Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity

Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and thermal denaturation, as well as proteolytic degradation. Despite its significance, specific mechanisms governing kinetic stability remain largely unknown, and few studies address the rational design of kinetic stability. Here, we describe a method for designing protein kinetic stability that uses protein long-range order, absolute contact order, and simulated free energy barriers of unfolding to quantitatively analyze and predict unfolding kinetics. We analyze two β-trefoil proteins: hisactophilin, a quasi-three-fold symmetric natural protein with moderate stability, and ThreeFoil, a designed three-fold symmetric protein with extremely high kinetic stability. The quantitative analysis identifies marked differences in long-range interactions across the protein hydrophobic cores that partially account for the differences in kinetic stability. Swapping the core interactions of ThreeFoil into hisactophilin increases kinetic stability with close agreement between predicted and experimentally measured unfolding rates. These results demonstrate the predictive power of readily applied measures of protein topology for altering kinetic stability and recommend core engineering as a tractable target for rationally designing kinetic stability that may be widely applicable.

A Bridge too Far? Comparison of Transition Metal Complexes of Dibenzyltetraazamacrocycles with and without Ethylene Cross-Bridges: X-ray Crystal Structures, Kinetic Stability, and Electronic Properties

Tetraazamacrocycles, cyclic molecules with four nitrogen atoms, have long been known to produce highly stable transition metal complexes. Cross-bridging such molecules with two-carbon chains has been shown to enhance the stability of these complexes even further. This provides enough stability to use the resulting compounds in applications as diverse and demanding as aqueous, green oxidation catalysis all the way to drug molecules injected into humans. Although the stability of these compounds is believed to result from the increased rigidity and topological complexity imparted by the cross-bridge, there is insufficient experimental data to exclude other causes. In this study, standard organic and inorganic synthetic methods were used to produce unbridged dibenzyl tetraazamacrocycle complexes of Co, Ni, Cu, and Zn that are analogues of known cross-bridged tetraazamacrocycles and their transition metal complexes to allow direct comparison of molecules that are identical except for the cross-bridge. The syntheses of the known tetraazamacrocycles and the new transition metal complexes were successful with high yields and purity. Initial chemical characterization of the complexes was conducted by UV-Visible spectroscopy, while cyclic voltammetry showed more marked differences in electronic properties from bridged versions. Direct comparison studies of the unbridged and bridged compounds' kinetic stabilities, as demonstrated by decomposition using high acid concentration and elevated temperature, showed that the cyclen-based complex stability did not benefit from cross-bridging. This is likely due to poor complementarity with the Cu²⁺ ion while cyclam-based complexes benefited greatly. We conclude that ligand-metal complementarity must be maintained in order for the topological and rigidity constraints imparted by the cross-bridge to contribute significantly to complex robustness.

Biochemical and biophysical properties of an unreported T96R mutation causing transthyretin cardiac amyloidosis

OBJECTIVES

We presented an unreported T96R mutation induced transthyretin cardiac amyloidosis (ATTR). The biochemical and biophysical properties were explored to support its pathogenicity.

BACKGROUND

Understanding the biochemical and biophysical nature of genetically mutated transthyretin (TTR) proteins is key to provide precise medical cares for ATTR patients.

RESULTS

Genetic testing showed heterozygosity for the T96R pathogenic variant c.347C > G (ATTR p.T116R) after myocardial biopsy confirmed amyloid deposition. Biochemical characterizations revealed slight perturbation of its thermodynamic stability (C_m=3.7 M for T96R, 3.4 M for WT and 2.3 M for L55P (commonly studied TTR mutant)) and kinetic stability (t_1/2=39.8 h for T96R, 42 h for WT and 4.4 h in L55P). Crosslinking experiment demonstrated heterozygous subunit exchange between wild-type and TTR T96R protein destabilized the tetramer. Inhibitory effect of tafamidis and diflunisal on TTR T96R fibril formation was slightly less effective compared to WT and L55P.

CONCLUSIONS

A novel T96R mutation was identified for TTR protein. Biochemical and biophysical analyses revealed slightly destabilized kinetic stability. T96R mutation destabilized heterozygous protein but not proteolytic degradation, explaining its pathogenicity. Inhibitory effect of small molecule drugs on T96R mutation was different, suggesting personalized treatment may be required.

