Phase-Separation Propensity of Non-ionic Amino Acids in Peptide-Based Complex Coacervation Systems

Uncovering the sequence-encoded molecular grammar that governs the liquid-liquid phase separation (LLPS) of proteins is a crucial issue to understand dynamic compartmentalization in living cells and the emergence of protocells. Here, we present a model LLPS system that is induced by electrostatic interactions between anionic nucleic acids and cationic oligolysine peptides modified with 12 different non-ionic amino acids, with the aim of creating an index of "phase-separation propensity" that represents the contribution of non-ionic amino acids to LLPS. Based on turbidimetric titrations and microscopic observations, the lower critical peptide concentrations where LLPS occurs (C_crit) were determined for each peptide. A correlation analysis between these values and known amino acid indices unexpectedly showed that eight non-ionic amino acids inhibit the generation of LLPS, whereby the extent of inhibition increases with increasing hydrophobicity of the amino acids. However, three aromatic amino acids deviate from this trend and rather markedly promote LLPS despite their high hydrophobicity. A comparison with double-stranded DNA and polyacrylic acid revealed that this is primarily due to interactions with DNA nucleobases. Our approach to quantify the contribution of non-ionic amino acids can be expected to help to provide a more accurate description and prediction of the LLPS propensity of peptides/proteins.

Strategy for Fast Decision on Material System Suitability for Continuous Crystallization Inside a Slug Flow Crystallizer

There is an increasing focus on two-phase flow in micro- or mini-structured apparatuses for various manufacturing and measurement instrumentation applications, including the field of crystallization as a separation technique. The slug flow pattern offers salient features for producing high-quality products, since narrow residence time distribution of liquid and solid phases, intensified mixing and heat exchange, and an enhanced particle suspension are achieved despite laminar flow conditions. Due to its unique features, the slug flow crystallizer (SFC) represents a promising concept for small-scale continuous crystallization achieving high-quality active pharmaceutical ingredients (API). Therefore, a time-efficient strategy is presented in this study to enable crystallization of a desired solid product in the SFC as quickly as possible and without much experimental effort. This strategy includes pre-selection of the solvent/solvent mixture using heuristics, verifying the slug flow stability in the apparatus by considering the static contact angle and dynamic flow behavior, and modeling the temperature-dependent solubility in the supposed material system using perturbed-chain statistical associating fluid theory (PC-SAFT). This strategy was successfully verified for the amino acids l-alanine and l-arginine and the API paracetamol for binary and ternary systems and, thus, represents a general approach for using different material systems in the SFC.

Investigating adsorption of model low-MW AOM components onto different types of activated carbon - influence of temperature and pH value

Low molecular weight algal organic matter (AOM), as a frequent water contaminant with poor coagulation efficiency, adversely affects the quality of produced water and serves as a source of potentially carcinogenic disinfection by-products. AOM removal from water is inevitable to eliminate the negative health and environmental impacts. This research evaluates the removal of arginine, phenylalanine and aspartic acid, which are amino acids abundant in AOM. Adsorption experiments were performed at 10, 18 and 25 °C and pH 5, 7 and 9 using two different activated carbons (FTL, PIC). Amino acids showed endothermic adsorption behaviour, with a higher removal at higher temperature. Higher temperature increased the diffusion of amino acid molecules, reduced the solution viscosity, or enhanced the hydrophobic interactions contributing to adsorption. The effect of temperature manifested differently during experiments depending on the chemical nature of the amino acids, the pH value and the surface properties of the carbon. Phenylalanine isotherms showed specific waves (Langmuir type 4). pH had a greater effect on arginine adsorption than did temperature. Aspartic acid isotherms exhibited a decrease in adsorption at higher pH values and higher temperatures. The principal mechanisms involved in amino acid adsorption were hydrophobic interactions, electrostatic interactions or hydrogen bonds.

