Advancing oil-water separation: Design and efficiency of amphiphilic hyperbranched demulsifiers.

HYPOTHESIS: An innovative strategy for designing high-performance demulsifiers is proposed. It hypothesizes that integrating mesoscopic molecular simulations with macroscopic physicochemical experiments can enhance the understanding and effectiveness of demulsifiers. Specifically, it is suggested that amphiphilic hyperbranched polyethyleneimine (CHPEI) could act as an efficient demulsifier in oil-water systems, with its performance influenced by its adsorption behaviors at the oil-water interface and its ability to disrupt asphaltene-resin aggregates. EXPERIMENTS: Several coarse-grained models of oil-water systems, with CHPEI, are constructed using dissipative particle dynamics (DPD) simulation. Following the insights gained from the simulations, a series of CHPEI-based demulsifiers are designed and synthesized. Demulsification experiments are conducted on both simulated and crude oil emulsions, with the process monitored using laser scanning confocal microscopy. Additionally, adsorption kinetics and small angle X-ray scattering are employed to reveal the inherent structural characteristics of CHPEI demulsifiers. FINDINGS: CHPEI demonstrates over 96.7 % demulsification efficiency in high acid-alkali-salt systems and maintains its performance even after multiple reuse cycles. The simulations and macroscopic experiments collectively elucidate that the effectiveness of a demulsifier is largely dependent on its molecular weight and the balance of hydrophilic and hydrophobic groups. These factors are crucial in providing sufficient interfacial active functional groups while avoiding adsorption sites for other surfactants. Collaborative efforts between DPD simulation and macroscopic measurements deepen the understanding of how demulsifiers can improve oil-water separation efficiency in emulsion treatment.

Large language model to multimodal large language model: A journey to shape the biological macromolecules to biological sciences and medicine.

After ChatGPT was released, large language models (LLMs) became more popular. Academicians use ChatGPT or LLM models for different purposes, and the use of ChatGPT or LLM is increasing from medical science to diversified areas. Recently, the multimodal LLM (MLLM) has also become popular. Therefore, we comprehensively illustrate the LLM and MLLM models for a complete understanding. We also aim for simple and extended reviews of LLMs and MLLMs for a broad category of readers, such as researchers, students in diversified fields, and other academicians. The review article illustrates the LLM and MLLM models, their working principles, and their applications in diversified fields. First, we demonstrate the technical concept of LLMs, working principle, Black Box, and the evolution of LLMs. To explain the working principle, we discuss the tokenization process, token representation, and token relationships. We also extensively demonstrate the application of LLMs in biological macromolecules, medical science, biological science, and other areas. We illustrate the multimodal applications of LLMs or MLLMs. Finally, we illustrate the limitations, challenges, and future prospects of LLMs. The review acts as a booster dose for clinicians, a primer for molecular biologists, and a catalyst for scientists, and also benefits diversified academicians.

DNA-Based Complexes and Composites: A Review of Fabrication Methods, Properties, and Applications.

Deoxyribonucleic acid (DNA), a macromolecule that stores genetic information in organisms, has recently been gradually developed into a building block for new materials due to its stable chemical structure and excellent biocompatibility. The efficient preparation and functional integration of various molecular complexes and composite materials based on nucleic acid skeletons have been successfully achieved. These versatile materials possess excellent physical and chemical properties inherent to certain inorganic or organic molecules but are endowed with specific physiological functions by nucleic acids, demonstrating unique advantages and potential applications in materials science, nanotechnology, and biomedical engineering in recent years. However, issues such as the production cost, biological stability, and potential immunogenicity of DNA have presented some unprecedented challenges to the application of these materials in the field. This review summarizes the cutting-edge manufacturing techniques and unique properties of DNA-based complexes and composites and discusses the trends, challenges, and opportunities for the future development of nucleic acid-based materials.

Excipient-free nanotransformation of hydrophilic macromolecules using aqueous counter collision for enhanced bioavailability.

