Doxorubicin catalyses self-assembly of p53 by phase separation.

Liquid-liquid phase separation plays a crucial role in cellular physiology, as it leads to the formation of membrane-less organelles in response to various internal stimuli, contributing to various cellular functions. However, the influence of exogenous stimuli on this process in the context of disease intervention remains unexplored. In this current investigation, we explore the impact of doxorubicin on the abnormal self-assembly of p53 using a combination of biophysical and imaging techniques. Additionally, we shed light on the potential mechanisms behind chemoresistance in cancer cells carrying mutant p53. Our findings reveal that doxorubicin co-localizes with both wild-type p53 (WTp53) and its mutant variants. Our in vitro experiments indicate that doxorubicin interacts with the N-terminal-deleted form of WTp53 (WTp53ΔNterm), inducing liquid-liquid phase separation, ultimately leading to protein aggregation. Notably, the p53 variants at the R273 position exhibit a propensity for phase separation even in the absence of doxorubicin, highlighting the destabilizing effects of point mutations at this position. The strong interaction between doxorubicin and p53 variants, along with its localization within the protein condensates, provides a potential explanation for the development of chemotherapy resistance. Collectively, our cellular and in vitro studies emphasize the role of exogenous agents in driving phase separation-mediated p53 aggregation.

A single shell protein plays a major role in choline transport across the shell of the choline utilization microcompartment of Escherichia coli 536.

Bacterial microcompartments (MCPs) are widespread protein-based organelles that play important roles in the global carbon cycle and in the physiology of diverse bacteria, including a number of pathogens. MCPs consist of metabolic enzymes encapsulated within a protein shell. The main roles of MCPs are to concentrate enzymes together with their substrates (to increase reaction rates) and to sequester harmful metabolic intermediates. Prior studies indicate that MCPs have a selectively permeable protein shell, but the mechanisms that allow selective transport across the shell are not fully understood. Here we examine transport across the shell of the choline utilization (Cut) MCP of Escherichia coli 536, which has not been studied before. The shell of the Cut MCP is unusual in consisting of one pentameric and four hexameric bacterial microcompartment (BMC) domain proteins. It lacks trimeric shell proteins, which are thought to be required for the transport of larger substrates and enzymatic cofactors. In addition, its four hexameric BMC domain proteins are very similar in amino acid sequence. This raises questions about how the Cut MCP mediates the selective transport of the substrate, products and cofactors of choline metabolism. In this report, site-directed mutagenesis is used to modify the central pores (the main transport channels) of all four Cut BMC hexamers to assess their transport roles. Our findings indicate that a single shell protein, CmcB, plays the major role in choline transport across the shell of the Cut MCP and that the electrostatic properties of the CmcB pore also impact choline transport. The implications of these findings with regard to the higher-order structure of MCPs are discussed.

Innate and engineered attributes of bacterial microcompartments for applications in bio-materials science.

Bacterial microcompartments (BMCs) are sophisticated all-protein bionanoreactors widely spread in bacterial phyla. BMCs facilitate diverse metabolic reactions, which assist bacterial survivability in normal (by fixing carbon dioxide) and energy dearth conditions. The past seven decades have uncovered numerous intrinsic features of BMCs, which have attracted researchers to tailor them for customised applications, including synthetic nanoreactors, scaffold nano-materials for catalysis or electron conduction, and delivery vehicles for drug molecules or RNA/DNA. In addition, BMCs provide a competitive advantage to pathogenic bacteria and this can pave a new path for antimicrobial drug design. In this review, we discuss different structural and functional aspects of BMCs. We also highlight the potential employment of BMCs for novel applications in bio-material science.

Self-assembly of shell protein and native enzyme in a crowded environment leads to catalytically active phase condensates.

