The Molecular Basis of the Sodium Dodecyl Sulfate Effect on Human Ubiquitin Structure: A Molecular Dynamics Simulation Study

Revealing the interaction between alpha-chymotrypsin and eugenol: An integrated multi-spectral and dynamic simulation approach

The study aims to explore the effects of Eugenol (EUG) as an antioxidant on α-Chymotrypsin (α-Chy) and its interaction mechanism, with potential implications for new therapy development. The interaction between EUG and α-Chy was demonstrated through ultraviolet (UV) spectroscopy, which resulted in a shift in absorption with docking energies of -22.76 kJ/mol. An increase in fluorescence intensity indicated that the Trp residues moved to a less polar environment, which is consistent with the changes in accessible surface area (ASA) values. The presence of EUG led to a decrease in α-helix, β-turn, and random coil structures as shown by circular dichroism (CD) and Fourier-transform infrared (FTIR) analysis. Additionally, there was a slight increase in β-sheet structures, indicating a decrease in enzyme stability. However, tests for thermal stability showed a decrease in folding upon the introduction of EUG, which contradicted the results obtained from molecular dynamics (MD) simulations. The docking studies revealed that EUG forms hydrogen bonds and van der Waals forces with the enzyme, indicating the interaction mechanism. Kinetic studies confirmed that EUG acts as a mixed inhibitor. However, further research involving live organisms is necessary to fully understand its potential.

QbD Approach-Based Preparation and Optimization of Hydrophobic Ion-Pairing Complex of Lysozyme with Sodium Dodecyl Sulphate to Enhance Stability in Lipid-Based Carriers

Hydrophobic ion pairing (HIP) complexation was found to be an efficient approach in modulating the release and enhancing the stability and encapsulation of hydrophilic macromolecules such as proteins in hydrophobic nano/microcarriers. The present work strives to develop and optimize the preparation of the HIP complex of the antimicrobial enzyme lysozyme (LYZ) with the ion-pairing agent (IPA) sodium dodecyl sulphate (SDS) relying on the quality-by-design (QbD) approach. The quality target product profile (QTPP) includes the achievement of maximal lipophilicity in a reversible manner to enable the maintenance of biological activity. The related critical quality attributes (CQAs) were defined as complexation efficacy, complex stability, enzyme recovery and activity. Three risk assessment (RA) tools were used to identify and rank the critical process parameters (CPPs) and critical material attributes (CMAs). From this assessment, the pH of the medium, LYZ:SDS molar ratio and drying conditions were determined as high-risk factors that need to be investigated. To the best of our knowledge, for the first time, electrostatic titration was used as a smart approach to determine the optimum molar ratio at different pH values. Based on the predefined CQAs, pH 8 with an LYZ/SDS molar ratio of 1:8 was found to be the optimal condition for complexation efficiency and recovery (%) of a biologically active enzyme. A cost-effective drying process based on a ventilated oven was developed, which resulted in complex qualities comparable to those obtained by the commonly used freeze-drying method. In a nutshell, the optimum conditions for the preparation of the LYZ/SDS HIP complex were efficiently facilitated by the rational application of QbD principles and the utilization of efficient electrostatic titration and ventilated oven-drying methods.

Molecular dynamics simulation of the effect of temperature on the conformation of ubiquitin protein

CONTENT

Ubiquitin, a ubiquitous small protein found in all living organisms, is crucial for tagging proteins earmarked for degradation and holds pivotal importance in biomedicine. Protein functionality is intricately linked to its structure. To comprehend the impact of diverse temperatures on ubiquitin protein structure, our study delved into the energy landscape, hydrogen bonding, and overall structural stability of ubiquitin protein at varying temperatures. Through meticulous analysis of root mean square deviation and root mean square fluctuation, we validated the robustness of the simulation conditions employed. Within our simulated system, the bonding energy and electrostatic potential energy exhibited linear augmentation, while the van der Waals energy demonstrated a linear decline. Additionally, our findings highlighted that the α-Helix secondary structure of the ubiquitin protein gradually transitions toward helix destabilization under high-temperature conditions. The secondary structure of ubiquitin protein experiences distinct changes under varying temperatures. The outcomes of our molecular simulations offer a theoretical framework that enhances our comprehension of how temperature impacts the structural stability of ubiquitin protein. These insights contribute not only to a deeper understanding of iniquity's behavior but also hold broader implications in the realm of biomedicine and beyond.