Rheology of dispersions and emulsions composed of chia mucilage and the application of chia in food

Chia mucilage (CM) is an emerging resource in food applications. However, the mechanism of this biopolymer as a stabilizer/emulsifier ingredient has not yet been well defined. A non-uniform viscoelastic tridimensional network was observed on emulsions with CM, while the surface activity of the CM ingredient has been associated with its protein content. To understand its functionality in food, this review focused on discussing and summarizing the rheological properties of dispersions and emulsions composed of CM under different conditions, such as pH, temperature, salt content, and mucilage content. For example, emulsions and dispersions with CM showed pseudoplastic behavior. An increase in the CM concentration increased the viscosity and the consistency index and decreased the behavior index. The consistency index of dispersions with CM increased with pH. The future evaluation of emulsions and dispersions properties, such as viscoelastic properties and microstructure, is particularly important for the successful use of CM in the food industry. The principal studies have evaluated the use of CM in dairy and meat systems as an emulsifier, stabilizer, or lipid replacer. The nutritional quality of the products with CM was maintained or improved, but sometimes an undesirable darkening was observed. Future evaluation of the cold extraction method of CM might improve the color and overall sensory acceptability of food products with CM. Integrated chia seed processing, including mucilage, oil, and protein extraction could be carried out to make chia seed industrial processing viable. © 2022 Society of Chemical Industry.

Polydopamine-Modified Nanolime with High Kinetic Stability in Water for the Consolidation of Stone Relics

As a promising inorganic nanomaterial for the conservation of arenaceous sandstone-based relics such as wall painting, ancient building, stone heritage etc., nanolime (NL) has drawn increasing attention in recent years. Usually, NL needs to be dispersed into an alcoholic solution when applied. Nevertheless, a back-migration phenomenon of NL to the surface of the stone and delayed carbonation of NL enabled by alcohol do not guarantee good preservation effects. Dispersing NL into water can avoid the above issues. However, NL water suspension shows extremely poor kinetic stability, greatly restricting the penetration of NL into stone relics as well as bringing unfavorable impacts to the treated stone heritage. Here, we develop a facile method to synthesize polydopamine (PDA)-modified NL (PDA@NL). Characterizations demonstrate that PDA is uniformly distributed on the surface of NL particles though hydrogen bonds. In addition, the presence of PDA reduces the size of NL particles and achieves the highest specific surface area of NL reported to date. More importantly, water suspension of PDA@NL is far more stable than that of pure NL. The kinetic stability mechanism of PDA@NL in water is attributed to the lessened spatial interactions between NL particles, which is realized by the coverage of PDA on the surface of NL particles. Furthermore, the coverage of PDA does not inhibit carbonation. Within 105 h, NL in PDA@NL completes carbonation and obtains 93.7% calcite, which is comparable to that of NL suspension. Permeability tests prove that the PDA@NL suspension penetrates far deeper through stone specimens compared with the NL suspension. Additionally, PDA@NL presents good consolidation performances for stone samples. Our work opens a new direction for the modification of NL that will boost the studies of NL-modified materials as well as the conservation of cultural heritage.

Expanding the toolbox for predictive parameters describing antibody stability considering thermodynamic and kinetic determinants

PURPOSE

Introduction of the activation energy (E_a) as a kinetic parameter to describe and discriminate monoclonal antibody (mAb) stability.

METHODS

E_a is derived from intrinsic fluorescence (IF) unfolding thermograms. An apparent irreversible three-state fit model based on the Arrhenius integral is developed to determine E_a of respective unfolding transitions. These activation energies are compared to the thermodynamic parameter of van´t Hoff enthalpies (∆H_vh). Using a set of 34 mAbs formulated in four different formulations, both the apparent thermodynamic and kinetic parameters together with apparent melting temperatures are correlated collectively with each other to storage stabilities to evaluate its predictive power with respect to long-term effects potentially reflected in shelf-life.

