Interaction mechanism and binding mode of phycocyanin to lysozyme: Molecular docking and molecular dynamics simulation

In this study, multispectral analysis and molecular simulations were performed to investigate the interaction mechanism between phycocyanin (PC) and lysozyme (Lys). The interaction was examined using surface plasmon resonance (SPR), and the structural changes were analyzed using Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), and transmission electron microscopy (TEM). The results suggest that the interaction between PC and Lys was primarily driven by electrostatic, hydrophobic, and hydrogen bonding forces. Molecular dynamics (MD) simulation revealed that Lys preferentially binds between the two subunits, alpha (α) and beta (β), of PC, with residues ASP-13, GLU-106, and GLU-115 on PC and ARG-119, ARG-107, and ARG-98 on Lys being the main contributors to the binding interaction. Additionally, the formation of the PC-Lys complex resulted in increased kinetic and improved thermal stability of PC, which have important implications for PC applications.

Biochemical and biophysical properties of a rare TTRA81V mutation causing mild transthyretin amyloid cardiomyopathy

AIMS

We conducted a presentation on an 84-year-old male patient who has been diagnosed with TTRA81V (p. TTRA101V) hereditary transthyretin cardiac amyloidosis (hATTR-CM). In order to establish its pathogenicity, we extensively investigated the biochemical and biophysical properties of the condition.

METHODS AND RESULTS

Transthyretin amyloid cardiomyopathy (ATTR-CM) is an increasingly acknowledged progressive infiltrative cardiomyopathy that leads to heart failure and potentially fatal arrhythmias. Gaining a comprehensive understanding of the biochemical and biophysical characteristics of genetically mutated TTR proteins serves as the fundamental cornerstone for delivering precise medical care to individuals affected by ATTR. Laboratory assessments indicated a brain natriuretic peptide of 200.12 ng/L (normal range: 0-100 ng/L) and high-sensitivity cardiac troponin I of 0.189 μg/L (normal range: 0-0.1 μg/L). Echocardiography identified left atrial enlargement, symmetrical left ventricular hypertrophy (16 mm septal and 16 mm posterior wall), and a left ventricular ejection fraction of 56%. Cardiac-enhanced magnetic resonance imaging revealed subendocardial late gadolinium enhancement. Tc-99m-PYP nuclear scintigraphy confirmed grade 3 myocardial uptake, showing an increased heart-to-contralateral ratio (H/CL = 2.33). Genetic testing revealed a heterozygous missense mutation in the TTR gene (c.302C>T), resulting in an alanine-to-valine residue change (p. Ala81Val, following the first 20 residues of signal sequence nomenclature). Biochemical analysis of this variant displayed compromised kinetic stability in both the TTRA81V:WT (wild-type) heterozygote protein (half-life, t1/2  = 21 h) and the TTRA81V homozygote protein (t1/2  = 17.5 h). The kinetic stability fell between that of the TTRWT (t1/2  = 42 h) and the early-onset TTRL55P mutation (t1/2  = 4.4 h), indicating the patient's late-onset condition. Kinetic stabilizers (Tafamidis, Diflunisal, and AG10) all exhibited the capacity to inhibit TTRA81V acid- and mechanical force-induced fibril formation, albeit less effectively than with TTRWT. Chromatographic assessment of the patient's serum TTR tetramers indicated a slightly lower concentration (3.0 μM) before oral administration of Tafamidis compared with the normal range (3.6-7.2 μM).

CONCLUSIONS

We identified a patient with hATTR-CM who possesses a rare TTRA81V mutation solely associated with cardiac complications. The slightly reduced kinetic stability of this mutation indicates its late-onset nature and contributes to the gradual progression of the disease.

