Comparative analysis of brain proteins from p53-deficient mice by two-dimensional electrophoresis

p53 is a tumor suppressor protein that regulates many cellular processes including the cell cycle, DNA repair, and apoptosis. It also serves as a critical regulator of neuronal apoptosis in the central nervous system (CNS). To elucidate the role of p53 in the CNS, brain proteins of p53 knock-out mice (p53-/-) were analyzed by two-dimensional gel electrophoresis (2-DE) and compared with those from p53 wild type (p53+/+) mice. Six types of brain tissue (temporal cortex, cerebellum, hippocampus, striatum, olfactory bulb, and cervical spinal cord) and other control tissues (lung and blood) from 18-week-old non-stress-induced mice were analyzed. The morphology of brains from p53-/- mice appeared to be normal and identical to that of p53+/+ mice, although lungs showed diffuse tumors that may have been caused by p53 deficiency. Comparative 2-D gel analysis showed that, on average, 7 of 886 spots from brain tissue were p53-/- specific, whereas 12 of 1008 spots from lung tissue were p53-/- specific. N-terminal amino acid sequence was determined for p53-/- specific proteins. In all brain tissues from p53-/- mice, a newly identified mouse mitochondrial NADH-ubiquinone oxidoreductase 24 kDa subunit showed decreased expression, and apolipoprotein A1 acidic forms showed increased expression. In addition, brain-type creatine kinase B chain and tubulin beta-5 N-terminal fragment were increased in the p53-/- cerebellum, and a new protein in mouse, hydroxyacylglutathione hydrolase (glyoxalase II) was decreased in the temporal cortex of p53-/- mice. The alterations in protein expression identified in this study may imply a p53-related brain function. This is the first proteomic analysis on the p53-/- mouse brain, and further information based on this study will provide new insights into the p53 function in the CNS.     

Native PAGE to study the interaction between the oncosuppressor p53 and its protein ligands

In the present study, we investigated a new approach for studying the interaction between p53 and MDM2/X (where MDM is murine double minute protein). The method is based on the different mobility between the interacting domains of the oncosuppressor p53 and its protein ligands MDM2/X on polyacrylamide gels under native conditions. While the two proteins MDM2/X alone were able to enter the gel, the formation of a binary complex between p53 and MDM2/X prevented the gel entry. The novel technique is reliable for determining the different affinity elicited by MDM2 or MDMX toward p53, and can be useful for analyzing the dissociation power exerted by other molecules on the p53–MDM2/X complex.     

Single-molecule analysis of interaction between p53TAD and MDM2 using aerolysin nanopores

Protein–protein interactions (PPIs) are regarded as important, but undruggable targets. Intrinsically disordered p53 transactivation domain (p53TAD) mediates PPI with mouse double minute 2 (MDM2), which is an attractive anticancer target for therapeutic intervention. Here, using aerolysin nanopores, we probed the p53TAD peptide/MDM2 interaction and its modulation by small-molecule PPI inhibitors or p53TAD phosphorylation. Although the p53TAD peptide showed short-lived (<100 ms) translocation, the protein complex induced the characteristic extraordinarily long-lived (0.1 s ∼ tens of min) current blockage, indicating that the MDM2 recruitment by p53TAD peptide almost fully occludes the pore. Simultaneously, the protein complex formation substantially reduced the event frequency of short-lived peptide translocation. Notably, the addition of small-molecule PPI inhibitors, Nutlin-3 and AMG232, or Thr18 phosphorylation of p53TAD peptide, were able to diminish the extraordinarily long-lived events and restore the short-lived translocation of the peptide rescued from the complex. Taken together, our results elucidate a novel mechanism of single-molecule sensing for analyzing PPIs and their inhibitors using aerolysin nanopores. This novel methodology may contribute to remarkable improvements in drug discovery targeted against undruggable PPIs.

Using aerolysin nanopores, we probed protein–protein interaction (PPI) between p53TAD and MDM2 and its modulation by small-molecule PPI inhibitors and p53TAD phosphorylation.     

Helical beta-peptide inhibitors of the p53-hDM2 interaction

hDM2 is recognized in vivo by a short alpha-helix within the p53 trans-activation domain (p53AD). Disruption of the p53.hDM2 interaction is an important goal for cancer therapy. A functional epitope comprised of three residues on one face of the p53AD helix (F19, W23, and L26) contributes heavily to the binding free energy. We hypothesized that the p53AD functional epitope would be recapitulated if the side chains of F19, W23, and L26 were presented at successive positions three residues apart on a stabilized beta3-peptide 14-helix. Here, we report a set of beta3-peptides that possess significant 14-helix structure in water; one recognizes a cleft on the surface of hDM2 with nanomolar affinity. The strategy for beta3-peptide design that we describe is general and may have advantages over one in which individual or multiple beta-amino acid substitutions are introduced into a functional alpha-peptide, because it is based on homology at the level of secondary structure, not primary sequence.     

