Negative regulation of a protein tyrosine phosphatase by tyrosine phosphorylation

The low molecular weight protein tyrosine phosphatase (LMW-PTP) is a ubiquitously expressed enzyme with several proposed roles in cell signaling. Previously, two tyrosine phosphorylation modifications of LMW-PTP at sites Tyr-131 and Tyr-132 in response to growth factor stimulation have been mapped and suggested to stimulate LMW-PTP phosphatase activity. Biochemical analysis of tyrosine phosphorylation of a tyrosine phosphatase is challenging because of the intrinsic instability of these modifications. Here we used expressed protein ligation to site-specifically incorporate a phosphotyrosine mimic (phosphonomethylenephenylalanine, Pmp) at the Tyr-131 and Tyr-132 positions and measured the catalytic activity of these semisynthetic LMW-PTPs. The phosphonate-modified LMW-PTPs were 10- to 23-fold less active in dephosphorylating phosphotyrosine peptides derived from the PDGF receptor and p190RhoGap, two putative cellular substrates. These findings suggest the first example of a tyrosine phosphatase that is inhibited by tyrosine phosphorylation and provide a new model for the regulation of LMW-PTP and its role in cell adhesion.     

Development of a fluorogenic probe with a transesterification switch for detection of histone deacetylase activity

Histone deacetylases (HDACs) are key enzymatic regulators of many cellular processes such as gene expression, cell cycle, and tumorigenesis. These enzymes are attractive targets for drug development. However, very few simple methods for monitoring HDAC activity have been reported. Here, we have developed a fluorogenic probe, K4(Ac)-CCB, which consists of the histone H3 peptide containing acetyl-Lys and a coumarin fluorophore with a carbonate ester. By the simple addition of the probe to a HDAC solution, enzyme activity was clearly detected through spontaneous intramolecular transesterification, which renders the probe fluorescent. In addition, K4(Ac)-CCB can be applied to the evaluation of HDAC inhibitor activity. This is the first report to demonstrate the monitoring of HDAC activity by using a one-step procedure. Thus, our novel fluorogenic probe will provide a powerful tool for epigenetic research and the discovery of HDAC-targeted drugs.     

Dynamical regulation of ligand migration by a gate-opening molecular switch in truncated hemoglobin-N from Mycobacterium tuberculosis

Truncated hemoglobin-N is believed to constitute a defense mechanism of Mycobacterium tuberculosis against NO produced by macrophages, which is converted to the harmless nitrate anion. This process is catalyzed very efficiently, as the enzyme activity is limited by ligand diffusion. By using extended molecular dynamics simulations we explore the mechanism that regulates ligand diffusion and, particularly, the role played by residues that assist binding of O2 to the heme group. Our data strongly support the hypothesis that the access of NO to the heme cavity is dynamically regulated by the TyrB10-GlnE11 pair, which acts as a molecular switch that controls opening of the ligand diffusion tunnel. Binding of O2 to the heme group triggers local conformational changes in the TyrB10-GlnE11 pair, which favor opening of the PheE15 gate residue through global changes in the essential motions of the protein skeleton. The complex pattern of conformational changes triggered upon O2 binding is drastically altered in the GlnE11-->Ala and TyrB10-->Phe mutants, which justifies the poor enzymatic activity observed experimentally for the TyrB10-->Phe form. The results support a molecular mechanism evolved to ensure access of NO to the heme cavity in the oxygenated form of the protein, which should warrant survival of the microorganism under stress conditions.     

Application of two-dimensional gel electrophoresis in the study of cytoskeletal protein regulation during growth activation and differentiation

Two-dimensional gel electrophoresis was used to study the regulation of cytoskeletal protein synthesis during growth activation and development of the differentiated phenotype. We demonstrated a correlation between the state of organization and the expression of the respective cytoskeletal protein by showing that depolymerization of microtubules leads to a rapid decrease in new tubulin synthesis. We found that the synthesis of vimentin in both fibroblasts and epithelial cells correlates with extensive cell spreading on the substrate, while cytokeratin synthesis is maximal when cell to cell contacts are abundant. The analysis of cytoskeletal elements, involved directly in the formation of cell contacts, revealed that the level of vinculin synthesis is dependent on the extent of adherent type of cell contacts formed. Moreover, we found that the transient disappearance of vinculin from adhesion plaques of quiescent fibroblasts in response to serum factors was followed by an induction of vinculin mRNA and protein synthesis. The morphological changes associated with establishment of the differentiated phenotype were also found to include changes in the expression of the cytoskeletal-extracellular matrix complex. This was demonstrated in several differentiating systems: in 3T3 preadipocytes which change their shape from a fibroblastic to a spherical shape when stimulated to differentiate with adipogenic medium, we observed a decrease in mRNA levels and in the synthesis of fibronectin, beta-integrin, and the microfilament proteins, vinculin, alpha-actinin, tropomyosin and actin. The culturing of these cells on a certain extracellular matrix prevented the morphological changes occurring in the presence of adipogenic medium and blocked the shifts in cytoskeletal- and differentiation-related gene expression. Similar changes in the organization and expression of cytoskeletal proteins were identified during maturation of primary ovarian granulosa cell cultures, stimulated with gonadotropic hormones to form highly steroidogenic cells. The cell rounding and aggregation occurring during this process were associated with a decreased synthesis of vinculin, alpha-actinin, actin and the nonmuscle tropomyosins. The physiological relevance of these changes was suggested by the observation that the level of tropomyosin mRNA was lower in follicles of animals at late stages of granulosa cell maturation when compared to earlier stages. The expression of tissue-specific and cytoskeletal proteins was also determined in primary cultures of liver hepatocytes, maintained under conditions either favorable for growth or for expression of liver-specific functions. When DNA synthesis was elevated, cytoskeletal protein synthesis was high and that of liver-specific proteins was low.(ABSTRACT TRUNCATED AT 400 WORDS)     

