RNA: interactions drive functionalities

RNA is produced from the majority of human genomic sequences, although only a relatively small portion of these transcripts has known functions. Diverse RNA species interact with RNA, DNA, proteins, lipids, and metabolites to form intricate molecular networks. In this review, we attempt to delineate diverse RNA functions by interaction types between RNA and other macromolecules. Through such interactions RNAs participate in essentially every major molecular function and process, including information flow and storage, environment sensing, signal transduction, and gene regulation at transcriptional and posttranscriptional levels. Through such interactions, RNAs promote or inhibit diverse biological processes, and act as catalyzer or quencher to modulate the pace of these progresses. Alterations and personal variations of these interactions are mechanistically coupled with disease etiology and phenotypical variations for clinical use.

Targeting Macromolecules to CNS and Other Hard-to-Treat Organs Using Lectin-Mediated Delivery

The greatest challenges for therapeutic efficacy of many macromolecular drugs that act on intracellular are delivery to key organs and tissues and delivery into cells and subcellular compartments. Transport of drugs into critical cells associated with disease, including those in organs protected by restrictive biological barriers such as central nervous system (CNS), bone, and eye remains a significant hurdle to drug efficacy and impacts commercial risk and incentives for drug development for many diseases. These limitations expose a significant need for the development of novel strategies for macromolecule delivery. RTB lectin is the non-toxic carbohydrate-binding subunit B of ricin toxin with high affinity for galactose/galactosamine-containing glycolipids and glycoproteins common on human cell surfaces. RTB mediates endocytic uptake into mammalian cells by multiple routes exploiting both adsorptive-mediated and receptor-mediated mechanisms. In vivo biodistribution studies in lysosomal storage disease models provide evidence for the theory that the RTB-lectin transports corrective doses of enzymes across the blood–brain barrier to treat CNS pathologies. These results encompass significant implications for protein-based therapeutic approaches to address lysosomal and other diseases having strong CNS involvement.

Disordered chromatin packing regulates phenotypic plasticity

Three-dimensional supranucleosomal chromatin packing plays a profound role in modulating gene expression by regulating transcription reactions through mechanisms such as gene accessibility, binding affinities, and molecular diffusion. Here, we use a computational model that integrates disordered chromatin packing (CP) with local macromolecular crowding (MC) to study how physical factors, including chromatin density, the scaling of chromatin packing, and the size of chromatin packing domains, influence gene expression. We computationally and experimentally identify a major role of these physical factors, specifically chromatin packing scaling, in regulating phenotypic plasticity, determining responsiveness to external stressors by influencing both intercellular transcriptional malleability and heterogeneity. Applying CPMC model predictions to transcriptional data from cancer patients, we identify an inverse relationship between patient survival and phenotypic plasticity of tumor cells.

Macromolecular crowding effects on transcription and translation are regulated by free magnesium ion

Cell-free metabolic engineering is an emerging and promising alternative platform for the production of fuels and chemicals. In recent years, macromolecular crowding effect, which is an important function in living cells but ignored in cell-free systems, has been transferred to cell-free protein synthesis (CFPS). However, inhibitory effects of crowding agents on CFPS were frequently observed, and the mechanism is unclear. In this study, free Mg2+ was found to be a key factor that can regulate the macromolecular crowding effect on in vitro transcription, in vitro translation, and coupled transcript/translation. Addition of crowding agents (20% of Ficoll-70 or Ficoll-400) enhanced in vitro transcription at an index of free Mg2+ concentration (IFMC) below 2 mM but inhibited the transcription when the IFMC was higher than 2 mM. Similarly, Ficoll-400 enhanced in vitro translation and coupled transcription/translation at a lower IFMC (0.1-2 mM) and inhibited the reactions at higher IFMC (>2 mM). Based on the results, CFPS systems could be further optimized by adjusting the content of crowding agents and the IFMC. Besides, the results also indicate that macromolecular crowding effect is important for maintaining the efficiency of in vivo transcription and translation which occur at a low intracellular IFMC (<1 mM).