The demand for sustainable, eco-friendly biopolymer transdermal delivery systems has increased owing to growing environmental awareness. In this study, we used aqueous counter collision (ACC), a nontoxic nanotransformation method, to convert high- and ultrahigh-molecular-weight hydrophilic macromolecules into their corresponding nanoparticles (NPs). Hyaluronic acid (HA) and crosslinked HA (CLHA) were chosen as the model compounds. Their NPs exhibited particle sizes in the range of 10-100 nm and negative zeta potentials (-20 to -30 mV). Transmission electron microscopy revealed that the NPs were nearly spherical with smooth surfaces. Fourier-transform infrared and proton nuclear magnetic resonance spectroscopy and agarose gel electrophoresis confirmed that the structures and molecular weights of HA and CLHA remained unaltered after ACC. However, the storage and loss moduli of HANPs and CLHANPs were significantly lower than those of HA and CLHA, respectively. Furthermore, the permeation of HANPs and CLHANPs in reconstructed human skin and human cadaver skin was visualized and quantified. HANPs and CLHANPs penetrated deeper into the skin, whereas HA and CLHA were mainly found in the stratum corneum. The total skin absorption (permeation and deposition) of HANPs and CLHANPs was approximately 2.952 and 5.572 times those of HA and CLHA, respectively. Furthermore, HANPs and CLHANPs exhibited resistance to enzyme and free radical degradation. Our findings reveal ACC as a promising, sustainable hydrophilic macromolecule delivery system compared with the chemical hydrolysis of HA.

Polysaccharide-based chondroitin sulfate macromolecule loaded hydrogel/scaffolds in wound healing- A comprehensive review on possibilities, research gaps, and safety assessment.

Wound healing is an intricate multifactorial process that may alter the extent of scarring left by the wound. A substantial portion of the global population is impacted by non-healing wounds, imposing significant financial burdens on the healthcare system. The conventional dosage forms fail to improve the condition, especially in the presence of other morbidities. Thus, there is a pressing requirement for a type of wound dressing that can safeguard the wound site and facilitate skin regeneration, ultimately expediting the healing process. In this context, Chondroitin sulfate (CS), a sulfated glycosaminoglycan material, is capable of hydrating tissues and further promoting the healing. Thus, this comprehensive review article delves into the recent advancement of CS-based hydrogel/scaffolds for wound healing management. The article initially summarizes the various physicochemical characteristics and sources of CS, followed by a brief understanding of the importance of hydrogel and CS in tissue regeneration processes. This is the first instance of such a comprehensive summarization of CS-based hydrogel/scaffolds in wound healing, focusing more on the mechanistic wound healing process, furnishing the recent innovations and toxicity profile. This contemporary review provides a profound acquaintance of strategies for contemporary challenges and future direction in CS-based hydrogel/scaffolds for wound healing.

Mild three-stage alkali-oxygen treatment preserving the native macromolecular structure of lignin for effective disassembling of tobacco stalk.

Tobacco stalks, as one of the annual economic crops rich in biomacromolecules such as cellulose and hemicellulose, are more difficult to decompose into cellulose fibers due to their high degree of lignification compared to other ordinary straw feedstocks, resulting in their underutilization. In this study, we developed a mild three-stage alkali­oxygen (AO) process to efficiently deconstruct the tobacco stalk cell walls. The process, involving alkaline dosages of 15 %, 10 %, and 3 % at each stage, effectively dissociated the cell walls and yielded cellulose fibers with high brightness (42.0 % ISO). The organics in the spent liquor, including lignin, hemicellulose, and small-molecular extracts, were isolated through acid/ethanol precipitation and organic solvent extraction. Lignin characterization by 2D HSQC NMR indicated that the majority of native ß-aryl ether linkages were preserved after AO treatment, making it suitable for producing chemicals or biofuels via depolymerization. Additionally, the small-molecular extracts contained numerous depolymerized products from lignin and carbohydrates, as well as bioactive compounds derived from the tobacco stalk. Overall, this mild, efficient, and eco-friendly process offers a promising approach for the valorization of tobacco stalks and similar biomass resources.

A Carrier Phase Ultrafiltration and Backflow Recovery Technique for Purification of Biological Macromolecules.

A simple carrier phase based ultrafiltration technique that is akin to liquid chromatography and is suitable for medium-to-large volume sample preparation in the laboratory is discussed in this paper. A membrane module was integrated with a liquid chromatography system in a "plug and play" mode for ease of sample handling, and recovery of species retained by the membrane. The sample injector and pump were used for feed injection and for driving ultrafiltration, while the sensors and detectors were used for real-time monitoring of the separation process. The concentration of retained species was enriched by utilizing controlled concentration polarization. The recovery of the retained and enriched species was enhanced by backflow of carrier phase through the membrane using appropriate combination of valves. The backflow of carrier phase also cleaned the membrane and limited the extent of membrane fouling. Proof-of-concept of the proposed technique was provided by conducting different types of protein ultrafiltration experiments. The technique was shown to be suitable for carrying out protein fractionation, desalting, buffer exchange and concentration enrichment. Adoption of this approach is likely to make ultrafiltration easier to use for non-specialized users in biological research laboratories. Other advantages include enhanced product recovery, significant reduction in the number of diavolumes of buffer needed for conducting desalting and buffer exchange, minimal membrane fouling and the potential for repeated use of the same module for multiple separation cycles.