Chromatographic investigations into the interaction between proteins and polymer matrices

Summary Chromatographic investigations with two enzymes and selected low-molecular-weight compounds of different pk_a on three different inert gels (matrices) commonly used for enzyme separation and immobilization showed that considerable deviations from the theoretical elution volumes occur at low ionic strength. These deviations are explained in terms of ionic and hydrophobic interaction between gel matrix and solute.     

How protonation modulates the interaction between proteins and pH-responsive hydrogel films

Hydrogels of pH-responsive polymers are promising candidates for the design of functional biomaterials. In this context, understanding the complexity of the interaction between these materials and proteins is essential. A recently developed molecular-level equilibrium theory for protein adsorption on hydrogels of cross-linked polyacid chains allows for modeling size, shape, charge distribution, protonation state and conformational degrees of freedom of all chemical species in the system; proteins are described using a coarse-grained model of their crystallographic structure. This review summarizes our recent studies, which have focused on understanding how the interaction between proteins and pH-responsive hydrogel films depends on the pH and salt concentration, both in single protein solutions and mixtures. In particular, we discuss the key role that protonation plays in mediating the polymer-protein electrostatic attractions that drive adsorption. Deprotonation of the polyacid network modifies the nano-environment inside the hydrogel; the local pH drops inside the film. In single protein solutions, protonation of amino acid residues in this lower-pH environment favors adsorption to the hydrogel. Upon adsorption, the net charge of the protein can be several units more positive than in the solution. The various amino acids protonate differently, in a non-trivial way, which gives flexibility to the protein to enhance its positive charge and favor adsorption under a wide range of conditions. In binary and ternary protein solutions, amino acid protonation is the decisive factor for selective adsorption under certain conditions. We show that the polymer network composition and the solution pH can be used to separate and localize proteins within nanometer-sized regions.     

Binding of an inhibitor of the p53/MDM2 interaction to MDM2

The mode of action of the secondary metabolite chlorofusin, which antagonises the interaction between p53 and MDM2, involves direct binding to the N-terminal domain of MDM2.     

Allosteric inhibition of the protein-protein interaction between the leukemia-associated proteins Runx1 and CBFbeta

The two subunits of core binding factor (Runx1 and CBFbeta) play critical roles in hematopoiesis and are frequent targets of chromosomal translocations found in leukemia. The binding of the CBFbeta-smooth muscle myosin heavy chain (SMMHC) fusion protein to Runx1 is essential for leukemogenesis, making this a viable target for treatment. We have developed inhibitors with low micromolar affinity which effectively block binding of Runx1 to CBFbeta. NMR-based docking shows that these compounds bind to CBFbeta at a site displaced from the binding interface for Runx1, that is, these compounds function as allosteric inhibitors of this protein-protein interaction, a potentially generalizable approach. Treatment of the human leukemia cell line ME-1 with these compounds shows decreased proliferation, indicating these are good candidates for further development.     

An integrated in silico screening strategy for identifying promising disruptors of p53-MDM2 interaction

The p53 protein, also called guardian of the genome, plays a critical role in the cell cycle regulation and apoptosis. This protein is frequently inactivated in several types of human cancer by abnormally high levels of its negative regulator, mouse double minute 2 (MDM2). As a result, restoration of p53 function by inhibiting p53-MDM2 protein–protein interaction has been pursued as a compelling strategy for cancer therapy. To date, a limited number of small-molecules have been reported as effective p53−MDM2 inhibitors. X-ray structures of MDM2 in complex with some ligands are available in Protein Data Bank and herein, these data have been exploited to efficiently identify new p53-MDM2 interaction antagonists through a hierarchical virtual screening strategy. For this purpose, the first step was aimed at compiling a focused library of 686,630 structurally suitable compounds, from PubChem database, similar to two known effective inhibitors, Nutlin-3a and DP222669. These compounds were subjected to the subsequent structure-based approaches (quantum polarized ligand docking and molecular dynamics simulation) to select potential compounds with highest binding affinity for MDM2 protein. Additionally, ligand binding energy, ADMET properties and PAINS analysis were also considered as filtering criteria for selecting the most promising drug-like molecules. On the basis of these analyses, three top-ranked hit molecules, CID_118439641, CID_60452010 and CID_3106907, were found to have acceptable pharmacokinetics properties along with superior in silico inhibitory ability towards the p53-MDM2 interaction compared to known inhibitors. Molecular docking and molecular dynamics results well confirmed the interactions of the final selected compounds with critical residues within p53 binding site on the MDM2 hydrophobic clefts with satisfactory thermodynamics stability. Consequently, the new final scaffolds identified by the presented computational approach could offer a set of guidelines for designing promising anti-cancer agents targeting p53-MDM2 interaction.     

