Self-assembly of amphiphilic Janus dendrimers into uniform onion-like dendrimersomes with predictable size and number of bilayers

A constitutional isomeric library synthesized by a modular approach has been used to discover six amphiphilic Janus dendrimer primary structures, which self-assemble into uniform onion-like vesicles with predictable dimensions and number of internal bilayers. These vesicles, denoted onion-like dendrimersomes, are assembled by simple injection of a solution of Janus dendrimer in a water-miscible solvent into water or buffer. These dendrimersomes provide mimics of double-bilayer and multibilayer biological membranes with dimensions and number of bilayers predicted by the Janus compound concentration in water. The simple injection method of preparation is accessible without any special equipment, generating uniform vesicles, and thus provides a promising tool for fundamental studies as well as technological applications in nanomedicine and other fields.Most living organisms contain single-bilayer membranes composed of lipids, glycolipids, cholesterol, transmembrane proteins, and glycoproteins (1). Gram-negative bacteria (2, 3) and the cell nucleus (4), however, exhibit a strikingly special envelope that consists of a concentric double-bilayer membrane. More complex membranes are also encountered in cells and their various organelles, such as multivesicular structures of eukaryotic cells (5) and endosomes (6), and multibilayer structures of endoplasmic reticulum (7, 8), myelin (9, 10), and multilamellar bodies (11, 12). This diversity of biological membranes inspired corresponding biological mimics. Liposomes (Fig. 1) self-assembled from phospholipids are the first mimics of single-bilayer biological membranes (13–16), but they are polydisperse, unstable, and permeable (14). Stealth liposomes coassembled from phospholipids, cholesterol, and phospholipids conjugated with poly(ethylene glycol) exhibit improved stability, permeability, and mechanical properties (17–20). Polymersomes (21–24) assembled from amphiphilic block copolymers exhibit better mechanical properties and permeability, but are not always biocompatible and are polydisperse. Dendrimersomes (25–28) self-assembled from amphiphilic Janus dendrimers and minidendrimers (26–28) have also been elaborated to mimic single-bilayer biological membranes. Amphiphilic Janus dendrimers take advantage of multivalency both in their hydrophobic and hydrophilic parts (23, 29–32). Dendrimersomes are assembled by simple injection (33) of a solution of an amphiphilic Janus dendrimer (26) in a water-soluble solvent into water or buffer and produce uniform (34), impermeable, and stable vesicles with excellent mechanical properties. In addition, their size and properties can be predicted by their primary structure (27). Amphiphilic Janus glycodendrimers self-assemble into glycodendrimersomes that mimic the glycan ligands of biological membranes (35). They have been demonstrated to be bioactive toward biomedically relevant bacterial, plant, and human lectins, and could have numerous applications in nanomedicine (20).Open in a separate windowFig. 1.Strategies for the preparation of single-bilayer vesicles and multibilayer onion-like vesicles.More complex and functional cell mimics such as multivesicular vesicles (36, 37) and multibilayer onion-like vesicles (38–40) have also been discovered. Multivesicular vesicles compartmentalize a larger vesicle (37) whereas multibilayer onion-like vesicles consist of concentric alternating bilayers (40). Currently multibilayer vesicles are obtained by very complex and time-consuming methods that do not control their size (39) and size distribution (40) in a precise way. Here we report the discovery of “single–single” (28) amphiphilic Janus dendrimer primary structures that self-assemble into uniform multibilayer onion-like dendrimersomes (Fig. 1) with predictable size and number of bilayers by simple injection of their solution into water or buffer.     

Solid-phase peptide synthesis and solid-phase fragment coupling mediated by isonitriles

The synthesis of polypeptides on solid phase via mediation by isonitriles is described. The acyl donor is a thioacid, which presumably reacts with the isonitrile to generate a thio-formimidate carboxylate mixed anhydride intermediate. Applications of this chemistry to reiterative solid-phase peptide synthesis as well as solid-phase fragment coupling are described.Amide bond formations are arguably among the most important constructions in organic chemistry (1, 2). The centrality of the amide linkage, as found in polypeptides and proteins, in the maintenance of life hardly needs restatement. Numerous strategies, resulting in a vast array of protocols to synthesize biologically active polypeptides and proteins, have been demonstrated (3, 4). Central to reiterative polypeptide bond formations was the discovery and remarkable development of solid-phase peptide synthesis (SPPS) (5, 6). The extraordinary impact of SPPS in fostering enhanced access to homogeneous polypeptides is clear to everyone in the field.As we have described elsewhere, by classical, mechanistic reasoning, we were led to conjecture about some hitherto-unexplored possibilities relevant to the chemistry of isonitriles (7–14). It was anticipated that isonitriles might be able to mediate the acylation of amines, thus giving rise to amides (15). Early experiments focused on free carboxylic acids as the acylating agents. As our studies progressed, it was found that the combination of thioacids, amines, and isonitriles leads to the efficient formation of amide bonds under stoichiometric or near-stoichiometric conditions (7–13, 16, 17). Although there remain unresolved issues of detail and nuance, the governing mechanism for amide formation under these conditions involves reaction of the thioacid, 1, with an isonitrile, 2, to generate a thio-formimidate carboxylate mixed anhydride (thio-FCMA), 3, which is intercepted by the “acyl-accepting” amine to generate amide, 5, and thioformamide, 6 (Fig. 1). The efficiency of the amidation was further improved through the use of hydroxybenzotriazole (HOBt) (18), which could well give rise to HOBt ester 7, although this pathway has not been mechanistically proven.Open in a separate windowFig. 1.Isonitrile-mediated amidation; structure of OT.The potentialities of the isonitrile-mediated amidation method were foreshadowed via its application to the synthesis of cyclosporine (19). The power of the method was particularly well demonstrated in the context of our recent total synthesis of oxytocin (OT) (20), wherein isonitrile mediation was used in each of the peptide bond constructions, leading to the synthesis of the hormone in high yield and excellent purity. This nonapeptide is involved in a range of biological functions including parturition and lactation (21, 22). Signaling of OT to its receptor (OTR) is apparently an important factor in quality maintenance of various CNS functions (23). The ability to synthesize such modestly sized, but bio-impactful peptides in both native (wild-type) form, and as strategically modified variants, is one of the current missions of our laboratory, with the objective of possible applications to the very serious problem of autism (24–26).     