Amorphous solid dispersions of curcumin in a poly(ester amide): Antiplasticizing effect on the glass transition and macromolecular relaxation dynamics, and controlled release

In order to exploit the pharmacological potential of natural bioactive molecules with low water solubility, such as curcumin, it is necessary to develop formulations, such as amorphous polymer dispersions, which allow a constant release rate and at the same time avoid possible toxicity effects of the crystalline form of the molecule under scrutiny. In this study, polymer dispersions of curcumin were obtained in PADAS, a biodegradable semicrystalline copolymer based on 1,12-dodecanediol, sebacic acid and alanine. The dispersions were fully characterized by means of differential scanning calorimetry and broadband dielectric spectroscopy, and the drug release profile was measured in a simulated body fluid. Amorphous homogeneous binary dispersions were obtained for curcumin mass fraction between 30 and 50%. Curcumin has significantly higher glass transition temperature Tg (≈ 347 K) than the polymer matrix (≈274-277 K depending on the molecular weight), and dispersions displayed Tg's intermediate between those of the pure amorphous components, implying that curcumin acts as an effective antiplasticizer for PADAS. Dielectric spectroscopy was employed to assess the relaxation dynamics of the binary dispersion with 30 wt% curcumin, as well as that of each (amorphous) component separately. The binary dispersion was characterized by a single structural relaxation, a single Johari-Goldstein process, and two local intramolecular processes, one for each component. Interestingly, the latter processes scaled with the Tg of the sample, indicating that they are viscosity-sensitive. In addition, both the pristine polymer and the dispersion exhibited an interfacial Maxwell-Wagner relaxation, likely due to spatial heterogeneities associated with phase disproportionation in this polymer. The release of curcumin from the dispersion in a simulated body fluid followed a Fickian diffusion profile, and 51% of the initial curcumin content was released in 48 h.

Baru oil (Dipteryx alata vog.) applied in the formation of O/W nanoemulsions: A study of physical-chemical, rheological and interfacial properties

The oil extracted from baru (Dipteryx alata Vog.) seeds is in bioactive compounds and it presents potential to be used in food and cosmetic industries. Therefore, this study aims to provide insights into the stability of baru oil-in-water (O/W) nanoemulsions. For this purpose, the effects of the ionic strength (0, 100 and 200 mM), pH (6, 7 and 8), and storage time (28 days) on the kinetic stability of these colloidal dispersions were evaluated. The nanoemulsions were characterized in terms of interfacial properties, rheology, zeta potential (ζ), average droplet diameter, polydispersity index (PDI), microstructure, and creaming index. In general, for samples, the equilibrium interfacial tension ranged from 1.21 to 3.4 mN.m^-1, and the interfacial layer presented an elastic behavior with low dilatational viscoelasticity. Results show that the nanoemulsions present a Newtonian flow behavior, with a viscosity ranging from 1.99 to 2.39 mPa.s. The nanoemulsions presented an average diameter of 237-315 nm with a low polydispersity index (<0.39), and a ζ-potential ranging from 39.4 to 50.3 mV after 28 days of storage at 25 °C. The results obtained for the ζ-potential suggest strong electrostatic repulsions between the droplets, which is an indicative of relative kinetic stability. In fact, macroscopically, all the nanoemulsions were relatively stable after 28 days of storage, except the nanoemulsions added with NaCl. Nanoemulsions produced with baru oil present a great potential to be used in the food, cosmetic, and pharmaceutical industries.

Mercury ions impact the kinetic and thermal stabilities of human lens γ-crystallins via direct metal-protein interactions

Loss of metal homeostasis may be involved in several age-related diseases, such as cataracts. Cataracts are caused by the aggregation of lens proteins into light-scattering high molecular weight complexes that impair vision. Environmental exposure to heavy metals, such as mercury, is a risk factor for cataract development. Indeed, mercury ions induce the non-amyloid aggregation of human γC- and γS crystallins, while human γD-crystallin is not sensitive to this metal. Using Differential Scanning Calorimetry (DSC), we evaluate the impact of mercury ions on the kinetic stability of the three most abundant human γ-crystallins. The metal/crystallin interactions were characterized using Isothermal Titration Calorimetry (ITC). Human γD-crystallins exhibited kinetic stabilization due to the presence of mercury ions, despite its thermal stability being decreased. In contrast, human γC- and γS-crystallins are both, thermally and kinetically destabilized by this metal, consistent with their sensitivity to mercury-induced aggregation. The interaction of human γ-crystallins with mercury ions is highly exothermic and complex, since the protein interacts with the metal at more than three sites. The isolated domains of human γ-D and its variant with the H22Q mutation were also studied, revealing the importance of these regions in the mercury-induced stabilization by a direct metal-protein interaction.