Design of aggregation-induced emission materials for biosensing of molecules and cells.

In recent years, aggregation-induced emission (AIE) materials have gained significant attention and have been developed for various applications in different fields including biomedical research, chemical analysis, optoelectronic devices, materials science, and nanotechnology. AIE is a unique luminescence phenomenon, and AIEgens are fluorescent moieties with relatively twisted structures that can overcome the aggregation-caused quenching (ACQ) effect. Additionally, AIEgens offer advantages such as non-washing properties, deep tissue penetration, minimal damage to biological structures, high signal-to-noise ratio, and excellent photostability. Fluorescent probes with AIE characteristics exhibit high sensitivity, short response time, simple operation, real-time detection capability, high selectivity, and excellent biocompatibility. As a result, they have been widely applied in cellular imaging, luminescent sensing, detection of physiological abnormalities in the human body, as well as early diagnosis and treatment of diseases. This review provides a comprehensive summary and discussion of the progress over the past four years regarding the detection of metal ions, small chemical molecules, biomacromolecules, microbes, and cells based on AIE materials, along with discussing their potential applications and future development prospects.

The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches.

In wastewater treatment plants (WWTPs), complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1,000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota has a high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme cytochromes suggest capabilities for extracellular electron transfer by various taxa, including some Bacteroidota that encode undescribed cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning.IMPORTANCEWastewater treatment plants (WWTPs) are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for the recovery of resources. They function primarily by the activity of microorganisms, which act as a "living sponge," taking up and transforming nutrients, organic material, and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.

Microcapsules based on biological macromolecules for intestinal health: A review.

Intestinal dysfunction is becoming increasingly associated with neurological and endocrine issues, raising concerns about its impact on world health. With the introduction of several breakthrough technologies for detecting and treating intestinal illnesses, significant progress has been made in the previous few years. On the other hand, traditional intrusive diagnostic techniques are expensive and time-consuming. Furthermore, the efficacy of conventional drugs (not capsules) is reduced since they are more likely to degrade before reaching their target. In this context, microcapsules based on different types of biological macromolecules have been used to encapsulate active drugs and sensors to track intestinal ailments and address these issues. Several biomacromolecules/biomaterials (natural protein, alginate, chitosan, cellulose and RNA etc.) are widely used for make microcapsules for intestinal diseases, and can significantly improve the therapeutic effect and reduce adverse reactions. This article systematically summarizes microencapsulated based on biomacromolecules material for intestinal health control and efficacy enhancement. It also discusses the application and mechanism research of microencapsulated biomacromolecules drugs in reducing intestinal inflammation, in addition to covering the preparation techniques of microencapsulated drug delivery systems used for intestinal health. Microcapsule delivery systems' limits and potential applications for intestinal disease diagnosis, treatment, and surveillance were highlighted.

Microbial ice-binding structures: A review of their applications.

Microorganisms' ice-binding structures (IBS) are macromolecules with potential commercial value in agriculture, food technology, material technology, cryobiology, and medicine. Microbial ice-structuring or microbial ice-binding particles, with their multi-applications, are simple to use, effective in low amounts, non-toxic, and environmentally friendly. Due to their source and composition diversities, microbial ice-binding structures are gaining attention because they are useable in various conditions. Some microorganisms also produce structures with dual ice-nucleating and anti-freezing properties. Structures that promote ice formation (ice nucleating particles- INPs) act as ice nuclei, lowering the energy barrier between supercooled liquid and ice, causing ice crystals to form. In contrast, anti-freeze particles (AFPs) prevent ice formation and recrystallization through several mechanisms, including disturbing the formation of string hydrogen bonds amongst water molecules, melting already formed ice crystals, and preventing crystal formation by binding to specific sites. Knowledge of the type and function of microbial ice-binding structures lends fundamental insight for possible scaling the production of cheap, functional, and advanced microbial structure-inspired mimics and by-products. This review focuses on microbial ice-binding structures and their potential uses in the food, medicinal, environmental, and agricultural sectors.

