Short peptides are uniquely versatile building blocks for self-assembly. Supramolecular peptide assemblies can be used to construct functional hydrogel biomaterials-an attractive approach for neural tissue engineering. Here, we report a new class of short, five-residue peptides that form hydrogels with nanofiber structures. Using rheology and spectroscopy, we describe how sequence variations, pH, and peptide concentration alter the mechanical properties of our pentapeptide hydrogels. We find that this class of seven unmodified peptides forms robust hydrogels from 0.2-20 kPa at low weight percent (less than 3 wt. %) in cell culture media, and undergoes shear-thinning and rapid self-healing. The peptides self-assemble into long fibrils with sequence-dependent fibrillar morphologies. These fibrils exhibit a unique twisted ribbon shape, as visualized by TEM and Cryo-EM imaging, with diameters in the low tens of nanometers and periodicities similar to amyloid fibrils. Experimental gelation behavior corroborates our molecular dynamics simulations, which demonstrate peptide assembly behavior, an increase in -sheet content, and patterns of variation in solvent accessibility. Our Rapidly Assembling Pentapeptides for Injectable Delivery (RAPID) hydrogels are syringe-injectable and support cytocompatible encapsulation of oligodendrocyte progenitor cells (OPCs), as well as their proliferation and threedimensional process extension. Furthermore, RAPID gels protect OPCs from mechanical membrane disruption and acute loss of viability when ejected from a syringe needle, highlighting the protective capability of the hydrogel as potential cell carriers for transplantation therapies. The tunable mechanical and structural properties of these supramolecular assemblies are shown to be permissive to cell expansion and remodeling, making this hydrogel system suitable as an injectable material for cell delivery and tissue engineering applications.

Background Given that an individual’s age and gender are strongly predictive of coronavirus disease 2019 (COVID-19) outcomes, do such factors imply anything about preferable therapeutic options? Methods An analysis of electronic health records for a large (68,466-case), international COVID-19 cohort, in 5-year age strata, revealed age-dependent sex differences. In particular, we surveyed the effects of systemic hormone administration in women. The primary outcome for estradiol therapy was death. Odds ratios (ORs) and Kaplan-Meier survival curves were analyzed for 37,086 COVID-19 women in two age groups: pre- (15–49 years) and peri-/post-menopausal (> 50 years). Results The incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is higher in women than men (by about + 15%) and, in contrast, the fatality rate is higher in men (about + 50%). Interestingly, the relationships between these quantities are linked to age: pre-adolescent girls and boys had the same risk of infection and fatality rate, while adult premenopausal women had a significantly higher risk of infection than men in the same 5-year age stratum (about 16,000 vs. 12,000 cases). This ratio changed again in peri- and postmenopausal women, with infection susceptibility converging with men. While fatality rates increased continuously with age for both sexes, at 50 years, there was a steeper increase for men. Thus far, these types of intricacies have been largely neglected. Because the hormone 17ß-estradiol influences expression of the human angiotensin-converting enzyme 2 (ACE2) protein, which plays a role in SARS-CoV-2 cellular entry, propensity score matching was performed for the women’s sub-cohort, comparing users vs. non-users of estradiol. This retrospective study of hormone therapy in female COVID-19 patients shows that the fatality risk for women > 50 years receiving estradiol therapy (user group) is reduced by more than 50%; the OR was 0.33, 95% CI [0.18, 0.62] and the hazard ratio (HR) was 0.29, 95% CI [0.11,0.76]. For younger, pre-menopausal women (15–49 years), the risk of COVID-19 fatality is the same irrespective of estradiol treatment, probably because of higher endogenous estradiol levels. Conclusions As of this writing, still no effective drug treatment is available for COVID-19; since estradiol shows such a strong improvement regarding fatality in COVID-19, we suggest prospective studies on the potentially more broadly protective roles of this naturally occurring hormone.

Immune dysregulation is characteristic of the more severe stages of SARS-CoV-2 infection. Understanding the mechanisms by which the immune system contributes to COVID-19 severity may open new avenues to treatment. Here we report that elevated interleukin-13 (IL-13) was associated with the need for mechanical ventilation in two independent patient cohorts.In addition, patients who acquired COVID-19 while prescribed Dupilumab, a mAb that blocks IL-13 and IL-4 signaling, had less severe disease. In SARS-CoV-2 infected mice, IL-13 neutralization reduced death and disease severity without affecting viral load, demonstrating an immunopathogenic role for this cytokine. Following anti-IL-13 treatment in infected mice, hyaluronan synthase 1 (Has1) was the most downregulated gene and accumulation of the hyaluronan polysaccharide was decreased in the lung. In patients with COVID-19, hyaluronan was increased in the lungs and plasma. Blockade of the hyaluronan receptor, CD44, reduced mortality in infected mice, supporting the importance of hyaluronan as a pathogenic mediator.Finally, hyaluronan was directly induced in the lungs of mice by administration of IL-13, indicating a new role for IL-13 in lung disease. Understanding the role of IL-13 and hyaluronan has important implications for therapy of COVID-19 and potentially other pulmonary diseases.Summary: IL-13 levels were elevated in patients with severe COVID-19. In a mouse model of disease, IL-13 neutralization reduced disease and decreased lung hyaluronan deposition.Administration of IL-13 induced hyaluronan in the lung. Blockade of the hyaluronan receptor CD44 prevented mortality, highlighting a novel mechanism for IL-13-mediated hyaluronan synthesis in pulmonary pathology.

