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1.
Mol Pharm ; 21(5): 2250-2271, 2024 May 06.
Artículo en Inglés | MEDLINE | ID: mdl-38661388

RESUMEN

Charges and their contribution to protein-protein interactions are essential for the key structural and dynamic properties of monoclonal antibody (mAb) solutions. In fact, they influence the apparent molecular weight, the static structure factor, the collective diffusion coefficient, or the relative viscosity, and their concentration dependence. Further, charges play an important role in the colloidal stability of mAbs. There exist standard experimental tools to characterize mAb net charges, such as the measurement of the electrophoretic mobility, the second virial coefficient, or the diffusion interaction parameter. However, the resulting values are difficult to directly relate to the actual overall net charge of the antibody and to theoretical predictions based on its known molecular structure. Here, we report the results of a systematic investigation of the solution properties of a charged IgG1 mAb as a function of concentration and ionic strength using a combination of electrophoretic measurements, static and dynamic light scattering, small-angle X-ray scattering, and tracer particle-based microrheology. We analyze and interpret the experimental results using established colloid theory and coarse-grained computer simulations. We discuss the potential and limits of colloidal models for the description of the interaction effects of charged mAbs, in particular pointing out the importance of incorporating shape and charge anisotropy when attempting to predict structural and dynamic solution properties at high concentrations.


Asunto(s)
Anticuerpos Monoclonales , Coloides , Inmunoglobulina G , Coloides/química , Anticuerpos Monoclonales/química , Inmunoglobulina G/química , Viscosidad , Soluciones/química , Concentración Osmolar , Dispersión del Ángulo Pequeño , Dispersión Dinámica de Luz , Simulación por Computador , Difracción de Rayos X/métodos
2.
Mol Pharm ; 21(4): 1719-1728, 2024 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-38411904

RESUMEN

Therapeutic proteins with a high concentration and low viscosity are highly desirable for subcutaneous and certain local injections. The shape of a protein is known to influence solution viscosity; however, the precise quantification of protein shape and its relative impact compared to other factors like charge-charge interactions remains unclear. In this study, we utilized seven model proteins of varying shapes and experimentally determined their shape factors (v) based on Einstein's viscosity theory, which correlate strongly with the ratios of the proteins' surface area to the 2/3 power of their respective volumes, based on protein crystal structures resolved experimentally or predicted by AlphaFold. This finding confirms the feasibility of computationally estimating protein shape factors from amino acid sequences alone. Furthermore, our results demonstrated that, in high-concentration electrolyte solutions, a more spherical protein shape increases the protein's critical concentration (C*), the transition concentration beyond which protein viscosity increases exponentially relative to concentration increases. In summary, our work elucidates protein shape as a key determinant of solution viscosity through quantitative analysis and comparison with other contributing factors. This provides insights into molecular engineering strategies to optimize the molecular design of therapeutic proteins, thus optimizing their viscosity.


Asunto(s)
Anticuerpos Monoclonales , Electrólitos , Anticuerpos Monoclonales/química , Viscosidad , Soluciones/química
3.
Biochem Biophys Res Commun ; 701: 149600, 2024 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-38309151

RESUMEN

The hydrophobicity of solutes measures the intensity of a solute's interaction with aqueous environment. The aqueous environment may change with its composition, leading to changes in its solvent properties largely characterized by polarity. As a result, the relative hydrophobicity of a solute is a function of the solute structure and the properties of the water-based solvent determined by the total composition of the aqueous phase. This aspect is commonly ignored by medicinal chemists even though it is essential for drug distribution between different biological tissues. Partitioning of solutes in aqueous two-phase systems provides the relative hydrophobicity estimates for any water-soluble compounds that can be used to improve predictions of the toxicity and other biological effects of these compounds.