RESULTS

E_a allows for the discrimination of (i) different parent mAbs, (ii) different variants that originate from parent mAbs, and (iii) different formulations. Interestingly, we observed that the E_a of the CH₂ unfolding transition shows strongest correlations with monomer and aggregate content after storage at accelerated and stress conditions when collectively compared to ∆H_vh and T_m of the CH₂ transition. Moreover, the predictive parameters determined for the CH₂ domain show generally stronger correlations with monomer and aggregate content than those derived for the Fab. Qualitative assessment by ranking E_a of the Fab domain showed good agreement with monomer content in storage stabilities of individual mAb sub-sets.

CONCLUSION

E_a from IF unfolding transitions can be used in addition to other commonly used thermodynamic predictive parameters to discriminate and characterize thermal stability of different mAbs in different formulations. Hence, it shows great potential for antibody engineering and formulation scientists.

Biodegradable Amphoteric Surfactants in Titration-Ultrasound Formulation of Oil-in-Water Nanoemulsions: Rational Design, Development, and Kinetic Stability

Amphoteric amphiphilic compounds, due to their unique properties, may represent a group of safe and biocompatible surface-active agents for effective colloidal stabilization of nanoformulations. For this reason, the aim of this work was to develop and characterize the oil-in-water nanoemulsions based on two betaine-derived surfactants with high biodegradability, i.e., cocamidopropyl betaine and coco-betaine. In the first step, we investigated ternary phase diagrams of surfactant-oil-water systems containing different weight ratios of surfactant and oil, as the betaine-type surfactant entity (S), linoleic acid, or oleic acid as the oil phase (O), and the aqueous phase (W) using the titration-ultrasound approach. All the received nanoemulsion systems were then characterized upon droplets size (dynamic light scattering), surface charge (electrophoretic light scattering), and morphology (transmission electron as well as atomic force microscopy). Thermal and spinning tests revealed the most stable compositions, which were subjected to further kinetic stability analysis, including turbidimetric evaluation. Finally, the backscattering profiles revealed the most promising candidate with a size <200 nm for potential delivery of active agents in the future cosmetic, pharmaceutical, and biomedical applications.

Direct Visualization of Atomic-Scale Heterogeneous Structure Dynamics in MnO2 Nanowires

Manganese oxides are attracting great interest owing to their rich polymorphism and multiple valent states, which give rise to a wide range of applications in catalysis, capacitors, ion batteries, and so forth. Most of their functionalities are connected to transitions among the various polymorphisms and Mn valences. However, their atomic-scale dynamics is still a great challenge. Herein, we discovered a strong heterogeneity in the crystalline structure and defects, as well as in the Mn valence state. The transitions are studied by in situ transmission electron microscopy (TEM), and they involve a complex ordering of [MnO₆] octahedra as the basic building tunnels. MnO₂ nanowires synthesized using solution-based hydrothermal methods usually exhibit a large number of multiple polymorphism impurities with different tunnel sizes. Upon heating, MnO₂ nanowires undergo a series of stoichiometric polymorphism changes, followed by oxygen release toward an oxygen-deficient spinel and rock-salt phase. The impurity polymorphism exhibits an abnormally high stability with interesting small-large-small tunnel size transition, which is attributed to a preferential stabilizer (K⁺) concentration, as well as a strong competition of kinetics and thermodynamics. Our results unveil the complicated intergrowth of polymorphism impurities in MnO₂, which provide insights into the heterogeneous kinetics, thermodynamics, and transport properties of the tunnel-based building blocks.

Filling the Gap in the Metallacrown Family: The 9-MC-3 Chromium Metallacrown

In this work, we report on a long‐sought missing complex in the metallacrown family. We synthesized and characterized the novel chromium metallacrown (MC) complex {Cr^III(μ₂‐piv)₃[9‐MC_{Cr(III)N(shi)}‐3](morph)₃}⋅MeOH (in which shi³⁻=salicyl hydroxamate, piv=pivalate, and morph=morpholine). The MC with a 9‐MC‐3 cavity of kinetically inert chromium(III) ions was synthesized by a solvothermal reaction. Magnetization measurements reveal a high spin ground state.