Current knowledge in the field of algal organic matter adsorption onto activated carbon in drinking water treatment

The increasing occurrence of algal and cyanobacterial blooms and the related formation of algal organic matter (AOM) is a worldwide issue that endangers the quality of freshwater sources and affects water treatment processes. The associated problems involve the production of toxins or taste and odor compounds, increasing coagulant demand, inhibition of removal of other polluting compounds, and in many cases, AOM acts as a precursor of disinfection by-products. Previous research has shown that for sufficient AOM removal, the conventional drinking water treatment based on coagulation/flocculation must be often accompanied by additional polishing technologies such as adsorption onto activated carbon (AC). This state-of-the-art review is intended to serve as a summary of the most current research on the adsorption of AOM onto AC concerning drinking water treatment. It summarizes emerging trends in this field with an emphasis on the type of AOM compounds removed and on the adsorption mechanisms and influencing factors involved. Additionally, also the principles of competitive adsorption of AOM and other organic pollutants are elaborated. Further, this paper also synthesizes previous knowledge on combining AC adsorption with other treatment techniques for enhanced AOM removal in order to provide a practical resource for researchers, water treatment plant operators and engineers. Finally, research gaps regarding the AOM adsorption onto AC are identified, including, e.g., adsorption of AOM residuals recalcitrant to coagulation/flocculation, suitability of pre-oxidation of AOM prior to the AC adsorption, relationships between the solution properties and AOM adsorption behaviour, or AOM as a cause of competitive adsorption. Also, focus should be laid on continuous flow column experiments using water with multi-component composition, because these would greatly contribute to transferring the theoretical knowledge to practice.

Solubility Parameters of Amino Acids on Liquid-Liquid Phase Separation and Aggregation of Proteins

The solution properties of amino acids determine the folding, aggregation, and liquid–liquid phase separation (LLPS) behaviors of proteins. Various indices of amino acids, such as solubility, hydropathy, and conformational parameter, describe the behaviors of protein folding and solubility both in vitro and in vivo. However, understanding the propensity of LLPS and aggregation is difficult due to the multiple interactions among different amino acids. Here, the solubilities of aromatic amino acids (SAs) were investigated in solution containing 20 types of amino acids as amino acid solvents. The parameters of SAs in amino acid solvents (PSASs) were varied and dependent on the type of the solvent. Specifically, Tyr and Trp had the highest positive values while Glu and Asp had the lowest. The PSAS values represent soluble and insoluble interactions, which collectively are the driving force underlying the formation of droplets and aggregates. Interestingly, the PSAS of a soluble solvent reflected the affinity between amino acids and aromatic rings, while that of an insoluble solvent reflected the affinity between amino acids and water. These findings suggest that the PSAS can distinguish amino acids that contribute to droplet and aggregate formation, and provide a deeper understanding of LLPS and aggregation of proteins.

Buffers, Especially the Good Kind

Fifty-five years ago, Norman Good and colleagues authored a paper that fundamentally advanced wet biochemistry [Good, N. E., Winget, G. D., Winter, W., Connolly, T. N., Izawa, S., and Singh, R. M. M. (1966) Hydrogen ion buffers for biological research. Biochemistry 5, 467-477] and in doing so has amassed more than 2500 citations. They laid out the properties required for useful, biochemically relevant hydrogen-ion buffers and then synthesized and tested 10 of them. Soon after, these buffers became commercially available. Since then, most of us never gave them a second thought. We just use them. Here, I discuss some of the background regarding the genesis of "Good's buffers", make a few (disparaging) observations about the non-Good's buffer, Tris, and suggest that we synthesize new buffers by combining the ideas of Good et al. with results from the past 60 years of protein chemistry.

