Ion Mobility Mass Spectrometry Measures the Conformational Landscape of p27 and its Domains and how this is Modulated upon Interaction with Cdk2/cyclin A

Intrinsically disordered proteins have been reported to undergo disorder‐to‐order transitions upon binding to their partners in the cell. The extent of the ordering upon binding and the lack of order prior to binding is difficult to visualize with classical structure determination methods. Binding of p27 to the Cdk2/cyclin A complex is accompanied by partial folding of p27 in the KID domain, with the retention of dynamic behavior for function, particularly in the C‐terminal half of the protein. Herein, native ion mobility mass spectrometry (IM‐MS) is employed to measure the intrinsic dynamic properties of p27, both in isolation and within the trimeric complex with Cdk2/cyclin A. The trimeric Cdk2/cyclin A/p27‐KID complex possesses significant structural heterogeneity compared to Cdk2/cyclin A. These findings support the formation of a fuzzy complex in which both the N‐ and C‐termini of p27 interact with Cdk2/cyclin A in multiple, closely associated states.     

Native Top‐Down Mass Spectrometry of TAR RNA in Complexes with a Wild‐Type tat Peptide for Binding Site Mapping

Ribonucleic acids (RNA) frequently associate with proteins in many biological processes to form more or less stable complex structures. The characterization of RNA–protein complex structures and binding interfaces by nuclear magnetic resonance (NMR) spectroscopy, X‐ray crystallography, or strategies based on chemical crosslinking, however, can be quite challenging. Herein, we have explored the use of an alternative method, native top‐down mass spectrometry (MS), for probing of complex stoichiometry and protein binding sites at the single‐residue level of RNA. Our data show that the electrostatic interactions between HIV‐1 TAR RNA and a peptide comprising the arginine‐rich binding region of tat protein are sufficiently strong in the gas phase to survive phosphodiester backbone cleavage of RNA by collisionally activated dissociation (CAD), thus allowing its use for probing tat binding sites in TAR RNA by top‐down MS. Moreover, the MS data reveal time‐dependent 1:2 and 1:1 stoichiometries of the TAR–tat complexes and suggest structural rearrangements of TAR RNA induced by binding of tat peptide.     

Dual‐Targeting Nanovesicles for In Situ Intracellular Imaging of and Discrimination between Wild‐type and Mutant p53

p53 is a tumor‐suppressor protein related to the cell cycle and programmed cell apoptosis. Herein, dual‐targeting nanovesicles are designed for in situ imaging of intracellular wild‐type p53 (WTp53) and mutant p53 (MUp53). Nanovesicle‐encapsulated plasmonic gold nanoparticles (AuNPs) were functionalized with consensus DNA duplexes, and a fluorescein isothiocyanate (FITC)‐marked anti‐MUp53 antibody was conjugated to the nanovesicle surface. After entering the cytoplasm, the released AuNPs aggregated through recognition of WTp53 and the double‐stranded DNA. The color changes of AuNPs were observed using dark‐field microscopy, which showed the intracellular WTp53 distribution. The MUp53 location was detected though the immunological recognition between FITC‐labeled anti‐MUp53 and MUp53. Thus, a one‐step incubation method for the in situ imaging of intracellular WTp53 and MUp53 was obtained; this was used to monitor the p53 level under a drug treatment.     

Electrochemical Determination of the p53 Tumor Suppressor Gene Using a Gold Nanoparticle-Graphene Nanocomposite Modified Glassy Carbon Electrode

A novel sensitive and simple electrochemical DNA sensor is reported for the determination of p53 tumor suppressor gene. A gold nanoparticle/graphene nanocomposite-modified glassy carbon electrode was prepared and methylene blue was used as the hybridization redox indicator. Scanning electron microscopic and electrochemical characterization demonstrated that the gold nanoparticles and graphene were present on the electrode. The resulting sensor provided suitable electrochemical response to the p53 tumor suppressor gene with a linear dynamic range from 0.1 to 1000?nM. The limit of detection was 0.012?nM. The sensor was able to differentiate a complete complementary DNA sequence, single-base mismatched DNA sequence, and a three-base mismatched DNA sequence. The precision of the device was satisfactory, with a relative standard deviation of 4.1% for 11 measurements. The combination of gold nanoparticles and a graphene nanocomposite provided enhanced capabilities for the determination of DNA for clinical applications.     

