Exploration of HIV-1 fusion peptide-antibody VRC34.01 binding reveals fundamental neutralization sites.

Antibody binding to a vulnerable site of HIV envelope glycoprotein (Env), the eight N-terminal residues of the gp41 fusion peptide, renders robust HIV neutralization. Here, we theoretically investigate HIV-1 fusion peptide binding to the neutralizing antibody N123-VRC34.01. We explore numerous fusion peptide mutations using all-atom molecular dynamics simulation with explicit-solvent models. Simulation results show that the hydrophobic interaction between Ile515 in the HIV-1 fusion peptide and the antibody VRC34.01 Fab plays an important role in antibody binding. Furthermore, we verify by free energy perturbation (FEP) calculations that two point mutations of Ile515Thr or Ile515Ala can dramatically weaken the binding affinity. Our findings provide new insights into fusion peptide-VRC34.01 binding, which can ultimately be utilized to design effective HIV vaccines.

Different protonated states at the C-terminal of the amyloid-ß peptide modulate the stability of S-shaped protofibril.

Studies have found strong correlations between polymorphism and structural variations in amyloid-ß (Aß) fibrils and the diverse clinical subtypes of Alzheimer's disease (AD). Thus, a detailed understanding of the conformational behavior of Aß fibrils may be an aid to elucidate the pathological mechanisms involved in AD. However, a key point that has been inadvertently underestimated or dismissed is the role of the protonated state at the C-terminal residue of amyloid-ß peptides, which can give rise to intrinsic differences in the morphology and stability of the fibrils. For instance, the effects of the salt bridge formed between the C-terminal residue A42 and the residue K28 on the S-shaped Aß protofibril structure remain unknown and may be different from those in the U-shaped Aß protofibril structures. To address this effect, we explore the stability of the S-shaped protofibrils capped with different C-terminal modifications, including carboxyl group in its deprotonated (COO-) and protonated (COOH) states, by using molecular dynamics simulations. Our findings indicated that the C-terminal deprotonated protofibril is significantly more stable than its C-terminal protonated counterpart due to a well-defined and highly stable zipper-like salt-bridge-chain formed by the ε-NH3 + groups on the sidechain of residue K28 and the C-terminal COO- group at the A42 residue. The revealed underlying molecular mechanism for the different stability of the protofibrils provides insights into the diversity of polymorphism in Aß fibrils.

Mechanism by which DHA inhibits the aggregation of KLVFFA peptides: A molecular dynamics study.

Docosahexaenoic acid (DHA) is one of the omega-3 polyunsaturated fatty acids, which has shown promising applications in lowering Aß peptide neurotoxicity in vitro by preventing aggregation of Aß peptides and relieving accumulation of Aß fibrils. Unfortunately, the underlying molecular mechanisms of how DHA interferes with the aggregation of Aß peptides remain largely enigmatic. Herein, aggregation behaviors of amyloid-ß(Aß)16-21 peptides (KLVFFA) with or without the presence of a DHA molecule were comparatively studied using extensive all-atom molecular dynamics simulations. We found that DHA could effectively suppress the aggregation of KLVFFA peptides by redirecting peptides to unstructured oligomers. The highly hydrophobic and flexible nature of DHA made it randomly but tightly entangled with Leu-17, Phe-19, and Phe-20 residues to form unstructured but stable complexes. These lower-ordered unstructured oligomers could eventually pass through energy barriers to form ordered ß-sheet structures through large conformational fluctuations. This study depicts a microscopic picture for understanding the role and mechanism of DHA in inhibition of aggregation of Aß peptides, which is generally believed as one of the important pathogenic mechanisms of Alzheimer's disease.

Comparison of the safety and efficacy of the wild-type and lpxL/lpxM mutant inactivated vaccine against the avian pathogenic Escherichia coli O1, O2, and O78 challenge.