METHODS

All the MD simulations were performed using the GROMACS software with GROMOS96 force field and SPC for water. The ubiquitin protein was put in the center of a cubic box with a length of 8 nm, a setting that allowed > 0.8 nm in the minimal distance between the protein surface and the box wall. To remove the possible coordinate collision of the configurations, in the beginning, the steepest descent method was used until the maximum force between atoms was under 100 kJ/mol·nm with a 0.01 nm step size. Minimization was followed by 30 ps of position-restrained MD simulation. The protein was restrained to its initial position, and the solvent was freely equilibrated. The product phase was obtained with the whole system simulated for 10 ns without any restraint using an integral time step of 1 fs with different temperatures. The cutoff for short-range electronic interaction was set to 1.5 nm. The long-range interactions were treated with a particle-mesh Ewald (PME) method with a grid width of 1.2 nm.

Evaluating and optimizing Acid-pH and Direct Lysis RNA extraction for SARS-CoV-2 RNA detection in whole saliva

COVID-19 has been a global public health and economic challenge. Screening for the SARS-CoV-2 virus has been a key part of disease mitigation while the world continues to move forward, and lessons learned will benefit disease detection beyond COVID-19. Saliva specimen collection offers a less invasive, time- and cost-effective alternative to standard nasopharyngeal swabs. We optimized two different methods of saliva sample processing for RT-qPCR testing. Two methods were optimized to provide two cost-efficient ways to do testing for a minimum of four samples by pooling in a 2.0 mL tube and decrease the need for more highly trained personnel. Acid-pH-based RNA extraction method can be done without the need for expensive kits. Direct Lysis is a quick one-step reaction that can be applied quickly. Our optimized Acid-pH and Direct Lysis protocols are reliable and reproducible, detecting the beta-2 microglobulin (B2M) mRNA in saliva as an internal control from 97 to 96.7% of samples, respectively. The cycle threshold (Ct) values for B2M were significantly higher in the Direct Lysis protocol than in the Acid-pH protocol. The limit of detection for N1 gene was higher in Direct Lysis at ≤ 5 copies/μL than Acid-pH. Saliva samples collected over the course of several days from two COVID-positive individuals demonstrated Ct values for N1 that were consistently higher from Direct Lysis compared to Acid-pH. Collectively, this work supports that each of these techniques can be used to screen for SARS-CoV-2 in saliva for a cost-effective screening platform.

CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation

Molecular modeling and simulation play important roles in biomedical research as they provide molecular-level insight into the underlying mechanisms of biological functions that are difficult to elucidate only with experiments. CHARMM-GUI (https://charmm-gui.org) is a web-based cyberinfrastructure that is widely used to generate various molecular simulation system and input files and thus facilitates and standardizes the usage of common and advanced simulation techniques. In particular, PDB Manipulator provides various chemical modification options as the starting point for most input generation modules in CHARMM-GUI. Here, we discuss recent additions to PDB Manipulator, such as non-standard amino acids/RNA substitutions, ubiquitylation and SUMOylation, Lys/Arg post-translational modifications, lipidation, peptide stapling, and improved parameterization options of small molecules. These additional features are expected to make complex PDB modifications easy for biomolecular modeling and simulation.

Green Chemistry to Modify Functional Properties of Crambe Protein Isolate-Based Thermally Formed Films

Proteins are promising precursors to be used in production of sustainable materials with properties resembling plastics, although protein modification or functionalization is often required to obtain suitable product characteristics. Here, effects of protein modification were evaluated by crosslinking behavior using high-performance liquid chromatography (HPLC), secondary structure using infrared spectroscopy (IR), liquid imbibition and uptake, and tensile properties of six crambe protein isolates modified in solution before thermal pressing. The results showed that a basic pH (10), especially when combined with the commonly used, although moderately toxic, crosslinking agent glutaraldehyde (GA), resulted in a decrease in crosslinking in unpressed samples, as compared to acidic pH (4) samples. After pressing, a more crosslinked protein matrix with an increase in β-sheets was obtained in basic samples compared to acidic samples, mainly due to the formation of disulfide bonds, which led to an increase in tensile strength, and liquid uptake with less material resolved. A treatment of pH 10 + GA, combined either with a heat or citric acid treatment, did not increase crosslinking or improve the properties in pressed samples, as compared to pH 4 samples. Fenton treatment at pH 7.5 resulted in a similar amount of crosslinking as the pH 10 + GA treatment, although with a higher degree of peptide/irreversible bonds. The strong bond formation resulted in lack of opportunities to disintegrate the protein network by all extraction solutions tested (even for 6 M urea + 1% sodium dodecyl sulfate + 1% dithiothreitol). Thus, the highest crosslinking and best properties of the material produced from crambe protein isolates were obtained by pH 10 + GA and pH 7.5 + Fenton, where Fenton is a greener and more sustainable solution than GA. Therefore, chemical modification of crambe protein isolates is effecting both sustainability and crosslinking behavior, which might have an effect on product suitability.