Native Mass Spectrometry Analysis of Affinity-Captured Endogenous Yeast RNA Exosome Complexes

Native mass spectrometry (MS) enables direct mass measurement of intact protein assemblies generating relevant subunit composition and stoichiometry information. Combined with cross-linking and structural data, native MS-derived information is crucial for elucidating the architecture of macromolecular assemblies by integrative structural methods. The exosome complex from budding yeast was among the first endogenous protein complexes to be affinity isolated and subsequently characterized by this technique, providing improved understanding of its composition and structure. We present a protocol that couples efficient affinity capture of yeast exosome complexes and sensitive native MS analysis, including rapid affinity isolation of the endogenous exosome complex from cryolysed yeast cells, elution in nondenaturing conditions by protease cleavage, depletion of the protease, buffer exchange, and native MS measurements using an Orbitrap-based instrument (Exactive Plus EMR).

TADs and Their Borders: Free Movement or Building a Wall?

The tridimensional (3D) organization of mammalian genomes combines structures from different length scales. Within this organization, Topologically Associating Domains (TADs) are visible in Hi-C heat maps at the sub-megabase scale. The integrity of TADs is important for correct gene expression, but in a context-dependent and variable manner. The correct structure and function of TADs require the binding of the CTCF protein at both borders, which appears to block an active and dynamic mechanism of "Cohesin-mediated loop extrusion." As a result, mammalian TADs appear as so-called "loop domains" in Hi-C data, which are the focus of this review. Here, we present a reanalysis of TADs from three "golden-standard" mammalian Hi-C data sets. Despite the prominent presence of TADs in Hi-C heat maps from all studies, we find consistently that regions within these domains are only moderately insulated from their surroundings. Moreover, single-cell Hi-C and superresolution microscopy have revealed that the structure of TADs and the position of their borders can vary from cell to cell. The function of TADs as units of gene regulation may thus require additional aspects, potentially incorporating the mechanism of loop extrusion as well. Recent developments in single-cell and multi-contact genomics and superresolution microscopy assays will be instrumental to link TAD formation and structure to their function in transcriptional regulation.

Analyzing acoustoelastic effect of shear wave elastography data for perfused and hydrated soft tissues using a macromolecular network inspired model

Shear wave elastography (SWE) has enhanced our ability to non-invasively make in vivo measurements of tissue elastic properties of animal and human tissues. Recently, researchers have taken advantages of acoustoelasticity in SWE to extract nonlinear elastic properties from soft biological tissues. However, most investigations of the acoustoelastic effects of SWE data (AE-SWE) rely on classic hyperelastic models for rubber-like (dry) materials. In this paper, we focus solely on understanding acoustoelasticity in soft hydrated tissues using SWE data and propose a straightforward approach to modeling the constitutive behavior of soft tissue that has a direct microstructural/macromolecular interpretation. Our approach incorporates two constitutive features relevant to biological tissues into AE-SWE: static dilation of the medium associated with nonstructural components (e.g. tissue hydration and perfusion) and finite extensibility derived from an ideal network of biological filaments. We evaluated the proposed method using data from an in-house tissue-mimicking phantom experiment, and ex vivo and in vivo AE-SWE data available in the SWE literature. In conclusion, predictions made by our approach agreed well with measurements obtained from phantom, ex vivo and in vivo tissue experiments.

Natural Variation Reveals a Key Role for Rhamnogalacturonan I in Seed Outer Mucilage and Underlying Genes