Ngn (Ng= Ne, Ar, Kr, Xe, and Rn; n=1, 2) encapsulated porphyrin-like porous C24N24 fullerene: A quantum chemical study

This study focused on the theoretical viability of Ng_n@C₂₄N₂₄ (Ng = Ne, Ar, Kr, Xe, and Rn; n = 1, 2) complexes using density functional theory at the computational level of ωB97X-D/def2-TZVP. Thermodynamic and kinetic stabilities of these complexes have been evaluated by calculating the interaction energy of Ng atoms encapsulated C₂₄N₂₄ cage (ΔE_int), and the corresponding dissociation energy barrier (ΔG^‡), respectively. The obtained results predict that although these complexes are thermodynamically unstable compared to their dissociation into free Ng atoms and the bare C₂₄N₂₄ cage, but once formed, they are protected by the activation energy barrier of the corresponding dissociation process. Furthermore, natural population analysis (NPA) and topological analysis of the electron density have been employed to investigate the nature of Ng-Ng and Ng-cage interactions. The results demonstrate that these interactions are highly significant compared to similar cases in the free state; and the amounts of energy of the interaction gradually increases as the Ng atom becomes heavier. Surprisingly in the Kr₂@C₂₄N₂₄ complex the Kr-Kr bond is somewhat covalent in nature relative to non-bonded interaction in Kr₂ free dimer.

Polymeric micelles in drug delivery: An insight of the techniques for their characterization and assessment in biorelevant conditions

Polymeric micelles, i.e. aggregation colloids formed in solution by self-assembling of amphiphilic polymers, represent an innovative tool to overcome several issues related to drug administration, from the low water-solubility to the poor drug permeability across biological barriers. With respect to other nanocarriers, polymeric micelles generally display smaller size, easier preparation and sterilization processes, and good solubilization properties, unfortunately associated with a lower stability in biological fluids and a more complicated characterization. Particularly challenging is the study of their interaction with the biological environment, essential to predict the real in vivo behavior after administration. In this review, after a general presentation on micelles features and properties, different characterization techniques are discussed, from the ones used for the determination of micelles basic characteristics (critical micellar concentration, size, surface charge, morphology) to the more complex approaches used to figure out micelles kinetic stability, drug release and behavior in the presence of biological substrates (fluids, cells and tissues). The techniques presented (such as dynamic light scattering, AFM, cryo-TEM, X-ray scattering, FRET, symmetrical flow field-flow fractionation (AF4) and density ultracentrifugation), each one with their own advantages and limitations, can be combined to achieve a deeper comprehension of polymeric micelles in vivo behavior. The set-up and validation of adequate methods for micelles description represent the essential starting point for their development and clinical success.

Kinetically-stable small-molecule prodrug nanoassemblies for cancer chemotherapy

Self-delivering nanocarrier based on the small-molecule prodrug nanoassemblies (NAs) have been widely used for the efficient delivery of chemotherapeutics, but the effect of kinetic stability of NAs on their delivery performance has not been illuminated. In this study, two camptothecin (CPT)-oleic acid (OA) prodrugs were used to fabricate self-assembling nanorods with similar size distribution, zeta potential and morphology but having sharply different kinetic stability, which provided an ideal platform to investigate the effects of kinetic stability. It is found that the nanorods with high kinetic stability showed a lower in vitro cytotoxicity, but were more effective to inhibit the tumor growth probably by decreasing the premature CPT release and subsequent generation of the inactive carboxylate CPT. However, such kinetically stable nanorods also resulted in the increased toxicity, probably due to the high prodrug accumulation in tissues after multiple injections. These results outlined the pivotal role of kinetic stability in determining antitumor efficacy of prodrug NAs, which provided a new insight into the delivery mechanism for the small-molecule prodrug self-delivering nanosystems.