Relaxation-allowed nuclear magnetic resonance transitions by interference between the quadrupolar coupling and the paramagnetic interaction

Of the various ways in which nuclear spin systems can relax to their ground states, the processes involving an interference between different relaxation mechanisms, such as dipole-dipole coupling and chemical shift anisotropy, have become of great interest lately. The authors show here that the interference between the quadrupolar coupling and the paramagnetic interaction (cross-correlated relaxation) gives rise to nuclear spin transitions that would remain forbidden otherwise. In addition, frequency shifts arise. These would be reminiscent of residual anisotropic interactions when there are none. While interesting from a fundamental point of view, these processes may become relevant in magnetic resonance imaging experiments which involve quadrupolar spins, such as (23)Na, in the presence of contrast agents. Geometrical constraints in paramagnetic molecule structures may likewise be derived from these interference effects.     

Proteomimetic libraries: design, synthesis, and evaluation of p53-MDM2 interaction inhibitors

The p53-MDM2 interaction regulates p53-mediated cellular responses to DNA damage, and MDM2 is overexpressed in 7% of all cancers. Structure-based computational design was applied to this system to design libraries centered on a scaffold that projects side chain functionalities with distance and angular relationships equivalent to those seen in the MDM2 interacting motif of p53. A library of 173 such compounds was synthesized using solution phase parallel chemistry. The in vitro competitive ability of the compounds to block p53 peptide binding to MDM2 was determined using a fluorescence polarization competition assay. The most active compound bound with K(d) = 12 microM, and its binding was characterized by (15)N-(1)H HSQC NMR.     

In vitro study on the interaction between thiophanate methyl and human serum albumin

Thiophanate methyl (MT) is one of the widely used fungicides to control important fungal diseases of crops, which has led to potential toxicological risk to public health. Several different transport proteins exist in blood plasma, but albumin only is bound by a wide diversity of xenobiotics reversibly with high affinity. We studied the interaction of MT with human serum albumin by using spectroscopic methods including fluorescence quenching technology, UV and Fourier transform infrared (FT-IR) spectroscopy under simulative physiological conditions. The result of fluorescence titration revealed that MT could quench the intrinsic fluorescence of HSA. The binding process was exothermic and spontaneous, as indicated by the thermodynamic analyses. In addition, the studies of FT-IR spectroscopy showed that the binding of MT to HSA changed molecular conformation of HSA. The results obtained from molecular modeling showed that the interaction between MT and HSA was dominated by hydrophobic force, and there was also hydrogen bond interaction between the pesticide and the residues of HSA, which was in good agreement with the result of binding mode.     

Involvement of JNK-initiated p53 accumulation and phosphorylation of p53 in pseudolaric acid B induced cell death

A terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay was used to determine that apoptosis causes HeLa cell death induced by pseudolaric acid B. The c-Jun N-terminal kinase (JNK) inhibitor SP600125 decreased p53 protein expression during exposure to pseudolaric acid B. SP600125 decreased the phosphorylation of p53 during pseudolaric acid B exposure, indicating that JNK mediates phosphorylation of p53 during the response to pseudolaric acid B. SP600125 reversed pseudolaric acid B-induced down-regulation of phosphorylated extracellular signal-regulated protein kinase (ERK), and protein kinase C (PKC) was activated by pseudolaric acid B, whereas staurosporine, calphostin C, and H7 partly blocked this effect. These results indicate that p53 is partially regulated by JNK in pseudolaric acid B-induced HeLa cell death and that PKC participates in pseudolaric acid B-induced HeLa cell death.     

A rapid and sensitive method for the determination of trace proteins based on the interaction between proteins and Ponceau 4R

The interactions between proteins and Ponceau 4R (PR) in aqueous solution have been studied by the techniques of resonance light scattering (RLS) spectroscopy, the absorption spectroscopy, zeta potential assay and circular dichroism (CD) spectrum. The dry PR can assemble on the surface of protein via electrostatic and hydrophobic forces to produce an associated compound of protein-PR, this compound can enhance the RLS of protein. Based on this fact, a simple, rapid, and sensitive method has been developed for the determination of proteins at nanogram level by RLS technique with a common spectrofluorimeter. Under optimum conditions, the linear range is 0.10-39.2 μg mL⁻¹ for the determination of both bovine serum albumin (BSA) and human serum albumin (HSA). The detection limits (S/N = 3) are 6.96 ng mL⁻¹ for BSA and 5.71 ng mL⁻¹ for HSA, respectively. There is almost no interference from amino acids, most of the metal ions, and other coexistent substances. The method has been satisfactorily applied to the direct determination of the total protein in human serum.     

p53 induction in normal human skin in vitro following exposure to solar simulated UV and UV-B irradiation.