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping

DNA polymorphisms are important markers in genetic analyses and are increasingly detected by using genome resequencing. However, the presence of repetitive sequences and structural variants can lead to false positives in the identification of polymorphic alleles. Here, we describe an analysis strategy that minimizes false positives in allelic detection and present analyses of recently published resequencing data from Arabidopsis meiotic products and individual humans. Our analysis enables the accurate detection of sequencing errors, small insertions and deletions (indels), and structural variants, including large reciprocal indels and copy number variants, from comparisons between the resequenced and reference genomes. We offer an alternative interpretation of the sequencing data of meiotic products, including the number and type of recombination events, to illustrate the potential for mistakes in single-nucleotide polymorphism calling. Using these examples, we propose that the detection of DNA polymorphisms using resequencing data needs to account for nonallelic homologous sequences.DNA polymorphisms are ubiquitous genetic variations among individuals and include single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and other larger rearrangements (1–3) (Fig. 1 A and B). They can have phenotypic consequences and also serve as molecular markers for genetic analyses, facilitating linkage and association studies of genetic diseases, and other traits in humans (4–6), animals, plants, (7–10) and other organisms. Using DNA polymorphisms for modern genetic applications requires low-error, high-throughput analytical strategies. Here, we illustrate the use of short-read next-generation sequencing (NGS) data to detect DNA polymorphisms in the context of whole-genome analysis of meiotic products.Open in a separate windowFig. 1.(A) SNPs and small indels between two ecotype genomes. (B) Possible types of SVs. Col genotypes are marked in blue and Ler in red. Arrows indicate DNA segments involved in SVs between the two ecotypes. (C) Meiotic recombination events including a CO and a GC (NCO). Centromeres are denoted by yellow dots.There are many methods for detecting SNPs (11–14) and structural variants (SVs) (15–25), including NGS, which can capture nearly all DNA polymorphisms (26–28). This approach has been widely used to analyze markers in crop species such as rice (29), genes associated with diseases (6, 26), and meiotic recombination in yeast and plants (30, 31). However, accurate identification of DNA polymorphisms can be challenging, in part because short-read sequencing data have limited information for inferring chromosomal context.Genomes usually contain repetitive sequences that can differ in copy number between individuals (26–28, 31); therefore, resequencing analyses must account for chromosomal context to avoid mistaking highly similar paralogous sequences for polymorphisms. Here, we use recently published datasets to describe several DNA sequence features that can be mistaken as allelic (32, 33) and describe a strategy for differentiating between repetitive sequences and polymorphic alleles. We illustrate the effectiveness of these analyses by examining the reported polymorphisms from the published datasets.Meiotic recombination is initiated by DNA double-strand breaks (DSBs) catalyzed by the topoisomerase-like SPORULATION 11 (SPO11). DSBs are repaired as either crossovers (COs) between chromosomes (Fig. 1C), or noncrossovers (NCOs). Both COs and NCOs can be accompanied by gene conversion (GC) events, which are the nonreciprocal transfer of sequence information due to the repair of heteroduplex DNA during meiotic recombination. Understanding the control of frequency and distribution of CO and NCO (including GC) events has important implications for human health (including cancer and aneuploidy), crop breeding, and the potential for use in genome engineering. COs can be detected relatively easily by using polymorphic markers in the flanking sequences, but NCO products can only be detected if they are accompanied by a GC event. Because GCs associated with NCO result in allelic changes at polymorphic sites without exchange of flanking sequences, they are more difficult to detect. Recent advances in DNA sequencing have made the analysis of meiotic NCOs more feasible (30–32, 34); however, SVs present a challenge in these analyses. We recommend a set of guidelines for detection of DNA polymorphisms by using genomic resequencing short-read datasets. These measures improve the accuracy of a wide range of analyses by using genomic resequencing, including estimation of COs, NCOs, and GCs.     

Tuning a riboswitch response through structural extension of a pseudoknot

Structural and dynamic features of RNA folding landscapes represent critical aspects of RNA function in the cell and are particularly central to riboswitch-mediated control of gene expression. Here, using single-molecule fluorescence energy transfer imaging, we explore the folding dynamics of the preQ₁ class II riboswitch, an upstream mRNA element that regulates downstream encoded modification enzymes of queuosine biosynthesis. For reasons that are not presently understood, the classical pseudoknot fold of this system harbors an extra stem–loop structure within its 3′-terminal region immediately upstream of the Shine–Dalgarno sequence that contributes to formation of the ligand-bound state. By imaging ligand-dependent preQ₁ riboswitch folding from multiple structural perspectives, we reveal that the extra stem–loop strongly influences pseudoknot dynamics in a manner that decreases its propensity to spontaneously fold and increases its responsiveness to ligand binding. We conclude that the extra stem–loop sensitizes this RNA to broaden the dynamic range of the ON/OFF regulatory switch.A variety of small metabolites have been found to regulate gene expression in bacteria, fungi, and plants via direct interactions with distinct mRNA folds (1–4). In this form of regulation, the target mRNA typically undergoes a structural change in response to metabolite binding (5–9). These mRNA elements have thus been termed “riboswitches” and generally include both a metabolite-sensitive aptamer subdomain and an expression platform. For riboswitches that regulate the process of translation, the expression platform minimally consists of a ribosomal recognition site [Shine–Dalgarno (SD)]. In the simplest form, the SD sequence overlaps with the metabolite-sensitive aptamer domain at its downstream end. Representative examples include the S-adenosylmethionine class II (SAM-II) (10) and the S-adenosylhomocysteine (SAH) riboswitches (11, 12), as well as prequeuosine class I (preQ₁-I) and II (preQ₁-II) riboswitches (13, 14). The secondary structures of these four short RNA families contain a pseudoknot fold that is central to their gene regulation capacity. Although the SAM-II and preQ₁-I riboswitches fold into classical pseudoknots (15, 16), the conformations of the SAH (17) and preQ₁-II counterparts are more complex and include a structural extension that contributes to the pseudoknot architecture (14). Importantly, the impact and evolutionary significance of these “extra” stem–loop elements on the function of the SAH and preQ₁-II riboswitches remain unclear.PreQ₁ riboswitches interact with the bacterial metabolite 7-aminomethyl-7-deazaguanine (preQ₁), a precursor molecule in the biosynthetic pathway of queuosine, a modified base encountered at the wobble position of some transfer RNAs (14). The general biological significance of studying the preQ₁-II system stems from the fact that this gene-regulatory element is found almost exclusively in the Streptococcaceae bacterial family. Moreover, the preQ₁ metabolite is not generated in humans and has to be acquired from the environment (14). Correspondingly, the preQ₁-II riboswitch represents a putative target for antibiotic intervention. Although preQ₁ class I (preQ₁-I) riboswitches have been extensively investigated (18–28), preQ₁ class II (preQ₁-II) riboswitches have been largely overlooked despite the fact that a different mode of ligand binding has been postulated (14).The consensus sequence and the secondary structure model for the preQ₁-II motif (COG4708 RNA) (Fig. 1A) comprise ∼80–100 nt (14). The minimal Streptococcus pneumoniae R6 aptamer domain sequence binds preQ₁ with submicromolar affinity and consists of an RNA segment forming two stem–loops, P2 and P4, and a pseudoknot P3 (Fig. 1B). In-line probing studies suggest that the putative SD box (AGGAGA; Fig. 1) is sequestered by pseudoknot formation, which results in translational-dependent gene regulation of the downstream gene (14).Open in a separate windowFig. 1.PreQ₁ class II riboswitch. (A) Chemical structure of 7-aminomethyl-7-deazaguanosine (preQ₁); consensus sequence and secondary structure model for the COG4708 RNA motif (adapted from reference 14). Nucleoside presence and identity as indicated. (B) S. pneumoniae R6 preQ₁-II RNA aptamer investigated in this study. (C) Schematics of an H-type pseudoknot with generally used nomenclature for comparison.Here, we investigated folding and ligand recognition of the S. pneumoniae R6 preQ₁-II riboswitch, using complementary chemical, biochemical, and biophysical methods including selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE), mutational analysis experiments, 2-aminopurine fluorescence, and single-molecule fluorescence resonance energy transfer (smFRET) imaging. In so doing, we explored the structural and functional impact of the additional stem–loop element in the context of its otherwise “classical” H-type pseudoknot fold (29–32) (Fig. 1C). Our results reveal that the unique 3′-stem–loop element in the preQ₁-II riboswitch contributes to the process of SD sequestration, and thus the regulation of gene expression, by modulating both its intrinsic dynamics and its responsiveness to ligand binding.     