In vitro and in silico characterization of a novel glutamate carboxypeptidase from Cohnella sp. A01

Glutamate carboxypeptidase is a bacterial enzyme of metallopeptidase superfamily. This enzyme is an exo-peptidase that catalyzes the hydrolysis of glutamate residues at the C-terminus of folic acid. The rCP302 is a novel zinc ion-dependent recombinant glutamate carboxypeptidase derived from a thermophilic bacterium, Cohnella sp. A01 (PTCC No: 1921). By simulating the structure of rCP302, analyzing its activity in various environmental settings, and contrasting it with that of related enzymes, we wanted to evaluate the heterologous production, purification, and characterization of this enzyme. The bioinformatics study showed that rCP302 had maximum similarity to M20 family of metallopeptidases. The purified rCP302 molecular weight was about 41.6 kDa. The optimum temperature and pH for the catalytic activity of rCP302 were 50 °C and 7.2, respectively. Fluorescence spectroscopy data elucidated the secondary structure of rCP302 and determined conformational changes caused by alterations in ambient conditions. Using folate as a substrate, K_m and specific activity values were calculated as 0.108 μM and 687 μmol/min/mg, respectively. The enzyme activity was strongly inhibited when EDTA sequestered zinc ions. The half-life of this enzyme at 30 °C was 2012 min. Regarding the ability of rCP302 to degrade folic acid, and its long half-life at 37 °C, the normal temperature of many mammals, this enzyme can be introduced for further study for use in the pharmaceutical industry.

Brave new surfactant world revisited by thermoalkalophilic lipases: computational insights into the role of SDS as a substrate analog

Non-ionic surfactants were shown to stabilize the active conformation of thermoalkalophilic lipases by mimicking the lipid substrate while the catalytic interactions formed by anionic surfactants have not been well characterized. In this study, we combined μs-scale molecular dynamics (MD) simulations and lipase activity assays to analyze the effect of ionic surfactant, sodium dodecyl sulfate (SDS), on the structure and activity of thermoalkalophilic lipases. Both the open and closed lipase conformations that differ in geometry were recruited to the MD analysis to provide a broader understanding of the molecular effect of SDS on the lipase structure. Simulations at 298 K showed the potential of SDS for maintaining the active lipase through binding to the sn-1 acyl-chain binding pocket in the open conformation or transforming the closed conformation to an open-like state. Consistent with MD findings, experimental analysis showed increased lipase activity upon SDS incubation at ambient temperature. Notably, the lipase cores stayed intact throughout 2 μs regardless of an increase in the simulation temperature or SDS concentration. However, the surface structures were unfolded in the presence of SDS and at elevated temperature for both conformations. Simulations of the dimeric lipase were also carried out and showed reduced flexibility of the surface structures which were unfolded in the monomer, indicating the insulating role of dimer interactions against SDS. Taken together, this study provides insights into the possible substrate mimicry by the ionic surfactant SDS for the thermoalkalophilic lipases without temperature elevation, underscoring SDS's potential for interfacial activation at ambient temperatures.

Effects of Chemical Additives in Refolding Buffer on Recombinant Human BMP-2 Dimerization and the Bioactivity on SaOS-2 Osteoblasts