The self-assembly of bacterial microcompartments is the result of several genetic, biochemical, and physical stimuli orchestrating inside the bacterial cell. In this work, we use 1,2-propanediol utilization microcompartments as a paradigm to identify the factors that physically drive the self-assembly of MCP proteins in vitro using its major shell protein and major encapsulated enzyme. We find that a major shell protein PduBB' tends to self-assemble under macromolecular crowded environment and suitable ionic strength. Microscopic visualization and biophysical studies reveal phase separation to be the principle mechanism behind the self-association of shell protein in the presence of salts and macromolecular crowding. The shell protein PduBB' interacts with the enzyme diol-dehydratase PduCDE and co-assemble into phase separated liquid droplets. The co-assembly of PduCDE and PduBB' results in the enhancement of catalytic activity of the enzyme. The shell proteins that make up PduBB' (PduB and PduB') have contrasting self-assembly behavior. While N-terminal truncated PduB' has a high self-associating property and forms solid assemblies that separates out of solution, the longer component of the shell protein PduBM38L is more soluble and shows least tendency to undergo phase separation. A combination of spectroscopic, imaging and biochemical techniques shows the relevance of divalent cation Mg2+ in providing stability to intact PduMCP. Together our results suggest a combination of protein-protein interactions and phase separation guiding the self-assembly of Pdu shell protein and enzyme in the solution phase.

Disordered regions endow structural flexibility to shell proteins and function towards shell-enzyme interactions in 1,2-propanediol utilization microcompartment.

Intrinsically disordered regions in proteins have been functionally linked to the protein-protein interactions and genesis of several membraneless organelles. Depending on their residual makeup, hydrophobicity or charge distribution they may remain in extended form or may assume certain conformations upon biding to a partner protein or peptide. The present work investigates the distribution and potential roles of disordered regions in the integral proteins of 1,2-propanediol utilization microcompartments. We use bioinformatics tools to identify the probable disordered regions in the shell proteins and enzyme of the 1,2-propanediol utilization microcompartment. Using a combination of computational modelling and biochemical techniques we elucidate the role of disordered terminal regions of a major shell protein and enzyme. Our findings throw light on the importance of disordered regions in the self-assembly, providing flexibility to shell protein and mediating its interaction with a native enzyme.Communicated by Ramaswamy H. Sarma.

Barrier-free liquid condensates of nanocatalysts as effective concentrators of catalysis.

Traditional methods of molecular confinement have physicochemical barriers that restrict the free passage of substrates/products. Here, we explored liquid-liquid phase separation as a method to restrain protein-metal nanocomposites within barrier-free condensates. Confinement within liquid droplets was independent of the protein's native conformation and amplified the catalytic efficiency of metal nanocatalysts by one order of magnitude.

Light-controlled shape-changing azomacrocycles exhibiting reversible modulation of pyrene fluorescence emission.

We report the design, synthesis, and study of light-induced shape-changing azomacrocycles. These systems have been incorporated with azobenzene photoswitches using alkoxy tethers and triazole units to afford flexibility and binding. We envision that such azomacrocycles are capable of reversibly binding with the guest molecule. Remarkably, we have demonstrated fully light-controlled fluorescence quenching and enhancement in the monomeric emission of pyrene (guest). Such modulations have been achieved by the photoisomerization of the azomacrocycle and, in turn, host-guest interactions. Also, the azomacrocycles tend to aggregate and can also be controlled by light or heat. We uncovered such phenomena using spectroscopic, microscopic, and isothermal titration calorimetry (ITC) studies and computations.

A Major Shell Protein of 1,2-Propanediol Utilization Microcompartment Conserves the Activity of Its Signature Enzyme at Higher Temperatures.

A classic example of an all-protein natural nano-bioreactor, the bacterial microcompartment is a prokaryotic organelle that confines enzymes in a small volume enveloped by an outer protein shell. These protein compartments metabolize specific organic molecules, allowing bacteria to survive in restricted nutrient environments. In this work, 1,2-propanediol utilization microcompartment (PduMCP) was used as a model to study the effect of molecular confinement on the stability and catalytic activity of native enzymes in the microcompartment. A combination of enzyme assays, spectroscopic techniques, binding assays, and computational analysis were used to evaluate the impact of the major shell protein PduBB' on the stability and activity of PduMCP's signature enzyme, dioldehydratase PduCDE. While free PduCDE shows ∼45 % reduction in its optimum activity (activity at 37 °C) when exposed to a temperature of 45 °C, it retains similar activity up to 50 °C when encapsulated within PduMCP. PduBB', a major component of the outer shell of PduMCP, preserves the catalytic efficiency of PduCDE under thermal stress and prevents temperature-induced unfolding and aggregation of PduCDE in vitro. We observed that while both PduB and PduB' interact with the enzyme with micromolar affinity, only the PduBB' combination influences its activity and stability, highlighting the importance of the unique PduBB' combination in the functioning of PduMCP.

