Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance

The net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the S10-spc cluster show an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea. In non-halophilic bacteria, the S10-spc cluster r-proteins are generally basic (positively charged), while the rest of the proteomes in these strains are generally acidic.

Evaluating quantum alchemy of atoms with thermodynamic cycles: Beyond ground electronic states

Due to the sheer size of chemical and materials space, high throughput computational screening thereof will require the development of new computational methods that are accurate, efficient, and transferable. These methods need to be applicable to electron configurations beyond ground states. To this end, we have systematically studied the applicability of quantum alchemy predictions using a Taylor series expansion on quantum mechanics (QM) calculations for single atoms with different electronic structures arising from different net charges and electron spin multiplicities. We first compare QM method accuracy to experimental quantities including first and second ionization energies, electron affinities, and multiplet spin energy gaps for a baseline understanding of QM reference data. We then investigate the intrinsic accuracy of an approach we call "manual" quantum alchemy schemes compared to the same QM reference data, which employ QM calculations where the basis set of a different element is used for an atom as the limit case of quantum alchemy. We then discuss the reliability of quantum alchemy based on Taylor series approximations at different orders of truncation. Overall, we find that the errors from finite basis set treatments in quantum alchemy are significantly reduced when thermodynamic cycles are employed, which points out a route to improve quantum alchemy in explorations of chemical space. This work establishes important technical aspects that impact the accuracy of quantum alchemy predictions using a Taylor series and provides a foundation for further quantum alchemy studies.

Net charges of the ribosomal proteins of the S10 and spc clusters of halophiles are inversely related to the degree of halotolerance

Net positive charge(s) on ribosomal proteins (r-proteins) have been reported to influence the assembly and folding of ribosomes. A high percentage of r-proteins from extremely halophilic archaea are known to be acidic or even negatively charged. Those proteins that remain positively charged are typically far less so. Herein the analysis is extended to the non-archaeal halophilic bacteria, eukaryotes and halotolerant archaea. The net charges (pH 7.4) of r-proteins that comprise the S10-spc operon/cluster from individual microbial and eukaryotic genomes were estimated and intercompared. It was observed that as a general rule, as the salt tolerance of the bacterial strains increased from 5 to 15%, the net charges of the individual proteins remained mostly basic. The most striking exceptions were the extremely halophilic bacterial strains, Salinibacter ruber SD01, Acetohalobium arabaticum DSM 5501 and Selenihalanaerobacter shriftii ATCC BAA-73, which are reported to require a minimum of 18%-21% of salt for their growth. All three strains have a higher number of acidic S10-spc cluster r-proteins than what is seen in the moderate halophiles or the halotolerant strains. Of the individual proteins, only uL2 never became acidic. uS14 and uL16 also seldom became acidic. The net negative charges on several of the S10-spc cluster r-proteins is a feature generally shared by all extremely halophilic archaea and bacteria. The S10-spc cluster r-proteins of halophilic fungi and algae (eukaryotes) were exceptions. They were positively charged despite the halophilicity of the organisms.

Silicon Nanowire Field-Effect Transistor as Label-Free Detection of Hepatitis B Virus Proteins with Opposite Net Charges

The prevalence of hepatitis B virus (HBV) is a global healthcare threat, particularly chronic hepatitis B (CHB) that might lead to hepatocellular carcinoma (HCC) should not be neglected. Although many types of HBV diagnosis detection methods are available, some technical challenges, such as the high cost or lack of practical feasibility, need to be overcome. In this study, the polycrystalline silicon nanowire field-effect transistors (pSiNWFETs) were fabricated through commercial process technology and then chemically functionalized for sensing hepatitis B virus surface antigen (HBsAg) and hepatitis B virus X protein (HBx) at the femto-molar level. These two proteins have been suggested to be related to the HCC development, while the former is also the hallmark for HBV diagnosis, and the latter is an RNA-binding protein. Interestingly, these two proteins carried opposite net charges, which could serve as complementary candidates for evaluating the charge-based sensing mechanism in the pSiNWFET. The measurements on the threshold voltage shifts of pSiNWFETs showed a consistent correspondence to the polarity of the charges on the proteins studied. We believe that this report can pave the way towards developing an approachable tool for biomedical applications.