Single-molecule spectroscopy reveals how calmodulin activates NO synthase by controlling its conformational fluctuation dynamics

Mechanisms that regulate the nitric oxide synthase enzymes (NOS) are of interest in biology and medicine. Although NOS catalysis relies on domain motions, and is activated by calmodulin binding, the relationships are unclear. We used single-molecule fluorescence resonance energy transfer (FRET) spectroscopy to elucidate the conformational states distribution and associated conformational fluctuation dynamics of the two electron transfer domains in a FRET dye-labeled neuronal NOS reductase domain, and to understand how calmodulin affects the dynamics to regulate catalysis. We found that calmodulin alters NOS conformational behaviors in several ways: It changes the distance distribution between the NOS domains, shortens the lifetimes of the individual conformational states, and instills conformational discipline by greatly narrowing the distributions of the conformational states and fluctuation rates. This information was specifically obtainable only by single-molecule spectroscopic measurements, and reveals how calmodulin promotes catalysis by shaping the physical and temporal conformational behaviors of NOS.Although proteins adopt structures determined by their amino acid sequences, they are not static objects and fluctuate among ensembles of conformations (1). Transitions between these states can occur on a variety of length scales (Å to nm) and time scales (ps to s) and have been linked to functionally relevant phenomena such as allosteric signaling, enzyme catalysis, and protein–protein interactions (2–4). Indeed, protein conformational fluctuations and dynamics, often associated with static and dynamic inhomogeneity, are thought to play a crucial role in biomolecular functions (5–11). It is difficult to characterize such spatially and temporally inhomogeneous dynamics in bulk solution by an ensemble-averaged measurement, especially in proteins that undergo multiple-conformation transformations. In such cases, single-molecule spectroscopy is a powerful approach to analyze protein conformational states and dynamics under physiological conditions, and can provide a molecular-level perspective on how a protein’s structural dynamics link to its functional mechanisms (12–21).A case in point is the nitric oxide synthase (NOS) enzymes (22–24), whose nitric oxide (NO) biosynthesis involves electron transfer reactions that are associated with relatively large-scale movement (tens of Å) of the enzyme domains (Fig. 1A). During catalysis, NADPH-derived electrons first transfer into an FAD domain and an FMN domain in NOS that together comprise the NOS reductase domain (NOSr), and then transfer from the FMN domain to a heme group that is bound in a separate attached “oxygenase” domain, which then enables NO synthesis to begin (22, 25–27). The electron transfers into and out of the FMN domain are the key steps for catalysis, and they appear to rely on the FMN domain cycling between electron-accepting and electron-donating conformational states (28, 29) (Fig. 1B). In this model, the FMN domain is suggested to be highly dynamic and flexible due to a connecting hinge that allows it to alternate between its electron-accepting (FAD→FMN) or closed conformation and electron-donating (FMN→heme) or open conformation (Fig. 1 A and B) (28, 30–36). In the electron-accepting closed conformation, the FMN domain interacts with the NADPH/FAD domain (FNR domain) to receive electrons, whereas in the electron donating open conformation the FMN domain has moved away to expose the bound FMN cofactor so that it may transfer electrons to a protein acceptor like the NOS oxygenase domain, or to a generic protein acceptor like cytochrome c. In this way, the reductase domain structure cycles between closed and open conformations to deliver electrons, according to a conformational equilibrium that determines the movements and thus the electron flux capacity of the FMN domain (25, 28, 32, 34, 35, 37). A similar conformational switching mechanism is thought to enable electron transfer through the FMN domain in the related flavoproteins NADPH-cytochrome P450 reductase and methionine synthase reductase (38–42).Open in a separate windowFig. 1.(A) The nNOSr ribbon structure (from PDB: 1TLL) showing bound FAD (yellow) in FNR domain (green), FMN (orange) in FMN domain (yellow), connecting hinge (blue), and the Cy3–Cy5 label positions (pink) and distance (42 Å, dashed line). (B) Cartoon of an equilibrium between the FMN-closed and FMN-open states, with Cy dye label positions indicated. (C) Cytochrome c reductase activity of nNOSr proteins in their CaM-bound and CaM-free states. Color scheme of bar graphs: Black, WT nNOSr unlabeled; Red, Cys-lite (CL) nNOSr unlabeled; Blue, E827C/Q1268C CL nNOSr unlabeled; and Dark cyan, E827C/Q1268C CL nNOSr labeled.NOS enzymes also contain a calmodulin (CaM) binding domain that is located just before the N terminus of the FMN domain (Fig. 1B), and this provides an important layer of regulation (25, 27). CaM binding to NOS enzymes increases electron transfer from NADPH through the reductase domain and also triggers electron transfer from the FMN domain to the NOS heme as is required for NO synthesis (31, 32). The ability of CaM, or similar signaling proteins, to regulate electron transfer reactions in enzymes is unusual, and the mechanism is a topic of interest and intensive study. It has long been known that CaM binding alters NOSr structure such that, on average, it populates a more open conformation (43, 44). Recent equilibrium studies have detected a buildup of between two to four discreet conformational populations in NOS enzymes and in related flavoproteins, and in some cases, have also estimated the distances between the bound FAD and FMN cofactors in the different species (26, 36, 37, 39, 40), and furthermore, have confirmed that CaM shifts the NOS population distribution toward more open conformations (34, 36, 45). Although valuable, such ensemble-averaged results about conformational states cannot explain how electrons transfer through these enzymes, or how CaM increases the electron flux in NOS, because answering these questions requires a coordinate understanding of the dynamics of the conformational fluctuations. Indeed, computer modeling has indicated that a shift toward more open conformations as is induced by CaM binding to nNOS should, on its own, actually diminish electron flux through nNOS and through certain related flavoproteins (38). Despite its importance, measuring enzyme conformational fluctuation dynamics is highly challenging, and as far as we know, there have been no direct measures on the NOS enzymes or on related flavoproteins, nor studies on how CaM binding might influence the conformational fluctuation dynamics in NOS.To address this gap, we used single-molecule fluorescence energy resonance transfer (FRET) spectroscopy to characterize individual molecules of nNOSr that had been labeled at two specific positions with Cyanine 3 (Cy3) donor and Cyanine 5 (Cy5) acceptor dye molecules, regarding their conformational states distribution and the associated conformational fluctuation dynamics, which in turn enabled us to determine how CaM binding impacts both parameters. This work provides a unique perspective and a novel study of the NOS enzymes and within the broader flavoprotein family, which includes the mammalian enzymes methionine synthase reductase (MSR) and cytochrome P450 reductase (CPR), and reveals how CaM’s control of the conformational behaviors may regulate the electron transfer reactions of NOS catalysis.     