Doxorubicin induced aggregation of α-synuclein: Insights into the mechanism of drug induced Parkinsonism.

The aggregation of α-synuclein is a prominent feature of Parkinson's disease. It is induced by factors such as genetic mutations and presence of metal salts leading to Parkinson's like symptoms. Existing case studies show that patients undergoing cancer chemotherapeutics are also prone to developing Parkinson's like symptoms. However, the underlying cause behind onset of these symptoms is not understood. It is not clear whether the administration of chemotherapeutic drugs alter the structural stability of α-synuclein. In the present study, we address this question by looking into the effect of chemotherapeutic drug namely doxorubicin on the α-synuclein stability. Using complementary spectroscopic, molecular docking and imaging techniques, we observe that doxorubicin interacted with central aggregation prone region of α-synuclein and induces destabilization leading to aggregation. We also show that the combination of doxorubicin and L-DOPA drugs impedes the α-synuclein aggregation. This may explain the reason behind the effectiveness of using L-DOPA against Parkinson's like symptoms.

Varying protein architectures in 3-dimensions for scaffolding and modulating properties of catalytic gold nanoparticles.

Fabrication and development of nanoscale materials with tunable structural and functional properties require a dynamic arrangement of nanoparticles on architectural templates. The function of nanoparticles not only depends on the property of the nanoparticles but also on their spatial orientations. Proteins with self-assembling properties which can be genetically engineered to varying architectural designs for scaffolds can be used to develop different orientations of nanoparticles in three dimensions. Here, we report the use of naturally self-assembling bacterial micro-compartment shell protein (PduA) assemblies in 2D and its single-point mutant variant (PduA[K26A]) in 3D architectures for the reduction and fabrication of gold nanoparticles. Interestingly, the different spatial organization of gold nanoparticles resulted in a smaller size in the 3D architect scaffold. Here, we observed a two-fold increase in catalytic activity and six-fold higher affinity toward TMB (3,3',5,5'-tetramethylbenzidine) substrate as a measure of higher peroxidase activity (nanozymatic) in the case of PduA[K26A] 3D scaffold. This approach demonstrates that the hierarchical organization of scaffold enables the fine-tuning of nanoparticle properties, thus paving the way toward the design of new nanoscale materials.

Biophysical approaches to understand and re-purpose bacterial microcompartments.

Bacterial microcompartments represent a modular class of prokaryotic organelles associated with metabolic processes. They harbor a congregation of enzymes that work in cascade within a small, confined volume. These sophisticated nano-engineered crafts of nature offer a tempting paradigm for the fabrication of biosynthetic nanoreactors. Repurposing bacterial microcompartments to develop nanostructures with desired functions requires a careful manipulation in their structural makeup and composition. This calls for a comprehensive understanding of all the interactions of the physical components which frame such molecular architectures. Over recent years, several biophysical techniques have been essential in illuminating the role played by bacterial microcompartments within cells, and have revealed crucial details regarding the morphology, physical properties and functions of their constituent proteins. This has promoted contemplation of ideas for engineering microcompartments inspired biomaterials with novel features and functions.

Factors deciding the assembly and thermostability of the DmrB cage.

Dihydromethanopterin reductase (DmrB), is a naturally occurring cage protein found in various archaeal and a few bacterial species. It exists as 24mer with cubic geometry where 8 trimeric subunits are present at the corners of each cube. Each trimer is made up of three monomeric units and six FMN, where two molecules of FMN are present at the interface of each monomer. DmrB is involved in the conversion of dihydromethanopterin to tetrahydromethanopterin using FMN as a redox equivalent. In the present study, we have used spectroscopic and biochemical techniques along with complementary bio-informatic work to understand the assembly principles of the DmrB. Our results show a concentration dependant self-assembly of DmrB which is mediated by ionic interactions. The co-factor FMN stabilizes and preserves the secondary and quaternary structure of DmrB against thermal insult, indicating that the higher order assembly of DmrB is very thermostable. Our work provides an interesting piece of information regarding the role of the co-factors in the thermostability of these classes of cage proteins. The understanding of the assembly and disassembly of this thermostable cage would enable the downstream usage of this system in various nano-biotechnological applications.