Improving the kinetic stability of a hyperthermostable β-mannanase by a rationally combined strategy

Feasible and easily accessible methods for the rational design of enzyme engineering strategies remain to be established. Thus, a new rationally combined strategy based on disulfide bond engineering and HotSpot Wizard 3.0 was proposed and experimentally demonstrated to be effective using a hyperthermostable β-mannanase. Ten of 42 mutants showed prominent enhancement of kinetic stability with 26.4%-39.9% increases in t_1/2 (75 °C) compared with the parent enzyme ManAKH. The best mutant, D273-V308, showed apparent increases in both optimal temperature (5 °C) and T₅₀ (6.8 °C), as well as advanced catalytic efficiency. The low rate of inactive mutants and the high rate of positive mutants indicated that newly introduced screening factors (distance from catalytic residues, Gibbs free energy term, molecular simulation, and visual inspections) greatly enhance the design of thermostable β-mannanase. Moreover, these findings further advance the industrial application of β-mannanase (ManAK) in food and food-related applications.

Different unfolding pathways of homologous alpha amylases from Bacillus licheniformis (BLA) and Bacillus amyloliquefaciens (BAA) in GdmCl and urea

Understanding the factors governing stability of proteins is fundamentally and industrially important topic in protein science. Bacterial alpha amylases are industrially important enzymes which are involved in the breakage of α-1, 4-glycosidic bonds in starch. Current study is focussed on elucidating the role of non-covalent interactions in the differential stability of alpha amylases from thermophilic like Bacillus licheniformis (BLA) and mesophilic Bacillus amyloliquefaciens (BAA). The conformational stability of BLA is slightly higher than BAA in GdmCl which are 2.94 and 2.53 kcal/mol respectively. BLA does not unfold even in 8.0 M urea at pH 7.0, while for BAA, the conformational stability in urea is calculated to be 2.22 kcal/mol. A structure-function relationship study of BLA reveals the non-coincidental unfolding by far UV-CD, enzyme activity and tryptophan fluorescence which indicates the presence of partially unfolded intermediates. The existence of intermediates in BLA during GdmCl induced unfolding was further confirmed by ANS fluorescence. The unfolding kinetics of both enzymes showed biphasic nature with slower unfolding of BLA compare to BAA pointing towards the higher kinetic stability of BLA than BAA. Taken together, our work demonstrates that the higher stability of BLA is mainly due to the combination of ionic and hydrophobic interactions.

Viscosity of ASDs at humid conditions

Many amorphous solid dispersions (ASDs) are thermodynamically unstable. Thus, the active pharmaceutical ingredient (API) might crystallize over time. The crystallization kinetics and therewith the long-term stability of ASDs depends on the storage conditions temperature and relative humidity (RH) as they determine the molecular mobility of the API in the polymer. To quantify the molecular mobility, the rheological behavior of two different ASDs with ibuprofen and either poly(vinyl acetate) or poly(vinylpyrrolidone-co-vinyl acetate) was analyzed as function of temperature and relative humidity by means of an oscillatory rheometer. The plasticizing effect of ibuprofen and absorbed water on the zero-shear viscosity of the polymer could be fully explained by the reduction of the glass-transition temperature of the mixture compared to the one of the pure polymer. Moreover, this work proposes an approach to predict the zero-shear viscosity of an ASD based on only the temperature dependence of the zero-shear viscosity of the pure polymer as well as the predicted water content in the ASD at certain RH using the Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT).

Does the trihydrate of atorvastatin calcium possess a melting point?