Structural Insights into the Mechanisms Underlying the Kinetic Stability of GH28 Endo-Polygalacturonase

Thermostability is a key property of industrial enzymes. Endo-polygalacturonases of the glycoside hydrolase family 28 have many practical applications, but only few of their structures have been determined, and the reasons for their stability remain unclear. We identified and characterized the Talaromyces leycettanus JCM12802 endo-polygalacturonase TlPGA, which differs from other GH28 family members because of its high catalytic activity, with an optimum temperature of 70 °C. Distinctive features were revealed by comparison of thermophilic TlPGA and all known structures of fungal endo-polygalacturonases, including a relatively large exposed polar accessible surface area in thermophilic TlPGA. By mutating potentially important residues in thermophilic TlPGA, we identified Thr284 as a critical residue. Mutant T284A was comparable to thermophilic TlPGA in melting temperature but exhibited a significantly lower half-life and half-inactivation temperature, implicating residue Thr284 in the kinetic stability of thermophilic TlPGA. Structure analysis of thermophilic TlPGA and mutant T284A revealed that a carbon-oxygen hydrogen bond between the hydroxyl group of Thr284 and the Cα atom of Gln255, and the stable conformation adopted by Gln255, contribute to its kinetic stability. Our results clarify the mechanism underlying the kinetic stability of GH28 endo-polygalacturonases and may guide the engineering of thermostable enzymes for industrial applications.

Repairing Creep-Resistant and Kinetically Inert Hydrogels via Yeast Activity-Regulated Energy Dissipation

Energy dissipation, a ubiquitous process in biological systems, has been intensively studied and widely used to guide the transient assembly of natural or synthetic molecules, but very few examples of material transient healability controlled by this important process have been reported. Herein, we realize the healing of creep-resistant and kinetically inert polymer hydrogels that is driven by the respiration of baker's yeast (Saccharomyces cerevisiae) and spontaneous energy dissipation. The entire healing process can be simply controlled by a single variable: sucrose concentration. Due to the high activity and stability of yeast in the hydrogels, multiple local healing events become possible and healing of damaged hydrogels is also efficient after a long waiting time. All these results indicate that our yeast-containing polymer hydrogels are kinetically stable materials, which can be readily healable on demand.

Bioinspired Self-Healing of Kinetically Inert Hydrogels Mediated by Chemical Nutrient Supply

Dynamic stability and self-healing ability are two inherently compatible properties for living organisms. By contrast, kinetic stability and intrinsic healability are two desired but mostly incompatible properties for synthetic materials. This is because the healing of these materials heavily relies on the kinetic lability of the chemical bonds or physical interactions in materials. Inspired by the hierarchically and temporally controlled wound healing in biological systems, here, we report the intrinsic healing of kinetically stable hydrogels, regulated by the consumption of chemical nutrients. The acylhydrazone-based polymer hydrogels with preinstalled urease and urea were formed at a low initial pH, followed by in situ enzymatic generation of a base to deactivate the dynamic bonds, allowing efficient fabrication of kinetically stable hydrogels. The healing of damaged hydrogels was effective when fed with proper chemical nutrients (i.e., acidic urea solutions), in which case a transient acidic pH state was temporally programmed by combining a fast acidic activator (for structural healing) with the slow, biocatalytic generation of a base (for property recovery). The ability to regulate both hydrogel fabrication and healing via a single enzymatic reaction could provide a new approach to create kinetically stable materials capable of healing damages on demand.

A simple protocol to characterize bacterial cell-envelope lipoproteins in a native-like environment

Physiological conditions in living cells are strictly regulated to allow, optimize, and coordinate biological processes. The bacterial cell envelope is the compartment where the communication with the external environment takes place. This involves membrane proteins, key players in many biological processes that ensure bacterial survival. The biochemical characterization of membrane proteins, either integral, lipidated or peripheral is challenging due to their mixed protein-lipid nature, making it difficult to purify and obtain considerable amounts of samples. In contrast to integral membrane proteins, lipidated proteins are usually purified as truncated soluble versions, neglecting the impact of the membrane environment. Here we report a simple and robust protocol to characterize bacterial lipidated proteins in spheroplasts from Escherichia coli using a β-lactamase as a model. The Metallo-β-lactamase NDM-1 is an enzyme anchored to the inner leaflet of the outer membrane of Gram-negative bacteria. Kinetic parameters and stability of the lipidated NDM-1 and the soluble unbound version (NDM-1 C26A) were measured in spheroplasts and periplasm, respectively. These studies revealed that membrane anchoring increases the K_M of the enzyme, consequently decreasing the catalytic efficiency, while not affecting its kinetic stability. This approach can be used to characterize lipidated proteins avoiding the purification step while mimicking its native environment. This approach also helps in filling the gap between in vitro and in vivo studies.