Bone morphogenetic protein-2 (BMP-2) is a promising osteogenic agent in tissue engineering. BMP-2 is usually expressed in Escherichia coli owing to the high yield and low cost, but the protein is expressed as inclusion bodies. Thus, the bottleneck for BMP-2 production in E. coli is the refolding process. Here, we explored the effects of the refolding buffer composition on BMP-2 refolding. The BMP-2 inclusion body was solubilized in urea and subjected to refolding by the dilution method. Various additives were investigated to improve the BMP-2 refolding yield. Nonreducing SDS-PAGE showed that BMP-2 dimers, the presumably biologically active form, were detected at approximately 25 kDa. The highest yield of the BMP-2 dimers was observed in the refolding buffer that contained ionic detergents (sarkosyl and cetylpyridinium chloride) followed by zwitterionic and nonionic detergents (NDSB-195, NP-40, and Tween 80). In addition, sugars (glucose, sorbitol, and sucrose) in combination with anionic detergents (sodium dodecyl sulfate and sarkosyl) reduced BMP-2 oligomers and increased the BMP-2 dimer yield. Subsequently, the refolded BMP-2s were tested for their bioactivity using the alkaline phosphatase assay in osteogenic cells (SaOS-2), as well as the luciferase reporter assay and the calcium assays. The refolded BMP-2 showed the activities in the calcium deposition assay and the luciferase reporter assay but not in the alkaline phosphatase activity assay or the intracellular calcium assay even though the dimers were clearly detected. Therefore, the detection of the disulfide-linked dimeric BMP-2 in nonreducing SDS-PAGE is an inadequate proxy for the bioactivity of BMP-2.

Advancements in antimicrobial nanoscale materials and self-assembling systems

Antimicrobial resistance is directly responsible for more deaths per year than either HIV/AIDS or malaria and is predicted to incur a cumulative societal financial burden of at least $100 trillion between 2014 and 2050. Already heralded as one of the greatest threats to human health, the onset of the coronavirus pandemic has accelerated the prevalence of antimicrobial resistant bacterial infections due to factors including increased global antibiotic/antimicrobial use. Thus an urgent need for novel therapeutics to combat what some have termed the 'silent pandemic' is evident. This review acts as a repository of research and an overview of the novel therapeutic strategies being developed to overcome antimicrobial resistance, with a focus on self-assembling systems and nanoscale materials. The fundamental mechanisms of action, as well as the key advantages and disadvantages of each system are discussed, and attention is drawn to key examples within each field. As a result, this review provides a guide to the further design and development of antimicrobial systems, and outlines the interdisciplinary techniques required to translate this fundamental research towards the clinic.

How do surfactants unfold and refold proteins?

Although the anionic surfactant sodium dodecyl sulfate, SDS, has been used for more than half a century as a versatile and efficient protein denaturant for protein separation and size estimation, there is still controversy about its mode of interaction with proteins. The term "rod-like" structures for the complexes that form between SDS and protein, originally introduced by Tanford, is not sufficiently descriptive and does not distinguish between the two current vying models, namely protein-decorated micelles a.k.a. the core-shell model (in which denatured protein covers the surface of micelles) versus beads-on-a-string model (where unfolded proteins are surrounded by surfactant micelles). Thanks to a combination of structural, kinetic and computational work particularly within the last 5-10 years, it is now possible to rule decisively in favor of the core-shell model. This is supported unambiguously by a combination of calorimetric and small-angle X-ray scattering (SAXS) techniques and confirmed by increasingly sophisticated molecular dynamics simulations. Depending on the SDS:protein ratio and the protein molecular mass, the formed structures can range from multiple partly unfolded protein molecules surrounding a single shared micelle to a single polypeptide chain decorating multiple micelles. We also have much new insight into how this species forms. It is preceded by the binding of small numbers of SDS molecules which subsequently grow by accretion. Time-resolved SAXS analysis reveals an asymmetric attack by SDS micelles followed by distribution of the increasingly unfolded protein around the micelle. The compactness of the protein chain continues to evolve at higher SDS concentrations according to single-molecule studies, though the protein remains completely denatured on the tertiary structural level. SDS denaturation can be reversed by addition of nonionic surfactants that absorb SDS forming mixed micelles, leaving the protein free to refold. Refolding can occur in parallel tracks if only a fraction of the protein is initially stripped of SDS. SDS unfolding is nearly always reversible unless carried out at low pH, where charge neutralization can lead to superclusters of protein-surfactant complexes. With the general mechanism of SDS denaturation now firmly established, it largely remains to explore how other ionic surfactants (including biosurfactants) may diverge from this path.