Macromolecule-Nanoparticle-Based Hybrid Materials for Biosensor Applications.

Biosensors function as sophisticated devices, converting biochemical reactions into electrical signals. Contemporary emphasis on developing biosensor devices with refined sensitivity and selectivity is critical due to their extensive functional capabilities. However, a significant challenge lies in the binding affinity of biosensors to biomolecules, requiring adept conversion and amplification of interactions into various signal modalities like electrical, optical, gravimetric, and electrochemical outputs. Overcoming challenges associated with sensitivity, detection limits, response time, reproducibility, and stability is essential for efficient biosensor creation. The central aspect of the fabrication of any biosensor is focused towards forming an effective interface between the analyte electrode which significantly influences the overall biosensor quality. Polymers and macromolecular systems are favored for their distinct properties and versatile applications. Enhancing the properties and conductivity of these systems can be achieved through incorporating nanoparticles or carbonaceous moieties. Hybrid composite materials, possessing a unique combination of attributes like advanced sensitivity, selectivity, thermal stability, mechanical flexibility, biocompatibility, and tunable electrical properties, emerge as promising candidates for biosensor applications. In addition, this approach enhances the electrochemical response, signal amplification, and stability of fabricated biosensors, contributing to their effectiveness. This review predominantly explores recent advancements in utilizing macrocyclic and macromolecular conjugated systems, such as phthalocyanines, porphyrins, polymers, etc. and their hybrids, with a specific focus on signal amplification in biosensors. It comprehensively covers synthetic strategies, properties, working mechanisms, and the potential of these systems for detecting biomolecules like glucose, hydrogen peroxide, uric acid, ascorbic acid, dopamine, cholesterol, amino acids, and cancer cells. Furthermore, this review delves into the progress made, elucidating the mechanisms responsible for signal amplification. The Conclusion addresses the challenges and future directions of macromolecule-based hybrids in biosensor applications, providing a concise overview of this evolving field. The narrative emphasizes the importance of biosensor technology advancement, illustrating the role of smart design and material enhancement in improving performance across various domains.

Effects of Alkaline Extraction pH on Amino Acid Compositions, Protein Secondary Structures, Thermal Stability, and Functionalities of Brewer's Spent Grain Proteins.

A high alkaline pH was previously demonstrated to enhance the extraction yield of brewer's spent grains (BSG) proteins. The effects of extraction pH beyond the extraction yield, however, has not been investigated before. The present work examined the effects of extraction pH (pH 8-12) on BSG proteins' (1) amino acid compositions, (2) secondary structures, (3) thermal stability, and (4) functionalities (i.e., water/oil holding capacity, emulsifying, and foaming properties). The ideal extraction temperature (60 °C) and BSG-to-solvent ratio (1:20 w/v) for maximizing the extraction yield were first determined to set the conditions for the pH effect study. The results showed that a higher extraction pH led to more balanced compositions between hydrophilic and hydrophobic amino acids and higher proportions of random coils structures indicating increased protein unfolding. This led to superior emulsifying properties of the extracted proteins with more than twofold improvement between pH 8 and a pH larger than 10. The extraction pH, nevertheless, had minimal impact on the water/oil holding capacity, foaming properties, and thermal denaturation propensity of the proteins. The present work demonstrated that a high alkaline pH at pH 11-12 was indeed ideal for both maximizing the extraction yield (37-46 wt.%) and proteins' functionalities.

Design and fabrication of 3D-printed in situ crystallization plates for probing microcrystals in an external electric field.

X-ray crystallography is an established tool to probe the structure of macromolecules with atomic resolution. Compared with alternative techniques such as single-particle cryo-electron microscopy and micro-electron diffraction, X-ray crystallography is uniquely suited to room-temperature studies and for obtaining a detailed picture of macromolecules subjected to an external electric field (EEF). The impact of an EEF on proteins has been extensively explored through single-crystal X-ray crystallography, which works well with larger high-quality protein crystals. This article introduces a novel design for a 3D-printed in situ crystallization plate that serves a dual purpose: fostering crystal growth and allowing the concurrent examination of the effects of an EEF on crystals of varying sizes. The plate's compatibility with established X-ray crystallography techniques is evaluated.

