a material orgânico no osso desproteinizado a 100°C. Esses materiais, ambos biocompatíveis, podem ser usados como de preenchimento ósseo-substitutos ou potenciais carreadores de proteínas morfogenéticas do osso.