Hormonal regulation of the adrenocortical cell

Monolayer cultures of bovine and human adrenocortical cells have been used to study regulation of growth and function. Homogeneous bovine adrenocortical cells exhibit a finite life span of approximately 60 generations in culture. Full maintenance of differentiated function (steroid hormone synthesis) requires an inducer such as ACTH and antioxidizing conditions. Full induction of differentiated function occurs only when cellular hypertrophy is stimulated by growth factors such as fibroblast growth factor and serum. ACTH and other agents that increase cellular cAMP inhibit replication but do not block growth factor-induced cellular hypertrophy. ACTH and growth factors together result in a hypertrophied, hyperfunctional cell. Replication ensues only when desensitization to the growth inhibitory effects of ACTH occurs. Cultures of the definitive and fetal zones of the human fetal adrenal cortex synthesize the steroids characteristic of the two zones in vivo. ACTH stimulates production of dehydroepiandrosterone (DHA), the major steroid product of the fetal zone, and of cortisol, the characteristic steroid product of the definitive zone. Prolonged ACTH treatment of fetal zone cultures results in a preferential increase in cortisol production so that the pattern of steroid synthesis becomes that of the definitive zone. The preferential increase in cortisol production by fetal Zone cultures results from induction of 3 beta-hydroxysteroid dehydrogenase, delta 4,5 isomerase activity, which is limiting in fetal zone cells. ACTH thus causes a phenotypic change in fetal zone cells to that of definitive zone cells. In both bovine and human adrenocortical cells, the principal effect of ACTH is to induce full expression of differentiated function. This occurs only under conditions where growth substances and nutrients permit full amplification.     

Chemically targeting the emergent properties of a chaperone complex

In this issue, Chang et?al. (2011) report a small molecule screen against the reconstituted DnaK-DnaJ-GrpE chaperone cycle. Through this approach, they identified myricetin as an inhibitor of DnaJ-stimulated DnaK ATPase activity, indicating the potential for their screening approach to identify modulators of emergent properties of protein complexes.     

Rational control of a polyacetylene helix by a pendant rotaxane switch

Polyacetylene bearing a pendant rotaxane moiety with an optically active wheel component was synthesized to realize reversible structural control of its helical structure by position control of the wheel component. Polyacetylene formed a one-handed helical structure only when the optically active wheel component moved close to the main chain.     

Control of a multisubunit DNA motor by a thermoresponsive polymer switch

The conjugation of thermoresponsive polymers to multisubunit, multifunctional hybrid type 1 DNA restriction-modification (R-M) enzymes enables temperature-controlled "switching" of DNA methylation by the conjugate. Polymers attached to the enzyme at a subunit distal to the methylation subunit allow retention of DNA recognition and ATPase activity while controlling methylation of plasmid DNA. This regulation of enzyme activity arises from the coil-globule phase transitions of the polymer as shown in light scattering and gel retardation assays.     

Photoinduced conformational switch of enantiopure azobenzenes controlled by a sulfoxide

Two series of enantiopure azobenzenes with a p-tolylsulfoxide at the ortho or meta position with respect to the azo group, have been regioselectively synthesized. Both can act as enantiopure molecular switches showing different structural features owing to the presence of the stereogenic sulfur. The photoisomerization process, studied by UV-vis, circular dichroism (CD), NMR, and chiral HPLC evidenced a double role of the sulfoxide. A transfer of chirality from the sulfoxide to the azo system was observed by CD in both cis and trans-isomers of the meta sulfinyl derivatives 3, whereas this perturbation was evident for the ortho sulfinyl series 7 only in the cis isomer. The NMR study evidenced that the s-cis rigid conformation of the bisaromatic sulfoxide was fixing a different orientation of the overall system in each series both in the trans and cis isomers, by forcing a final U-shaped structure in cis-3 and an S-shaped structure in cis-7. Very different values of specific optical rotations were measured in both trans and cis isomers, also reflecting the existence of distinct chiral entities in the photostationary states. The easy and reversible changes occurring between different conformational states could find applications in the photocontrol of several molecular switches.     