Global Isomeric Survey of Elusive Cyclopropanetrione: Unknown but Viable Isomers

Despite the great interest in energy storage application, stable neutral C_nO_n (n > 1) structures either in thermodynamics or kinetics have yet been largely limited due to the rather high tendency to release the very stable CO molecule. The neutral cyclopropanetrione (C₃O₃) cluster has long remained elusive since no isomer with sufficient kinetic stability has been found either experimentally or theoretically. In this work, we constructed the first global potential energy surface of singlet C₃O₃ at the CCSD(T)/aug-cc-pVTZ//B3LYP/aug-cc-pVTZ level, from which the kinetic stability of a wide range of C₃O₃ isomers can be determined by investigating their isomerization and fragmentation pathways. Amongst, a three-membered ring structure 01 is the global C₃O₃ isomer with a barrier of 10.6 kcal/mol at the sophisticated W1BD level. In particular, two carbene-type isomers 02 and 04 possess appreciable destruction barriers of 20.3 and 24.7 kcal/mol at W1BD, respectively. Thus, 02 and 04 can be useful building blocks for constructing larger high-energy density carbon-oxygen clusters. Moreover, with the carbene center, both might effectively functionalize various nano-materials while retaining the electrochemical active carbonyl and epoxyl moieties that are very desirable in alkali metal-ion batteries.

Designing the Backbone of Hexasilabenzene Derivatives with a High Unimolecular Kinetic Stability

It is an important subject to theoretically predict the kinetic stability of transient species. In this study, we have studied the kinetic stability of hexasilabenzene Si₆ H₆ and its derivatives, that is, decasilanaphthalene Si₁₀ H₈ and Li-substituted hexasilabenzene Si₆ Li₆ , theoretically by the artificial force induced reaction (AFIR) method combined with the rate constant matrix contraction (RCMC) method. Molecular design was further conducted to extend the unimolecular lifetime of hexasilabenzene derivatives. Although both Si₁₀ H₈ and Si₆ Li₆ were shown to possess shorter lifetimes than Si₆ H₆ , we found that the lifetimes of Si₆ Li₆ changed depending on arrangements of Li atoms around the monocyclic Si₆ backbone. Based on this knowledge, we found that a compound of an atomic composition Si₆ H₄ Li₂ with a planar, monocyclic Si₆ backbone has a relatively long unimolecular lifetime. Moreover, substitution of the two Li atoms by Na atoms further increased the lifetime.

Enhancing the Kinetic Stability and Lifetime of Organic Light-Emitting Diodes based on Bipolar Hosts by using Spiroconjugation

We examined how to enhance the lifetime of organic light-emitting diodes (OLEDs) based on bipolar host molecules ET-HT, where ET and HT refer to electron- and hole-transporting units, respectively, by analyzing their thermodynamic and kinetic stabilities. Our DFT calculations reveal that the thermodynamic stability of ET-HT is determined by that of its anion, which is difficult to improve by chemical modifications of ET and HT. The kinetic stability of ET-HT can be enhanced by the spiroconjugation between ET and HT, which occurs when their π-frameworks are extended and have an orthogonal arrangement. Green OLED devices were fabricated by using ET-HTs with and without spiroconjugation, to find that the device with spiroconjugation has a lifetime that is approximately 6 times longer than the one without spiroconjugation.

Unusual duplication mutation in a surface loop of human transthyretin leads to an aggressive drug-resistant amyloid disease