To decide whether an active pharmaceutical ingredient can be used in its amorphous form in drug formulations, often the glass transition is studied in relation to the melting point of the pharmaceutical. If the glass transition temperature is high enough and found relatively close to the melting point, the pharmaceutical is considered to be a good glass former. However, it is obviously important that the observed melting point and glass transition involve exactly the same system, otherwise the two temperatures cannot be compared. Although this may seem trivial, in the case of hydrates, where water may leave the system on heating, the composition of the system may not be evident. Atorvastatin calcium is a case in point, where confusing terminology, absence of a proper anhydrate form, and loss of water on heating lead to several doubtful conclusions in the literature. However, considering that no anhydrate crystal has ever been observed and that the glass transition of the anhydrous system is found at 144 °C, it can be concluded that if the system is kept isolated from water, the chances that atorvastatin calcium crystallises at room temperature is negligible. The paper discusses the various thermal effects of atorvastatin calcium on heating and proposes a tentative binary phase diagram with water.

Ultrasound-assisted oil-in-water nanoemulsion produced from Pereskia aculeata Miller mucilage

For the preparation of nanoemulsions, the correct choice of emulsifiers, together with the emulsification methods, directly influences the final product quality. The present study reports the ultrasound-assisted preparation of oil-in-water nanoemulsions produced with mucilage extracted from leaves of Pereskia aculeata Miller (ora-pro-nobis; OPN). The OPN mucilage (%) and soybean oil (%) concentration range, and the process operating parameters, ultrasonic power amplitude (%) and sonication time (min), were optimized based on the mean droplet diameter (d₃₂). The effect of the mucilage and oil concentrations was also investigated by the response variables such as polydispersity, density, turbidity, viscosity, zeta-potential, and interfacial tension. The higher OPN mucilage concentrations (%) with lower amounts of soybean oil (%) favored nanoemulsion formations (116 ≤ d₃₂ ≤ 171 nm) and increased polydispersity, density, and zeta-potential. On increasing OPN mucilage and soybean oil the turbidity of the dispersions increased. All colloidal systems showed Newtonian behavior, and the viscosity in the systems increased due to the greater OPN mucilage concentration in the aqueous phase at a certain oil concentration. In addition, lower values of equilibrium interfacial tension were found with increasing OPN mucilage concentrations. Finally, from the stability test, it can be pointed out that the OPN mucilage concentration should be between 1.0 and 1.5% and the oil concentration should be less than 5%, so that lower d₃₂ values are maintained over time. Therefore, mucilage extracted from OPN and the ultrasound technique can be used in the preparation of nanoemulsions.

Estimation of the thermal and photochemical stabilities of pheromones

The correlation between the kinetic stability of molecules against temperature and variations in their geometric structure under optical excitation is investigated by the example of different organic pheromone molecules sensitive to temperature or ultraviolet radiation using the density functional theory. The kinetic stability is determined by the previously developed method based on the calculation of the probability of extension of any structural bond by a value exceeding the limit value L_мах corresponding to the breaking of the bond under temperature excitation. The kinetic stability calculation only requires the eigenfrequencies and vibrational mode vectors in the molecule ground state to be calculated, without determining the transition states. The weakest bonds in molecules determined by the kinetic stability method are compared with the bond length variations in molecules in the excited state upon absorption of light by a molecule. Good agreement between the results obtained is demonstrated and the difference between them is discussed. The universality of formulations within both approaches used to estimate the stability of different pheromone molecules containing strained cycles and conjugated, double, and single bonds allows these approaches to be applied for studying other molecules. Graphical Abstract Estimation of the thermal and photochemical stabilities of pheromones.