Micelle Dynamic Reconstruction to Effectively Modulate the Transmission of Smart Windows

Micelles are extremely dynamic equilibrium aggregates. The size and shape of micelles are subject to appreciable structural fluctuations with the introduction of foreign ions, temperature, etc. The highly dynamic character has for a long time hugely attracted the interest of researchers to investigate the mechanism of micellar structure change and the dependence of their optical properties on the structure change. Herein, taking the most common sodium dodecyl sulfate (SDS) as an example, the aggregation behavior of SDS with excess K⁺ and the effect of temperature on the K⁺/SDS mixed system were detailed and systematically investigated by combining with molecular dynamics simulations and experiments. The addition of K⁺ leads to a reconfiguration of the original micelle structure, resulting in a significant change in micelle size from the nanoscale up to the microscale. And simultaneously, temperature can induce a dynamic process of conjugation/deconjugation of K⁺/SDS micelles in the mixed solution, which is manifested macroscopically by the change of transmittance. Finally, a temperature-responsive smart gel was prepared by introducing K⁺/SDS into a polyacrylamide (PAM) gel, which showed an excellent tunable performance in transmittance (ΔT_550 nm = 60.1%, ΔT_808 nm = 42.72%). The designed smart window shows potential applications in room temperature control (Δt = 4.1 °C) and excellent stability over the course of 50 cycles.

Structure based innovative approach to analyze aptaprobe-GPC3 complexes in hepatocellular carcinoma

Background

Glypican-3 (GPC3), a membrane-bound heparan sulfate proteoglycan, is a biomarker of hepatocellular carcinoma (HCC) progression. Aptamers specifically binding to target biomolecules have recently emerged as clinical disease diagnosis targets. Here, we describe 3D structure-based aptaprobe platforms for detecting GPC3, such as aptablotting, aptaprobe-based sandwich assay (ALISA), and aptaprobe-based imaging analysis.

Results

For preparing the aptaprobe–GPC3 platforms, we obtained 12 high affinity aptamer candidates (GPC3_1 to GPC3_12) that specifically bind to target GPC3 molecules. Structure-based molecular interactions identified distinct aptatopic residues responsible for binding to the paratopic nucleotide sequences (nt-paratope) of GPC3 aptaprobes. Sandwichable and overlapped aptaprobes were selected through structural analysis. The aptaprobe specificity for using in HCC diagnostics were verified through Aptablotting and ALISA. Moreover, aptaprobe-based imaging showed that the binding property of GPC3_3 and their GPC3 specificity were maintained in HCC xenograft models, which may indicate a new HCC imaging diagnosis.

Conclusion

Aptaprobe has the potential to be used as an affinity reagent to detect the target in vivo and in vitro diagnosing system.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-022-01391-z.

Chemical Cleaning Process of Polymeric Nanofibrous Membranes

Membrane fouling is one of the most significant issues to overcome in membrane-based technologies as it causes a decrease in the membrane flux and increases operational costs. This study investigates the effect of common chemical cleaning agents on polymeric nanofibrous membranes (PNM) prepared by polyvinylidene fluoride (PVDF), polyacrylonitrile (PAN), and polyamide 6 (PA6) nanofibers. Common alkaline and acid membrane cleaners were selected as the chemical cleaning agents. Membrane surface morphology was investigated. The PAN PNM were selected and fouled by engine oil and then cleaned by the different chemical cleaning agents at various ratios. The SEM results indicated that the use of chemical agents had some effects on the surface of the nanofibrous membranes. Moreover, alkaline cleaning of the fouled membrane using the Triton X 100 surfactant showed a two to five times higher flux recovery than without using a surfactant. Among the tested chemical agents, the highest flux recovery rate was obtained by a binary solution of 5% sodium hydroxide + Triton for alkaline cleaning, and an individual solution of 1% citric acid for acidic cleaning. The results presented here provide one of the first investigations into the chemical cleaning of nanofiber membranes.

Stereoisomeric Pam2CS Based TLR2 Agonists: Synthesis, Structural Modelling and Activity as Vaccine Adjuvants

Lipopeptides including diacylated Pam2CSK4 as well as triacylated Pam3CSK4 act as ligands of Toll-like receptor (TLR)-2, a promising target for the development of vaccine adjuvants. The highly investigated Pam2CSK4 and...

Optimizing Decellularization Strategies for the Efficient Production of Whole Rat Kidney Scaffolds

BACKGROUND

Renal dysfunction remains a global issue, with chronic kidney disease being the 18th most leading cause of death, worldwide. The increased demands in kidney transplants, led the scientific society to seek alternative strategies, utilizing mostly the tissue engineering approaches. Unlike to perfusion decellularization of kidneys, we proposed alternative decellularization strategies to obtain acellular kidney scaffolds. The aim of this study was the evaluation of two different decellularization approaches for producing kidney bioscaffolds.