Structural insight into HIV-1 capsid recognition by rhesus TRIM5α

Tripartite motif protein isoform 5 alpha (TRIM5α) is a potent antiviral protein that restricts infection by HIV-1 and other retroviruses. TRIM5α recognizes the lattice of the retrovirus capsid through its B30.2 (PRY/SPRY) domain in a species-specific manner. Upon binding, TRIM5α induces premature disassembly of the viral capsid and activates the downstream innate immune response. We have determined the crystal structure of the rhesus TRIM5α PRY/SPRY domain that reveals essential features for capsid binding. Combined cryo-electron microscopy and biochemical data show that the monomeric rhesus TRIM5α PRY/SPRY, but not the human TRIM5α PRY/SPRY, can bind to HIV-1 capsid protein assemblies without causing disruption of the capsid. This suggests that the PRY/SPRY domain alone constitutes an important pattern-sensing component of TRIM5α that is capable of interacting with viral capsids of different curvatures. Our results provide molecular insights into the mechanisms of TRIM5α-mediated retroviral restriction.TRIM5α potently inhibits infection by HIV-1 and other retroviruses at an early postentry stage in a species-specific manner (1). Rhesus TRIM5α (rhTRIM5α) potently blocks HIV-1 infection (2). In contrast, human TRIM5α (huTRIM5α) only weakly inhibits HIV-1, but potently restricts N-tropic murine leukemia viruses (N-MLV) (3, 4). TRIM5α is able to induce premature capsid disassembly (5) and activate downstream innate immune responses upon recognizing the retroviral capsid lattice (6).TRIM5α is composed of RING, B-box 2, coiled-coil (CC), and B30.2 (PRY/SPRY) domains (Fig. 1A), similar to many tripartite/RBCC motif (TRIM) family members (7). The RING domain functions as an E3 ubiquitin ligase (8); the B-box 2 domain mediates formation of higher-order structure and self-association (9, 10); and the coiled-coil domain mediates dimerization (11) and facilitates the formation of the hexagonal lattice (12). The PRY/SPRY domain is essential for recognition of retroviral capsids and determines the specificity of restriction (13, 14). Two linker regions, L1 and L2, separate RING/B-box 2 and coiled-coil/(PRY/SPRY) domains, respectively (Fig. 1A). The antiviral potency of TRIM5α has been shown to correlate with its affinity for the viral capsid lattice (5). Interestingly, a single amino acid change from arginine to proline at residue 332 (R332P) in the PRY/SPRY domain of huTRIM5α conferred the ability to restrict HIV-1 (14–16).Open in a separate windowFig. 1.(A) Schematic depiction of dimeric TRIM5α. The four domains are colored differently and their respective molecular masses are indicated. The two linker regions are labeled L1 and L2. (B) Size-exclusion chromatograms of rhesus (solid) and human (dashed) MBP-TRIM5α PRY/SPRY. The molecular masses of protein standards are indicated at the top.HIV-1 capsid (CA) proteins can assemble into closed fullerene cones or helical tubes; other structurally homologous retrovirus CA proteins form cylindrical or spherical capsids (17–19). Despite the diverse array of retroviral capsids, different shapes are recognized by the same TRIM5α protein or highly homologous orthologs (20). The binding interaction requires an assembled capsid lattice as individual CA molecules do not have an appreciable affinity to TRIM5α (21). This broad, yet specific lattice pattern-sensing ability resides in the capsid-recognition PRY/SPRY domain of TRIM5α (5, 13, 14, 16, 22). A TRIM5α truncation construct containing the coiled-coil and the PRY/SPRY domains (CC-SPRY) is sufficient to bind and disrupt HIV-1 CA assembly (23). However, the lack of detailed structural data on TRIM5α PRY/SPRY poses an obstacle to understanding the pattern-sensing mechanism by which TRIM5α interacts with the retrovirus capsid. Here we report the crystal structure of the rhTRIM5α PRY/SPRY domain that reveals important features for viral capsid recognition. Both our EM and biochemical data demonstrate that rhTRIM5α PRY/SPRY (PRY/SPRY_rh) alone is able to recognize HIV-1 capsid tubes, whereas huTRIM5α PRY/SPRY (PRY/SPRY_hu) cannot. These findings provide a structural framework that enables us to begin understanding the capsid pattern-recognition mechanisms of TRIM5α.     

Structural and functional analysis of two di-domain aromatase/cyclases from type II polyketide synthases

Aromatic polyketides make up a large class of natural products with diverse bioactivity. During biosynthesis, linear poly-β-ketone intermediates are regiospecifically cyclized, yielding molecules with defined cyclization patterns that are crucial for polyketide bioactivity. The aromatase/cyclases (ARO/CYCs) are responsible for regiospecific cyclization of bacterial polyketides. The two most common cyclization patterns are C7–C12 and C9–C14 cyclizations. We have previously characterized three monodomain ARO/CYCs: ZhuI, TcmN, and WhiE. The last remaining uncharacterized class of ARO/CYCs is the di-domain ARO/CYCs, which catalyze C7–C12 cyclization and/or aromatization. Di-domain ARO/CYCs can further be separated into two subclasses: “nonreducing” ARO/CYCs, which act on nonreduced poly-β-ketones, and “reducing” ARO/CYCs, which act on cyclized C9 reduced poly-β-ketones. For years, the functional role of each domain in cyclization and aromatization for di-domain ARO/CYCs has remained a mystery. Here we present what is to our knowledge the first structural and functional analysis, along with an in-depth comparison, of the nonreducing (StfQ) and reducing (BexL) di-domain ARO/CYCs. This work completes the structural and functional characterization of mono- and di-domain ARO/CYCs in bacterial type II polyketide synthases and lays the groundwork for engineered biosynthesis of new bioactive polyketides.The biosynthesis of type II aromatic polyketide natural products has been extensively investigated because of the versatile pharmacological properties of these compounds (1–7). The type II polyketide synthase (PKS) is composed of dissociated enzymes that are used iteratively and are responsible for the elongation, cyclization, and modification of the polyketide chain (Fig. 1) (3, 4, 8, 9). The regiospecific cyclization of an acyl carrier protein (ACP)-linked linear poly-β-ketone intermediate is a key transformation catalyzed by type II PKSs. However, the enzymatic mechanism of cyclization remains poorly understood (10–14). Without such knowledge, the polyketide cyclization pattern cannot be predicted; a full understanding of this process at the molecular level is essential for future biosynthetic engineering efforts.Open in a separate windowFig. 1.Schematic diagram of ARO/CYC activity and cyclization specificity in representative type II PKSs. The monodomain ARO/CYCs TcmN (PDB ID 2RER) and WhiE (PDB ID 3TVR) act on unreduced polyketide intermediates to generate C9–C14 cyclized and aromatized products. The monodomain ARO/CYC ZhuI (PDB ID 3TFZ) and di-domain ARO/CYC StfQ act on unreduced polyketide intermediates to generate C7–C12 cyclized and aromatized products. The di-domain ARO/CYC BexL acts on C9 reduced, C7–C12 cyclized intermediates and catalyzes the aromatization of the C7–12 cyclized ring by dehydration of the C9 hydroxyl group.In 2008, we reported the crystal structure of the first aromatase/cyclase (ARO/CYC) (TcmN ARO/CYC), which is a single-domain protein (15). On the basis of the structural analysis and mutagenesis results, we proposed that monodomain ARO/CYCs contain an active site and are capable of catalyzing polyketide cyclization and aromatization. Since then, we have performed structural and biochemical studies of two other monodomain ARO/CYCs: WhiE and ZhuI (Fig. 1) (16, 17). These studies provided strong evidence supporting our hypothesis that ARO/CYC is the site of polyketide cyclization. However, many type II PKSs contain di-domain ARO/CYCs that have two seemingly identical domains (18–23). Why these enzymes require two domains (as opposed to just one) and how they conduct the cyclization/aromatization are not understood.The di-domain ARO/CYCs are found in both nonreducing and reducing PKSs (18, 24). In nonreducing systems, the di-domain ARO/CYCs regiospecifically cyclize a polyketide between C7 and C12, followed by aromatization (18). In reducing systems, a ketoreductase (KR) first regiospecifically cyclizes the linear poly-β-ketone from C12 to C7, followed by a highly specific C9-carbonyl reduction (7, 25). A di-domain ARO/CYC then catalyzes the dehydration of the C9 hydroxyl, followed by first-ring aromatization (Fig. 1) (14). Therefore, in a nonreducing system, the growing poly-β-ketone intermediate is transported directly from the ketosynthase (KS) to the ARO/CYC. In contrast, in a reducing system, the intermediate needs to be transported from KS to KR and then to ARO/CYC. Before this study, there was no knowledge of whether there is any difference between the di-domain ARO/CYCs in reducing versus nonreducing PKSs, nor any information on the role that ARO/CYCs may play in determining the product specificity of reducing and nonreducing PKSs. The key issue that has hampered the investigation of this group of enzymes is the difficulty in protein crystallization.To critically compare the reducing and nonreducing di-domain ARO/CYCs, we have chosen StfQ as a model nonreducing di-domain ARO/CYC and BexL as a model reducing di-domain ARO/CYC (Fig. 1). StfQ is a di-domain ARO/CYC from Streptomyces steffisburgensis and is part of the nonreducing PKS catalyzing the biosynthesis of steffimycin, which shows promising antitumor activities (26–28). StfQ is the enzyme responsible for the C7–C12 first-ring cyclization and aromatization of the elongated poly-β-ketone substrate. In contrast, BexL is a di-domain ARO/CYC in the reducing PKS responsible for the biosynthesis of the anticancer agent BE-7585A. The linear poly-β-ketone precursor of BE-7585A is first cyclized, then reduced at the C9 position by KR, and then aromatized by BexL (Fig. 1) (24). Both StfQ and BexL use 20-carbon poly-β-ketone substrates; therefore, the structural enzymology of these two ARO/CYCs offers a great opportunity for side-by-side comparison with insight into the catalytic mechanisms of di-domain ARO/CYCs. Here we present the first structural and biochemical characterization, to our knowledge, of two di-domain ARO/CYCs, StfQ and BexL, using X-ray crystallography, structure-based mutagenesis, in silico docking, and in vitro functional assays.     

