Engineering Antimicrobial Peptides with Improved Antimicrobial and Hemolytic Activities

The rapid rise of antibiotic resistance in pathogens becomes a serious and growing threat to medicine and public health. Naturally occurring antimicrobial peptides (AMPs) are an important line of defense in the immune system against invading bacteria and microbial infection. In this work, we present a combined computational and experimental study of the biological activity and membrane interaction of the computationally designed Bac2A-based peptide library. We used the MARTINI coarse-grained molecular dynamics with adaptive biasing force method and the umbrella sampling technique to investigate the translocation of a total of 91 peptides with different amino acid substitutions through a mixed anionic POPE/POPG (3:1) bilayer and a neutral POPC bilayer, which mimic the bacterial inner membrane and the human red blood cell (hRBC) membrane, respectively. Potential of mean force (PMF, free energy profile) was obtained to measure the free energy barrier required to transfer the peptides from the bulk water phase to the water–membrane interface and to the bilayer interior. Different PMF profiles can indeed identify different membrane insertion scenarios by mapping out peptide–lipid energy landscapes, which are correlated with antimicrobial activity and hemolytic activity. Computationally designed peptides were further tested experimentally for their antimicrobial and hemolytic activities using bacteria growth inhibition assay and hemolysis assay. Comparison of PMF data with cell assay results reveals a good correlation of the peptides between predictive transmembrane activity and antimicrobial/hemolytic activity. Moreover, the most active mutants with the balanced substitutions of positively charged Arg and hydrophobic Trp residues at specific positions were discovered to achieve the improved antimicrobial activity while minimizing red blood cell lysis. Such substitutions provide more effective and cooperative interactions to distinguish the peptide interaction with different lipid bilayers. This work provides a useful computational tool to better understand the mechanism and energetics of membrane insertion of AMPs and to rationally design more effective AMPs

DataSheet1_Carbon dots with light-responsive oxidase-like activity for colorimetric detection of dopamine and the catalytic mechanism.DOCX

Introduction: Dopamine is one of the most significant neurotransmitters and plays an important role in the management of cognitive functions such as learning, memory, and behavior. The disorder of dopamine is associated with many major mental diseases. It is necessary to develop selective methods for the detection of dopamine.Methods: In this work, carbon dots (CDs) were synthesized by a solvothermal route using glutathione, L-histidine, and formamide as sources.Results: Under light irradiation, The CDs convert dissolved oxygen to singlet oxygen (1O2), which could oxidize TMB. When reduced dopamine was present, it suppressed the catalysis of CDs, then the absorption of the CDs-coupled TMB complex at 652 nm was diminished. Furthermore, it was revealed that the surface groups including hydroxyl, amino, carbonyl, and carboxyl groups of CDs were related to their light-responsive catalytic activity by surface modification. In the range of 0.5-15 μM, the CDs could afford a LOD of 0.25 μM for dopamine detection with fine linearity, also showing good selectivity.Discussion: The results from fetal bovine serum indicated the good applicability of the CDs in the determination of dopamine.</p

Probing the Structural Dependence of Carbon Space Lengths of Poly(<i>N</i>‑hydroxyalkyl acrylamide)-Based Brushes on Antifouling Performance

Numerous biocompatible antifouling polymers have been developed for a wide variety of fundamental and practical applications in drug delivery, biosensors, marine coatings, and many other areas. Several antifouling mechanisms have been proposed, but the exact relationship among molecular structure, surface hydration property, and antifouling performance of antifouling polymers still remains elusive. Here this work strives to provide a better understanding of the structure–property relationship of poly­(<i>N</i>-hydroxyalkyl acrylamide)-based materials. We have designed, synthesized, and characterized a series of polyHAAA brushes of various carbon spacer lengths (CSLs), that is, poly­(<i>N</i>-hydroxymethyl acrylamide) (polyHMAA), poly­(<i>N</i>-(2-hydroxyethyl)­acrylamide) (polyHEAA), poly­(<i>N</i>-(3-hydroxypropyl)­acrylamide) (polyHPAA), and poly­(<i>N</i>-(5-hydroxypentyl)­acrylamide) (polyHPenAA), to study the structural dependence of CSLs on their antifouling performance. HMAA, HEAA, HPAA, and HPenAA monomers contained one, two, three, and five methylene groups between hydroxyl and amide groups, while the other groups in polymer backbones were the same as each other. The relation of such small structural differences of polymer brushes to their surface hydration and antifouling performance was studied by combined experimental and computational methods including surface plasmon resonance sensors, sum frequency generation (SFG) vibrational spectroscopy, cell adhesion assay, and molecular simulations. Antifouling results showed that all polyHAAA-based brushes were highly surface resistant to protein adsorption from single protein solutions, undiluted blood serum and plasma, as well as cell adhesion up to 7 days. In particular, polyHMAA and polyHEAA with the shorter CSLs exhibited higher surface hydration and better antifouling ability than polyHPMA and polyHPenAA. SFG and molecular simulations further revealed that the variation of CSLs changed the ratio of hydrophobicity/hydrophilicity of polymers, resulting in different hydration characteristics. Among them, polyHMAA and polyHEAA with the shorter CSLs showed the highest potency for surface hydration and antifouling abilities, while polyHPenAA showed the lowest potency. The combination of both hydroxyl and amide groups in the same polymer chain provides a promising structural motif for the design of new effective antifouling materials