Transthyretin (TTR) is a globular tetrameric transport protein in plasma. Nearly 140 single amino acid substitutions in TTR cause life-threatening amyloid disease. We report a one-of-a-kind pathological variant featuring a Glu51, Ser52 duplication mutation (Glu51_Ser52dup). The proband, heterozygous for the mutation, exhibited an unusually aggressive amyloidosis that was refractory to treatment with the small-molecule drug diflunisal. To understand the poor treatment response and expand therapeutic options, we explored the structure and stability of recombinant Glu51_Ser52dup. The duplication did not alter the protein secondary or tertiary structure but decreased the stability of the TTR monomer and tetramer. Diflunisal, which bound with near-micromolar affinity, partially restored tetramer stability. The duplication had no significant effect on the free energy and enthalpy of diflunisal binding, and hence on the drug-protein interactions. However, the duplication induced tryptic digestion of TTR at near-physiological conditions, releasing a C-terminal fragment 49-129 that formed amyloid fibrils under conditions in which the full-length protein did not. Such C-terminal fragments, along with the full-length TTR, comprise amyloid deposits in vivo. Bioinformatics and structural analyses suggested that increased disorder in the surface loop, which contains the Glu51_Ser52dup duplication, not only helped generate amyloid-forming fragments but also decreased structural protection in the amyloidogenic residue segment 25-34, promoting misfolding of the full-length protein. Our studies of a unique duplication mutation explain its diflunisal-resistant nature, identify misfolding pathways for amyloidogenic TTR variants, and provide therapeutic targets to inhibit amyloid fibril formation by variant TTR.

Modification of the kinetic stability of immunoglobulin G by solvent additives

Biophysical properties of antibody-based biopharmaceuticals are a critical part of their release criteria. In this context, finding the appropriate formulation is equally important as optimizing their intrinsic biophysical properties through protein engineering, and both are mutually dependent. Most previous studies have empirically tested the impact of additives on measures of colloidal stability, while mechanistic aspects have usually been limited to only the thermodynamic stability of the protein. Here we emphasize the kinetic impact of additives on the irreversible denaturation steps of immunoglobulins G (IgG) and their antigen-binding fragments (Fabs), as these are the key committed steps preceding aggregation, and thus especially informative in elucidating the molecular parameters of activity loss. We examined the effects of ten additives on the conformational kinetic stability by differential scanning calorimetry (DSC), using a recently developed three-step model containing both reversible and irreversible steps. The data highlight and help to rationalize different effects of the additives on the properties of full-length IgG, analyzed by onset and aggregation temperatures as well as by kinetic parameters derived from our model. Our results further help to explain the observation that stabilizing mutations in the antigen-binding fragment (Fab) significantly affect the kinetic parameters of its thermal denaturation, but not the aggregation properties of the full-length IgGs. We show that the proper analysis of DSC scans for full-length IgGs and their corresponding Fabs not only helps in ranking their stability in different formats and formulations, but provides important mechanistic insights for improving the conformational kinetic stability of IgGs.

Physical Stability of Amorphous Solid Dispersions: a Physicochemical Perspective with Thermodynamic, Kinetic and Environmental Aspects

PURPOSE

Amorphous solid dispersions (ASDs) have been widely used in the pharmaceutical industry for solubility enhancementof poorly water-soluble drugs. The physical stability, however, remainsone of the most challenging issues for the formulation development.Many factors can affect the physical stability via different mechanisms, and therefore an in-depth understanding on these factors isrequired.

METHODS

In this review, we intend to summarize the physical stability of ASDsfrom a physicochemical perspective whereby factors that can influence the physical stability areclassified into thermodynamic, kinetic and environmental aspects.

RESULTS

The drug-polymer miscibility and solubility are consideredas the main thermodynamicfactors which may determine the spontaneity of the occurrence of the physical instabilityof ASDs. Glass-transition temperature,molecular mobility, manufacturing process,physical stabilityof amorphous drugs, and drug-polymerinteractionsareconsideredas the kinetic factors which areassociated with the kinetic stability of ASDs on aging. Storage conditions including temperature and humidity could significantly affect the thermodynamicand kineticstabilityof ASDs.

CONCLUSION

When designing amorphous solid dispersions, it isrecommended that these thermodynamic, kinetic and environmental aspects should be completely investigatedand compared to establish rationale formulations for amorphous solid dispersions with high physical stability.

Interplay between Protein Thermal Flexibility and Kinetic Stability

Kinetic stability is a key parameter to comprehend protein behavior and it plays a central role to understand how evolution has reached the balance between function and stability in cell-relevant timescales. Using an approach that includes simulations, protein engineering, and calorimetry, we show that there is a clear correlation between kinetic stability determined by differential scanning calorimetry and protein thermal flexibility obtained from a novel method based on temperature-induced unfolding molecular dynamics simulations. Thermal flexibility quantitatively measures the increment of the conformational space available to the protein when energy in provided. The (β/α)₈ barrel fold of two closely related by evolution triosephosphate isomerases from two trypanosomes are used as model systems. The kinetic stability-thermal flexibility correlation has predictive power for the studied proteins, suggesting that the strategy and methodology discussed here might be applied to other proteins in biotechnological developments, evolutionary studies, and the design of protein based therapeutics.