Avian pathogenic Escherichia coli (APEC) is primarily responsible for causing septicemia, pneumonitis, peritonitis, swollen head syndrome, and salpingitis in poultry, leading to significant losses in the poultry sector, particularly within the broiler industry. The removal of the lpxL and lpxM genes led to an eightfold decrease in the endotoxin levels of wild APEC strains. In this study, mutant strains of lpxL/lpxM and their O1, O2, and O78 wild-type strains were developed for an inactivated vaccine (referred to as the mutant vaccine and the wild-type vaccine, respectively), and the safety and effectiveness of these two prototype vaccines were assessed in white Leghorn chickens. Findings indicated that chickens immunized with the mutant vaccine showed a return of appetite sooner post-immunization and experienced earlier disappearance of nodules at the injection site compared to those immunized with the wild-type vaccine. Pathological examinations revealed that lesions were still present in the liver, lung, and injection site in chickens vaccinated with the wild-type vaccine 14 days post-vaccination (dpv), whereas no lesions were found in chickens vaccinated with the mutant vaccine at 14 dpv. There were no significant differences in antibody levels on the challenge day or in mortality or lesion scores between challenged birds immunized with either the mutant vaccine or the wild-type vaccine at the same dose. In this study, the safety of a single dose or overdose of the mutant vaccine and its efficacy at one dose were evaluated in broilers, and the results showed that the mutant vaccine had no adverse effects on or protected vaccinated broilers from challenge with the APEC O1, O2, or O78 strains. These results demonstrated that the mutant polyvalent inactivated vaccine is a competitive candidate against APEC O1, O2, and O78 infection compared to the wild-type vaccine.

Soil Nutrients, Enzyme Activities, and Microbial Communities along a Chronosequence of Chinese Fir Plantations in Subtropical China.

Forests undergo a long-term development process from young to mature stages, yet the variations in soil nutrients, enzyme activities, microbial diversity, and community composition related to forest ages are still unclear. In this study, the characteristics of soil bacterial and fungal communities with their corresponding soil environmental factors in the young, middle, and mature stages (7, 15, and 25-year-old) of Chinese fir plantations (CFP) in the subtropical region of China were investigated in 2021. Results showed that the alpha diversity indices (Chao1 and Shannon) of soil bacteria and fungi were higher in 15 and 25-year-old stands than in 7-year-old stand of CFP, while the soil pH, soil water content, soil organic carbon, total nitrogen, total phosphorus, sucrase, urease, acid phosphatase, catalase, and microbial biomass carbon, nitrogen, and phosphorus showed higher in 7-year-old stand than other two stands of CFP. The nonmetric multidimensional scaling analysis revealed that the soil microbial species composition was significantly different in three stand ages of CFP. The redundancy and canonical correspondence analysis indicated that the soil urease and microbial biomass nitrogen were the main factors affecting soil bacterial and fungal species composition. Our findings suggested that soil microbial diversity and community structure were inconsistent with changes in soil nutrients and enzyme activities during CFP development, and enhancing stand nurturing and soil nutrient accumulation in the mid-development stage were beneficial to the sustainable management of CFP.

A soft neuroprosthetic hand providing simultaneous myoelectric control and tactile feedback.

Neuroprosthetic hands are typically heavy (over 400 g) and expensive (more than US$10,000), and lack the compliance and tactile feedback of human hands. Here, we report the design, fabrication and performance of a soft, low-cost and lightweight (292 g) neuroprosthetic hand that provides simultaneous myoelectric control and tactile feedback. The neuroprosthesis has six active degrees of freedom under pneumatic actuation, can be controlled through the input from four electromyography sensors that measure surface signals from residual forearm muscles, and integrates five elastomeric capacitive sensors on the fingertips to measure touch pressure so as to enable tactile feedback by eliciting electrical stimulation on the skin of the residual limb. In a set of standardized tests performed by two individuals with transradial amputations, we show that the soft neuroprosthetic hand outperforms a conventional rigid neuroprosthetic hand in speed and dexterity. We also show that one individual with a transradial amputation wearing the soft neuroprosthetic hand can regain primitive touch sensation and real-time closed-loop control.

