Structural and Functional Mimicry of the Antimicrobial Defensin Plectasin by Analogues with Engineered Backbone Composition.

The threat posed by bacteria resistant to common antibiotics creates an urgent need for novel antimicrobials. Non-ribosomal peptide natural products that bind Lipid II, such as vancomycin, represent a promising source for such agents. The fungal defensin plectasin is one of a family of ribosomally produced miniproteins that also exert antimicrobial activity via Lipid II binding.

Application of artificial backbone connectivity in the development of metalloenzyme mimics.

Metal-dependent enzymes are abundant and vital catalytic agents in nature. The functional versatility of metalloenzymes has made them common targets for improvement by protein engineering as well as mimicry by de novo designed sequences. In both strategies, the incorporation of non-canonical cofactors and/or non-canonical side chains has proved a useful tool.

Backbone Modification in a Protein Hydrophobic Core.

Targeted protein backbone modification can recreate tertiary structures reminiscent of folds found in nature on artificial scaffolds with improved biostability. Incorporation of altered monomers in such entities is typically limited to sites distant from the hydrophobic core to avoid potential disruptions to folding. This is limiting, as it is advantageous in some applications to incorporate artificial connectivity at buried sites.

How warm are political interactions? A new measure of affective fractionalization.

Affective polarization measures account for partisans' feelings towards their own party versus its opponent(s), but not for how likely partisans are to encounter co-partisans versus out-partisans. However, the intensity of out-party dislike and the probability with which this comes into play both determine the social impact of cross-party hostility. We develop an affective fractionalization measure that accounts for both factors, and apply it to longitudinal survey data from 20 Western publics.

Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein.

Sequence-encoded protein folding is a ubiquitous biological process that has been successfully engineered in a range of oligomeric molecules with artificial backbone chemical connectivity. A remarkable aspect of protein folding is the contrast between the rapid rates at which most sequences in nature fold and the vast number of conformational states possible in an unfolded chain with hundreds of rotatable bonds. Research efforts spanning several decades have sought to elucidate the fundamental chemical principles that dictate the speed and mechanism of natural protein folding.

Probing effects of site-specific aspartic acid isomerization on structure and stability of GB1 through chemical protein synthesis.

Chemical modifications of long-lived proteins, such as isomerization and epimerization, have been evoked as prime triggers for protein-damage related diseases. Deamidation of Asn residues, which results in formation of a mixture of l- and d-Asp and isoAsp via an intermediate aspartyl succinimide, can result in the disruption of cellular proteostasis and toxic protein depositions. In contrast to extensive data on the biological prevalence and functional implications of aspartyl succinimide formation, much less is known about the impact of the resulting altered backbone composition on properties of individual proteins at a molecular level.

Effects of chirality and side chain length in C-dialkylated residues on β-hairpin peptide folded structure and stability.

Strategic incorporation of achiral C-dialkylated amino acids with bulky substituents into peptides can be used to promote extended strand conformations and inhibit protein-protein interactions associated with amyloid formation. In this work, we evaluate the thermodynamic impact of chiral C monomers on folding preferences in such systems through introduction of a series of C-methylated and C-ethylated residues into a β-hairpin host sequence. Depending on stereochemical configuration of the artificial monomer and potential for additional hydrophobic packing, a C-ethyl-C-propyl glycine residue can provide similar or enhanced folded stability relative to an achiral C-diethyl analogue.

Chemical Shifts of Artificial Monomers Used to Construct Heterogeneous-Backbone Protein Mimetics in Random Coil and Folded States.

The construction of protein-sized synthetic chains that blend natural amino acids with artificial monomers to create so-called heterogeneous-backbones is a powerful approach to generate complex folds and functions from bio-inspired agents. A variety of techniques from structural biology commonly used to study natural proteins have been adapted to investigate folding in these entities. In NMR characterization of proteins, proton chemical shift is a straightforward to acquire, information-rich metric that bears directly on a variety of properties related to folding.

Protein Backbone Alteration in Non-Hairpin β-Turns: Impacts on Tertiary Folded Structure and Folded Stability.

The importance of β-turns to protein folding has motivated extensive efforts to stabilize the motif with non-canonical backbone connectivity. Prior work has focused almost exclusively on turns between strands in a β-sheet (i. e.