Unusual heme-histidine bond in the active site of a chaperone

The heme chaperone CcmE is essential for the delivery of heme to c-type cytochromes. It forms an unusual transient, yet covalent, bond between an essential histidine, H130, and heme. We report on the discovery of the chemical structure of this bond solved by NMR, where the heme vinyl is cross-linked at the beta carbon to the Ndelta1 of H130. As this type of heme linkage has not been described previously in any cytochrome or hemoprotein, it represents a novel type of heme-histidine complex.     

Differential scanning calorimetric examination of the human skeletal muscle in a compartment syndrome of the lower extremities

The compartment syndrome—conditions of elevated intramuscular pressure—is one of the most serious complications of the injuries of the lower extremities. Early diagnosis is important, as delayed treatment leads to significant complications. The diagnosis of compartment syndrome is most commonly made by clinical examination and direct measurement of the intra-compartmental pressure. Our hypothesis was that in different stages of compartment syndrome there is a clear pathological abnormality in the tissue elements of the affected muscles, which is responsible for seriousness of the disease, and could be monitored besides the classical histological methods by differential scanning calorimetry. The thermal denaturation of different parts of human samples was monitored by a SETARAM Micro DSC-II calorimeter. All the experiments were performed between 0 and 100 °C. The heating rate was 0.3 K/min. DSC scans clearly demonstrated significant differences between the different types and conditions of samples (control: T_m = 55.5; 59.9 °C and ΔH_cal = 0.52 J/g, Gr. I.: T_m = 58.1; 62.2 °C and ΔH_cal = 0.28 J/g, Gr. II.: T_m = 57.45; 61.5 °C and ΔH_cal = 0.24 J/g, Volkmann’s ischemic contracture T_m = 57.75; 61.8; 65.8 °C and ΔH_cal = 0.74 J/g). These observations could be explained with the structural alterations caused by the biochemical processes. The heat capacity change between native and denatured states of muscle samples was significant, indicating significant water loosing during denaturation, but independent from the structural alterations.     

Micelle density regulated by a reversible switch of protein secondary structure

Protein secondary structures may exhibit reversible transitions that occur in an abrupt and controllable manner. In this report, we demonstrate that such transitions may be utilized in the design of a "smart" protein micellar system, in which a stimulus-induced change in protein structure triggers a rapid change in micelle compacticity and size. Specifically, recombinant DNA methods were used to prepare a protein triblock copolymer containing a central hydrophilic block and two hydrophobic end blocks derived from elastin-mimetic peptide sequences. Below the copolymer inverse transition temperature (T(t)), dilute solutions of this amphiphilic protein formed monodispersed micelles in a narrow range of R(H) of approximately 100 nm. When the the temperature was raised above T(t), an abrupt increase in micelle internal density was observed with a concomitant reduction in micelle size. This reversible change in micelle compacticity was triggered by helix-to-sheet protein folding transition. Significantly, these protein polymer-based micelles, which are rapidly responsive to environmental stimuli, establish a new mechanism for the design of controlled drug delivery vehicles.     

In situ monitoring of a trace intermediate during DNA phosphorylation by T4 polynucleotide kinase for transient kinetic studies

Formation and decomposition of the enzyme-substrate (ES) complex during phosphorylation by T4 polynucleotide kinase (T4 PNK) of dsDNAs were monitored using a highly sensitive quartz crystal microbalance (QCM) to determine kinetic parameters, which were characterised in comparison with those of other enzymes such as DNA polymerase and exo- and endo-nucleases.     

Reaction dynamics of a molecular switch unveiled by coherent two-dimensional electronic spectroscopy

Coherent two-dimensional electronic spectroscopy is usually employed on molecular species with fixed geometric configuration. Here we present two-dimensional Fourier-transform electronic spectra of dissolved 6,8-dinitro-1',3',3'-trimethylspiro[2H-1-benzopyran-2,2'-indoline] (6,8-dinitro-BIPS), a photochromic system present in two ring-open forms differing in the cis/trans configuration of a double bond, which both undergo a photoinduced ring closure. The two-dimensional spectra, recorded with 20 fs pump pulses centered at 605 nm and a supercontinuum probe covering the complete visible spectral range, allow for a detailed analysis of the photophysics and photochemistry of the two isomers and directly reveal that cis/trans isomerization among them does not play a major role. This experiment demonstrates the potential of two-dimensional electronic spectroscopy for reactive processes.