De novo production of the plant-derived alkaloid strictosidine in yeast

The monoterpene indole alkaloids are a large group of plant-derived specialized metabolites, many of which have valuable pharmaceutical or biological activity. There are ∼3,000 monoterpene indole alkaloids produced by thousands of plant species in numerous families. The diverse chemical structures found in this metabolite class originate from strictosidine, which is the last common biosynthetic intermediate for all monoterpene indole alkaloid enzymatic pathways. Reconstitution of biosynthetic pathways in a heterologous host is a promising strategy for rapid and inexpensive production of complex molecules that are found in plants. Here, we demonstrate how strictosidine can be produced de novo in a Saccharomyces cerevisiae host from 14 known monoterpene indole alkaloid pathway genes, along with an additional seven genes and three gene deletions that enhance secondary metabolism. This system provides an important resource for developing the production of more complex plant-derived alkaloids, engineering of nonnatural derivatives, identification of bottlenecks in monoterpene indole alkaloid biosynthesis, and discovery of new pathway genes in a convenient yeast host.Monoterpene indole alkaloids (MIAs) are a diverse family of complex nitrogen-containing plant-derived metabolites (1, 2). This metabolite class is found in thousands of plant species from the Apocynaceae, Loganiaceae, Rubiaceae, Icacinaceae, Nyssaceae, and Alangiaceae plant families (2, 3). Many MIAs and MIA derivatives have medicinal properties; for example, vinblastine, vincristine, and vinflunine are approved anticancer therapeutics (4, 5). These structurally complex compounds can be difficult to chemically synthesize (6, 7). Consequently, industrial production relies on extraction from the plant, but these compounds are often produced in small quantities as complex mixtures, making isolation challenging, laborious, and expensive (8–10). Reconstitution of plant pathways in microbial hosts is proving to be a promising approach to access plant-derived compounds as evidenced by the successful production of terpenes, flavonoids, and benzylisoquinoline alkaloids in microorganisms (11–19). Microbial hosts can also be used to construct hybrid biosynthetic pathways to generate modified natural products with potentially enhanced bioactivities (8, 20, 21). Across numerous plant species, strictosidine is believed to be the core scaffold from which all 3,000 known MIAs are derived (1, 2). Strictosidine undergoes a variety of redox reactions and rearrangements to form the thousands of compounds that comprise the MIA natural product family (Fig. 1) (1, 2). Due to the importance of strictosidine, the last common biosynthetic intermediate for all known MIAs, we chose to focus on heterologous production of this complex molecule (1). Therefore, strictosidine reconstitution represents the necessary first step for heterologous production of high-value MIAs.Open in a separate windowFig. 1.Strictosidine, the central intermediate in monoterpene indole alkaloid (MIA) biosynthesis, undergoes a series of reactions to produce over 3,000 known MIAs such as vincristine, quinine, and strychnine.     