Protein morphology drives the structure and catalytic activity of bio-inorganic hybrids.

Bio-hybrid materials have received a lot of attention in view of their bio-mimicking nature. One such biomimetic material with catalytic activity are the protein derived floral nanohybrid. Copper phosphate coordinated flakes can be curated to distinct floral morphology using proteins. Structurally two different proteins with similar size and with no known enzymatic activity are used to evaluate the role of protein structure and morphology, on the structure-activity relationship of the developed hybrid nanoflowers. Globular protein BSA and bacterial microcompartment domain protein PduBB' are selected. PduBB' because of self-assembling nature forms extended sheets, whereas BSA lacks specific assembly. The developed hybrid NFs differ in their morphology and also in their mimicry as a biological catalyst. The present investigation highlights the importance of the quaternary structure of proteins in tailoring the structure and function of the h-NFs. The results in this manuscript will motivate and guide designing, engineering and selection of glue material for fabricating biomacromolecule derived biohybrid material to mimic natural enzymes of potential industrial application.

Probe into a multi-protein prokaryotic organelle using thermal scanning assay reveals distinct properties of the core and the shell.

BACKGROUND: Bacterial microcompartments represent the only reported category of prokaryotic organelles that are capable of functioning as independent bioreactors. In this organelle, a biochemical pathway with all the enzyme machinery is encapsulated within an all protein shell. The shell proteins and the enzymes have distinct structural features. It is hypothesized that flat shell proteins align sideways to form extended sheets and, the globular enzymes fill up the central core of the organelle. METHODS: Using differential scanning fluorimetry, we explored the structure and functional alteration of Pdu BMC, involving tertiary or quaternary structures. RESULTS: Our findings exhibit that these intact BMCs as a whole behave similar to a globular protein with a rich hydrophobic core, which is exposed upon thermal insult. The encapsulated enzymes itself have a strong hydrophobic core, which is in line with the hydrophobic-collapse model of protein folding. The shell proteins, on the other hand, do not have a strong hydrophobic core and show a significant portion of exposed hydrophobic patches. CONCLUSION: We show for the first time the thermal unfolding profile of the BMC domain proteins and the unique exposure of hydrophobic patches in them might be required for anchoring the enzymes leading to better packaging of the micro-compartments. GENERAL SIGNIFICANCE: These observations indicate that the genesis of these unique bacterial organelles is driven by the hydrophobic interactions between the shell and the enzymes. Insights from this work will aid in the genetic and biochemical engineering of thermostable efficient enzymatic biomaterials.

Variable Mutations at the p53-R273 Oncogenic Hotspot Position Leads to Altered Properties.

Mutations in p53 protein, especially in the DNA-binding domain, is one of the major hallmarks of cancer. The R273 position is a DNA-contact position and has several oncogenic variants. Surprisingly, cancer patients carrying different mutant variants of R273 in p53 have different survival rates, indicating that the DNA-contact inhibition may not be the sole reason for reduced survival with R273 variants. Here, we probed the properties of three major oncogenic variants of the wild-type (WT) p53: [R273H]p53, [R273C]p53, and [R273L]p53. Using a series of biophysical, biochemical, and theoretical simulation studies, we observe that these oncogenic variants of the p53 not only suffer a loss in DNA binding, but they also show distinct structural stability, aggregation, and toxicity profiles. The WTp53 and the [R273H]p53 show the least destabilization and aggregation propensity. [R273C]p53 aggregation is disulfide mediated, leading to cross-ß, thioflavin-T-positive aggregates, whereas hydrophobic interactions dominate self-assembly in [R273L]p53, leading to a mixture of amyloid and amorphous aggregates. Molecular dynamics simulations indicate different contact maps and secondary structures for the different variants along the course of the simulations. Our study indicates that each of the R273 variants has its own distinct property of stability and self-assembly, the molecular basis of which may lead to different types of cancer pathogenesis in vivo. These studies will aid the design of therapeutic strategies for cancer using residue-specific or process-specific protein aggregation as a target.

Functional protein shells fabricated from the self-assembling protein sheets of prokaryotic organelles.