Coherent and Compact Zinc Electrodeposition Enabled by Compressing the Electric Double Layer of the Deposits

The porous hexagonal-platelet Zinc (Zn) deposits exacerbate the chemical corrosion and deteriorate the reversibility of the Zn electrodes in aqueous electrolytes. Based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, to turn the messy Zn deposits into agglomerate ones, the challenge is to weaken the electric double layer repulsive force, which is the main reason preventing the dense Zn deposits, between the electrodeposited Zn particles. Here, we proposed a strategy to compress the electric double layer and regulate the forces between the electrodeposited Zn particles by introducing inert charges to the surface of the Zn deposits. The results of the electron microscopies revealed dense and coherent electrodeposition of Zn, indicating that the van der Waals attraction between the deposits becomes governing during electrodeposition. Such results could be attributed to the adsorbed inert charges on Zn deposits decrease the net charges and weaken the electric double layer repulsive force. This design enables the Zn||Zn cells a long-term plating/stripping stability for > 1200 h, a high average Coulombic Efficiency of 99.9% for > 2100 h, and steady charge/discharge responses even under a draconian deep-discharge condition of 80% depth of discharge of Zn (DODZn). In addition, the Zn||VS2 full cells demonstrate significantly improved electrochemical reversibility and capacity retention.

Efficiency and Quantitative Structure-Activity Relationship of Monoaromatics Oxidation by Quinone-Activated Persulfate

Quinones and quinone-containing organics have potential of activating persulfate to produce sulfate radical. In this work, the optimal condition for quinone activation of persulfate was investigated. It was found representative monoaromatics were degraded fastest in alkaline environment (pH 10.0), but excessive alkalinity restrained the reaction instead. The mechanisms to explain this phenomenon were speculated. The effect of initial quinone concentration on persulfate oxidation was also investigated at pH 10.0. In addition, a quantitative structure-activity relationship model was established with 15 kinds of monoaromatics, which revealed the most negative atomic net charges on carbon atom played an important role on degradation rates. Chemicals with a smaller qC- were easier oxidized in quinone-activate system. This finding helps further exploration of effective activator in alkaline environment.

Study on the Structure-Activity Relationship of an Antimicrobial Peptide, Brevinin-2GUb, from the Skin Secretion of Hylarana guentheri

Antimicrobial peptides (AMPs) are considered potential alternatives to antibiotics due to their advantages in solving antibiotic resistance. Brevinin-2GUb, which was extracted from the skin secretion of Hylarana guentheri, is a peptide with modest antimicrobial activity. Several analogues were designed to explore the structure–activity relationship and enhance its activity. In general, the Rana box is not an indispensable motif for the bioactivity of Brevinin-2GUb, and the first to the 19th amino acids at the N-terminal end are active fragments, such that shortening the peptide while maintaining its bioactivity is a promising strategy for the optimisation of peptides. Keeping a complete hydrophobic face and increasing the net charges are key factors for antimicrobial activity. With the increase of cationic charges, α-helical proportion, and amphipathicity, the activity of t-Brevinin-2GUb-6K (tB2U-6K), in combatting bacteria, drastically improved, especially against Gram-negative bacteria, and the peptide attained the capacity to kill clinical isolates and fungi as well, which made it possible to address some aspects of antibiotic resistance. Thus, peptide tB2U-6K, with potent antimicrobial activity against antibiotic-resistant bacteria, the capacity to inhibit the growth of biofilm, and low toxicity against normal cells, is of value to be further developed into an antimicrobial agent.