Asunto(s)
Agua , Solventes/química , Soluciones/química , Agua/química , Interacciones Hidrofóbicas e Hidrofílicas
4.
Langmuir ; 40(9): 4615-4622, 2024 03 05.
Artículo en Inglés | MEDLINE | ID: mdl-38387073

RESUMEN

The cellular environment is crowded with macromolecules of different shapes and sizes. The effect of this macromolecular crowding has been studied in a variety of synthetic crowding environments: two popular examples are the compact colloid-like Ficoll macromolecule and the globular protein bovine serum albumin (BSA). Recent studies have indicated that a significant component of bound or surface-associated water in these crowders reduces the available free volume. In this work, Brillouin light scattering experiments were performed on aqueous solutions of Ficoll 70 and Ficoll 400 with concentrations ranging from 1 to 35 wt % and BSA with concentrations of 1 to 27 wt %. From the dependence of spectral peak parameters on polymer concentration, we determined fundamental solution properties: hypersound velocity, adiabatic bulk modulus and compressibility, apparent viscosity, and hypersound attenuation. The existing theory that ignores intermolecular interactions can capture only the observed linear trends in the frequency shift up to a threshold concentration, beyond which a quadratic term accounting for intermolecular interactions is necessary. This likely indicates a transition from the dilute to semidilute regime. In the Ficoll solutions (but not BSA), we see evidence for a central mode, which is indicative of relaxation in the hydration shell of Ficoll.


Asunto(s)
Albúmina Sérica Bovina , Agua , Ficoll/química , Albúmina Sérica Bovina/química , Sustancias Macromoleculares , Análisis Espectral , Soluciones/química
5.
J Am Chem Soc ; 146(4): 2701-2710, 2024 Jan 31.
Artículo en Inglés | MEDLINE | ID: mdl-38291994

RESUMEN

Macromolecular crowding is the usual condition of cells. The implications of the crowded cellular environment for protein stability and folding, protein-protein interactions, and intracellular transport drive a growing interest in quantifying the effects of crowding. While the properties of crowded solutions have been extensively studied, less attention has been paid to the interaction of crowders with the cellular boundaries, i.e., membranes. However, membranes are key components of cells and most subcellular organelles, playing a central role in regulating protein channel and receptor functions by recruiting and binding charged and neutral solutes. While membrane interactions with charged solutes are dominated by electrostatic forces, here we show that significant charge-induced forces also exist between membranes and neutral solutes. Using neutron reflectometry measurements and molecular dynamics simulations of poly(ethylene glycol) (PEG) polymers of different molecular weights near charged and neutral membranes, we demonstrate the roles of surface dielectrophoresis and counterion pressure in repelling PEG from charged membrane surfaces. The resulting depletion zone is expected to have consequences for drug design and delivery, the activity of proteins near membrane surfaces, and the transport of small molecules along the membrane surface.


Asunto(s)
Polímeros , Proteínas , Membrana Celular , Polímeros/química , Proteínas/química , Polietilenglicoles/química , Soluciones/química
6.
J Pharm Sci ; 113(4): 982-989, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-37967652

RESUMEN

Hydrophobic bonding is a phenomenon wherein the adsorption of solutes from aqueous solutions is driven largely by the desire of solvent molecules to interact with each other, thus squeezing out solute molecules onto the adsorbent surface. A novel computational analysis of hydration shell water dynamics was used to study the driving force for the hydrophobic bonding of five small drug molecules to activated carbon. It was demonstrated that the solvation of these drug molecules produced hydration shells of lower density and molecular mobility than bulk water, up to 10.5-14 Å distance. Excellent correlations were found between the simulated water-water hydrogen bonding lifetimes in the hydration shell and the experimental capacity constants of hydrophobic bonding (KHB) obtained from the Two-Mechanism Langmuir-Like Equation. KHB also correlated well with the solute-solvent vdW interaction energies in a manner that could allow future predictions of KHB values from simple simulations. Such correlations were not found with the capacity constant of the well-known enthalpy-driven adsorption. The driving force for hydrophobic bonding has entropic origins due to the elimination of water structuring in the hydration shells. However, unlike a typical entropy-driven process, hydrophobic bonding to activated carbon was also associated with a large exothermic enthalpy change when studied with isoperibol calorimetry.