Thymol's modulation of cellular macromolecules, oxidative stress, DNA damage, and NF-kB/caspase-3 signaling in the liver of imidacloprid-exposed rats.

We evaluated whether thymol (THY) (30 mg/kg b.wt) could relieve the adverse effects of the neonicotinoid insecticide imidacloprid (IMD) (22.5 mg/kg b.wt) on the liver in a 56-day oral experiment and the probable underlying mechanisms. THY significantly suppressed the IMD-associated increase in hepatic enzyme leakage. Besides, the IMD-induced dyslipidemia was considerably corrected by THY. Moreover, THY significantly repressed the IMD-induced hepatic oxidative stress, lipid peroxidation, DNA damage, and inflammation. Of note, the Feulgen, mercuric bromophenol blue, and PAS-stained hepatic tissue sections analysis declared that treatment with THY largely rescued the IMD-induced depletion of the DNA, total proteins, and polysaccharides. Moreover, THY treatment did not affect the NF-kB p65 immunoexpression but markedly downregulated the Caspase-3 in the hepatocytes of the THY+IMD-treated group than the IMD-treated group. Conclusively, THY could efficiently protect against IMD-induced hepatotoxicity, probably through protecting cellular macromolecules and antioxidant, antiapoptotic, and anti-inflammatory activities.

Chemical and Physical Architecture of Macromolecular Gels for Fracturing Fluid Applications in the Oil and Gas Industry; Current Status, Challenges, and Prospects.

Hydraulic fracturing is vital in recovering hydrocarbons from oil and gas reservoirs. It involves injecting a fluid under high pressure into reservoir rock. A significant part of fracturing fluids is the addition of polymers that become gels or gel-like under reservoir conditions. Polymers are employed as viscosifiers and friction reducers to provide proppants in fracturing fluids as a transport medium. There are numerous systems for fracturing fluids based on macromolecules. The employment of natural and man-made linear polymers, and also, to a lesser extent, synthetic hyperbranched polymers, as additives in fracturing fluids in the past one to two decades has shown great promise in enhancing the stability of fracturing fluids under various challenging reservoir conditions. Modern innovations demonstrate the importance of developing chemical structures and properties to improve performance. Key challenges include maintaining viscosity under reservoir conditions and achieving suitable shear-thinning behavior. The physical architecture of macromolecules and novel crosslinking processes are essential in addressing these issues. The effect of macromolecule interactions on reservoir conditions is very critical in regard to efficient fluid qualities and successful fracturing operations. In future, there is the potential for ongoing studies to produce specialized macromolecular solutions for increased efficiency and sustainability in oil and gas applications.

Revealing the Effect of Stereocontrol on Intermolecular Interactions between Abiotic, Sequence-Defined Polyurethanes and a Ligand.

The development of precision polymer synthesis has facilitated access to a diverse library of abiotic structures wherein chiral monomers are positioned at specific locations within macromolecular chains. These structures are anticipated to exhibit folding characteristics similar to those of biotic macromolecules and possess comparable functionalities. However, the extensive sequence space and numerous variables make selecting a sequence with the desired function challenging. Therefore, revealing sequence-function dependencies and developing practical tools are necessary to analyze their conformations and molecular interactions. In this study, we investigate the effect of stereochemistry, which dictates the spatial location of backbone and pendant groups, on the interaction between sequence-defined oligourethanes and bisphenol A ligands. Various methods are explored to analyze the receptor-like properties of model oligomers and the ligand. The accuracy of molecular dynamics simulations and experimental techniques is assessed to uncover the impact of discrete changes in stereochemical arrangements on the structures of the resulting complexes and their binding strengths. Detailed computational investigations providing atomistic details show that the formed complexes demonstrate significant structural diversity depending on the sequence of stereocenters, thus affecting the oligomer-ligand binding strength. Among the tested techniques, the fluorescence spectroscopy data, fitted to the Stern-Volmer equation, are consistently aligned with the calculations, thus validating the developed simulation methodology. The developed methodology opens a way to engineer the structure of sequence-defined oligomers with receptor-like functionality to explore their practical applications, e.g., as sensory materials.

Development of Stable Water-Soluble Supratomic Silver Clusters Utilizing A Polyoxoniobate-Protected Strategy: Giant Core-Shell-Type Ag8@Nb162 Fluorescent Nanocluster.

