Biochemical characterization of actin assembly mechanisms with ALS-associated profilin variants

Eight separate mutations in the actin-binding protein profilin-1 have been identified as a rare cause of amyotrophic lateral sclerosis (ALS). Profilin is essential for many neuronal cell processes through its regulation of lipids, nuclear signals, and cytoskeletal dynamics, including actin filament assembly. Direct interactions between profilin and actin monomers inhibit actin filament polymerization. In contrast, profilin can also stimulate polymerization by simultaneously binding actin monomers and proline-rich tracts found in other proteins. Whether the ALS-associated mutations in profilin compromise these actin assembly functions is unclear. We performed a quantitative biochemical comparison of the direct and formin-mediated impact for the eight ALS-associated profilin variants on actin assembly using classic protein-binding and single-filament microscopy assays. We determined that the binding constants of each profilin for actin monomers generally correlates with the actin nucleation strength associated with each ALS-related profilin. In the presence of formin, the A20T, R136W, Q139L, and C71G variants failed to activate the elongation phase of actin assembly. This diverse range of formin-activities is not fully explained through profilin-PLP interactions, as all ALS-associated variants bind a formin-derived PLP peptide with similar affinities. However, chemical denaturation experiments suggest that the folding stability of these profilins impact some of these effects on actin assembly. Thus, changes in profilin protein stability and alterations in actin filament polymerization may both contribute to the profilin-mediated actin disruptions in ALS.

Molecular Recognition by Pillar[5]arenes: Evidence for Simultaneous Electrostatic and Hydrophobic Interactions

The formation of inclusion complexes between alkylsulfonate guests and a cationic pillar[5]arene receptor in water was investigated by NMR and ITC techniques. The results show the formation of host-guest complexes stabilized by electrostatic interactions and hydrophobic effects with binding constants of up to 107 M−1 for the guest with higher hydrophobic character. Structurally, the alkyl chain of the guest is included in the hydrophobic aromatic cavity of the macrocycle while the sulfonate groups are held in the multicationic portal by ionic interactions.

Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing

The power of sensing molecules is often characterized in part by determining their thermodynamic/dynamic properties, in particular the binding constant of a guest to a host. In many studies, traditional nonlinear regression analysis has been used to determine the binding constants, which cannot be applied to complex systems and limits the reliability of such calculations. Supramolecular sensor systems include many interactions that make such chemical systems complicated. The challenges in creating sensing molecules can be significantly decreased through the availability of detailed mathematical models of such systems. Here, we propose uncovering accurate thermodynamic parameters of chemical reactions using better-defined mathematical modeling-fitting analysis is the key to understanding molecular assemblies and developing new bio/sensing agents. The supramolecular example we chose for this investigation is a self-assembled sensor consists of a synthesized receptor, DPA (DPA = dipicolylamine)-appended phenylboronic acid (1) in combination with Zn2+(1.Zn) that forms various assemblies with a fluorophore like alizarin red S (ARS). The self-assemblies can detect multi-phosphates like pyrophosphate (PPi) in aqueous solutions. We developed a mathematical model for the simultaneous quantitative analysis of twenty-seven intertwined interactions and reactions between the sensor (1.Zn-ARS) and the target (PPi) for the first time, relying on the Newton-Raphson algorithm. Through analyzing simulated potentiometric titration data, we describe the concurrent determination of thermodynamic parameters of the different guest-host bindings. Various values of temperatures, initial concentrations, and starting pHs were considered to predict the required measurement conditions for thermodynamic studies. Accordingly, we determined the species concentrations of different host-guest bindings in a generalized way. This way, the binding capabilities of a set of species can be quantitatively examined to systematically measure the power of the sensing system. This study shows analyzing supramolecular self-assemblies with solid mathematical models has a high potential for a better understanding of molecular interactions within complex chemical networks and developing new sensors with better sensing effects for bio-purposes.