Asunto(s)
Carbón Orgánico , Simulación de Dinámica Molecular , Entropía , Adsorción , Solventes/química , Agua/química , Soluciones/química , Interacciones Hidrofóbicas e Hidrofílicas , Enlace de Hidrógeno
7.
Eur Phys J E Soft Matter ; 46(12): 119, 2023 Dec 05.
Artículo en Inglés | MEDLINE | ID: mdl-38051398

RESUMEN

It is well established that deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) exhibit a reentrant condensation (RC) phase behavior in the presence of the trivalent hexamine cobalt(III) cations (Hac) which can be important for their packing and folding. A similar behavior can be observed for negatively charged globular proteins in the presence of trivalent metal cations, such as Y3+ or La3+. This phase behavior is mainly driven by charge inversion upon an increasing salt concentration for a fixed protein concentration (cp). However, as Hac exhibits structural differences compared to other multivalent metal cations, with six ammonia ligands (NH3) covalently bonded to the central cobalt atom, it is not clear that Hac can induce a similar phase behavior for proteins. In this work, we systematically investigate whether negatively charged globular proteins ß-lactoglobulin (BLG), bovine serum albumin (BSA), human serum albumin (HSA) and ovalbumin (OVA) feature Hac-induced RC. Effective protein-protein interactions were investigated by small-angle X-ray scattering. The reduced second virial coefficient (B2/B2HS) was obtained as a function of salt concentration. The virial coefficient analysis performed confirms the reentrant interaction (RI) behavior for BLG without actually inducing RC, given the insufficient strengths of the interactions for the latter to occur. In contrast, the strength of attraction for BSA, HSA and OVA are too weak to show RC. Model free analysis of the inverse intensity [Formula: see text] also supports this finding. Looking at different q-range by employing static (SLS) and dynamic light scattering experiments, the presence of RI behavior can be confirmed. The results are further discussed in view of metal cation binding sites in nucleic acids (DNA and RNA), where Hac induced RC phase behavior.


Asunto(s)
Cloruros , Cobalto , Humanos , Cloruros/química , Metenamina , Albúmina Sérica Bovina/química , Cationes/química , ADN , ARN , Soluciones/química
8.
Mol Pharm ; 20(12): 6420-6428, 2023 Dec 04.
Artículo en Inglés | MEDLINE | ID: mdl-37906640

RESUMEN

During the developability assessment of therapeutic monoclonal antibody (mAb) candidates, utilization of robust high-throughput predictive assays enables rapid selection of top candidates with low risks for late-stage development. Predicting the viscosities of highly concentrated mAbs using limited materials is an important aspect of developability assessment because high viscosity can complicate manufacturability, stability, and administration. Here, we report a high-throughput assay measuring protein-protein interactions to predict mAb viscosity. The diffusion interaction parameter (kD) measures colloidal self-association in dilute solutions and has been reported to be predictive of the mAb viscosity at high concentrations. However, kD of Amgen early stage IgG1 mAb candidates measured in 10 mM acetate at pH 5.2 containing sucrose and polysorbate (denoted A52SuT) shows only weak correlation to their viscosities at 140 mg/mL in A52SuT. We hypothesize that kD measured in A52SuT reflects primarily long-range electrostatic repulsions because most of these mAb candidates carry strong net positive charges in this low ionic strength formulation with pH (5.2) well below pI values of mAb candidates. However, the viscosities of high concentration mAbs depend heavily on short-range molecular interactions. We propose an improved kD method in which salt is added to suppress charge repulsions and to allow for detection of key short-range interactions in dilute solutions. Salt types and salt concentrations were screened, and an optimal salt condition was identified. This optimized method was further validated using two test mAb sets. Overall, the method improves the Pearson R2 between kD and viscosity (6-230 cP) from 0.24 to 0.80 for a data set consisting of 37 mAbs.