Preparation and Evaluation of Co-amorphous Formulations of Telmisartan-Amino Acids as a Potential Method for Solubility and Dissolution Enhancement

Telmisartan (TLM) is a potent antihypertensive drug with pH-dependent aqueous solubility. This work aimed to enhance the solubility and dissolution rate of TLM by the co-amorphous drug amino acid (AA) approach by combining TLM, with different types and ratios of AAs. The co-amorphous TLM-AA blends were prepared by freeze-drying and investigated for solid-state characteristics like the dissolution rate enhancement of TLM. Among the prepared co-amorphous formulations, TLM-arginine (ARG) exhibited the greatest enhancement in solubility with increasing the molar ratio of ARG. The TLM-ARG at 1:2 ratio showed about a 57-fold increase in solubility of TLM and the highest dissolution percentage in phosphate buffer (pH7.5) (100% in 20 minutes) compared to both crystalline TLM (20% in 60 min) and physical mixture. Powder XRD, DSC, FTIR analysis and SEM demonstrated the formation of amorphous form within the co-amorphous formulations. Only TLM:ARG (1:0.5) were stable at (40°C, 75% RH) for a minimum of 90 days. In conclusion, ARG was able to stabilize the amorphous form of TLM and enhances its aqueous solubility and dissolution. The 1:2 w/w ratio of TLM-ARG co-amorphous showed the best solubility and dissolution rate while the 1:0.5 w/w ratio showed the best stability.

Unravelling the nature of citric acid:L-arginine:water mixtures: the bifunctional role of water

The use of water as a component of deep eutectic systems (DES) has raised some questions regarding its influence on the nature of the mixture. Does it form a DES or an aqueous solution and what is the role of water? In this work, the nature of citric acid:l-arginine:water mixtures was explored through phase equilibria studies and spectroscopic analysis. In a first step, PC-SAFT was validated as a predictive tool to model the water influence on the solid liquid equilibria (SLE) of the DES reline using the individual-component approach. Hence, activity coefficients in the ternary systems citric acid:l-arginine:water and respective binary combinations were studied and compared using ePC-SAFT. It was observed that the water-free mixtures citric acid:l-arginine showed positive deviation from Raoult's law, while upon addition of water strong negative deviation from Raoult's law was found, yielding melting depressions around 100 K. Besides these strong interactions, pH was found to become acidic (pH = 3.5) upon water addition, which yields the formation of charged species ([H2Cit]- and [l-arg]+). Thus, the increased interactions between the molecules upon water addition might be caused by several mechanisms such as hydrogen bonding or ionic forces, both being induced by water. For further investigation, the liquid mixtures citric acid:l-arginine:water were studied by FTIR and NMR spectroscopy. FTIR spectra disproved a possible solubility enhancement caused by salt formation between citric acid and l-arginine, while NMR spectra supported the formation of a hydrogen bonding network different from the binary systems citric acid:water and l-arginine:water. Either being a DES or other type of non-ideal solution, the liquefaction of the studied systems is certainly caused by a water-mediator effect based on the formation of charged species and cross interactions between the mixture constituents.

Chirality-Dependent Amino Acid Modulation of RNA Folding

The preponderance of a specific d- or l-chirality in fats, sugars, amino acids, nucleic acids, and so on is ubiquitous in nature, yet the biological origin of such chiral dominance (i.e., with one enantiomer overwhelmingly present) remains an open question. One plausible proposal for the predominance of l-chirality in amino acids could be through evolutionary templating of chiral RNA-folding via chaperone activity. To help evaluate this possibility, single molecule fluorescence experiments have been performed that measure the chiral dependence of chaperone folding dynamics for the simple tetraloop-tetraloop receptor (TL-TLR) tertiary binding motif in the presence of a series of chiral amino acids. Specifically, d- vs l-arginine is found to accelerate the unfolding of this RNA motif in a chirally selective fashion, with temperature-dependent studies of the kinetics performed to extract free energy, enthalpy, and entropy landscapes for the underlying thermodynamics. Furthermore, all-atom molecular dynamics (MD) simulations are pursued to provide additional physical insight into this chiral sensitivity, which reveal enantiomer-specific sampling of nucleic acid surfaces by d- vs l-arginine and support a putative mechanism for chirally specific denaturation of RNA tertiary structure by arginine but not other amino acids.