Aptamer photoregulation in vivo

The in vivo application of aptamers as therapeutics could be improved by enhancing target-specific accumulation while minimizing off-target uptake. We designed a light-triggered system that permits spatiotemporal regulation of aptamer activity in vitro and in vivo. Cell binding by the aptamer was prevented by hybridizing the aptamer to a photo-labile complementary oligonucleotide. Upon irradiation at the tumor site, the aptamer was liberated, leading to prolonged intratumoral retention. The relative distribution of the aptamer to the liver and kidney was also significantly decreased, compared to that of the free aptamer.Aptamers are single-stranded nucleic acids that have emerged as a promising class of therapeutics owing to their relative ease of synthesis and high affinity and selectivity toward a range of targets including small molecules, proteins, viral particles, and living cells (1–6). Aptamers can fold into well-defined conformations and are more resistant to enzymatic degradation than other oligonucleotides (7–9). Aptamers have been suggested for imaging applications because their relatively small size and molecular mass (∼10 kDa) allow fast tissue penetration and clearance from blood (10, 11). The same characteristics make aptamers promising for effective delivery of diagnostic and therapeutic agents to tissues or organs. However, nonspecific accumulation of aptamers in normal tissues is undesirable (12–15) because it diminishes the proportion of aptamer that targets the desired tissue. This can adversely affect the therapeutic index of the aptamer; this may be particularly true if the aptamer is conjugated to a drug or drug delivery device. Moreover, aptamers themselves can have nonspecific toxic effects (16, 17). Ideally aptamers would achieve a high concentration in a pathological tissue of interest while maintaining low levels elsewhere. The activity of aptamers can be modulated in vivo by binding to polymers or complementary oligonucleotide sequences (18–20), but spatiotemporal regulation of aptamer activity in vivo has not been achieved, whereby activity would be enhanced in target tissues and not others. Here, we report a strategy to provide light-triggered control of aptamer function and distribution in vivo.Light is an excellent means of providing external spatiotemporal control of biological systems (21–26). Many strategies have been developed to incorporate photosensitive groups in nucleotides that can control cellular function or affect biological pathways or gene expression by light (24–29). Of particular interest, such approaches can be used to provide spatiotemporal control of gene activation (24). Here we hypothesized that light triggering can be used to achieve spatiotemporal control of binding of an aptamer injected systemically to its target tissue in vivo, which would have implications for control of delivery of therapeutic aptamers and/or conjugated drugs or drug delivery systems. We designed a photo-triggerable system whereby the aptamer of interest is inactivated by hybridization to a photo-labile complementary oligonucleotide. Upon irradiation, the complementary sequence breaks down, releasing the functional aptamer (Fig. 1). The aptamer of interest is the single-stranded DNA 26-mer aptamer AS1411 (A₁₄₁₁; sequence: 5′-GGT GGT GGT GGT TGT GGT GGT GGT GG-3′) that binds with high affinity and selectivity to nucleolin (30–32), which is overexpressed on the cell membrane of several types of cancer cells, including the 4T1 breast cancer cells used here (33–35). A₁₄₁₁ has been used for cancer targeting in vitro and in vivo (35, 36). A complementary photo-triggerable inhibitory oligonucleotide (OliP) was designed [sequence: 5′-CCA CCA//CCA CCA//CAA CCA C-3′, where // indicates photo-labile 1-(2-nitrophenyl)ethyl bonds (37); Scheme S1].Open in a separate windowFig. 1.The AS1411 aptamer (A₁₄₁₁, red DNA strand) is hybridized to a complementary oligonucleotide (OliP, green DNA strand) containing photo-cleavable bonds (black dots). The hybridized complex cannot bind cells. The A₁₄₁₁ can be released by light-triggered breakage of the OliP, allowing binding to cell surfaces.     

Multiaddressable molecular rectangles with reversible host–guest interactions: Modulation of pH-controlled guest release and capture

A series of multiaddressable platinum(II) molecular rectangles with different rigidities and cavity sizes has been synthesized by endcapping the U-shaped diplatinum(II) terpyridine moiety with various bis-alkynyl ligands. The studies of the host–guest association with various square planar platinum(II), palladium(II), and gold(III) complexes and the related low-dimensional gold(I) complexes, most of which are potential anticancer therapeutics, have been performed. Excellent guest confinement and selectivity of the rectangular architecture have been shown. Introduction of pH-responsive functionalities to the ligand backbone generates multifunctional molecular rectangles that exhibit reversible guest release and capture on the addition of acids and bases, indicating their potential in controlled therapeutics delivery on pH modulation. The reversible host–guest interactions are found to be strongly perturbed by metal–metal and π–π interactions and to a certain extent, electrostatic interactions, giving rise to various spectroscopic changes depending on the nature of the guest molecules. Their binding mode and thermodynamic parameters have been determined by 2D NMR and van’t Hoff analysis and supported by computational study.The study of metal–metal interactions has drawn enormous attention since the past two decades because of the intriguing spectroscopic and photophysical properties arising from the close proximity of the metal centers (1, 2). Square planar d⁸ platinum(II) complexes with coordination unsaturation are one of the important classes of metal complexes that have been extensively explored because of their capability to exhibit metal–metal interactions and display rich photophysical properties (3–26). Platinum(II) terpyridine complexes have been found to exhibit rich polymorphism in the solid state (16–20) owing to their square planar coordination geometry, which permits facile access to Pt(II)···Pt(II) interactions as well as π–π interactions between the chromophores. It was not until 2001 that the first successful synthesis of platinum(II) terpyridine alkynyl complexes, which possess enhanced solubility and luminescence compared with the chloro counterpart, was reported (16). Additional efforts have been devoted to the use of the system to respond to external stimuli, such as variation in solvent composition (17, 18), pH (19, 20), temperature (21, 22), addition of ionic (24–26), and polymeric species (27, 28), in which spectral changes induced by strong Pt(II)···Pt(II) and π−π interactions have been displayed.In the past few decades, enormous efforts have been devoted to the construction of molecular architectures by fusing the organic framework to the transition metal centers through self-assembly processes (29–57). There has been continuous interest in the construction of stimuli-responsive metallosupramolecular architectures with diverse sizes, shapes, and symmetries to rationalize the criteria for molecular recognition and impart them on unique areas of applications, such as stereoselective guest encapsulation and molecular transporting devices (45–65). Although such a variety of metal–organic macrocyclic architectures has been reported, those involving the use of noncovalent interactions other than those of hydrogen bonding, donor–acceptor, electrostatic, and hydrophobic–hydrophobic interactions as well as luminescence changes that depend on the nature of the guests, which would be attractive for chemo- and biosensing, have been rare and are rather underexplored. Examples of such systems that can exhibit reversible host–guest association are also limited.Since the discovery of anticancer properties of cisplatin in 1969 (58), the coordination chemistry and the development of related species with enhanced properties and reduced cytotoxicity have received enormous attention. Although the potency and cytotoxicity studies are important, the availability of the drugs and their transport and release to the site of action are equally important. Thus, the design of smart drug delivery systems has been an area of growing interest. The first phosphorescent molecular tweezers making use of the alkynylplatinum(II) terpyridine moiety have been reported by our group to show their host–guest interactions with transition metal complexes (57). However, the opened structures of the tweezers have limited their selectivity and functionality. To accomplish the controlled drug delivery functionalities, the first main strategy is to rigidify the molecular architecture of the host from tweezers to a rectangle, so that the guest molecules would be better accommodated within the cavity, which may lead to a more selective encapsulation of guests within a definite size and steric environment. The possibility of introducing responsive functionalities into the molecular rectangles, which may serve as models for the study of on-demand controlled guest capture and release systems, has also been explored. pH-sensitive pyridine moieties have, therefore, been incorporated into the backbone of the rectangle to modulate the reversible host–guest interaction within the constrained rectangle environment on protonation/deprotonation of the pyridine nitrogen atom to achieve multiaddressable functions that would not have been readily achievable with the molecular tweezers structure. Additionally, the use of various platinum and gold complexes as guest molecules, which have been shown to display anticancer therapeutic behavior (58–65), may lead to the design of a smart multiaddressable molecular rectangle system that could capture and release specific guest molecules under different pH conditions to achieve proof-of-principle on-demand controlled drug delivery. Herein, the design and synthesis of a series of alkynylplatinum(II) terpyridine molecular rectangles (Fig. 1) with different geometries, topologies and electronic properties are reported. Moreover, the encapsulation of various guest molecules is also investigated in detail to provide a proof-of-principle model for the design of artificial drug delivery systems with the modulation of drug release by pH.Open in a separate windowFig. 1.Molecular structures of rectangles 1−4.     

