N-Glycosylation-Induced Pathologic Protein Conformations as a Tool to Guide the Selection of Biologically Active Small Molecules.

Post-translational modifications such as protein N-glycosylation, significantly influence cellular processes. Dysregulated N-glycosylation, exemplified in Grp94, a member of the Hsp90 family, leads to structural changes and the formation of epichaperomes, contributing to pathologies. Targeting N-glycosylation-induced conformations offers opportunities for developing selective chemical tools and drugs for these pathologic forms of chaperones. We here demonstrate how a specific Grp94 conformation induced by N-glycosylation, identified previously via molecular dynamics simulations, rationalizes the distinct behavior of similar ligands. Integrating dynamic ligand unbinding information with SAR development, we differentiate ligands productively engaging the pathologic Grp94 conformers from those that are not. Additionally, analyzing binding site stereoelectronic properties and QSAR models using cytotoxicity data unveils relationships between chemical, conformational properties, and biological activities. These findings facilitate the design of ligands targeting specific Grp94 conformations induced by abnormal glycosylation, selectively disrupting pathogenic protein networks while sparing normal mechanisms.

Experimental traumatic brain injury increases epichaperome formation.

Under normal conditions, heat shock proteins work in unison through dynamic protein interactions collectively referred to as the "chaperome." Recent work revealed that during cellular stress, the functional interactions of the chaperome are modified to form the "epichaperome," which results in improper protein folding, degradation, aggregation, and transport. This study is the first to investigate this novel mechanism of protein dishomeostasis in traumatic brain injury (TBI). Male and female adult, Sprague-Dawley rats received a lateral controlled cortical impact (CCI) and the ipsilateral hippocampus was collected 24 h 1, 2, and 4 weeks after injury. The epichaperome complex was visualized by measuring HSP90, HSC70 and HOP expression in native-PAGE and normalized to monomeric protein expression. A two-way ANOVA examined the effect of injury and sex at each time-point. Native HSP90, HSC70 and HOP protein expression showed a significant effect of injury effect across all time-points. Additionally, HSC70 and HOP showed significant sex effects at 24 h and 4 weeks. Altogether, controlled cortical impact significantly increased formation of the epichaperome across all proteins measured. Further investigation of this pathological mechanism can lead to a greater understanding of the link between TBI and increased risk of neurodegenerative disease and targeting the epichaperome for therapeutics.

General Expression for the Size-Dependent Optical Properties of Quantum Dots.

While initial theories on quantum confinement in colloidal quantum dots (QDs) led to analytical band gap/size relations or sizing functions, numerical methods describe size quantization more accurately. However, because of the lack of reliable sizing functions, researchers fit experimental band gap/size data sets using models with redundant, physically meaningless parameters that break down upon extrapolation. Here, we propose a new sizing function based on a proportional correction for nonparabolic bands. Using known bulk parameters, we predict size quantization for groups IV, III-V, II-VI, and IV-VI and metal-halide perovskite semiconductors, including straightforward adaptations for negative-gap semiconductors and nonspherical QDs. Refinement with respect to experimental data is possible using the Bohr diameter as a fitting parameter, by which we show a statistically relevant difference in the band gap/size relation for wurtzite and zinc blende CdSe. The general sizing function proposed here unifies the QD size calibration and enables researchers to assess bulk semiconductor parameters and predict the size quantization in unexplored materials.

The epichaperome is an integrated chaperome network that facilitates tumour survival.