METHODS

Rat kidneys from Wistar rats, were submitted to decellularization, followed two different strategies. The decellularization solutions used in both approaches were the same and involved the use of 3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate and sodium dodecyl sulfate buffers for 12 h each, followed by incubation in a serum medium. Both approaches involved 3 decellularization cycles. Histological analysis, biochemical and DNA quantification were performed. Cytotoxicity assay and repopulation of acellular kidneys were also applied.

RESULTS

Histological, biochemical and DNA quantification confirmed that the 2nd approach had the best outcome regarding the kidney composition and cell elimination. Acellular kidneys from both approaches were successfully recellularized.

CONCLUSION

Based on the above data, the production of kidney scaffolds with the proposed cost- effective decellularization approaches, was efficient.

Anticoagulation and antibacterial properties of heparinized nanosilver with different morphologies

Synthesis and characterization of nanoparticles with different morphologies coupled to minimal chemical interventions for sustainable applications is one of the contemporary topics in the field of nanotechnology. In the current study, heparinized silver nanoparticles were synthesized using a chemical reduction method. Different concentrations of heparin were used to investigate its role in the stability and morphological properties of silver nanoparticles. Interestingly, it has been observed that the concentration of the stabilizing agent heparin plays a pivotal role in dictating the size and shape of the nanosilver. As visualized under a transmission electron microscope, nanosilver with different morphological states such as triangles, truncated triangles, hexagon, and spheres has been experimentally trapped. Such modular property of heparin coated nanosilver has also exhibited substantial differences in their anticoagulation and antimicrobial activities.

Surface-Induced Crystallization of Sodium Dodecyl Sulfate (SDS) Micellar Solutions in Confinement

We investigate the role of confinement on the onset of crystallization in subcooled micellar solutions of sodium dodecyl sulfate (SDS), examining the impact of sample volume, substrate surface energy, and surface roughness. Using small angle neutron scattering (SANS) and dynamic light scattering (DLS), we measure the crystallization temperature upon cooling and the metastable zone width (MSZW) for bulk 10-30 wt% SDS solutions. We then introduce a microdroplet approach to quantify the impact of surface free energy (18-65 mN/m) and substrate roughness (R_α ≃ 0-60 μm) on the kinetics of surface-induced crystallization through measurements of induction time (t_i) under isothermal conditions. While t_i is found to decrease exponentially with decreasing temperature (increasing subcooling) for all tested surfaces, increasing the surface energy could cause a significant further reduction of up to ∼40 fold. For substrates with the lowest surface energy and longest t_i, microscale surface roughness is found to enhance crystal nucleation, in particular for R_α ≥ 10 μm. Finally, we demonstrate that tuning the surface energy and microscopic roughness can be effective routes to promote or delay nucleation in bulk-like volumes, thus greatly impacting the stability of surfactant solutions at lower temperatures.

Optimization of Protein Extraction Method for 2DE Proteomics of Goat's Milk

Two-dimensional electrophoretic (2DE)-based proteomics remains a powerful tool for allergenomic analysis of goat’s milk but requires effective extraction of proteins to accurately profile the overall causative allergens. However, there are several current issues with goat’s milk allergenomic analysis, and among these are the absence of established standardized extraction method for goat’s milk proteomes and the complexity of goat’s milk matrix that may hamper the efficacy of protein extraction. This study aimed to evaluate the efficacies of three different protein extraction methods, qualitatively and quantitatively, for the 2DE-proteomics, using milk from two commercial dairy goats in Malaysia, Saanen, and Jamnapari. Goat’s milk samples from both breeds were extracted by using three different methods: a milk dilution in urea/thiourea based buffer (Method A), a triphasic separation protocol in methanol/chloroform solution (Method B), and a dilution in sulfite-based buffer (Method C). The efficacies of the extraction methods were assessed further by performing the protein concentration assay and 1D and 2D SDS-PAGE profiling, as well as identifying proteins by MALDI-TOF/TOF MS/MS. The results showed that method A recovered the highest amount of proteins (72.68% for Saanen and 71.25% for Jamnapari) and produced the highest number of protein spots (199 ± 16.1 and 267 ± 10.6 total spots for Saanen and Jamnapari, respectively) with superior gel resolution and minimal streaking. Six milk protein spots from both breeds were identified based on the positive peptide mass fingerprinting matches with ruminant milk proteins from public databases, using the Mascot software. These results attest to the fitness of the optimized protein extraction protocol, method A, for 2DE proteomic and future allergenomic analysis of the goat’s milk.