Analysis of IgG kinetic stability by differential scanning calorimetry, probe fluorescence and light scattering

Monoclonal antibodies of the immunoglobulin G (IgG) type have become mainstream therapeutics for the treatment of many life-threatening diseases. For their successful application in the clinic and a favorable cost-benefit ratio, the design and formulation of these therapeutic molecules must guarantee long-term stability for an extended period of time. Accelerated stability studies, e.g., by employing thermal denaturation, have the great potential for enabling high-throughput screening campaigns to find optimal molecular variants and formulations in a short time. Surprisingly, no validated quantitative analysis of these accelerated studies has been performed yet, which clearly limits their application for predicting IgG stability. Therefore, we have established a quantitative approach for the assessment of the kinetic stability over a broad range of temperatures. To this end, differential scanning calorimetry (DSC) experiments were performed with a model IgG, testing chaotropic formulations and an extended temperature range, and they were subsequently analyzed by our recently developed three-step sequential model of IgG denaturation, consisting of one reversible and two irreversible steps. A critical comparison of the predictions from this model with data obtained by an orthogonal fluorescence probe method, based on 8-anilinonaphthalene-1-sulfonate binding to partially unfolded states, resulted in very good agreement. In summary, our study highlights the validity of this easy-to-perform analysis for reliably assessing the kinetic stability of IgGs, which can support accelerated formulation development of monoclonal antibodies by ranking different formulations as well as by improving colloidal stability models.

Adsorption of Antifungal Drugs Inside Pristine and Functionalized Fullerenes and Nanotubes: DFT Investigation

BACKGROUND

Econazole, sulconazole and tioconazole usage as antifungal agents is limited due to poor pharmacokinetic properties. Pristine and hydroxylated structures of the C240 fullerene and single walled carbon nanotube (SWCNT) were proposed as transporters of these imidazoles potentially enhancing their pharmacokinetics.

METHODS

To assess possibility of creation of the endohedral complexes of the azoles and carbon nanostructures, their adsorption and interaction energies were calculated with the hybrid exchange-correlation density functional B97-1 and 6-31(d,p) basis set. Interactions within the transporter - drug complexes were investigated with the Atoms in Molecules (AIM) Theory and Reduced Density Gradient (RDG).

RESULTS AND CONCLUSIONS

The adsorption energies of the studied azoles depend on type and surface modification of the transporter. Hydroxylation of the fullerene and nanotube surface makes an opportunity for chemisorption of the investigated antifungal drugs. The pristine and hydroxylated nanotube complexes exhibit thermodynamic stability. The complexes of the fullerenes are thermodynamically unstable but its kinetic stability could be significant thus allowing for the such structures to exist. The energetic instability would enhance liberation of the encapsulated molecule from the complex. It is advantageous in the context of drug release.

Advanced analyses of kinetic stabilities of iggs modified by mutations and glycosylation

The stability of Immunoglobulin G (IgG) affects production, storage and usability, especially in the clinic. The complex thermal and isothermal transitions of IgGs, especially their irreversibilities, pose a challenge to the proper determination of parameters describing their thermodynamic and kinetic stability. Here, we present a reliable mathematical model to study the irreversible thermal denaturations of antibody variants. The model was applied to two unrelated IgGs and their variants with stabilizing mutations as well as corresponding non-glycosylated forms of IgGs and Fab fragments. Thermal denaturations of IgGs were analyzed with three transitions, one reversible transition corresponding to C(H)2 domain unfolding followed by two consecutive irreversible transitions corresponding to Fab and C(H)3 domains, respectively. The parameters obtained allowed us to examine the effects of these mutations on the stabilities of individual domains within the full-length IgG. We found that the kinetic stability of the individual Fab fragment is significantly lowered within the IgG context, possibly because of intramolecular aggregation upon heating, while the stabilizing mutations have an especially beneficial effect. Thermal denaturations of non-glycosylated variants of IgG consist of more than three transitions and could not be analyzed by our model. However, isothermal denaturations demonstrated that the lack of glycosylation affects the stability of all and not just of the C(H)2 domain, suggesting that the partially unfolded domains may interact with each other during unfolding. Investigating thermal denaturation of IgGs according to our model provides a valuable tool for detecting subtle changes in thermodynamic and/or kinetic stabilities of individual domains.