Transient, multi-protein complexes are important facilitators of cellular functions. This includes the chaperome, an abundant protein family comprising chaperones, co-chaperones, adaptors, and folding enzymes-dynamic complexes of which regulate cellular homeostasis together with the protein degradation machinery. Numerous studies have addressed the role of chaperome members in isolation, yet little is known about their relationships regarding how they interact and function together in malignancy. As function is probably highly dependent on endogenous conditions found in native tumours, chaperomes have resisted investigation, mainly due to the limitations of methods needed to disrupt or engineer the cellular environment to facilitate analysis. Such limitations have led to a bottleneck in our understanding of chaperome-related disease biology and in the development of chaperome-targeted cancer treatment. Here we examined the chaperome complexes in a large set of tumour specimens. The methods used maintained the endogenous native state of tumours and we exploited this to investigate the molecular characteristics and composition of the chaperome in cancer, the molecular factors that drive chaperome networks to crosstalk in tumours, the distinguishing factors of the chaperome in tumours sensitive to pharmacologic inhibition, and the characteristics of tumours that may benefit from chaperome therapy. We find that under conditions of stress, such as malignant transformation fuelled by MYC, the chaperome becomes biochemically 'rewired' to form a network of stable, survival-facilitating, high-molecular-weight complexes. The chaperones heat shock protein 90 (HSP90) and heat shock cognate protein 70 (HSC70) are nucleating sites for these physically and functionally integrated complexes. The results indicate that these tightly integrated chaperome units, here termed the epichaperome, can function as a network to enhance cellular survival, irrespective of tissue of origin or genetic background. The epichaperome, present in over half of all cancers tested, has implications for diagnostics and also provides potential vulnerability as a target for drug intervention.

Single and Double Electron Spin-Flip Raman Scattering in CdSe Colloidal Nanoplatelets.

CdSe colloidal nanoplatelets are studied by spin-flip Raman scattering in magnetic fields up to 5 T. We find pronounced Raman lines shifted from the excitation laser energy by an electron Zeeman splitting. Their polarization selection rules correspond to those expected for scattering mediated by excitons interacting with resident electrons. Surprisingly, Raman signals shifted by twice the electron Zeeman splitting are also observed. The theoretical analysis and experimental dependences show that the mechanism responsible for the double flip involves two resident electrons interacting with a photoexcited exciton. Effects related to various orientations of the nanoplatelets in the ensemble and different orientations of the magnetic field are analyzed.

Chaperome heterogeneity and its implications for cancer study and treatment.

The chaperome is the collection of proteins in the cell that carry out molecular chaperoning functions. Changes in the interaction strength between chaperome proteins lead to an assembly that is functionally and structurally distinct from each constituent member. In this review, we discuss the epichaperome, the cellular network that forms when the chaperome components of distinct chaperome machineries come together as stable, functionally integrated, multimeric complexes. In tumors, maintenance of the epichaperome network is vital for tumor survival, rendering them vulnerable to therapeutic interventions that target critical epichaperome network components. We discuss how the epichaperome empowers an approach for precision medicine cancer trials where a new target, biomarker, and relevant drug candidates can be correlated and integrated. We introduce chemical biology methods to investigate the heterogeneity of the chaperome in a given cellular context. Lastly, we discuss how ligand-protein binding kinetics are more appropriate than equilibrium binding parameters to characterize and unravel chaperome targeting in cancer and to gauge the selectivity of ligands for specific tumor-associated chaperome pools.

Electron and Hole g-Factors and Spin Dynamics of Negatively Charged Excitons in CdSe/CdS Colloidal Nanoplatelets with Thick Shells.

We address spin properties and spin dynamics of carriers and charged excitons in CdSe/CdS colloidal nanoplatelets with thick shells. Magneto-optical studies are performed by time-resolved and polarization-resolved photoluminescence, spin-flip Raman scattering and picosecond pump-probe Faraday rotation in magnetic fields up to 30 T. We show that at low temperatures the nanoplatelets are negatively charged so that their photoluminescence is dominated by radiative recombination of negatively charged excitons (trions). Electron g-factor of 1.68 is measured, and heavy-hole g-factor varying with increasing magnetic field from -0.4 to -0.7 is evaluated. Hole g-factors for two-dimensional structures are calculated for various hole confining potentials for cubic- and wurtzite lattice in CdSe core. These calculations are extended for various quantum dots and nanoplatelets based on II-VI semiconductors. We developed a magneto-optical technique for the quantitative evaluation of the nanoplatelets orientation in ensemble.

Dynamic Evolution from Negative to Positive Photocharging in Colloidal CdS Quantum Dots.