Supplementary Data: Phylogenetic Analysis Result, EDS Elemental Map, and Limb Proportions of Gansubatrachus qilianensis from A cretaceous frog with eggs from northwestern China provides fossil evidence for sexual maturity preceding skeletal maturity in anurans

Mesozoic fossils of frogs are rare in the palaeontological record, particularly those exhibiting soft tissues that offer limited insights into early life-history characteristics. Here we report on a skeletally immature frog from the Lower Cretaceous of northwest China, with egg masses in the body and eggs in the oviduct, indicative of a gravid female. CT reconstruction of the specimen allows referral to Gansubatrachus qilianensis and we assign it as a paratype complementing the diagnosis of the type species. The new fossil, which might represent a younger individual than the holotype of Gansubatrachus, shows that sexual maturation occurred before full adulthood in this frog and provides evidence of death linked to mating behaviour. We also discuss other potential sources of variation and life-history traits of Gansubatrachus. The new finding represents the oldest Early Cretaceous frog preserving in situ eggs and provides a glimpse into ancient anuran development during Mesozoic times

Comparative Study of Graphene Hydrogels and Aerogels Reveals the Important Role of Buried Water in Pollutant Adsorption

Water as the universal solvent has well-demonstrated its ability to dissolve many substances, but buried water inside different nanoporous materials always exhibits some unusual behaviors. Herein, 3D porous graphene hydrogel (GH) is developed as a super-adsorbent to remove different pollutants (antibiotics, dyes, and heavy ions) for water purification. Due to its highly porous structure and high content of water, GH also demonstrated its super adsorption capacity for adsorbing and removing different pollutants (antibiotics, dyes, and heavy ions) as compared to conventional graphene aerogel (GA). More fundamentally, the buried-water enhanced adsorption mechanism was proposed and demonstrated, such that buried water in GH plays the combinatorial roles as (1) supporting media, (2) transport nanochannels, and (3) hydrogen bondings in promoting pollutant adsorption. In parallel, molecular dynamics simulations further confirm that buried water in GH has the stronger interaction with pollutants via hydrogen bonds than other buried alcohols. GH integrates the merit of both graphene (e.g., fine chemical resistance and excellent mechanical property) and hydrogel (e.g., high water content, porous structure, and simple solution-based processability and scalability), giving it promising potential for environmental applications

First fossil evidence for a new frog from the Early Cretaceous of the Jiuquan Basin, Gansu Province, north-western China

Based on a well-preserved incomplete skeleton, a new frog, Gansubatrachus qilianensis gen. et sp. nov., is described from the Lower Cretaceous Zhonggou Formation of Jiuquan Basin, Gansu Province, north-western China. This species differs from other frogs in a unique combination of characteristics, such as a robust and non-bifurcated alary process on the premaxilla, a ‘V’-shaped parahyoid, a paired sphenethmoid, eight presacral vertebrae, three pairs of free ribs, and unexpanded sacral diapophyses. Phylogenetic analysis based on parsimony suggests that Gansubatrachus is a basal Lalagobatrachia. This discovery of a new frog fossil from the Early Cretaceous of north-west China expands the diversity of fossil frogs in East Asia and provides new material for further studies on the distribution and evolutionary history of Cretaceous Asian anurans. http://zoobank.org/urn:lsid:zoobank.org:pub:A80B417A-F9C6-4704-B473-FBBA6CDC8C2B</p

Dual Salt- and Thermoresponsive Programmable Bilayer Hydrogel Actuators with Pseudo-Interpenetrating Double-Network Structures