Exposure of normal human breast skin ex vivo to physiological levels of UV-B and solar simulated UV results in a UV dose- and time-dependent increase in epidermal p53, as determined by PAGE analysis. Peak p53 levels are detected 12 to 24 h post irradiation with UV-B (470-1410 mJ cm-2) and solar simulated UV (5-12 minimal erythema dose (MED) equivalents). Irradiation with an FS20 UV-B lamp, contaminated with UV-A and UV-C (74-1111 mJ cm-2), also induces peak levels after 12 h incubation at 37 degrees C but these levels persist to 36 h post UV irradiation. In all cases p53 levels start to return to normal by 48 h culture. A significant positive correlation is demonstrated between UV-B dose (47-1645 mJ cm-2) and p53 level (p < 0.01, R > 0.977) in explants cultured for 24 h at 37 degrees C post irradiation. The FS20 induces a 'UV-B' dose-dependent increase in p53 to a maximum from 370 to 1111 mJ cm-2. Similarly, solar simulated UV induces a plateau of peak p53 induction between 5 and 15 MED equivalents. Immunohistochemical analysis using microwave retrieval on 5 microns sections shows the same pattern of p53 staining with UV-B and solar UV insult, but proves unreliable as a method of quantification. These results suggest that the skin explant model may be a useful tool in the evaluation of UV-induced epidermal cell damage, providing a valuable alternative to in vivo studies.     

Influence of Cu(II) on the interaction between sulfite and horseradish peroxidase in vitro

This paper discussed the quantitative influence of Cu(II) on the interaction between horseradish peroxidase (HRP) and sulfite (SO3(2-)), which is a derivate of sulfite dioxide in human bodies, by using fluorescence spectrum and ultraviolet (UV) absorption spectrometry in vitro. The results show that under the conditions of physiological pH and room-temperature, Cu(II) can bind strongly with both the protein part and the ferroporphyrin part in HRP at a low concentration (10(-4) mol L(-1)), and the combination constants are 2.047 x 10(3) and 7.66 x 10(2) L mol(-1), respectively. Under the same conditions, SO3(2-) at low concentrations (<0.15 mol L(-1)) has little quenching for the fluorescence of HRP at 330 nm, and the combination constant is 0.108 L mol(-1). While the fluorescence intensity at 440 nm enhance gradually with the increased concentration of SO3(2-) (<0.1 mol L(-1)), and the combination constant is 8.219 L mol(-1). These indicate that SO3(2-) at low concentration has little reaction with the enzyme protein part in HRP but obvious reaction with the ferroporphyrin part in HRP. After SO3(2-) at low concentrations is added into the HRP-Cu(II) binary system, the reaction constants between SO3(2-) and the enzyme protein part in HRP increase rapidly. Compared with the absence of Cu(II), the combination constant of SO3(2-) with the enzyme protein part in HRP increases nearly 70 times with a certain Cu(II) concentration (5.0 x 10(-4) mol L(-1)) in the system. However, the presence of Cu(II) in the system has little effect on the reaction constants between SO3(2-) and the ferroporphyrin part in HRP.     

Evaluation of the interaction between sitagliptin and cyclodextrin derivatives by capillary electrophoresis and nuclear magnetic resonance spectroscopy

An aqueous capillary electrophoretic method was developed for chiral analysis of the novel anti-diabetic drug, sitagliptin. The acid-base profiling of the analyte was carried out using both capillary electrophoresis and nuclear magnetic resonance pH titrations. The apparent complex stability and chiral separation properties were investigated with 30 different cyclodextrins under acidic conditions. The effect of concentration and pH of the BGE, temperature of the capillary, and the type and concentration of the chiral selector on the enantiomer resolution were thoroughly investigated. The effects of dual cyclodextrin systems on separation were also extensively studied. Complete separation of racemic sitagliptin with good resolution (R(S)=2.24) was achieved within a short time (15 min) with optimized parameters (10°C, pH=4.4, 40 mM phosphate buffer) of a sulfobutylether-β-cyclodextrin (averaged degree of substitution ~4) and native β-cyclodextrin dual system. The averaged stoichiometry of the inclusion complex was determined using the Job plot method with both (1)H and (19)F NMR experiments and resulted in a 1:1 complex. The structure of the inclusion complex was elucidated using 2-D ROESY NMR experiments.