On imbibition, Arabidopsis (Arabidopsis thaliana) seeds release polysaccharides from their epidermal cells that form a two-layered hydrogel, termed mucilage. Analysis of a publicly available data set of outer seed mucilage traits of over 300 accessions showed little natural variation in composition. This mucilage is almost exclusively made up of rhamnogalacturonan I (RGI), highlighting the importance of this pectin for outer mucilage function. In a genome-wide association study, observed variations in polymer amount and macromolecular characteristics were linked to several genome polymorphisms, indicating the complexity of their genetic regulation. Natural variants with high molar mass were associated with a gene encoding a putative glycosyltransferase called MUCILAGE-RELATED70 (MUCI70). muci70 insertion mutants produced many short RGI polymers that were highly substituted with xylan, confirming that polymorphism in this gene can affect RGI polymer size. A second gene encoding a putative copper amine oxidase of clade 1a (CuAOα1) was associated with natural variation in the amount of RGI present in the outer mucilage layer; cuaoα1 mutants validated its role in pectin production. As the mutant phenotype is unique, with RGI production only impaired for outer mucilage, this indicates that CuAOα1 contributes to a further mechanism controlling mucilage synthesis.

Fibrillar fibronectin plays a key role as nucleator of collagen I polymerization during macromolecular crowding-enhanced matrix assembly

Macromolecular crowding is used by tissue engineers to accelerate extracellular matrix assembly in vitro, however, most mechanistic studies focus on the impact of crowding on collagen fiber assembly and largely ignore the highly abundant provisional matrix protein fibronectin. We show that the accelerated collagen I assembly as induced by the neutral crowding molecule Ficoll is regulated by cell access to fibronectin. Ficoll treatment leads to significant increases in the amount of surface adherent fibronectin, which can readily be harvested by cells to speed up fibrillogenesis. FRET studies reveal that Ficoll crowding also upregulates the total amount of fibronectin fibers in a low-tension state through upregulating fibronectin assembly. Since un-stretched fibronectin fibers have more collagen binding sites to nucleate the onset of collagen fibrillogenesis, our data suggest that the Ficoll-induced upregulation of low-tension fibronectin fibers contributes to enhanced collagen assembly in crowded conditions. In contrast, chemical cross-linking of fibronectin to the glass substrate prior to cell seeding prevents early force mediated fibronectin harvesting from the substrate and suppresses upregulation of collagen I assembly in the presence of Ficoll, even though the crowded environment is known to drive enzymatic cleavage of procollagen and collagen fiber formation. To show that our findings can be exploited for tissue engineering applications, we demonstrate that the addition of supplemental fibronectin in the form of an adsorbed coating markedly improves the speed of tissue formation under crowding conditions.

TADs as the Caller Calls Them

Developments in proximity ligation methods and sequencing technologies have provided high-resolution views of the organization of the genome inside the nucleus. A prominent feature of Hi-C maps is regions of increased self-interaction called topologically associating domains (TADs). Despite the strong evolutionary conservation and clear link with gene expression, the exact role of TADs and even their definition remains debatable. Here, I review the discovery of TADs, how they are commonly identified, and the mechanisms that lead to their formation. Furthermore, I discuss recent results that have created a more nuanced view of the role of TADs in the regulation of genes. In light of this, I propose that when we define TADs, we also consider the mechanisms that shape them.

Macromolecular complex in recognition and proteolysis of amyloid precursor protein in Alzheimer's disease

Proteolysis of amyloid precursor protein (APP), first extracellularly by β-secretase and then within the membrane by γ-secretase, produces β-amyloid peptides (Aβ). Aβ accumulates in the brain to form amyloid plaques, a hallmark of Alzheimer's disease (AD). Mutations in APP and presenilin (the catalytic subunit of γ-secretase) result in early onset of AD. Cryogenic electron microscopy (cryo-EM) structures of substrate-free and substrate-bound γ-secretase, determined at atomic resolutions, reveal the physical basis of distinct substrate specificity. These advances, together with the discovery and characterization of multiple proteins that interact with APP or presenilin, have given rise to an optimistic scenario for future mechanistic understanding of AD.