Molecular dynamics studies of the protective and destructive effects of sodium dodecyl sulfate in thermal denaturation of hen egg-white lysozyme and bovine serum albumin

To investigate the protective and destructive effects of sodium dodecyl sulfate (SDS) in thermal denaturation of proteins, we carried out twelve independent atomistic molecular dynamics (MD) simulations of bovine serum albumin (BSA) and hen egg-white lysozyme (LYZ) in pure water and SDS solutions at 25 and 80 °C, using SDS concentrations of 0.01, 0.05, 0.1 and 1 M. In the case of the BSA in pure water and SDS solutions, it was found that its helicity decreased from 67.02% in reference structure to 35% in pure water at 80 °C due to thermal denaturation, whereas it increased to 49.34, 52.36 and 54% at 0.01, 0.05 and 0.1 M SDS, respectively, owing to the SDS protective effect. In 1 M SDS, however, the surfactant's protective effect was weak, and consequently the helicity of the BSA decreased to 47.01%. In contrast, no protection by SDS was observed for the LYZ in SDS solutions as the loss of its helices increased with SDS concentration from 0.01 to 1 M. In attempt to interpret the SDS effects molecularly, we calculated the diffusion coefficients of SDS in the protein solutions. The calculated values were found to decrease with increasing SDS concentration in the BSA solutions, but to increase with SDS concentration in the LYZ solutions. The decrease or increase in the diffusion coefficient of SDS was attributed to the net negative or positive charge on the proteins at neutral pH, indicating that electrostatic repulsions or attractions affect diffusivity significantly and can moderate SDS-proteins non-covalent interactions. Communicated by Ramaswamy H. Sarma.

A complete picture of protein unfolding and refolding in surfactants

Interactions between proteins and surfactants are of relevance in many applications including food, washing powder formulations, and drug formulation. The anionic surfactant sodium dodecyl sulfate (SDS) is known to unfold globular proteins, while the non-ionic surfactant octaethyleneglycol monododecyl ether (C₁₂E₈) can be used to refold proteins from their SDS-denatured state. While unfolding have been studied in detail at the protein level, a complete picture of the interplay between protein and surfactant in these processes is lacking. This gap in our knowledge is addressed in the current work, using the β-sheet-rich globular protein β-lactoglobulin (bLG). We combined stopped-flow time-resolved SAXS, fluorescence, and circular dichroism, respectively, to provide an unprecedented in-depth picture of the different steps involved in both protein unfolding and refolding in the presence of SDS and C₁₂E₈. During unfolding, core-shell bLG-SDS complexes were formed within ∼10 ms. This involved an initial rapid process where protein and SDS formed aggregates, followed by two slower processes, where the complexes first disaggregated into single protein structures situated asymmetrically on the SDS micelles, followed by isotropic redistribution of the protein. Refolding kinetics (>100 s) were slower than unfolding (<30 s), and involved rearrangements within the mixing deadtime (∼5 ms) and transient accumulation of unfolded monomeric protein, differing in structure from the original bLG-SDS structure. Refolding of bLG involved two steps: extraction of most of the SDS from the complexes followed by protein refolding. These results reveal that surfactant-mediated unfolding and refolding of proteins are complex processes with rearrangements occurring on time scales from sub-milliseconds to minutes.

Complete observation of all structural, conformational, and fibrillation transitions of monomeric globular proteins at submicellar sodium dodecyl sulfate concentrations

Although considerable information is available regarding protein-sodium dodecyl sulfate (SDS) interactions, it is still unclear as to how much SDS is needed to denature proteins. The role of protein charge and micellar surfactant concentration on amyloid fibrillation is also unclear. This study reports on equilibrium measurements of SDS interaction with six model proteins and analyzes the results to obtain a general understanding of conformational breakdown, reorganization and restructuring of secondary structure, and entry into the amyloid fibrillar state. Significantly, all of these responses are entirely resolved at much lower than the critical micellar concentration (CMC) of SDS. Electrostatic interaction of the dodecyl sulfate anion (DS^- ) with positive surface potential on the protein can completely unfold both secondary and tertiary structures, which is followed by protein chain restructuration to α-helices. All SDS-denatured proteins contain more α-helices than the corresponding native state. SDS interaction stochastically drives proteins to the aggregated fibrillar state.