The small b-barrel (SBB) is an ancient protein structural domain characterized by extremes: it features a broad range of structural varieties, a deeply intricate evolutionary history, and it is associated with a bewildering array of cellular pathways. Here, we present a thorough, survey-based analysis of the structural properties of SBBs. We first consider the defining properties of the SBB, including various systems of nomenclature used to describe it, and we introduce the unifying concept of an ''urfold.'' To begin elucidating how vast functional diversity can be achieved by a relatively simple domain, we explore the anatomy of the SBB and its representative structural variants. Many SBB proteins assemble into cyclic oligomers as the biologically functional units; these oligomers often bind RNA, and typically exhibit great quaternary structural plasticity (homomeric and heteromeric rings, variable subunit stoichiometries, etc.). We conclude with three themes that emerge from the rich structure 4 function versatility of the SBB.Strand b1 is red, b2 is orange, b3 is yellow, and b4 is green; for the SH3 and OB folds, the fifth strand is also shown (gray). Branches along a sample path in this digraph are highlighted in tan (subtree at right), yielding the 1 Zhang and Kim, 2000); these two sheets, near the center of the image, are drawn simply to illustrate tree traversal. The base of the overall tree (at center) is a decision between the two possible configurations (parallel, antiparallel) for the simplest possible sheet-i.e., a tandem pair of strands (⇨∿∿⇨). Traversing the tree from this split ''root'' to the leaves corresponds to building-up the sheet, and the tree's branching structure elucidates the n!• •2 nÀ2 unique topologies that are possible for a sheet of n strands; the successive branches of this unrooted k-ary tree are of degrees 2, 6, 2, 2, 2. The positions of the SH3 and OB folds are indicated by cyan and purple paths (subtree at left). Other features of b-sheets are also elucidated by this hierarchical representation, such as the fact that there are 24 unique arrangements of two sequentially adjacent b-hairpin motifs (red circles, left subtree). If the origin for strand numbering is taken as arbitrary (e.g., labeling a sequence 2/3/4 does not differ from 1/2/3), then the OB topology (pink path, left) can be seen to cluster closely with the SH3; the yellow region delimits a putative SBB ''urfold'' basin in fold-space, subsuming the SH3 and OB folds.

Sm proteins form the core of small nuclear ribonucleoprotein particles (snRNPs), making them key components of several mRNAprocessing assemblies, including the spliceosome. We report the 1.75-Å crystal structure of SmAP, an Sm-like archaeal protein that forms a heptameric ring perforated by a cationic pore. In addition to providing direct evidence for such an assembly in eukaryotic snRNPs, this structure (i) shows that SmAP homodimers are structurally similar to human Sm heterodimers, (ii) supports a gene duplication model of Sm protein evolution, and (iii) offers a model of SmAP bound to single-stranded RNA (ssRNA) that explains Sm binding-site specificity. The pronounced electrostatic asymmetry of the SmAP surface imparts directionality to putative SmAP-RNA interactions.E ukaryotic pre-mRNA processing is an intricate cellular task whose many steps include intron excision. This final maturation step occurs in the spliceosome, a large (Ϸ60 S), transiently stable ribonucleoprotein particle that ligates two exons and releases an intron lariat. The major spliceosome contains several small nuclear ribonucleoprotein particles (snRNPs; e.g., U1, U2, and U4͞U6⅐U5), and each U snRNP consists of a respective small nuclear RNA (snRNA; e.g., U1, U2) and many proteins (reviewed in refs. 1 and 2). The subset of proteins common to all spliceosomal U snRNPs is the Sm proteins. Discovered as a group of eight small antigens involved in autoimmune diseases such as systemic lupus erythematosus (3), these core snRNP Sm proteins have been found in most eukaryotes (4) and, recently, in a few archaeal species (ref. 5 and this report). Also, several sets of Sm-like (Lsm) proteins have been discovered in organisms with Sm proteins (4, 6). Biochemical characterization of Lsm proteins has verified their similarity to canonical Sm proteins (reviewed in ref. 7), and this report treats them as equivalent.Together with U snRNAs, canonical Sm proteins form snRNP core complexes. The molecular structure and function(s) of Sm assemblies and Sm-RNA interactions within these core complexes are unknown, but are presumably more generic than those of snRNP-specific proteins. Cytoplasmic Sm proteins associate with exported snRNAs at short single-stranded regions that are usually flanked by stem-loop structures (8, 9). The consensus sequence for the Sm binding site is RAU 4-6 GR (R ϭ purine), although this selectivity is not very stringent (10, 11). The core complex is thought to be a heteroheptamer of Sm proteins, and electron microscopic investigations of U snRNP core particles suggest that the Sm (12) and Lsm (13) cores are composed of a doughnut-shaped heteromer. The current paradigm is that seven Sm proteins (e.g., human B͞BЈ, D 1 , D 2 , D 3 , E, F, and G) assemble stepwise into a heteroheptameric ring with snRNA through various intermediates, such as D 1 ⅐D 2 and E⅐F⅐G heteromers. This snRNP core complex is then imported to the nucleus for completion of spliceosome assembly. Functional complexes of RNA and homologous Sm protein septets, such as t...