Dynamic Continuum of Molecular Assemblies for Controlling Cell Fates

Biological systems have evolved to create a structural and dynamic continuum of bio-macromolecular assemblies for the purpose of optimizing the system's functions. The formation of these dynamic higher-order assemblies is precisely controlled by biological cues. However, controlling the self-assembly of synthetic molecules spatiotemporally in or on live cells is still a big challenge, especially for performing functions. This concept article introduces the use of in situ reactions as a spatiotemporal control to form assemblies of small molecules that induce cell morphogenesis or apoptosis. After briefly introducing a representative example of a natural dynamic continuum of the higher-order assemblies, we describe enzyme-instructed self-assembly (EISA) for constructing dynamic assemblies of small molecules, then discuss the use of EISA for controlling cell morphogenesis and apoptosis. Finally, we provide a brief outlook to discuss the future perspective of this exciting new research direction.

Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology

Small-angle X-ray scattering (SAXS) has emerged as an enabling integrative technique for comprehensive analyses of macromolecular structures and interactions in solution. Over the past two decades, SAXS has become a mainstay of the structural biologist's toolbox, supplying multiplexed measurements of molecular shape and dynamics that unveil biological function. Here, we discuss evolving SAXS theory, methods, and applications that extend the field of small-angle scattering beyond simple shape characterization. SAXS, coupled with size-exclusion chromatography (SEC-SAXS) and time-resolved (TR-SAXS) methods, is now providing high-resolution insight into macromolecular flexibility and ensembles, delineating biophysical landscapes, and facilitating high-throughput library screening to assess macromolecular properties and to create opportunities for drug discovery. Looking forward, we consider SAXS in the integrative era of hybrid structural biology methods, its potential for illuminating cellular supramolecular and mesoscale structures, and its capacity to complement high-throughput bioinformatics sequencing data. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.

Spatiotemporal material functionalization via competitive supramolecular complexation of avidin and biotin analogs

Spatiotemporal control over engineered tissues is highly desirable for various biomedical applications as it emulates the dynamic behavior of natural tissues. Current spatiotemporal biomaterial functionalization approaches are based on cytotoxic, technically challenging, or non-scalable chemistries, which has hampered their widespread usage. Here we report a strategy to spatiotemporally functionalize (bio)materials based on competitive supramolecular complexation of avidin and biotin analogs. Specifically, an injectable hydrogel is orthogonally post-functionalized with desthiobiotinylated moieties using multivalent neutravidin. In situ exchange of desthiobiotin by biotin enables spatiotemporal material functionalization as demonstrated by the formation of long-range, conformal, and contra-directional biochemical gradients within complex-shaped 3D hydrogels. Temporal control over engineered tissue biochemistry is further demonstrated by timed presentation and sequestration of growth factors using desthiobiotinylated antibodies. The method's universality is confirmed by modifying hydrogels with biotinylated fluorophores, peptides, nanoparticles, enzymes, and antibodies. Overall, this work provides a facile, cytocompatible, and universal strategy to spatiotemporally functionalize materials.

Green alga cultivation with nanofibers as physical adsorbents of carbon dioxide: Evaluation of gas biofixation and macromolecule production

The objective of this study was to evaluate the biofixation and production of biocompounds by Chlorella fusca LEB 111 cultivated with different concentrations of carbon dioxide (CO₂) adsorbent nanofibers in their free form or retained. Cultures were grown in 15% (v v^-1) CO₂ with 0.1, 0.3 and 0.5 g L^-1 nanofibers developed with 10% (w v^-1) polyacrylonitrile (PAN)/dimethylformamide (DMF), with or without nanoparticles; retained or not. The addition of 0.1 g L^-1 nanofibers with nanoparticles in their free form to the cultures promoted the accumulation of approximately 3 times more carbon in the medium (46.6 mg L^-1), a 45% higher biofixation rate (89.2 mg L^-1 d^-1) and increased carbohydrate production by approximately 2.3% (w w^-1) of that observed in cultures grown without nanofibers. Therefore, nanofibers showed promising potential as physical adsorbents of CO₂ in the cultivation to increase gas fixation and promote the synthesis of macromolecules.