Implications of the unfolded state in the folding energetics of heterogeneous-backbone protein mimetics.

Sequence-encoded folding is the foundation of protein structure and is also possible in synthetic chains of artificial chemical composition. In natural proteins, the characteristics of the unfolded state are as important as those of the folded state in determining folding energetics. While much is known about folded structures adopted by artificial protein-like chains, corresponding information about the unfolded states of these molecules is lacking.

Effects of Desiccation and Freezing on Microbial Ionizing Radiation Survivability: Considerations for Mars Sample Return.

Increasingly, national space agencies are expanding their goals to include Mars exploration with sample return. To better protect Earth and its biosphere from potential extraterrestrial sources of contamination, as set forth in the Outer Space Treaty of 1967, international efforts to develop planetary protection measures strive to understand the danger of cross-contamination processes in Mars sample return missions. We aim to better understand the impact of the martian surface on microbial dormancy and survivability.

Heterogeneous-Backbone Proteomimetic Analogues of Lasiocepsin, a Disulfide-Rich Antimicrobial Peptide with a Compact Tertiary Fold.

The emergence of resistance to clinically used antibiotics by bacteria presents a significant problem in public health. Natural antimicrobial peptides (AMPs) are a valuable source of antibiotics that act by a mechanism less prone to the evolutionary development of resistance. In an effort to realize the promise of AMPs while overcoming limitations such as poor biostability, researchers have sought sequence-defined oligomers with artificial amide-based backbones that show membrane-disrupting functions similar to natural agents.

Comparison of Morphological and Histological Characteristics of Human and Sheep: Sheep as a Potential Model for Testing Midurethral Slings in vivo.

Introduction: The sheep was evaluated as a potential model for preclinical evaluation of urethral slings in vivo based on: (1) anatomical measurements of the sheep vagina and (2) histological tissue integration and host response to polypropylene (PP) slings.

Methods: Eight female, multiparous sheep were utilized. Three of 8 animals underwent surgery mimicking human tension-free vaginal tape protocols for midurethral slings and were euthanized at 6 months.

Small-Molecule Mn Antioxidants in Caenorhabditis elegans and Deinococcus radiodurans Supplant MnSOD Enzymes during Aging and Irradiation.

Denham Harman's oxidative damage theory identifies superoxide (O) radicals as central agents of aging and radiation injury, with Mn-dependent superoxide dismutase (MnSOD) as the principal O-scavenger. However, in the radiation-resistant nematode Caenorhabditis elegans, the mitochondrial antioxidant enzyme MnSOD is dispensable for longevity, and in the model bacterium Deinococcus radiodurans, it is dispensable for radiation resistance. Many radiation-resistant organisms accumulate small-molecule Mn-antioxidant complexes well-known for their catalytic ability to scavenge O, along with MnSOD, as exemplified by D.

Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics.

Recent years have seen a growing number of examples of designed oligomeric molecules with artificial backbone connectivity that are capable of adopting complex folded tertiary structures analogous to those seen in natural proteins. A range of experimental techniques from structural biology and biophysics have been brought to bear in the study of these proteomimetic agents. Here, we discuss some considerations encountered in the characterization of high-resolution folded structure as well as folding thermodynamics of protein-like artificial backbones.

Characterization of unique functionalities in c-Src domains required for osteoclast podosome belt formation.

Deletion of c-Src, a ubiquitously expressed tyrosine kinase, results in osteoclast dysfunction and osteopetrosis, in which bones harden into "stone." In contrast, deletion of the genes encoding other members of the Src family kinase (SFK) fails to produce an osteopetrotic phenotype. This suggests that c-Src performs a unique function in the osteoclast that cannot be compensated for by other SFKs.

High-dimensional profiling clusters asthma severity by lymphoid and non-lymphoid status.

Clinical definitions of asthma fail to capture the heterogeneity of immune dysfunction in severe, treatment-refractory disease. Applying mass cytometry and machine learning to bronchoalveolar lavage (BAL) cells, we find that corticosteroid-resistant asthma patients cluster largely into two groups: one enriched in interleukin (IL)-4 innate immune cells and another dominated by interferon (IFN)-γ T cells, including tissue-resident memory cells. In contrast, BAL cells of a healthier population are enriched in IL-10 macrophages.