Fabricating protein compartments from protein units is challenging and limited by the use of external stimuli and crosslinkers. Here we explore the fabrication of all-protein compartments using self-assembled proteins of prokaryotic organelles. These proteins have intrinsic interacting domains which are ionic in nature, and spontaneously self-assemble into sheets when over-expressed. Using a one-step approach, we maneuvered the formation of the protein shells from the sheets without any external stimuli or crosslinker. The spontaneous self-assembly of the native protein sheets into protein shells not only preserves the native functional properties of the protein but also enhances their thermal stability compared to the sheets. We further demonstrate that these compartments can encapsulate macromolecular enzymes and, more interestingly, permit the free exchange of small molecules and substrates through their intrinsic conduit channels. The porous nature of the shell housing active enzymes and allowing movement of small molecules makes them suitable as active bioreactors. Furthermore, to extend the tunability of these protein-compartments with respect to stability, enzyme-encapsulation, and permeability, we fabricated three different compartments using three different sheet proteins, PduA/B/B' and compared their properties. Interestingly we find that all three protein shells show similar behaviour with respect to an encapsulated diol-dehydratase enzyme and vitamin B12, which are native to the Pdu BMC system. Furthermore, for the non-native enzyme CytC, the small molecule R6G dye, doxorubicin, NR and curcumin they behave diversely. Insights from this analysis will allow us to design and develop sheet protein based synthetic active bioreactors requiring meticulous, compartmentalization in process optimization.

Cellulose-metallothionein matrix for metal binding.

In this report, we have modified bacterial cellulose to a metal binding matrix by covalently conjugating physiological metal chelators known as metallothioneins. The hydroxyl groups of the native bacterial cellulose from Gluconobacter xylinus are epoxidized, followed by the covalent conjugation with the amine groups of the proteins. For the first time, a covalent conjugation of protein with bacterial cellulose is achieved using the epoxy-amine conjugation chemistry. Using this protocol, 50% mass by mass of the metallothionein could be attached to bacterial cellulose. The morphological features and porosity of the modified cellulose are different compared to pristine bacterial cellulose. Also, the conjugated material has better thermal stability. A five-fold enhancement in the metal binding capacity of the metallothionein conjugated bacterial cellulose is achieved as compared to pristine bacterial cellulose. Cellular metabolic assay and membrane integrity assay on MCF and HeLa cell lines showed no significant toxicity of the conjugate material. This bacterial cellulose-metallothionein conjugate can be explored for health care applications where management of metal toxicity is crucial. Further, the epoxy-amine chemistry for covalent conjugation of protein can be applied for several other types of proteins to develop specific functional biocompatible and biodegradable cellulose matrices.

The Wrappers of the 1,2-Propanediol Utilization Bacterial Microcompartments.

The propanediol utilization bacterial microcompartments are specialized protein-based organelles in Salmonella that facilitate the catabolism of 1,2-propanediol when available as the sole carbon source. This smart prokaryotic cell organelle compartmentalizes essential enzymes and substrates in a volume of a few attoliters compared to the femtoliter volume of a bacterial cell thereby enhancing the enzyme kinetics and properly orchestrating the downstream pathways. A shell or coat, which is composed of a few thousand protein subunits, wraps a chain of consecutively acting enzymes and serves as ducts for the diffusion of substrates, cofactors, and products into and out of the core of the microcompartment. In this article we bring together the properties of the wrappers of the propanediol utilization bacterial microcompartments to update our understanding on the mechanism of the formation of these unique wraps, their assembly, and interaction with the encapsulated enzymes.

Selective molecular transport through the protein shell of a bacterial microcompartment organelle.

Bacterial microcompartments are widespread prokaryotic organelles that have important and diverse roles ranging from carbon fixation to enteric pathogenesis. Current models for microcompartment function propose that their outer protein shell is selectively permeable to small molecules, but whether a protein shell can mediate selective permeability and how this occurs are unresolved questions. Here, biochemical and physiological studies of structure-guided mutants are used to show that the hexameric PduA shell protein of the 1,2-propanediol utilization (Pdu) microcompartment forms a selectively permeable pore tailored for the influx of 1,2-propanediol (the substrate of the Pdu microcompartment) while restricting the efflux of propionaldehyde, a toxic intermediate of 1,2-propanediol catabolism. Crystal structures of various PduA mutants provide a foundation for interpreting the observed biochemical and phenotypic data in terms of molecular diffusion across the shell. Overall, these studies provide a basis for understanding a class of selectively permeable channels formed by nonmembrane proteins.