Restricted binding of a model protein on C3N4 nanosheets suggests an adequate biocompatibility of the nanomaterial.

Recently, C3N4, a carbon nitride nanomaterial, has attracted great attention in many scientific fields due to its outstanding properties. Specifically, this nanomaterial has displayed non- or low-toxicity in biological systems suggesting its excellent biocompatibility and biosafety. Nevertheless, few studies address the structural consequences from the direct interaction between C3N4 and biomolecules that could imply the physical origin of its bio-effect, particularly from the molecular level. Herein, we explored the interaction of a C3N4 nanosheet and a model protein, the λ-repressor protein. We found that the C3N4 nanosheet has a limited influence on the structure of the λ-repressor protein, which substantiates the outstanding biocompatibility of the nanomaterial. Detailed analyses showed that upon absorption on the C3N4 nanosheet, the λ-repressor protein remains located in a relatively fixed position without compromising the structural integrity of the protein. Furthermore, the protein-nanomaterial interaction is mediated by positively charged residues located on the surface of the protein and by the regional negatively charged center on the C3N4 nanosheet (i.e., N-rich defects). These findings provide further molecular-level insights into the good biocompatibility of the C3N4 nanomaterial and also suggest its potential usage as a protein drug delivery platform.

Fibrin-associate diffuse large B-Cell lymphoma arising in a left atrial myxoma: A case report and literature review✰,✰✰.

We report a 60-year-old male with fibrin-associated diffuse large B-cell lymphoma (fa-DLBCL) in left atrial myxoma. Echocardiography showed a mass (63 mm × 33 mm) in the left atrium. Histological inspection indicated fa-DLBCL on the surface of atrial myxoma incidentally, together with extensive fibrinous like exudation on myxoma surface. Malignant cells were localized in solid sheets and nests at the peripheral area of the fibrinous exudation which were positive for B-lineage markers (CD20+, CD79a+, PAX-5+) and in situ hybridization of EBV-encoded RNA (EBER). PCR amplification showed clonal rearrangement of immunoglobulin heavy chain (IgH) genes. The patient was still alive with no recurrence in the 35-month follow-up after surgery. We also did a detailed clinicopathological analysis and literature review, which indicated that fa-DLBCL was a heterogeneous entity.

Different platinum crystal surfaces show very distinct protein denaturation capabilities.

Different platinum (Pt) surfaces of nanocrystals usually exhibit significant distinctions with regard to various biological, physical, and chemical characteristics, such as bio-recognition, surface wetting, and catalytic activities. In this study, we report for the first time that two shape-controlled Pt nanocrystals with the most common low-index surfaces, Pt(100) and Pt(111), show very dissimilar protein denaturation capabilities based on all-atom molecular dynamics simulations employing the widely used model protein, villin headpiece (HP35). We demonstrate that HP35 is well preserved on the Pt(100) crystal surface, whereas it is severely disrupted on the Pt(111) crystal surface. This surprising difference originates from the distinct water behavior in the first solvation shell (FSS) of the two Pt crystal surfaces. Within the FSS of the Pt(100) crystal surface, water molecules form a very compact and stable monolayer through a highly uniform rhombic hydrogen-bond network. This water monolayer prefers the adsorption of acidic residues (such as Glu and Asp) and acts as a shield to prevent other residues from directly coming into contact with the metal surface. On the other hand, the hydrogen bond network in the water monolayer in the FSS of the Pt(111) crystal surface is very sparse and quite defective, which makes it more vulnerable to the penetration of various residues, particularly those with planar side chains such as Phe, Trp and Arg due to strong dispersion interactions, leading to subsequent protein unfolding. The binding free energy calculations for some key amino acids on the two different crystal surfaces further uncover the molecular origin behind their distinct protein denaturation capability. Our study reveals the vital importance of interfacial water in determining the structure of proteins when binding to different metal crystal surfaces. The discovered molecular mechanisms may be helpful for the future development of a bio-assisted programmable synthetic strategy of sophisticated Pt nanostructures for biomedical applications.