Robust efficiency and actuator saturation explain healthy heart rate control and variability

The correlation of healthy states with heart rate variability (HRV) using time series analyses is well documented. Whereas these studies note the accepted proximal role of autonomic nervous system balance in HRV patterns, the responsible deeper physiological, clinically relevant mechanisms have not been fully explained. Using mathematical tools from control theory, we combine mechanistic models of basic physiology with experimental exercise data from healthy human subjects to explain causal relationships among states of stress vs. health, HR control, and HRV, and more importantly, the physiologic requirements and constraints underlying these relationships. Nonlinear dynamics play an important explanatory role––most fundamentally in the actuator saturations arising from unavoidable tradeoffs in robust homeostasis and metabolic efficiency. These results are grounded in domain-specific mechanisms, tradeoffs, and constraints, but they also illustrate important, universal properties of complex systems. We show that the study of complex biological phenomena like HRV requires a framework which facilitates inclusion of diverse domain specifics (e.g., due to physiology, evolution, and measurement technology) in addition to general theories of efficiency, robustness, feedback, dynamics, and supporting mathematical tools.Biological systems display a variety of well-known rhythms in physiological signals (1–6), with particular patterns of variability associated with a healthy state (2–6). Decades of research demonstrate that heart rate (HR) in healthy humans has high variability, and loss of this high HR variability (HRV) is correlated with adverse states such as stress, fatigue, physiologic senescence, or disease (6–13). The dominant approach to analysis of HRV has been to focus on statistics and patterns in HR time series that have been interpreted as fractal, chaotic, scale-free, critical, etc. (6–17). The appeal of time series analysis is understandable as it puts HRV in the context of a broad and popular approach to complex systems (5, 18), all while requiring minimal attention to domain-specific (e.g., physiological) details. However, despite intense research activity in this area, there is limited consensus regarding causation or mechanism and minimal clinical application of the observed phenomena (10). This paper takes a completely different approach, aiming for more fundamental rigor (19–24) and methods that have the potential for clinical relevance. Here we use and model data from experimental studies of exercising healthy athletes, to add simple physiological explanations for the largest source of HRV and its changes during exercise. We also present methods that can be used to systematically pursue further explanations about HRV that can generalize to less healthy subjects.Fig. 1 shows the type of HR data analyzed, collected from healthy young athletes (n = 5). The data display responses to changes in muscle work rate on a stationary bicycle during mostly aerobic exercise. Fig. 1A shows three separate exercise sessions with identical workload fluctuations about three different means. With proper sleep, hydration, nutrition, and prevention from overheating, trained athletes can maintain the highest workload in Fig. 1 for hours and the lower and middle levels almost indefinitely. This ability requires robust efficiency: High workloads are sustained while robustly maintaining metabolic homeostasis, a particularly challenging goal in the case of the relatively large, metabolically demanding, and fragile human brain.Open in a separate windowFig. 1.HR responses to simple changes in muscle work rate on a stationary bicycle: Each experimental subject performed separate stationary cycle exercises of ∼10 min for each workload profile, with different means but nearly identical square wave fluctuations around the mean. A typical result is shown from subject 1 for three workload profiles with time on the horizontal axis (zoomed in to focus on a 6-min window). (A) HR (red) and workload (blue); linear local piecewise static fits (black) with different parameters for each exercise. The workload units (most strenuous exercise on top of graph) are shifted and scaled so that the blue curves are also the best global linear fit. (B) Corresponding dynamics fits, either local piecewise linear (black) or global linear (blue). Note that, on all time scales, mean HR increases and variability (HRV) goes down with the increasing workload. Breathing was spontaneous (not controlled).Whereas mean HR in Fig. 1A increases monotonically with workloads, both slow and fast fluctuations (i.e., HRV) in HR are saturating nonlinear functions of workloads, meaning that both high- and low-frequency HRV component goes down. Results from all subjects showed qualitatively similar nonlinearities (SI Appendix). We will argue that this saturating nonlinearity is the simplest and most fundamental example of change in HRV in response to stressors (11, 12, 25) [exercise in the experimental case, but in general also fatigue, dehydration, trauma, infection, even fear and anxiety (6–9, 11, 12, 25)].Physiologists have correlated HRV and autonomic tone (7, 11, 12, 14), and the (im)balance between sympathetic stimulation and parasympathetic withdrawal (12, 26–28). The alternation in autonomic control of HR (more sympathetic and less parasympathetic tone during exercise) serves as an obvious proximate cause for how the HRV changes as shown in Fig. 1, but the ultimate question remains as to why the system is implemented this way. It could be an evolutionary accident, or could follow from hard physiologic tradeoff requirements on cardiovascular control, as work in other systems suggests (1). Here, the explanation of HRV similarly involves hard physiological tradeoffs in robust efficiency and employs the mathematical tools necessary to make this explanation rigorous in the context of large measurement and modeling uncertainties.     

Remote loading of preencapsulated drugs into stealth liposomes

Loading drugs into carriers such as liposomes can increase the therapeutic ratio by reducing drug concentrations in normal tissues and raising their concentrations in tumors. Although this strategy has proven advantageous in certain circumstances, many drugs are highly hydrophobic and nonionizable and cannot be loaded into liposomes through conventional means. We hypothesized that such drugs could be actively loaded into liposomes by encapsulating them into specially designed cyclodextrins. To test this hypothesis, two hydrophobic drugs that had failed phase II clinical trials because of excess toxicity at deliverable doses were evaluated. In both cases, the drugs could be remotely loaded into liposomes after their encapsulation (preloading) into cyclodextrins and administered to mice at higher doses and with greater efficacy than possible with the free drugs.There is currently wide interest in the development of nanoparticles for drug delivery (1–7). This area of research is particularly relevant to cancer drugs, wherein the therapeutic ratio (dose required for effectiveness to dose causing toxicity) is often low. Nanoparticles carrying drugs can increase this therapeutic ratio over that achieved with the free drug through several mechanisms. In particular, drugs delivered by nanoparticles are thought to selectively enhance the concentration of the drugs in tumors as a result of the enhanced permeability and retention (EPR) effect (8–18). The enhanced permeability results from a leaky tumor vascular system, whereas the enhanced retention results from the disorganized lymphatic system that is characteristic of malignant tumors.Much current work in this field is devoted to designing novel materials for nanoparticle generation. This new generation of nanoparticles can carry drugs—particularly those that are insoluble in aqueous medium—that are difficult to incorporate into conventional nanoparticles such as liposomes. However, the older generation of nanoparticles has a major practical advantage in that they have been extensively tested in humans and approved by regulatory agencies such as the Food and Drug Administration in the United States and the European Medicines Agency in Europe. Unfortunately, many drugs cannot be easily or effectively loaded into liposomes, thereby compromising their general use.In general, liposomal drug loading is achieved by either passive or active methods (9, 19–22). Passive loading involves dissolution of dried lipid films in aqueous solutions containing the drug of interest. This approach can only be used for water-soluble drugs, and the efficiency of loading is often low. In contrast, active loading can be extremely efficient, resulting in high intraliposomal concentrations and minimal wastage of precious chemotherapeutic agents (9, 23, 24). In active loading, drug internalization into preformed liposomes is typically driven by a transmembrane pH gradient. The pH outside the liposome allows some of the drug to exist in an unionized form, able to migrate across the lipid bilayer. Once inside the liposome, the drug becomes ionized due to the differing pH and becomes trapped there (Fig. 1A). Many reports have emphasized the dependence of liposome loading on the nature of the transmembrane pH gradient, membrane–water partitioning, internal buffering capacity, aqueous solubility of the drug, lipid composition, and other factors (25–28). As described in a recent model (28), the aqueous solubility of the drug is one of the requirements for efficient active loading. Another key element for the success of remote loading is the presence of weakly basic functional groups on the small molecule.Open in a separate windowFig. 1.Schematic representation of active loading of a liposome. (A) Remote loading of an ionizable hydrophilic drug using a transmembrane pH results in efficient incorporation. (B) A poorly soluble hydrophobic drug results in meager incorporation into preformed liposomes under similar conditions. (C) Encapsulation of a poorly soluble drug into an ionizable cyclodextrin (R = H, ionizable alkyl or aryl groups) enhances its water solubility and permits efficient liposomal loading via a pH gradient.Only a small fraction of chemotherapeutic agents possesses the features required for active loading with established techniques. Attempts at active loading of such nonionizable drugs into preformed liposomes result in poor loading efficiencies (Fig. 1B). One potential solution to this problem is the addition of weakly basic functional groups to otherwise unloadable drugs, an addition that would provide the charge necessary to drive these drugs across the pH gradient. However, covalent modification of drugs often alters their biological and chemical properties, and is not desirable in many circumstances. We therefore attempted to develop a general strategy that would allow loading of unmodified hydrophobic chemotherapeutics devoid of weakly basic functional groups. For this purpose, we used modified β-cyclodextrins to facilitate the loading of such drugs into liposomes (Fig. 1C).Cyclodextrins are a family of cyclic sugars that are commonly used to solubilize hydrophobic drugs (29–32). They possess a hydrophobic cavity and a hydrophilic surface and are known to stably encapsulate a large variety of hydrophobic organic molecules in aqueous media. Cyclodextrins bind to their cargos strongly enough to form relatively stable complexes, but allow a slow efflux of the entrapped drug and consequent steady concentrations of free drug once administered in vivo (33, 34). Cyclodextrins are nontoxic and biologically inert, and several have been approved for use in humans (35–38).In this work, we synthesized cyclodextrins with multiple weakly basic or weakly acidic functional groups on their solvent-exposed surfaces. We hypothesized that these modified cyclodextrins would still be able to encapsulate chemotherapeutic agents and that the cyclodextrin–drug complexes could then be remotely loaded into liposomes using pH gradients that exploited ionizable groups on the cyclodextrins rather than on the drugs themselves.     