Asunto(s)
Anticuerpos Monoclonales , Cloruro de Sodio , Anticuerpos Monoclonales/química , Viscosidad , Difusión , Soluciones/química
9.
Nature ; 620(7972): 104-109, 2023 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-37532817

RESUMEN

Iron is important in regulating the ocean carbon cycle1. Although several dissolved and particulate species participate in oceanic iron cycling, current understanding emphasizes the importance of complexation by organic ligands in stabilizing oceanic dissolved iron concentrations2-6. However, it is difficult to reconcile this view of ligands as a primary control on dissolved iron cycling with the observed size partitioning of dissolved iron species, inefficient dissolved iron regeneration at depth or the potential importance of authigenic iron phases in particulate iron observational datasets7-12. Here we present a new dissolved iron, ligand and particulate iron seasonal dataset from the Bermuda Atlantic Time-series Study (BATS) region. We find that upper-ocean dissolved iron dynamics were decoupled from those of ligands, which necessitates a process by which dissolved iron escapes ligand stabilization to generate a reservoir of authigenic iron particles that settle to depth. When this 'colloidal shunt' mechanism was implemented in a global-scale biogeochemical model, it reproduced both seasonal iron-cycle dynamics observations and independent global datasets when previous models failed13-15. Overall, we argue that the turnover of authigenic particulate iron phases must be considered alongside biological activity and ligands in controlling ocean-dissolved iron distributions and the coupling between dissolved and particulate iron pools.


Asunto(s)
Hierro , Minerales , Agua de Mar , Hierro/análisis , Hierro/química , Hierro/metabolismo , Ligandos , Minerales/análisis , Minerales/química , Minerales/metabolismo , Ciclo del Carbono , Conjuntos de Datos como Asunto , Océano Atlántico , Agua de Mar/análisis , Agua de Mar/química , Bermudas , Factores de Tiempo , Estaciones del Año , Soluciones/química , Internacionalidad
10.
Int J Pharm ; 644: 123353, 2023 Sep 25.
Artículo en Inglés | MEDLINE | ID: mdl-37647976

RESUMEN

In recent years, advancements in bioengineering and materials science have witnessed increasing interest in synthetic polymers capable of fulfilling various applications. Owing to their distinctive properties, Pluronics can be used as nano-drug carriers, to deliver poorly water-soluble drugs, and as model systems to study colloidal science by tuning amphiphilic properties. In this work, we investigated the effect of diclofenac sodium on the self-assembly and thermoresponsive crystallization of Pluronic F68 in water solutions, by employing experimental rheology and Nuclear Magnetic Resonance (NMR). We built a complete phase diagram as a function of temperature and concentration for 45 wt% Pluronic F68 with various amounts of diclofenac sodium in water. The morphological transitions were followed as a function of temperature via linear rheology. We extrapolated the transition temperatures - identifying distinct phases - as a function of the drug concentration and proposed an empirical model for their prediction. NMR analysis provided further information on the structural characteristics of the systems, shedding light on the interactions between F68 and diclofenac sodium. Although dealing with a pharmaceutical salt, the study is focused on a colloidal system and its interaction with a binding molecule, that is of general interest for colloidal science.


Asunto(s)
Transición de Fase , Diclofenaco/química , Soluciones/química , Poloxámero/química , Reología , Temperatura , Espectroscopía de Resonancia Magnética , Difusión
11.
J Phys Chem B ; 127(27): 6197-6204, 2023 07 13.
Artículo en Inglés | MEDLINE | ID: mdl-37399586