Meiotic cellular rejuvenation is coupled to nuclear remodeling in budding yeast

Production of healthy gametes in meiosis relies on the quality control and proper distribution of both nuclear and cytoplasmic contents. Meiotic differentiation naturally eliminates age-induced cellular damage by an unknown mechanism. Using time-lapse fluorescence microscopy in budding yeast, we found that nuclear senescence factors - including protein aggregates, extrachromosomal ribosomal DNA circles, and abnormal nucleolar material - are sequestered away from chromosomes during meiosis II and subsequently eliminated. A similar sequestration and elimination process occurs for the core subunits of the nuclear pore complex in both young and aged cells. Nuclear envelope remodeling drives the formation of a membranous compartment containing the sequestered material. Importantly, de novo generation of plasma membrane is required for the sequestration event, preventing the inheritance of long-lived nucleoporins and senescence factors into the newly formed gametes. Our study uncovers a new mechanism of nuclear quality control and provides insight into its function in meiotic cellular rejuvenation.

MetalPDB in 2018: a database of metal sites in biological macromolecular structures

MetalPDB (http://metalweb.cerm.unifi.it/) is a database providing information on metal-binding sites detected in the three-dimensional (3D) structures of biological macromolecules. MetalPDB represents such sites as 3D templates, called Minimal Functional Sites (MFSs), which describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. The 2018 update of MetalPDB includes new contents and tools. A major extension is the inclusion of proteins whose structures do not contain metal ions although their sequences potentially contain a known MFS. In addition, MetalPDB now provides extensive statistical analyses addressing several aspects of general metal usage within the PDB, across protein families and in catalysis. Users can also query MetalPDB to extract statistical information on structural aspects associated with individual metals, such as preferred coordination geometries or aminoacidic environment. A further major improvement is the functional annotation of MFSs; the annotation is manually performed via a password-protected annotator interface. At present, ∼50% of all MFSs have such a functional annotation. Other noteworthy improvements are bulk query functionality, through the upload of a list of PDB identifiers, and ftp access to MetalPDB contents, allowing users to carry out in-depth analyses on their own computational infrastructure.

Encapsulation of anticancer drug doxorubicin inside dendritic macromolecular cavities: First-principles benchmarks

By using first-principles approaches based on Density Functional Theory, we explore the possibility of using dendritic macromolecular structures as carriers of the doxorubicin anticancer drug. In particular, we consider macromolecular cavities of different sizes composed of phenylene-, thiophene-, phenyl-cored thiophen- and thioazole-based dendrimers. The comparison between the optimized molecular geometries of the monomers and of the host-guest complexes reveals that only slight structural changes are observed in doxorubicin upon complexation. Also, the encapsulation energies for the host-guest complexes suggest that these systems are of potential use for pharmacology applications in vivo. The interaction of the guest doxorubicin with the macromolecular cavities exploits different types of weak intermolecular forces including σ, π and hydrogen bond interactions. The electronic structure of these complexes is discussed, with particular emphasis placed on the role of the charge distribution and the nature of the frontier molecular orbitals in the encapsulation process. Spectroscopic properties of these complexes are derived to facilitate their detection in laboratory and in vivo. These include IR vibrational frequencies, absorption wavelengths and relative oscillator strengths for the main transitions in the UV-Vis spectrum.

DNA-supramolecule conjugates in theranostics

The elegant properties of deoxyribonucleic acid (DNA), such as accurate recognition, programmability and addressability, make it a well-defined and promising material to develop various molecular probes, drug delivery carriers and theranostic systems for cancer diagnosis and therapy. In addition, supramolecular chemistry, also termed "chemistry beyond the molecule", is a promising research field that aims to develop functional chemical systems by bringing discrete molecular components together in a manner that invokes noncovalent intermolecular forces, such as hydrophobic interaction, hydrogen bonding, metal coordination, and shape or size matching. Thus, DNA-supramolecule conjugates (DSCs) combine accurate recognition, programmability and addressability of DNA with the greater toolbox of supramolecular chemistry. This review discusses the applications of DSCs in sensing, protein activity regulation, cell behavior manipulation, and biomedicine.