Respiratory virus transmission dynamics determine timing of asthma exacerbation peaks: Evidence from a population-level model

Asthma exacerbations exhibit a consistent annual pattern, closely mirroring the school calendar. Although respiratory viruses—the “common cold” viruses—are implicated as a principal cause, there is little evidence to link viral prevalence to seasonal differences in risk. We jointly fit a common cold transmission model and a model of biological and environmental exacerbation triggers to estimate effects on hospitalization risk. Asthma hospitalization rate, influenza prevalence, and air quality measures are available, but common cold circulation is not; therefore, we generate estimates of viral prevalence using a transmission model. Our deterministic multivirus transmission model includes transmission rates that vary when school is closed. We jointly fit the two models to 7 y of daily asthma hospitalizations in adults and children (66,000 events) in eight metropolitan areas. For children, we find that daily viral prevalence is the strongest predictor of asthma hospitalizations, with transmission reduced by 45% (95% credible interval =41–49%) during school closures. We detect a transient period of nonspecific immunity between infections lasting 19 (17–21) d. For adults, hospitalizations are more variable, with influenza driving wintertime peaks. Neither particulate matter nor ozone was an important predictor, perhaps because of the large geographic area of the populations. The school calendar clearly and predictably drives seasonal variation in common cold prevalence, which results in the “back-to-school” asthma exacerbation pattern seen in children and indirectly contributes to exacerbation risk in adults. This study provides a framework for anticipating the seasonal dynamics of common colds and the associated risks for asthmatics.Asthma is a chronic airway condition with increasing prevalence in many countries (1, 2). Exacerbations, the worsening of asthma symptoms, are a growing public health concern, resulting in millions of missed work and school days and $50 billion in direct healthcare costs in the United States each year (3–5). Prior studies have examined environmental correlates of asthma exacerbations, including air quality measures (6–8), whereas others have considered the role of respiratory virus infections in triggering asthma exacerbation (9–13). However, none have simultaneously considered both infectious and noninfectious factors that potentially influence the large-scale spatiotemporal dynamics of asthma exacerbations.Asthma-related hospitalizations exhibit an extraordinarily consistent seasonal pattern from year to year (14). In children, this pattern strongly reflects the school calendar (15–17). A wave of asthma exacerbations in children ensues shortly after the return to school after summer break (shown in Fig. 1 for Texas in mid-August). The return-to-school peak has been termed the “September epidemic of asthma” (14) and noted in the United Kingdom (18), Canada (17, 19), and elsewhere (20). Asthma hospitalizations also seem to rise after the 2-wk winter holiday (late December through early January) and 1-wk spring break (late March) (Fig. 1).Open in a separate windowFig. 1.Daily number of asthma hospitalizations. Total hospitalizations in the eight largest metropolitan areas in Texas from August of 2004 to August of 2005, where markers indicate the first day of the month. Daily count values (light gray) and a spline-smoothed value (dark gray) in (A) children ages 5–18 y old and (B) adults ages 19–55 y old. In 2004, most Texas schools started in mid-August, took a 2-wk winter break in late December to early January, and took a 1-wk spring break in late March.Respiratory virus infections, including those responsible for the common cold, are known to cause exacerbations in asthmatic children and to a lesser extent, adults suffering from respiratory diseases (11, 21, 22). In particular, rhinovirus has been widely implicated in asthma exacerbations and wheezing-related hospitalizations (13, 16, 23–29). Although asthma is not infectious, these aggravating viruses are infectious. Consequently, the dynamics of asthma hospitalizations can seem as if children are serving as transmission vectors for exacerbations (19). Data on the prevalence of these common viruses are infrequently available and are never available for large sample sizes.Common cold viruses spread rampantly—typically causing two to four relatively mild infections in adults and three to eight infections in children annually (30, 31). Although asthmatics tend to experience more severe and prolonged illness on infection, studies suggest that the frequency of infection is similar for asthmatics and nonasthmatics (21). However, little is known about the transmission dynamics of these viruses or the extent to which they account for the complex annual cycles of asthma exacerbations. Mathematical models of viral transmission are widely used for estimating epidemiological parameters, such as transmission rates, from disease surveillance data (32–34). Such data are rare for common colds, because most infections are subclinical, never entering the healthcare system. Here, we exploit asthmatics as a “sentinel” population for the common cold to infer the transmission dynamics of these viruses.Although viral infections are an important trigger for asthma exacerbations, they are not the only cause of asthma hospitalizations. In particular, poor air quality is thought to be a critical risk factor, and the link between pollution and asthma has been studied extensively (8, 35–39). Elevated particulate matter and ozone levels have both been associated with increased asthma exacerbations and hospitalization events.By fitting a mathematical model of viral transmission jointly with a model of noninfectious drivers to asthma hospitalization data from eight metropolitan populations in Texas, we are able to both estimate epidemiological characteristics of common cold viruses and rigorously assess the relative contributions of proposed infectious and noninfectious drivers of asthma exacerbations. Our analysis provides insight into the dynamics of common cold viruses and a robust framework for predicting times of heightened risk and thus, key periods for clinical intervention in the growing population of asthmatic people.