Proteomimetic Zinc Finger Domains with Modified Metal-binding β-Turns.

The mimicry of protein tertiary folds by chains artificial in backbone chemical composition leads to proteomimetic analogues with potential utility as bioactive agents and as tools to shed light on biomacromolecule behavior. Notable successes toward such molecules have been achieved; however, as protein structural diversity is vast, design principles must be continually honed as they are applied to new prototype folding patterns. One specific structure where a gap remains in understanding how to effectively generate modified backbone analogues is the metal-binding β-turn found in zinc finger domains.

Metal-Binding Foldamers.

Sequence-defined oligomeric molecules with discrete folding propensities, termed foldamers, are a versatile source of agents with tailored structure and function. An inspiration for the development of the foldamer paradigm are natural biomacromolecules, the sequence-encoded folding of which is the basis of life. Metal ions and clusters are common features in proteins, where the role of metal varies from supporting structure to enabling function.

Acquired mutations and transcriptional remodeling in long-term estrogen-deprived locoregional breast cancer recurrences.

Background: Endocrine therapy resistance is a hallmark of advanced estrogen receptor (ER)-positive breast cancer. In this study, we aimed to determine acquired genomic changes in endocrine-resistant disease.

Methods: We performed DNA/RNA hybrid-capture sequencing on 12 locoregional recurrences after long-term estrogen deprivation and identified acquired genomic changes versus each tumor's matched primary.

Biliary-Atresia-Associated Mannosidase-1-Alpha-2 Gene Regulates Biliary and Ciliary Morphogenesis and Laterality.

Background/aims: Infectious and genetic factors are invoked, respectively in isolated biliary atresia (BA), or syndromic BA, with major extrahepatic anomalies. However, isolated BA is also associated with minor extrahepatic gut and cardiovascular anomalies and multiple susceptibility genes, suggesting common origins.

Methods: We investigated novel susceptibility genes with genome-wide association, targeted sequencing and tissue staining in BA requiring liver transplantation, independent of BA subtype.

Interleukin-17-induced neutrophil extracellular traps mediate resistance to checkpoint blockade in pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy with an immunosuppressive microenvironment that is resistant to most therapies. IL17 is involved in pancreatic tumorigenesis, but its role in invasive PDAC is undetermined. We hypothesized that IL17 triggers and sustains PDAC immunosuppression.

Human Serum Phenylpyruvate Quantification Using Responsive 2D Photonic Crystal Hydrogels via Chemoselective Oxime Ligation: Progress toward Developing Phenylalanine-Sensing Elements.

There is a need to develop at-home phenylalanine (Phe) test kits, analogous to home glucose meters, for phenylketonuria patients who must measure their blood Phe levels frequently to adjust their diet. Unfortunately, such test kits are not available yet because of the lack of simple and inexpensive Phe-sensing elements. With the goal of developing a Phe-sensing element, we fabricated two-dimensional photonic crystal (2DPC) hydrogels that quantify human serum phenylpyruvate (PhPY), which is the product of the reaction between Phe and the enzyme phenylalanine dehydrogenase.

A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics.

We present a new force field, AMBER ff15ipq-m, for simulations of protein mimetics in applications from therapeutics to biomaterials. This force field is an expansion of the AMBER ff15ipq force field that was developed for canonical proteins and enables the modeling of four classes of artificial backbone units that are commonly used alongside natural α residues in blended or "heterogeneous" backbones: chirality-reversed D-α-residues, the C-methylated α-residue Aib, homologated β-residues (β) bearing proteinogenic side chains, and two cyclic β residues (β; APC and ACPC). The ff15ipq-m force field includes 472 unique atomic charges and 148 unique torsion terms.

Differential gene expression in peripheral blood mononuclear cells from children immunized with inactivated influenza vaccine.

The human immune response to inactivated influenza vaccine is dynamic and impacted by age and preexisting immunity. Our goal was to identify postvaccination transcriptomic changes in peripheral blood mononuclear cells from children. Blood samples were obtained before and at 3 or 7 days postvaccination with 2016-2017 quadrivalent inactivated influenza vaccine and RNA sequencing was performed.