Coupling of high-intensity ultrasound and mechanical stirring for producing food emulsions at low-energy densities

In this study, coupling of ultrasound (US) device and rotor-stator (RS), operating at low-energy densities, was studied as an alternative process to individual US and RS to produce modified starch-stabilized oil-in-water emulsions, as well as its potential use to encapsulate eugenol. To this aim, a full factorial design was employed to evaluate the effects of the US nominal power (0, 360 and 720 W) and RS nominal power (0, 150 and 300 W) on the physical properties, encapsulation efficiency and kinetic stability of emulsions produced. Firstly, the action of modified starch and eugenol onto interface oil-water was evaluated. The emulsifier was rapidly adsorbed on the interface water-sunflower oil reducing the interfacial tension from 25 to 16 mN/m, while eugenol did not show surface activity. The increase of energy density, in general, resulted in droplet size reduction, indicating the relevant role of the forces involved in the droplet breakup on emulsion stability. Coupling was more efficient on the droplets breakup producing smaller droplet size with narrower size distribution. While the coupled system work during 5 min for an energy density of 583 J/mL, the corresponding emulsification time for operating singly US and RS were 7.09 min and 17.04 min, respectively. Therefore, the main advantage associate to coupled process is the reduction of processing time to produce an emulsion with better kinetic stability.

Kinetic stability and sequence/structure studies of urine-derived Bence-Jones proteins from multiple myeloma and light chain amyloidosis patients

It is now accepted that the ability of a protein to form amyloid fibrils could be associated both kinetic and thermodynamic protein folding parameters. A recent study from our laboratory using recombinant full-length (encompassing the variable and constant domain) immunoglobulin light chains found a strong kinetic control of the protein unfolding for these proteins. In this study, we are extending our analysis by using urine-derived Bence Jones proteins (BJPs) from five patients with light chain (AL) amyloidosis and four patients with multiple myeloma (MM). We observed lower stability in κ proteins compared to λ proteins (for both MM and AL proteins) in agreement with previous studies. The kinetic component of protein stability is not a universal feature of BJPs and the hysteresis observed during refolding reactions could be attributed to the inability of the protein to refold all domains. The most stable proteins exhibited 3-state unfolding transitions. While these proteins do not refold reversibly, partial refolding shows 2-state partial refolding transitions, suggesting that one of the domains (possibly the variable domain) does not refold completely. Sequences were aligned with their respective germlines and the location and nature of the mutations were analyzed. The location of the mutations were analyzed and compared with the stability and amyloidogenic properties for the proteins in this study, increasing our understanding of light chain unfolding and amyloidogenic potential.

Role of cardiolipin in stability of integral membrane proteins

Cardiolipin (CL) is a unique phospholipid with a dimeric structure having four acyl chains and two phosphate groups found almost exclusively in certain membranes of bacteria and of mitochondria of eukaryotes. CL interacts with numerous proteins and has been implicated in function and stabilization of several integral membrane proteins (IMPs). While both functional and stabilization roles of CL in IMPs has been generally acknowledged, there are, in fact, only limited number of quantitative analysis that support this function of CL. This is likely caused by relatively complex determination of parameters characterizing stability of IMPs and particularly intricate assessment of role of specific phospholipids such as CL in IMPs stability. This review aims to summarize quantitative findings regarding stabilization role of CL in IMPs reported up to now.

Ultrasonic assisted formation and stability of mustard oil in water nanoemulsion: Effect of process parameters and their optimization

The present work reports the ultrasound assisted preparation of mustard oil in water nanoemulsion stabilized by Span 80 and Tween 80 at different operating conditions. Effects of various operating parameters such as HLB (Hydrophilic Lipophilic Balance) value, surfactant volume fraction (φ_S), oil volume fraction (φ_O) and power amplitude were investigated and optimized on the basis of droplet size and stability of nanoemulsions. It was observed that minimum droplet size of about 87.38nm was obtained within 30min of ultrasonication at an optimum HLB value of 10, φ_S of 0.08 (8%, v/v), φ_O of 0.1 (10%, v/v) and ultrasonic power amplitude of 40%. The stability of the nanoemulsion was measured through visual observation and it was found that the unstable emulsions got separated within 24h whereas, stable emulsions never showed any separation until 90days. In addition to that, the kinetic stability of the prepared nanoemulsions was also assessed under centrifuge and thermal stress conditions. The emulsion stability was found to be unaffected by these forces as the droplet size remained unchanged. The ultrasound prepared emulsion was found to be long term stable even after 3months of storage at ambient conditions without any visual evidence of creaming and phase separation and also remained kinetically stable. FTIR analysis of the emulsions at different sonication conditions was carried out to examine the possible impact of ultrasonically induced chemical effects on oil structure during emulsification and it was found that the oil molecular structure was unaffected by ultrasonication process. The present work illustrates the formation and stability of mustard oil in water nanoemulsion using ultrasound cavitation which may be useful in food and cosmetic based applications.