Protein unfolding rates correlate as strongly as folding rates with native structure

Although the folding rates of proteins have been studied extensively, both experimentally and theoretically, and many native state topological parameters have been proposed to correlate with or predict these rates, unfolding rates have received much less attention. Moreover, unfolding rates have generally been thought either to not relate to native topology in the same manner as folding rates, perhaps depending on different topological parameters, or to be more difficult to predict. Using a dataset of 108 proteins including two-state and multistate folders, we find that both unfolding and folding rates correlate strongly, and comparably well, with well-established measures of native topology, the absolute contact order and the long range order, with correlation coefficient values of 0.75 or higher. In addition, compared to folding rates, the absolute values of unfolding rates vary more strongly with native topology, have a larger range of values, and correlate better with thermodynamic stability. Similar trends are observed for subsets of different protein structural classes. Taken together, these results suggest that choosing a scaffold for protein engineering may require a compromise between a simple topology that will fold sufficiently quickly but also unfold quickly, and a complex topology that will unfold slowly and hence have kinetic stability, but fold slowly. These observations, together with the established role of kinetic stability in determining resistance to thermal and chemical denaturation as well as proteases, have important implications for understanding fundamental aspects of protein unfolding and folding and for protein engineering and design.

Protein Stability, Folding and Misfolding in Human PGK1 Deficiency

Conformational diseases are often caused by mutations, altering protein folding and stability in vivo. We review here our recent work on the effects of mutations on the human phosphoglycerate kinase 1 (hPGK1), with a particular focus on thermodynamics and kinetics of protein folding and misfolding. Expression analyses and in vitro biophysical studies indicate that disease-causing mutations enhance protein aggregation propensity. We found a strong correlation among protein aggregation propensity, thermodynamic stability, cooperativity and dynamics. Comparison of folding and unfolding properties with previous reports in PGKs from other species suggests that hPGK1 is very sensitive to mutations leading to enhance protein aggregation through changes in protein folding cooperativity and the structure of the relevant denaturation transition state for aggregation. Overall, we provide a mechanistic framework for protein misfolding of hPGK1, which is insightful to develop new therapeutic strategies aimed to target native state stability and foldability in hPGK1 deficient patients.

Modulating protein stability - directed evolution strategies for improved protein function

Protein engineering is widely used to generate proteins with novel or enhanced function. However, manipulating protein function in the laboratory can prove laborious, protracted and challenging. Recent developments in the understanding of protein evolutionary dynamics have unveiled the full extent by which the evolution of function is limited by protein stability - a revelation that may be applied to protein engineering on a whole. Thus, strategies that modulate protein stability and reduce its constraining effects may facilitate the engineering of protein function. A combinatorial approach involving the introduction of compensatory mutations and manipulation of the stability threshold by chaperone buffering during directed evolution can improve the functional adaptation of a protein, thereby fostering our ability to attain ever-more ambitious protein functions in the laboratory.

Molecular Orientation in Stable Glasses of Indomethacin

Spectroscopic ellipsometry has been used to measure the properties of indomethacin prepared by physical vapor deposition at Tsubstrate/Tg = 0.78, 0.84, and 0.90. The as-deposited glasses exhibited high kinetic stability and had densities 0.8-1.2% higher than the ordinary glass prepared by cooling the liquid at 1 K/min. Deposition at the higher temperatures yielded glasses with positive birefringence (up to Δn = 0.028), while the lowest-temperature sample was negatively birefringent (Δn = -0.015). These results indicate that substrate temperature can be used to manipulate molecular orientation in high-density and high-stability glasses. The data for the supercooled liquid and the ordinary glass of indomethacin are reasonably consistent with the Lorentz-Lorenz equation, but significant deviations are noted with the as-deposited materials.