Atomically precise low-nuclearity (n<10) silver nanoclusters (AgNCs) have garnered significant interest due to their size-dependent optical properties and diverse applications. However, their synthesis has remained challenging, primarily due to their inherent instability. The present study introduces a new feasible approach for clustering silver ions utilizing highly negative and redox-inert polyoxoniobates (PONbs) as all-inorganic ligands. This strategy not only enables the creation of novel Ag-PONb composite nanoclusters but also facilitates the synthesis of stable low-nuclearity AgNCs. Using this method, we have successfully synthesized a small octanuclear rhombic [Ag8]6+ AgNC stabilized by six highly negative [LiNb27O75]14- polyoxoanions. This marks the first PONb-protected superatomic AgNC, designated as {Ag8@(LiNb27O75)6} (Ag8@Nb162), with an aesthetically spherical core-shell structure. The crystalline Ag8@Nb162 is stable under ambient conditions, What's more, it is water-soluble and able to maintain its molecular cluster structure intact in water. Further, the stable small [Ag8]6+ AgNC has interesting temperature- and pH-dependent reversible fluorescence response, based on which a multiple optical encryption mode for anti-counterfeit technology was demonstrated. This work offers a promising avenue for the synthesis of fascinating and stable PONb-protected AgNCs and sheds light on the development of new-type optical functional materials.

In silico energetic and molecular dynamic simulations studies demonstrate potential effect of the point mutations with implications for protein engineering in BDNF.

Protein engineering by directed evolution is time-consuming. Hence, in silico techniques like FoldX-Yasara for ∆∆G calculation, and SNPeffect for predicting propensity for aggregation, amyloid formation, and chaperone binding are employed to design proteins. Here, we used in silico techniques to engineer BDNF-NTF3 interaction and validated it using mutations with known functional implications for NGF dimer. The structures of three mutants representing a positive, negative, or neutral ∆∆G involving two interface residues in BDNF and two mutations representing a neutral and positive ∆∆G in NGF, which is aligned with BDNF, were selected for molecular dynamics (MD) simulation. Our MD results conclude that the secondary structure of individual protomers of the positive and negative mutants displayed a similar or different conformation from the NTF3 monomer, respectively. The positive mutants showed fewer hydrophobic interactions and higher hydrogen bonds compared to the wild-type, negative, and neutral mutants with similar SASA, suggesting solvent-mediated disruption of hydrogen-bonded interactions. Similar results were obtained for mutations with known functional implications for NGF and BDNF. The results suggest that mutations with known effects in homologous proteins could help in validation, and in silico directed evolution experiments could be a viable alternative to the experimental technique used for protein engineering.

GABA-edited MEGA-PRESS at 3 T: Does a measured macromolecule background improve linear combination modeling?

PURPOSE: The J-difference edited γ-aminobutyric acid (GABA) signal is contaminated by other co-edited signals-the largest of which originates from co-edited macromolecules (MMs)-and is consequently often reported as "GABA+." MM signals are broader and less well-characterized than the metabolites, and are commonly approximated using a Gaussian model parameterization. Experimentally measured MM signals are a consensus-recommended alternative to parameterized modeling; however, they are relatively under-studied in the context of edited MRS. METHODS: To address this limitation in the literature, we have acquired GABA-edited MEGA-PRESS data with pre-inversion to null metabolite signals in 13 healthy controls. An experimental MM basis function was derived from the mean across subjects. We further derived a new parameterization of the MM signals from the experimental data, using multiple Gaussians to accurately represent their observed asymmetry. The previous single-Gaussian parameterization, mean experimental MM spectrum and new multi-Gaussian parameterization were compared in a three-way analysis of a public MEGA-PRESS dataset of 61 healthy participants. RESULTS: Both the experimental MMs and the multi-Gaussian parameterization exhibited reduced fit residuals compared to the single-Gaussian approach (p = 0.034 and p = 0.031, respectively), suggesting they better represent the underlying data than the single-Gaussian parameterization. Furthermore, both experimentally derived models estimated larger MM fractional contribution to the GABA+ signal for the experimental MMs (58%) and multi-Gaussian parameterization (58%), compared to the single-Gaussian approach (50%). CONCLUSIONS: Our results indicate that single-Gaussian parameterization of edited MM signals is insufficient and that both experimentally derived GABA+ spectra and their parameterized replicas improve the modeling of GABA+ spectra.