RESUMEN

Studying protein interactions at low temperatures has important implications for optimizing cryostorage processes of biological tissue, food, and protein-based drugs. One of the major issues is related to the formation of ice nanocrystals, which can occur even in the presence of cryoprotectants and can lead to protein denaturation. The presence of ice nanocrystals in protein solutions poses several challenges since, contrary to microscopic ice crystals, they can be difficult to resolve and can complicate the interpretation of experimental data. Here, using a combination of small- and wide-angle X-ray scattering (SAXS and WAXS), we investigate the structural evolution of concentrated lysozyme solutions in a cryoprotected glycerol-water mixture from room temperature (T = 300 K) down to cryogenic temperatures (T = 195 K). Upon cooling, we observe a transition near the melting temperature of the solution (T ≈ 245 K), which manifests both in the temperature dependence of the scattering intensity peak position reflecting protein-protein length scales (SAXS) and the interatomic distances within the solvent (WAXS). Upon thermal cycling, a hysteresis is observed in the scattering intensity, which is attributed to the formation of nanocrystallites in the order of 10 nm. The experimental data are well described by the two-Yukawa model, which indicates temperature-dependent changes in the short-range attraction of the protein-protein interaction potential. Our results demonstrate that the nanocrystal growth yields effectively stronger protein-protein attraction and influences the protein pair distribution function beyond the first coordination shell.


Asunto(s)
Hielo , Dispersión del Ángulo Pequeño , Difracción de Rayos X , Congelación , Solventes , Soluciones/química
12.
Nature ; 619(7971): 749-754, 2023 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-37380782

RESUMEN

Proton transfer is one of the most fundamental events in aqueous-phase chemistry and an emblematic case of coupled ultrafast electronic and structural dynamics1,2. Disentangling electronic and nuclear dynamics on the femtosecond timescales remains a formidable challenge, especially in the liquid phase, the natural environment of biochemical processes. Here we exploit the unique features of table-top water-window X-ray absorption spectroscopy3-6 to reveal femtosecond proton-transfer dynamics in ionized urea dimers in aqueous solution. Harnessing the element specificity and the site selectivity of X-ray absorption spectroscopy with the aid of ab initio quantum-mechanical and molecular-mechanics calculations, we show how, in addition to the proton transfer, the subsequent rearrangement of the urea dimer and the associated change of the electronic structure can be identified with site selectivity. These results establish the considerable potential of flat-jet, table-top X-ray absorption spectroscopy7,8 in elucidating solution-phase ultrafast dynamics in biomolecular systems.


Asunto(s)
Protones , Urea , Urea/química , Soluciones/química , Agua/química , Espectroscopía de Absorción de Rayos X , Teoría Cuántica , Factores de Tiempo
13.
Molecules ; 28(9)2023 May 05.
Artículo en Inglés | MEDLINE | ID: mdl-37175306

RESUMEN

Natural astaxanthin has been widely used in the food, cosmetic, and medicine industries due to its exceptional biological activity. Shrimp shell is one of the primary natural biological sources of astaxanthin. However, after astaxanthin recovery, there is still a lot of chitin contained in the residues. In this study, the residue from shrimp (Penaeus vannamei) shells after astaxanthin extraction using ionic liquid (IL) 1-ethyl-3-methyl-imidazolium acetate ([Emim]Ac) was used as a bioadsorbent to remove fluoride from the aqueous solution. The results show the IL extraction conditions, including the solid/liquid ratio, temperature, time, and particle size, all played important roles in the removal of fluoride by the shrimp shell residue. The shrimp shells treated using [Emim]Ac at 100 °C for 2 h exhibited an obvious porous structure, and the porosity showed a positive linear correlation with defluorination (DF, %). Moreover, the adsorption process of fluoride was nonspontaneous and endothermic, which fits well with both the pseudo-second-order and Langmuir models. The maximum adsorption capacity calculated according to the Langmuir model is 3.29 mg/g, which is better than most bioadsorbents. This study provides a low-cost and efficient method for the preparation of adsorbents from shrimp processing waste to remove fluoride from wastewater.