The optical properties of colloidal semiconductor nanocrystals are largely influenced by the trapping of charge carriers on the nanocrystal surface. Different concentrations of electron and hole traps and different rates of their capture to the traps provide dynamical charging of otherwise neutral nanocrystals. We study the photocharging formation and evolution dynamics in CdS colloidal quantum dots with native oleic acid surface ligands. A time-resolved technique with three laser pulses (pump, orientation, and probe) is developed to monitor the photocharging dynamics with picosecond resolution on wide time scales ranging from picoseconds to milliseconds. The detection is based on measuring the coherent spin dynamics of electrons, allowing us to distinguish the type of carrier in the QD core (electron or hole). We find that although initially negative photocharging happens because of fast hole trapping, it eventually evolves to positive photocharging due to electron trapping and hole detrapping. The positive photocharging lasts up to hundreds of microseconds at room temperature. These findings give insight into the photocharging process and provide valuable information for understanding the mechanisms responsible for the emission blinking in colloidal nanostructures.

Biexciton Auger Recombination in CdSe/CdS Core/Shell Semiconductor Nanocrystals.

A theoretical study of the positive and negative trion channels in the nonradiative Auger recombination of band-edge biexcitons (BXs) in CdSe/CdS core/shell nanocrystals (NCs) is presented. The theory takes into account the BX fine-structure produced by NC asymmetry and hole-hole exchange interaction. The calculations show that growth of CdS shell upon CdSe core suppresses the rate of the Auger recombination via negative trion channel, while the more efficient Auger recombination via positive trion channel shows much weaker dependence on the shell thickness. The demonstrated oscillatory dependence of the BX Auger rate on the core and shell sizes is explained qualitatively in terms of overlap of the ground and excited carrier wave functions. The calculations show that raise of temperature accelerates the Auger recombination in CdSe/CdS NCs due to reduction of the bulk energy gaps of CdSe and CdS.

Magnetic Properties of Nonmagnetic Nanostructures: Dangling Bond Magnetic Polaron in CdSe Nanocrystals.

We predict theoretically that nonmagnetic CdSe nanocrystals may possess macroscopic magnetic moments due to the formation of dangling-bond magnetic polarons (DBMPs). A DBMP is created in optically pumped nanocrystals by dynamic polarization of dangling bond spins (DBSs) at the nanocrystal surface during radiative recombination of the ground state "dark" exciton assisted by a spin-flip of the DBS. The formation of DBMPs suppresses the radiative recombination of the dark exciton and leads to a temperature-dependent contribution to the Stokes shift of the photoluminescence. This model consistently explains the experimentally observed low-temperature photoluminescence features of nonmagnetic CdSe nanocrystals as manifestations of their spin-related magnetic properties.

Nonradiative Auger recombination in semiconductor nanocrystals.

We calculate the rate of nonradiative Auger recombination in negatively charged CdSe nanocrystals (NCs). The rate is nonmonotonic, strongly oscillating with NC size, and sensitive to the NC surface. The oscillations result in nonexponential decay of carriers in NC ensembles. Using a standard single-exponential approximation of the decay dynamics, we determine the apparent size dependence of the Auger rate in an ensemble and derive CdSe surface parameters consistent with the experimental dependence on size.

Targeting the Hsp90-associated viral oncoproteome in gammaherpesvirus-associated malignancies.

PU-H71 is a purine-scaffold Hsp90 inhibitor that, in contrast to other Hsp90 inhibitors, displays unique selectivity for binding the fraction of Hsp90 that is preferentially associated with oncogenic client proteins and enriched in tumor cells (teHsp90). This property allows PU-H71 to potently suppress teHsp90 without inducing toxicity in normal cells. We found that lymphoma cells infected by Epstein-Barr virus or Kaposi sarcoma-associated herpes virus (KSHV) are exquisitely sensitive to this compound. Using PU-H71 affinity capture and proteomics, an unbiased approach to reveal oncogenic networks, we identified the teHsp90 interactome in KSHV(+) primary effusion lymphoma cells. Viral and cellular proteins were identified, including many involved in nuclear factor (NF)-κB signaling, apoptosis, and autophagy. KSHV vFLIP is a viral oncoprotein homologous to cFLIPs, with NF-κB-activating and antiapoptotic activities. We show that teHsp90 binds vFLIP but not cFLIPs. Treatment with PU-H71 induced degradation of vFLIP and IKKγ, NF-κB downregulation, apoptosis and autophagy in vitro, and more importantly, tumor responses in mice. Analysis of the interactome revealed apoptosis as a central pathway; therefore, we tested a BCL2 family inhibitor in primary effusion lymphoma cells. We found strong activity and synergy with PU-H71. Our findings demonstrate PU-H71 affinity capture identifies actionable networks that may help design rational combinations of effective therapies.

Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators.

Although androgen receptor (AR)-mediated signaling is central to prostate cancer, the ability to modulate AR signaling states is limited. Here we establish a chemical genomic approach for discovery and target prediction of modulators of cancer phenotypes, as exemplified by AR signaling. We first identify AR activation inhibitors, including a group of structurally related compounds comprising celastrol, gedunin, and derivatives. To develop an in silico approach for target pathway identification, we apply a gene expression-based analysis that classifies HSP90 inhibitors as having similar activity to celastrol and gedunin. Validating this prediction, we demonstrate that celastrol and gedunin inhibit HSP90 activity and HSP90 clients, including AR. Broadly, this work identifies new modes of HSP90 modulation through a gene expression-based strategy.

Synthesis and Characterization of Click Chemical Probes for Single-Cell Resolution Detection of Epichaperomes in Neurodegenerative Disorders.

Neurodegenerative disorders, including Alzheimer's disease (AD) and Parkinson's disease (PD), represent debilitating conditions with complex, poorly understood pathologies. Epichaperomes, pathologic protein assemblies nucleated on key chaperones, have emerged as critical players in the molecular dysfunction underlying these disorders. In this study, we introduce the synthesis and characterization of clickable epichaperome probes, PU-TCO, positive control, and PU-NTCO, negative control. Through comprehensive in vitro assays and cell-based investigations, we establish the specificity of the PU-TCO probe for epichaperomes. Furthermore, we demonstrate the efficacy of PU-TCO in detecting epichaperomes in brain tissue with a cellular resolution, underscoring its potential as a valuable tool for dissecting single-cell responses in neurodegenerative diseases. This clickable probe is therefore poised to address a critical need in the field, offering unprecedented precision and versatility in studying epichaperomes and opening avenues for novel insights into their role in disease pathology.

Phosphorylation-Driven Epichaperome Assembly: A Critical Regulator of Cellular Adaptability and Proliferation.

The intricate protein-chaperone network is vital for cellular function. Recent discoveries have unveiled the existence of specialized chaperone complexes called epichaperomes, protein assemblies orchestrating the reconfiguration of protein-protein interaction networks, enhancing cellular adaptability and proliferation. This study delves into the structural and regulatory aspects of epichaperomes, with a particular emphasis on the significance of post-translational modifications in shaping their formation and function. A central finding of this investigation is the identification of specific PTMs on HSP90, particularly at residues Ser226 and Ser255 situated within an intrinsically disordered region, as critical determinants in epichaperome assembly. Our data demonstrate that the phosphorylation of these serine residues enhances HSP90's interaction with other chaperones and co-chaperones, creating a microenvironment conducive to epichaperome formation. Furthermore, this study establishes a direct link between epichaperome function and cellular physiology, especially in contexts where robust proliferation and adaptive behavior are essential, such as cancer and stem cell maintenance. These findings not only provide mechanistic insights but also hold promise for the development of novel therapeutic strategies targeting chaperone complexes in diseases characterized by epichaperome dysregulation, bridging the gap between fundamental research and precision medicine.

Phosphorylation-driven epichaperome assembly is a regulator of cellular adaptability and proliferation.