Anti-lipopolysaccharide factor D from kuruma shrimp exhibits antiviral activity

Anti-lipopolysaccharide factors (ALFs) exhibit a potent antimicrobial activity against a broad range of bacteria, filamentous fungi, and viruses. In previous reports, seven groups of ALFs (groups A–G) were identified in penaeid shrimp. Among them, group D showed negative net charges and weak antimicrobial activity. Whether this group has antiviral function is not clear. In this study, the ALF sequences of penaeid shrimp were analyzed, and eight groups of ALF family (groups A–H) were identified. The four ALFs including MjALF-C2, MjALF-D1, MjALF-D2, and MjALF-E2 from kuruma shrimp Marsupenaeus japonicus were expressed recombinantly in Escherichia coli, and the antiviral activity was screened via injection of purified recombinant ALFs into shrimp following white spot syndrome virus (WSSV) infection. Results showed that the expression of Vp28 (WSSV envelope protein) decreased significantly in the MjALF-D2-injected shrimp only. Therefore, MjALF-D2 was chosen for further study. Expression pattern analysis showed that MjAlf-D2 was upregulated in shrimp challenged by WSSV. The WSSV replication was detected in RNA, genomic DNA, and protein levels using VP28 and Ie1 (immediate-early gene of WSSV) as indicators in MjALF-D2-injected shrimp following WSSV infection. Results showed that WSSV replication was significantly inhibited compared with that in the rTRX- or PBS-injected control groups. After knockdown of MjAlf-D2 in shrimp by RNA interference, the WSSV replication increased significantly in the shrimp. All these results suggested that MjALF-D2 has an antiviral function in shrimp immunity, and the recombinant ALF-D2 has a potential application for viral disease control in shrimp aquaculture.

Hydrophobic interactions control the self-assembly of DNA and cellulose

Desoxyribosenucleic acid, DNA, and cellulose molecules self-assemble in aqueous systems. This aggregation is the basis of the important functions of these biological macromolecules. Both DNA and cellulose have significant polar and nonpolar parts and there is a delicate balance between hydrophilic and hydrophobic interactions. The hydrophilic interactions related to net charges have been thoroughly studied and are well understood. On the other hand, the detailed roles of hydrogen bonding and hydrophobic interactions have remained controversial. It is found that the contributions of hydrophobic interactions in driving important processes, like the double-helix formation of DNA and the aqueous dissolution of cellulose, are dominating whereas the net contribution from hydrogen bonding is small. In reviewing the roles of different interactions for DNA and cellulose it is useful to compare with the self-assembly features of surfactants, the simplest case of amphiphilic molecules. Pertinent information on the amphiphilic character of cellulose and DNA can be obtained from the association with surfactants, as well as on modifying the hydrophobic interactions by additives.

Electric features of dislocations and electric force between dislocations

Dislocations and dislocation dynamics are the cores of material plasticity. In this work, the electric features of dislocations were investigated theoretically. An intrinsic electric field around a single dislocation was revealed. In addition to the well-known Peach–Koehler force, it was established that an important intrinsic electric force exists between dislocations, which is uncovered here for the first time and has been neglected since the discovery of dislocations. The electric forces may be large and sometimes could exceed the Peach–Koehler force for metals and some dielectric materials with large dielectric constant. Therefore, the electric force is anticipated to play a vital role in dislocation dynamics and material plasticity. Moreover, an external electric field could exert an electric force on dislocations and a threshold electric field was subsequently discovered above which this force enables dislocations to glide. Interestingly, it was found that some dislocations move in one direction, but others move in reverse in an identical electric field, which is in agreement with experimental observations. Despite dislocation motion under an electric field, to one’s surprise, both edge and screw dislocations do not carry net charges by themselves, which may tackle the long-standing puzzle on the charges of dislocations. These findings may supply people with new fundamental knowledge on dislocations as well as dislocation dynamics, and may assist people in understanding related phenomena.