Asunto(s)
Adsorción , Exoesqueleto , Fluoruros , Penaeidae , Contaminantes Químicos del Agua , Agua , Xantófilas , Animales , Exoesqueleto/química , Quitina/análisis , Quitina/química , Fluoruros/química , Fluoruros/aislamiento & purificación , Concentración de Iones de Hidrógeno , Líquidos Iónicos/química , Cinética , Tamaño de la Partícula , Penaeidae/química , Porosidad , Alimentos Marinos , Soluciones/química , Temperatura , Aguas Residuales/química , Agua/química , Contaminantes Químicos del Agua/química , Contaminantes Químicos del Agua/aislamiento & purificación , Xantófilas/aislamiento & purificación
14.
J Chromatogr A ; 1696: 463967, 2023 May 10.
Artículo en Inglés | MEDLINE | ID: mdl-37099825

RESUMEN

This report is the first of 2-part study of the effect of gradients in column parameters on the column performance. If t, x and p are, respectively, time since sample introduction, distance from column inlet and some parameter of solute migration along the column then ∂p/∂t and ∂p/∂x are, respectively, the rate of changing p and the gradient of p. Unified approach to study of gradients and rates in different chromatographic techniques (LC, GC, etc.) has been developed. To facilitate a unified approach, the umbrella term mobilization (y) representing column temperature (T) in GC, solvent composition (ϕ) in LC, etc. is introduced. Differential equations for migration of a solute band (collection of solute molecules) under the following conditions are formulated and solved:The key solutions describe the time of migration of a solute band and the band width - both as functions of the distance traveled by the band. The solutions are used in Part 2 for the study of the effects of the negative gradients in y on column performance in several practically important cases. A reduction of the key general solutions to much simpler equations for gradient LC has been demonstrated herein as an example.


Asunto(s)
Cromatografía , Solventes/química , Soluciones/química , Temperatura
15.
Environ Sci Technol ; 57(14): 5872-5880, 2023 04 11.
Artículo en Inglés | MEDLINE | ID: mdl-36976836

RESUMEN

The demand to effectively treat medical wastewater has escalated with the much greater use of antiviral drugs since the COVID-19 pandemic. Forward osmosis (FO) has great potential in wastewater treatment only when appropriate draw solutes are available. Here, we synthesize a series of smart organic-inorganic polyoxomolybdates (POMs), namely, (NH4)6[Mo7O24], (PrNH3)6[Mo7O24], (iPrNH3)6[Mo7O24], and (BuNH3)6[Mo7O24], for FO to treat antiviral-drug wastewater. Influential factors of separation performance have been systematically studied by tailoring the structure, organic characteristics, and cation chain length of POMs. POMs at 0.4 M produce water fluxes ranging from 14.0 to 16.4 LMH with negligible solute losses, at least 116% higher than those of NaCl, NH4HCO3, and other draw solutes. (NH4)6[Mo7O24] creates a water flux of 11.2 LMH, increased by more than 200% compared to that of NaCl and NH4HCO3 in long-term antiviral-drug wastewater reclamation. Remarkably, the drugs treated with NH4HCO3 and NaCl are either contaminated or denatured, while those with (NH4)6[Mo7O24] remain intact. Moreover, these POMs are recovered by sunlight-assisted acidification owing to their light and pH dual sensitivity and reusability for FO. POMs prove their suitability as draw solutes and demonstrate their superiority over the commonly studied draw solutes in wastewater treatment.


Asunto(s)
COVID-19 , Purificación del Agua , Humanos , Aguas Residuales , Cloruro de Sodio , Pandemias , Membranas Artificiales , Ósmosis , Soluciones/química , Agua/química
16.
J Pharm Sci ; 112(7): 1872-1887, 2023 07.
Artículo en Inglés | MEDLINE | ID: mdl-36780988

RESUMEN

The degradation kinetics of the glycopeptide antibiotic dalbavancin in solution are systematically evaluated over the pH range 1-12 at 70°C. The decomposition rate of dalbavancin was measured as a function of pH, buffer composition, temperature, ionic strength, and drug concentration. A pH-rate profile was constructed using pseudo first-order kinetics at 70°C after correcting for buffer effects; the observed pH-rate profile could be fitted with standard pseudo first order rate laws. The degradation reactions of dalbavancin were found to be strongly dependent on pH and were catalyzed by protons or hydroxyl groups at extreme pH values. Dalbavancin shows maximum stability in the pH region 4-5. Based on the Arrhenius equation, dalbavancin solution at pH 4.5 is predicted to have a maximum stability of thirteen years under refrigerated conditions, eight months at room temperature and one month at 40°C. Mannosyl Aglycone (MAG), the major thermal and acid degradation product, and DB-R6, an additional acid degradation product, were formed in dalbavancin solutions at 70°C due to hydrolytic cleavage at the anomeric carbons of the sugars. Through deamination and hydrolytic cleavage of dalbavancin, a small amount of DB-Iso-DP2 (RRT-1.22) degradation product was also formed under thermal stress at 70°C. A greater amount of the base degradation product DB-R2 forms under basic conditions at 70°C due to epimerization of the alpha carbon of phenylglycine residue 3.