The intricate network of protein-chaperone interactions is crucial for maintaining cellular function. Recent discoveries have unveiled the existence of specialized chaperone assemblies, known as epichaperomes, which serve as scaffolding platforms that orchestrate the reconfiguration of protein-protein interaction networks, thereby enhancing cellular adaptability and proliferation. This study explores the structural and regulatory aspects of epichaperomes, with a particular focus on the role of post-translational modifications (PTMs) in their formation and function. A key finding is the identification of specific PTMs on HSP90, particularly at residues Ser226 and Ser255 within an intrinsically disordered region, as critical determinants of epichaperome assembly. Our data demonstrate that phosphorylation of these serine residues enhances HSP90's interactions with other chaperones and co-chaperones, creating a microenvironment conducive to epichaperome formation. Moreover, we establish a direct link between epichaperome function and cellular physiology, particularly in contexts where robust proliferation and adaptive behavior are essential, such as in cancer and pluripotent stem cell maintenance. These findings not only provide mechanistic insights but also hold promise for the development of novel therapeutic strategies targeting chaperone assemblies in diseases characterized by epichaperome dysregulation, thereby bridging the gap between fundamental research and precision medicine.

Affinity-based proteomics reveal cancer-specific networks coordinated by Hsp90.

Most cancers are characterized by multiple molecular alterations, but identification of the key proteins involved in these signaling pathways is currently beyond reach. We show that the inhibitor PU-H71 preferentially targets tumor-enriched Hsp90 complexes and affinity captures Hsp90-dependent oncogenic client proteins. We have used PU-H71 affinity capture to design a proteomic approach that, when combined with bioinformatic pathway analysis, identifies dysregulated signaling networks and key oncoproteins in chronic myeloid leukemia. The identified interactome overlaps with the well-characterized altered proteome in this cancer, indicating that this method can provide global insights into the biology of individual tumors, including primary patient specimens. In addition, we show that this approach can be used to identify previously uncharacterized oncoproteins and mechanisms, potentially leading to new targeted therapies. We further show that the abundance of the PU-H71-enriched Hsp90 species, which is not dictated by Hsp90 expression alone, is predictive of the cell's sensitivity to Hsp90 inhibition.

Synthesis and evaluation of cell-permeable biotinylated PU-H71 derivatives as tumor Hsp90 probes.

The attachment of biotin to a small molecule provides a powerful tool in biology. Here, we present a systematic approach to identify biotinylated analogues of the Hsp90 inhibitor PU-H71 that are capable of permeating cell membranes so as to enable the investigation of Hsp90 complexes in live cells. The identified derivative 2g can isolate Hsp90 through affinity purification and, as we show, represents a unique and useful tool to probe tumor Hsp90 biology in live cells by affinity capture, flow cytometry and confocal microscopy. To our knowledge, 2g is the only reported biotinylated Hsp90 probe to have such combined characteristics.

Use of Native-PAGE for the Identification of Epichaperomes in Cell Lines.

Epichaperomes are disease-associated pathologic scaffolds, composed of tightly bound chaperones, co-chaperones, and other factors. They mediate anomalous protein-protein interactions inside cells, which aberrantly affects the function of protein networks, and in turn, cellular phenotypes. Epichaperome study necessitates the implementation of methods that retain these protein complexes in their native cellular states for analysis. Here we describe a protocol for detection and composition analysis of epichaperomes in cell homogenates through native polyacrylamide gel electrophoresis.

Coherent Spin Dynamics of Electrons in CdSe Colloidal Nanoplatelets.

Coherent spin dynamics of electrons in CdSe colloidal nanoplatelets are investigated by time-resolved pump-probe Faraday rotation at room and cryogenic temperatures. We measure electron spin precession in a magnetic field and determine g-factors of 1.83 and 1.72 at low temperatures for nanoplatelets with a thickness of 3 and 4 monolayers, respectively. The dephasing time of spin precession T2* amounts to a few nanoseconds and has a weak dependence on temperature, while the longitudinal spin relaxation time T1 exceeds 10 ns even at room temperature. Observations of single and double electron spin-flips confirm that the nanoplatelets are negatively charged. The spin-flip Raman scattering technique reveals g-factor anisotropy by up to 10% in nanoplatelets with thicknesses of 3, 4, and 5 monolayers. In the ensemble with a random orientation of nanoplatelets, our theoretical analysis shows that the measured Larmor precession frequency corresponds to the in-plane electron g-factor. We conclude that the experimentally observed electron spin dephasing and its acceleration in the magnetic field are not provided by the electron g-factor anisotropy and can be related to the localization of the resident electrons and fluctuations of the localization potential.