Increased levels of hyper-stable protein aggregates in plasma of older adults

Proteins that misfold into hyper-stable/degradation-resistant species during aging may accumulate and disrupt protein homeostasis (i.e., proteostasis), thereby posing a survival risk to any organism. Using the method diagonal two-dimensional (D2D) SDS-PAGE, which separates hyper-stable SDS-resistant proteins at a proteomics level, we analyzed the plasma of healthy young (<30 years) and older (60-80 years) adults. We discovered the presence of soluble SDS-resistant protein aggregates in the plasma of older adults, but found significantly lower levels in the plasma of young adults. We identified the inflammation-related chaperone protein haptoglobin as the main component of the hyper-stable aggregates. This observation is consistent with the growing link between accumulations of protein aggregates and aging across many organisms. It is plausible higher amounts of SDS-resistant protein aggregates in the plasma of older adults may reflect a compromise in proteostasis that may potentially indicate cellular aging and/or disease risk. The results of this study have implications for further understanding the link between aging and the accumulation of protein aggregates, as well as potential for the development of aging-related biomarkers. More broadly, this novel application of D2D SDS-PAGE may be used to identify, quantify, and characterize the degradation-resistant protein aggregates in human plasma or any biological system.

Differential scanning fluorimetry based assessments of the thermal and kinetic stability of peptide-MHC complexes

Measurements of thermal stability by circular dichroism (CD) spectroscopy have been widely used to assess the binding of peptides to MHC proteins, particularly within the structural immunology community. Although thermal stability assays offer advantages over other approaches such as IC50 measurements, CD-based stability measurements are hindered by large sample requirements and low throughput. Here we demonstrate that an alternative approach based on differential scanning fluorimetry (DSF) yields results comparable to those based on CD for both class I and class II complexes. As they require much less sample, DSF-based measurements reduce demands on protein production strategies and are amenable for high throughput studies. DSF can thus not only replace CD as a means to assess peptide/MHC thermal stability, but can complement other peptide-MHC binding assays used in screening, epitope discovery, and vaccine design. Due to the physical process probed, DSF can also uncover complexities not observed with other techniques. Lastly, we show that DSF can also be used to assess peptide/MHC kinetic stability, allowing for a single experimental setup to probe both binding equilibria and kinetics.

Knotted proteins: A tangled tale of Structural Biology

Knotted proteins have their native structures arranged in the form of an open knot. In the last ten years researchers have been making significant efforts to reveal their folding mechanism and understand which functional advantage(s) knots convey to their carriers. Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments. Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research.

Thermodynamic and fibril formation studies of full length immunoglobulin light chain AL-09 and its germline protein using scan rate dependent thermal unfolding

Light chain (AL) amyloidosis is a fatal disease where monoclonal immunoglobulin light chains deposit as insoluble amyloid fibrils. For many years it has been considered that AL amyloid deposits are formed primarily by the variable domain, while its constant domain has been considered not to be amyloidogenic. However recent studies identify full length (FL) light chains as part of the amyloid deposits. In this report, we compare the stabilities and amyloidogenic properties of two light chains, an amyloid-associated protein AL-09 FL, and its germline protein κ I O18/O8 FL (IGKV 1-33). We demonstrate that the thermal unfolding for both proteins is irreversible and scan rate dependent, with similar stability parameters compared to their VL counterparts. In addition, the constant domain seems to modulate their amyloidogenic properties and affect the morphology of the amyloid fibrils. These results allow us to understand the role of the kappa constant domain in AL amyloidosis.