Asunto(s)
Protones , Cinética , Concentración de Iones de Hidrógeno , Temperatura , Soluciones/química , Estabilidad de Medicamentos , Tampones (Química) , Cromatografía Líquida de Alta Presión
17.
J Chem Theory Comput ; 19(5): 1602-1614, 2023 Mar 14.
Artículo en Inglés | MEDLINE | ID: mdl-36791464

RESUMEN

Replica exchange with solute tempering (REST) is a highly effective variant of replica exchange for enhanced sampling in explicit solvent simulations of biomolecules. By scaling the Hamiltonian for a selected "solute" region of the system, REST effectively applies tempering only to the degrees of freedom of interest but not the rest of the system ("solvent"), allowing fewer replicas for covering the same temperature range. A key consideration of REST is how the solute-solvent interactions are scaled together with the solute-solute interactions. Here, we critically evaluate the performance of the latest REST2 protocol for sampling large-scale conformation fluctuations of intrinsically disordered proteins (IDPs). The results show that REST2 promotes artificial protein conformational collapse at high effective temperatures, which seems to be a designed feature originally to promote the sampling of reversible folding of small proteins. The collapse is particularly severe with larger IDPs, leading to replica segregation in the effective temperature space and hindering effective sampling of large-scale conformational changes. We propose that the scaling of the solute-solvent interactions can be treated as free parameters in REST, which can be tuned to control the solute conformational properties (e.g., chain expansion) at different effective temperatures and achieve more effective sampling. To this end, we derive a new REST3 protocol, where the strengths of the solute-solvent van der Waals interactions are recalibrated to reproduce the levels of protein chain expansion at high effective temperatures. The efficiency of REST3 is examined using two IDPs with nontrivial local and long-range structural features, including the p53 N-terminal domain and the kinase inducible transactivation domain of transcription factor CREB. The results suggest that REST3 leads to a much more efficient temperature random walk and improved sampling efficiency, which also further reduces the number of replicas required. Nonetheless, our analysis also reveals significant challenges of relying on tempering alone for sampling large-scale conformational fluctuations of disordered proteins. It is likely that more efficient sampling protocols will require incorporating more sophisticated Hamiltonian replica exchange schemes in addition to tempering.


Asunto(s)
Proteínas Intrínsecamente Desordenadas , Simulación de Dinámica Molecular , Conformación Proteica , Soluciones/química , Proteínas Intrínsecamente Desordenadas/química , Solventes
18.
Phys Chem Chem Phys ; 25(4): 3031-3041, 2023 Jan 27.
Artículo en Inglés | MEDLINE | ID: mdl-36607608

RESUMEN

Liquid-liquid phase separation (LLPS) of protein solutions is governed by highly complex protein-protein interactions. Nevertheless, it has been suggested that based on the extended law of corresponding states (ELCS), as proposed for colloids with short-range attractions, one can rationalize not only the thermodynamics, but also the structure and dynamics of such systems. This claim is systematically and comprehensively tested here by static and dynamic light scattering experiments. Spinodal lines, the isothermal osmotic compressibility κT and the relaxation rate of concentration fluctuations Γ are determined for protein solutions in the vicinity of LLPS. All these quantities are found to exhibit a corresponding-states behavior. This means that, for different solution conditions, these quantities are essentially the same if considered at similar reduced temperature or second virial coefficient. For moderately concentrated solutions, the volume fraction ϕ dependence of κT and Γ can be consistently described by Baxter's model of adhesive hard spheres. The off-critical, asymptotic T behavior of κT and Γ close to LLPS is consistent with the scaling laws predicted by mean-field theory. Thus, the present work aims at a comprehensive experimental test of the applicability of the ELCS to structural and dynamical properties of concentrated protein solutions.