Investigation on the Binding and Conformational Change of All-trans-Retinoic Acid with Peptidyl Prolyl cis/trans Isomerase Pin1 Using Spectroscopic and Computational Techniques

Binding and conformational change of all-trans-retinoic acid (ATRA) with peptidyl prolyl cis/trans isomerase Pin1 were investigated systematically by spectroscopic and computational techniques under experimentally optimized physiological conditions. The intrinsic fluorescence of Pin1 was quenched through a static quenching mechanism in the presence of ATRA with binding constants on the order of 105 mol/L. Thermodynamic parameters (ΔH = 15.76 kJ/mol and ΔS = 158.36 J/mol·K at 293 K) and computational results illustrated that the hydrophobic interactions played a significant role in the binding process of ATRA to Pin1, but electrostatic forces, weak van der Waals, and hydrogen bonds cannot be ignored. Circular dichroism, fluorescence spectra, and computational simulations revealed that ATRA interacted with residues Lys63 and Arg69 of Pin1 to affect its conformational changes. Molecular dynamic simulation, principal component analysis, and free energy landscape monitored the dynamical conformational characteristics of ATRA binding to Pin1. All in all, the present research might provide a reference for the development and design of retinoic acid drugs that inhibit the activity of Pin1.

Molecular Mechanisms of Anticancer Activity of N-Glycosides of Indolocarbazoles LCS-1208 and LCS-1269

Novel indolocarbazole derivatives named LCS were synthesized by our research group. Two of them were selected as the most active anticancer agents in vivo. We studied the mechanisms of anticancer activity in accordance with the previously described effects of indolocarbazoles. Cytotoxicity was estimated by MTT assay. We analyzed LCS-DNA interactions by circular dichroism in cholesteric liquid crystals and fluorescent indicator displacement assay. The effect on the activity of topoisomerases I and II was studied by DNA relaxation assay. Expression of interferon signaling target genes was estimated by RT-PCR. Chromatin remodeling was analyzed–the effect on histone H1 localization and reactivation of epigenetically silenced genes. LCS-induced change in the expression of a wide gene set was counted by means of PCR array. Our study revealed the cytotoxic activity of the compounds against 11 cancer cell lines and it was higher than in immortalized cells. Both compounds bind DNA; binding constants were estimated—LCS-1208 demonstrated higher affinity than LCS-1269; it was shown that LCS-1208 intercalates into DNA that is typical for rebeccamycin derivatives. LCS-1208 also inhibits topoisomerases I and IIα. Being a strong intercalator and topoisomerase inhibitor, LCS-1208 upregulates the expression of interferon-induced genes. In view of LCSs binding to DNA we analyzed their influence on chromatin stability and revealed that LCS-1269 displaces histone H1. Our analysis of chromatin remodeling also included a wide set of epigenetic experiments in which LCS-1269 demonstrated complex epigenetic activity. Finally, we revealed that the antitumor effect of the compounds is based not only on binding to DNA and chromatin remodeling but also on alternative mechanisms. Both compounds induce expression changes in genes involved in neoplastic transformation and target genes of the signaling pathways in cancer cells. Despite of being structurally similar, each compound has unique biological activities. The effects of LCS-1208 are associated with intercalation. The mechanisms of LCS-1269 include influence on higher levels such as chromatin remodeling and epigenetic effects.

Characterization of a G-quadruplex from hepatitis B virus and its stabilization by binding TMPyP4, BRACO19 and PhenDC3

Specific guanine rich nucleic acid sequences can form non-canonical structures, like the four stranded G-quadruplex (GQ). We studied the GQ-forming sequence (named HepB) found in the genome of the hepatitis B virus. Fluorescence-, infrared- and CD-spectroscopy were used. HepB shows a hybrid form in presence of K+, but Na+, Li+, and Rb+ induce parallel structure. Higher concentrations of metal ions increase the unfolding temperature, which was explained by a short thermodynamic calculation. Temperature stability of the GQ structure was determined for all these ions. Na+ has stronger stabilizing effect on HepB than K+, which is highly unusual. The transition temperatures were 56.6, 53.8, 58.5 and 54.4 °C for Na+, K+, Li+, and Rb+ respectively. Binding constants for Na+ and K+ were 10.2 mM and 7.1 mM respectively. Study of three ligands designed in cancer research for GQ targeting (TMPyP4, BRACO19 and PhenDC3) showed unequivocally their binding to HepB. Binding was proven by the increased stability of the bound form. The stabilization was higher than 20 °C for TMPyP4 and PhenDC3, while it was considerably lower for BRACO19. These results might have medical importance in the fight against the hepatitis B virus.