Supramolecular Assemblies of Peptides or Nucleopeptides for Gene Delivery

Using non-covalent interactions between nucleic acids (DNA, siRNA, miRNA, and mRNA) with peptides or nucleopeptides is a promising strategy to construct supramolecular assemblies for gene delivery and therapy. Comparing to conventional strategies for gene delivery, the assemblies of peptides or nucleopeptides provide several unique advantages: i) reversible interactions between the assemblies and the nucleic acids; ii) minimal immunogenicity; iii) biocompatibility. This field has advanced considerably in recent years so that it is worth summarizing the recent progresses and future challenges. In this review, we introduce the development of assemblies of peptides or nucleopeptides for applications in gene delivery and related fields. After introducing the promises of gene therapy and the current strategies for the delivery, we discuss the unique advantage of using peptide assemblies for gene delivery. Then we describe several representative strategies for gene delivery by the assemblies of peptides or nucleopeptides. Finally, we discuss the key factors for designing such assemblies for gene delivery, and speculate future directions and challenges in the field, particularly the rational design and the spatiotemporally controlled release in live cells.

AIE-based theranostic systems for detection and killing of pathogens

Pathogenic bacteria, fungi and viruses pose serious threats to the human health under appropriate conditions. There are many rapid and sensitive approaches have been developed for identification and quantification of specific pathogens, but many challenges still exist. Culture/colony counting and polymerase chain reaction are the classical methods used for pathogen detection, but their operations are time-consuming and laborious. On the other hand, the emergence and rapid spread of multidrug-resistant pathogens is another global threat. It is thus of utmost urgency to develop new therapeutic agents or strategies. Luminogens with aggregation-induced emission (AIEgens) and their derived supramolecular systems with unique optical properties have been developed as fluorescent probes for turn-on sensing of pathogens with high sensitivity and specificity. In addition, AIE-based supramolecular nanostructures exhibit excellent photodynamic inactivation (PDI) activity in aggregate, offering great potential for not only light-up diagnosis of pathogen, but also image-guided PDI therapy for pathogenic infection.

Advances in intracellular delivery through supramolecular self-assembly of oligonucleotides and peptides

Cells utilize natural supramolecular assemblies to maintain homeostasis and biological functions. Naturally inspired modular assembly of biomaterials are now being exploited for understanding or manipulating cell biology for treatment, diagnosis, and detection of diseases. Supramolecular biomaterials, in particular peptides and oligonucleotides, can be precisely tuned to have diverse structural, mechanical, physicochemical and biological properties. These merits of oligonucleotides and peptides as building blocks have given rise to the evolution of numerous nucleic acid- and peptide-based self-assembling nanomaterials for various medical applications, including drug delivery, tissue engineering, regenerative medicine, and immunotherapy. In this review, we provide an extensive overview of the intracellular delivery approaches using supramolecular self-assembly of DNA, RNA, and peptides. Furthermore, we discuss the current challenges related to subcellular delivery and provide future perspectives of the application of supramolecular biomaterials for intracellular delivery in theranostics.

Potential of Chlorella fusca LEB 111 cultivated with thermoelectric fly ashes, carbon dioxide and reduced supply of nitrogen to produce macromolecules

Fly ashes present several minerals that along with carbon dioxide (CO₂) represent a promising nutrient source and an alternative to reduce environmental problems. Thus, the objective of this study was to investigate if CO₂, thermoelectric fly ashes and reduction in nitrogen supply alters the production of macromolecules in Chlorella fusca LEB 111. For this purpose, 1.5 or 0.75 g L^-1 of NaNO₃, injection of 10% (v v^-1) of CO₂ as well as 0, 40 and 120 ppm of fly ashes were studied. The protein content was not impaired in cultivations with 0.75 g L^-1 of NaNO₃ since nitrogen was not fully consumed. Nevertheless, this cultivation strategy increased carbohydrate content by up to 25%, which could be fermented to produce bioethanol. Therefore, Chlorella fusca presented not only potential for CO₂ biofixation and assimilation of nutrients from fly ashes but also for enhancement of carbohydrates accumulation when the nitrogen supply was reduced.

Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications

Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for "generic" proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data.