Asunto(s)
Coloides , Proteínas , Temperatura , Termodinámica , Proteínas/química , Dispersión Dinámica de Luz , Soluciones/química
19.
J Biol Chem ; 299(2): 102799, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-36528062

RESUMEN

Collagen triple helices are critical in the function of mannan-binding lectin (MBL), an oligomeric recognition molecule in complement activation. The MBL collagen regions form complexes with the serine proteases MASP-1 and MASP-2 in order to activate complement, and mutations lead to common immunodeficiencies. To evaluate their structure-function properties, we studied the solution structures of four MBL-like collagen peptides. The thermal stability of the MBL collagen region was much reduced by the presence of a GQG interruption in the typical (X-Y-Gly)n repeat compared to controls. Experimental solution structural data were collected using analytical ultracentrifugation and small angle X-ray and neutron scattering. As controls, we included two standard Pro-Hyp-Gly collagen peptides (POG)10-13, as well as three more peptides with diverse (X-Y-Gly)n sequences that represented other collagen features. These data were quantitatively compared with atomistic linear collagen models derived from crystal structures and 12,000 conformations obtained from molecular dynamics simulations. All four MBL peptides were bent to varying degrees up to 85o in the best-fit molecular dynamics models. The best-fit benchmark peptides (POG)n were more linear but exhibited a degree of conformational flexibility. The remaining three peptides showed mostly linear solution structures. In conclusion, the collagen helix is not strictly linear, the degree of flexibility in the triple helix depends on its sequence, and the triple helix with the GQG interruption showed a pronounced bend. The bend in MBL GQG peptides resembles the bend in the collagen of complement C1q and may be key for lectin pathway activation.


Asunto(s)
Colágeno , Activación de Complemento , Lectina de Unión a Manosa , Colágeno/química , Lectina de Unión a Manosa/química , Lectina de Unión a Manosa/metabolismo , Soluciones/química , Conformación Proteica , Fragmentos de Péptidos/química , Fragmentos de Péptidos/metabolismo , Relación Estructura-Actividad , Estabilidad Proteica , Dispersión del Ángulo Pequeño , Difracción de Neutrones , Ultracentrifugación , Simulación de Dinámica Molecular , Cristalografía por Rayos X , Docilidad
20.
Mini Rev Med Chem ; 23(10): 1090-1117, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36029080

RESUMEN

Selenium (Se), a semi-metallic element, has chemical properties similar to sulfur; however, it has comparatively low electronegativity as well as a large atomic radius than sulfur. These features bestow selenium-containing compounds with extraordinary reactivity, sensitivity, and potential for several applications like chemical alteration, protein engineering, chemical (semi)synthesis, etc. Organoselenium chemistry is emerging fastly, however, examples of effective incorporation of Se into the peptides are relatively scarce. Providentially, there has been a drastic interest in synthesizing and applying selenoproteins and selenium-containing peptides over the last few decades. In this minireview, the synthetic methodologies of selenium-containing peptides and a brief description of their chemistry and biological activities are summarized. These methodologies enable access to various natural and unnatural selenium-containing peptides that have been used in a range of applications, from modulating protein characteristics to structure-activity relationship (SAR) studies for applications in nutraceuticals and drug development. This review aims at the audience interested in learning about the synthesis as well as will open new dimensions for their future research by aiding in the design of biologically interesting selenium-containing peptides.


Asunto(s)
Péptidos , Compuestos de Selenio/síntesis química , Compuestos de Selenio/química , Péptidos/síntesis química , Péptidos/química , Humanos , Animales , Azufre/química , Soluciones/química
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