RapA, a prokaryotic member of the SWI/SNF protein superfamily, is an integral part of the RNA polymerase transcription complex. RapA's function and catalytic mechanism have been linked to nucleic acid remodeling. In this work we show that mutations in the interface between RapA's SWI/SNF and double-stranded nucleic acid-binding domains significantly alter ATP hydrolysis in purified RapA. The effects of individual mutations on ATP hydrolysis loosely correlated with RapA's nucleic acid-remodeling activity, indicating that the interaction between these domains may be important for the RapA-mediated remodeling of nonproductive transcription complexes. In this study we introduced a model system for in vitro transcription of a full-length E. coli gene (slyD). To study the function of RapA, we fractionated and identified in vitro transcription reaction intermediates in the presence or absence of RapA. These experiments demonstrated that RapA contributes to the formation of free RNA species during in vitro transcription. This work further refines our models for RapA function in vivo and establishes a new role in RNA management for a representative of the SWI/SNF protein superfamily. KeywordsRapA; RNA polymerase; SWI/SNF; transcription; DNA-RNA; triplex Escherichia coli (E. coli) has served as a primary model system for the study of enzymes involved in RNA synthesis. A textbook example of polymerase function, the E. coli core RNA polymerase formed by the α 2 ββ'ω subunits is capable of transcription elongation and termination (1). Proteins called sigma factors (1-3) associate with the core enzyme and allow the resulting complex, referred to as the RNA polymerase holoenzyme, to bind DNA in a sequence-specific manner and initiate transcription from loosely homologous promoter sequences on the E. coli chromosome. Each sigma factor controls multiple groups of promoters; e.g, the key growth-related and housekeeping genes in E. coli are under control of σ 70 (4), the rpoD gene product. Approximately one-third of the core E. coli RNA polymerase molecules in a given cell form a high-affinity, stoichiometric complex with σ 70 under normal growth conditions; the α 2 ββ'ω and α 2 ββ'ωσ 70 enzyme species display a number of distinct properties and can be chromatographically separated (5,6). Apart from the sigma factors and relatively small proteins (which are unlikely to display mechanistically complex enzymatic activities), the key known interactors of the E. coli RNA polymerase established through biochemical studies are NusA (7,8) and RapA (6,9). NusA -an essential RNA-binding protein in E. coli -has been described in the existing literature as a * Correspondence: msoukhodol@my.lamar.edu, Phones: 409-880-7905 (office) 409-880-7906 (laboratory). NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2011 May 18. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript transcription elongation factor and a cofactor of antiterminators (10-13). The function of RapA (also known a...

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Novel aryl derivatives of benzamidine were synthesized and tested for their inhibitory potency against bovine trypsin, rat skin tryptase, human recombinant granzyme A, human thrombin, and human plasma kallikrein. All compounds show competitive inhibition against these proteases with Ki values in the micromolar range. X-ray structures were determined to 1.8 A resolution for trypsin complexed with two of the para-substituted benzamidine derivatives, 1-(4-amidinophenyl)-3-(4-chlorophenyl)urea (ACPU) and 1-(4-amidinophenyl)-3-(4-phenoxyphenyl)urea (APPU). Although the inhibitors do not engage in direct and specific interactions outside the S1 pocket, they do form intimate indirect contacts with the active site of trypsin. The inhibitors are linked to the enzyme by a sulfate ion that forms an intricate network of three-centered hydrogen bonds. Comparison of these structures with other serine protease structures with noncovalently bound oxyanions reveals a pair of highly conserved oxyanion-binding sites in the active site. The positions of noncovalently bound oxyanions, such as the oxygen atoms of sulfate, are distinct from the positions of covalent oxyanions of tetrahedral intermediates. Noncovalent oxyanion positions are outside the "oxyanion hole." Kinetics data suggest that protonation stabilizes the ternary inhibitor/oxyanion/protease complex. In sum, both cations and anions can mediate Ki. Cation mediation of potency of competitive inhibitors of serine proteases was previously reported by Stroud and co-workers [Katz, B. A., Clark, J. M., Finer-Moore, J. S., Jenkins, T. E., Johnson, C. R., Ross, M. J., Luong, C., Moore, W. R., and Stroud, R. M. (1998) Nature 391, 608-612].