An Activatable NIR Fluorescent Probe for NAD(P)H and Its Application to the Real-Time Monitoring of p53 Abnormalities In Vivo

NAD(P)H is crucial for biosynthetic reactions and antioxidant functions. However, the current probes developed for detecting NAD(P)H in vivo require intratumoral injection, which limited their application for animal imaging. To address this issue, we have developed a liposoluble cationic probe, KC8 , which exhibits excellent tumor-targeting ability and near-infrared (NIR) fluorescence after reaction with NAD(P)H. By using KC8 , it was demonstrated for the first time that the level of NAD(P)H in the mitochondria of living colorectal cancer (CRC) cells was highly related to the abnormality of the p53. Furthermore, KC8 was successfully used to differentiate not only between tumor and normal tissue but also between tumors with p53 abnormality and normal tumors when administered intravenously. Finally, we evaluated tumor heterogeneity through two fluorescent channels after treating a tumor with 5-Fu. This study provides a new tool for real-time monitoring of the p53 abnormality of CRC cells.     

Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling

The C‐terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non‐neutralized. Because of the flexibility of the unbound CTD, a free‐energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational sampling of CTD in the unbound state via virtual system coupled multicanonical molecular dynamics, in which the lysine was acetylated or nonacetylated and histidine was charged or neutralized. The fragments were expressed by an all‐atom model and were immersed in an explicit solvent. The acetylation and charge‐neutralization varied FEL greatly, which might be convenient to exert a hub property. The acetylation slightly enhanced alpha‐helix structures that are more compact than sheet/loop conformations. The charge‐neutralization produced hairpins. Additionally, circular dichroism experiments confirmed the computational results. We propose possible binding mechanisms of CTD to partners by investigating FEL. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Unveiling the “Three‐Finger Pharmacophore” Required for p53–MDM2 Inhibition by Saturation‐Transfer Difference (STD) NMR Initial Growth‐Rates Approach

Inhibitors of the p53‐MDM2 protein–protein interaction are emerging as a new and validated approach to treating cancer. Herein, we describe the synthesis and inhibitory evaluation of a series of isoquinolin‐1‐one analogues, and highlight the utility of an initial growth‐rates saturation‐transfer difference (STD) NMR approach supported by protein–ligand docking to investigate p53‐MDM2 inhibition. The approach is illustrated by the study of compound 1 , providing key insights into the binding mode of this kind of MDM2 ligands and, more importantly, readily unveiling the previously proposed three‐finger pharmacophore requirement for p53‐MDM2 inhibition.     

Nondenaturing polyacrylamide gel electrophoresis to study the dissociation of the p53·MDM2/X complex by potentially anticancer compounds

A new analytical method to study the dissociation of the complexes between the oncosuppressor p53 and its negative modulators murine double‐minute protein 2 (MDM2) or MDMX, is proposed. This technique is reliable to determine the dissociative power exerted by small molecules on the complex taking advantage of the appearance of migrating MDM2 or MDMX in a native polyacrylamide gel, when inhibitors are added to the complex mixture. Therefore, we propose this new approach to easily screen library of compounds, with potential pharmacological anticancer activity.     

Metal‐Directed Self‐Assembly of a Polyoxometalate‐Based Molecular Triangle: Using Powerful Analytical Tools to Probe the Chemical Structure of Complex Supramolecular Assemblies

A polyoxometalate‐based molecular triangle has been synthesized through the metal‐driven self‐assembly of covalent organic/inorganic hybrid oxo‐clusters with remote pyridyl binding sites. The new metallomacrocycle was unambiguously characterized by using a combination of ¹H NMR spectroscopy, 2D diffusion NMR spectroscopy (DOSY), electrospray ionization travelling wave ion mobility mass spectrometry (ESI‐TWIM‐MS), small‐angle X‐ray scattering (SAXS) and molecular modelling. The collision cross‐sections obtained from TWIM‐MS and the hydrodynamic radii derived from DOSY are in good agreement with the geometry‐optimized structures obtained by using theoretical calculations. Furthermore, SAXS was successfully employed and proved to be a powerful technique for characterizing such large supramolecular assemblies.