Identification and Affinity Determination of Protein-Antibody and Protein-Aptamer Epitopes by Biosensor-Mass Spectrometry Combination

Analytical methods for molecular characterization of diagnostic or therapeutic targets have recently gained high interest. This review summarizes the combination of mass spectrometry and surface plasmon resonance (SPR) biosensor analysis for identification and affinity determination of protein interactions with antibodies and DNA-aptamers. The binding constant (KD) of a protein–antibody complex is first determined by immobilizing an antibody or DNA-aptamer on an SPR chip. A proteolytic peptide mixture is then applied to the chip, and following removal of unbound material by washing, the epitope(s) peptide(s) are eluted and identified by MALDI-MS. The SPR-MS combination was applied to a wide range of affinity pairs. Distinct epitope peptides were identified for the cardiac biomarker myoglobin (MG) both from monoclonal and polyclonal antibodies, and binding constants determined for equine and human MG provided molecular assessment of cross immunoreactivities. Mass spectrometric epitope identifications were obtained for linear, as well as for assembled (“conformational”) antibody epitopes, e.g., for the polypeptide chemokine Interleukin-8. Immobilization using protein G substantially improved surface fixation and antibody stabilities for epitope identification and affinity determination. Moreover, epitopes were successfully determined for polyclonal antibodies from biological material, such as from patient antisera upon enzyme replacement therapy of lysosomal diseases. The SPR-MS combination was also successfully applied to identify linear and assembled epitopes for DNA–aptamer interaction complexes of the tumor diagnostic protein C-Met. In summary, the SPR-MS combination has been established as a powerful molecular tool for identification of protein interaction epitopes.

Rapid Screening and Estimation of Binding Constants for Interactions of Fe3+ with Two Metalloproteins, Apotransferrin and Transferrin, Using Affinity Mode of Capillary Electrophoresis

The interaction behavior of Fe3+ with transferrin and apotransferrin (iron-free form) was investigated in this study using affinity capillary electrophoresis. Change in the mass and charge of protein upon binding to the metal ion in the capillary tube led to variation in its migration time and was used to measure the noncovalent binding interactions by fast screening method. Acetanilide was used as the electroosmotic flow (EOF) marker to avoid possible errors due to the change in EOF during the experiment. The binding results were calculated from the mobility ratios of protein (Ri) and EOF marker (Rf) using the formula (Ri − Rf)/Rf or ∆R/Rf. For more comprehensive understanding, the kinetics of the interaction was studied and binding constants were calculated. Results showed that the Fe3+ displayed insignificant interaction with both proteins at lower metal ion concentrations (5–25 μmol/mL). However, transferrin exhibited significant interactions with the metal ion at 50 and 100 μmol/mL (ΔR/Rf = 0.0114 and 0.0201, resp.) concentrations and apotransferrin showed strong binding interactions (ΔR/Rf = −0.0254 and 0.0205, resp.) at relatively higher Fe3+ concentrations of 100 and 250 μmol/mL. The binding constants of 18.968 mmol−1 and −13.603 mmol−1 were recorded for Fe3+ interaction with transferrin and apotransferrin, respectively, showing significant interactions. Different binding patterns of Fe3+ with both proteins might be attributed to the fact that the iron-binding sites in transferrin have already been occupied, which was not the case in apotransferrin. The present study may be used as a reference for the investigation of protein-metal ion, drug-protein, drug-metal ion, and enzyme-metal ion interactions and may be helpful to provide preliminary insight into the new metal-based drug development.

Molecular Recognition by Pillar[5]arenes: Balance Between Hydrophobic and Electrostatic Interactions

The formation of inclusion complexes between alkylsulfonate guests and a cationic pillar[5]arene receptor in water was investigated by NMR and ITC techniques. The results show the formation of host-guest complexes stabilized by electrostatic interactions and hydrophobics effects with binding constants of up to 107 M-1 for the guest with higher hydrophobic character. Structurally, the alkyl chain of the guest is included in the hydrophobic aromatic cavity of the macrocycle while the sulfonate groups are hold in the multicationic portal by ionic interactions.