Development of smart soft actuators is highly important for fundamental research and industrial applications but has proved to be extremely challenging. In this work, we present a facile, one-pot, one-step method to prepare dual-responsive bilayer hydrogels, consisting of a thermoresponsive poly­(<i>N</i>-isopropylacrylamide) (polyNIPAM) layer and a salt-responsive poly­(3-(1-(4-vinylbenzyl)-1<i>H</i>-imidazol-3-ium-3-yl)­propane-1-sulfonate) (polyVBIPS) layer. Both polyNIPAM and polyVBIPS layers exhibit a completely opposite swelling/shrinking behavior, where polyNIPAM shrinks (swells) but polyVBIPS swells (shrinks) in salt solution (water) or at high (low) temperatures. By tuning NIPAM:VBIPS ratios, the resulting polyNIPAM/polyVBIPS bilayer hydrogels enable us to achieve fast and large-amplitude bidirectional bending in response to temperatures, salt concentrations, and salt types. Such bidirectional bending, bending orientation, and degree can be reversibly, repeatedly, and precisely controlled by salt- or temperature-induced cooperative swelling–shrinking properties from both layers. Based on their fast, reversible, and bidirectional bending behavior, we further design two conceptual hybrid hydrogel actuators, serving as a six-arm gripper to capture, transport, and release an object and an electrical circuit switch to turn on-and-off a lamp. Different from the conventional two- or multistep methods for preparation of bilayer hydrogels, our simple, one-pot, one-step method and a new bilayer hydrogel system provide an innovative concept to explore new hydrogel-based actuators through combining different responsive materials that allow us to program different stimuli for soft and intelligent materials applications

Dual Salt- and Thermoresponsive Programmable Bilayer Hydrogel Actuators with Pseudo-Interpenetrating Double-Network Structures

Development of smart soft actuators is highly important for fundamental research and industrial applications but has proved to be extremely challenging. In this work, we present a facile, one-pot, one-step method to prepare dual-responsive bilayer hydrogels, consisting of a thermoresponsive poly­(<i>N</i>-isopropylacrylamide) (polyNIPAM) layer and a salt-responsive poly­(3-(1-(4-vinylbenzyl)-1<i>H</i>-imidazol-3-ium-3-yl)­propane-1-sulfonate) (polyVBIPS) layer. Both polyNIPAM and polyVBIPS layers exhibit a completely opposite swelling/shrinking behavior, where polyNIPAM shrinks (swells) but polyVBIPS swells (shrinks) in salt solution (water) or at high (low) temperatures. By tuning NIPAM:VBIPS ratios, the resulting polyNIPAM/polyVBIPS bilayer hydrogels enable us to achieve fast and large-amplitude bidirectional bending in response to temperatures, salt concentrations, and salt types. Such bidirectional bending, bending orientation, and degree can be reversibly, repeatedly, and precisely controlled by salt- or temperature-induced cooperative swelling–shrinking properties from both layers. Based on their fast, reversible, and bidirectional bending behavior, we further design two conceptual hybrid hydrogel actuators, serving as a six-arm gripper to capture, transport, and release an object and an electrical circuit switch to turn on-and-off a lamp. Different from the conventional two- or multistep methods for preparation of bilayer hydrogels, our simple, one-pot, one-step method and a new bilayer hydrogel system provide an innovative concept to explore new hydrogel-based actuators through combining different responsive materials that allow us to program different stimuli for soft and intelligent materials applications

De Novo Design of Self-Assembled Hexapeptides as β‑Amyloid (Aβ) Peptide Inhibitors

The ability of peptides to construct specific secondary structures provides a useful function for biomaterial design that cannot be achieved with traditional organic molecules and polymers. Inhibition of amyloid formation is a promising therapeutic approach for the treatment of neurodegenerative diseases. Existing peptide-based inhibitors are mainly derived from original amyloid sequences, which have very limited sequence diversity and activity. It is highly desirable to explore other peptide-based inhibitors that are not directly derived from amyloid sequences. Here, we develop a hybrid high-throughput computational method to efficiently screen and design hexapeptide inhibitors against amyloid-β (Aβ) aggregation and toxicity from the first principle. Computationally screened/designed inhibitors are then validated for their inhibition activity using biophysical experiments. We propose and demonstrate a proof-of-concept of the “like-interacts-like” design principle that the self-assembling peptides are able to interact strongly with conformationally similar motifs of Aβ peptides and to competitively reduce Aβ–Aβ interactions, thus preventing Aβ aggregation and Aβ-induced toxicity. Such a de novo design can also be generally applicable to design new peptide inhibitors against other amyloid diseases, beyond traditional peptide inhibitors with homologous sequences to parent amyloid peptides

Two-Step Chemoenzymatic Detection of <i>N</i>‑Acetylneuraminic Acid−α(2-3)-Galactose Glycans

Sialic acids are typically linked α­(2-3) or α­(2-6) to the galactose that located at the non-reducing terminal end of glycans, playing important but distinct roles in a variety of biological and pathological processes. However, details about their respective roles are still largely unknown due to the lack of an effective analytical technique. Herein, a two-step chemoenzymatic approach for the rapid and sensitive detection of <i>N</i>-acetyl­neuraminic acid−α­(2-3)-galactose glycans is described