Melting properties of amino acids and their solubility in water

The state-of-the-art unit operation for separation and purification of amino acids is still crystallization, which requires solubility data and melting properties of pure compounds. Since measuring solubility is time-consuming, prediction tools are desired. Further, melting properties are not yet available due to decomposition of amino acids upon slow heating. In this work, melting properties of twenty amino acids (except Met) were measured by Fast Scanning Calorimetry (FSC) with heating rates up to 20 000 K s⁻¹. PC-SAFT was used to predict interactions in amino acid + water systems. Additionally, solubility, pH, and PXRD was measured. By combining FSC and PC-SAFT, the solubility of 15 amino acids was successfully predicted in a wide temperature range in good agreement with the experimental data. Thus, this work provides melting properties of amino acids for the first time and highlights the usefulness of such data to predict material properties such as aqueous solubility of amino acids.

We report the melting properties of amino acids for the first time and highlight the usefulness of such data to predict material properties such as aqueous solubility of amino acids.

Thermodynamic Impact of Mineral Surfaces on Amino Acid Polymerization: Aspartate Dimerization on Goethite

This article presents a thermodynamic predictive scheme for amino acid polymerization in the presence of minerals as a function of various environmental parameters (pH, ionic strength, amino acid concentration, and the solid/water ratio) using l-aspartate (Asp) and goethite as a model combination. This prediction is enabled by the combination of the surface adsorption constants of amino acid and its polymer, determined from the extended triple layer model characterization of the corresponding experimental results, with the thermodynamic data of these organic compounds in water reported in the literature. Calculations for the Asp-goethite system showed that the goethite surface drastically shifts the Asp monomer-dipeptide equilibrium toward the dipeptide side; when the dimerization of 0.1 mM Asp was considered in the presence of 10 m² L^-1 of goethite, an Asp dipeptide concentration around 10⁵ times larger was computed to be thermodynamically attainable compared with that in the absence of goethite at acidic pH (4-5) and low ionic strength (0.1 mM NaCl). Under this condition, the dipeptide-to-monomer molecular ratio in the adsorbed state reached 20%. In contrast, no significant enhancement by goethite was predicted at alkaline pH (>8), where the electrostatic interactions of the goethite surface with Asp and Asp dipeptide are weak. Thus, mineral surfaces should have had a significant impact on the thermodynamics of prebiotic peptide bond formation on the early Earth, although the influences likely depended largely on the environmental conditions. Future experimental studies for various amino acid-mineral interactions using our proposed methodology will provide a quantitative constraint on favorable geochemical settings for the chemical evolution on Earth. This approach can also offer important clues for future exploration of extraterrestrial life.

New experimental melting properties as access for predicting amino-acid solubility

New experimental melting properties combined with PC-SAFT allow quantitative solubility predictions of amino acids in water.

Evidence for cooperative Na+ and Cl− binding by strongly hydrated l-proline

Strongly hydrated l-proline cooperatively binds Na⁺ and Cl⁻ ions in aqueous solution.

Modeling solubility and acid-base properties of some amino acids in aqueous NaCl and (CH3)4NCl aqueous solutions at different ionic strengths and temperatures

New potentiometric experiments have been performed in NaCl and in (CH3)4NCl media, to determine the protonation constants, the protonation enthalpy changes and the solubility of six natural α-amino acids, namely Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Serine (Ser) and Phenylalanine (Phe). The aim of the work is the rationalization of the protonation thermodynamics (log [Formula: see text], solubility and [Formula: see text]) in NaCl, determining recommended, tentative or provisional values in selected experimental conditions and to report, for the first time, data in a weak interacting medium, as (CH3)4NCl. Literature data analysis was performed selecting the most reliable values, analyzed together with new data here reported. Significant trends and similarities were observed in the behavior of the six amino acids, and in some cases it was possible to determine common parameters for the ionic strength and temperature dependence. In general, the first protonation step, relative to the amino group, is significantly exothermic (average value is [Formula: see text] = -44.5 ± 0.4 kJ mol(-1) at infinite dilution and T = 298.15 K), and the second, relative to the carboxylate group, is fairly close to zero ([Formula: see text] = -2.5 ± 1.6, same conditions). In both cases, the main contribution to the proton binding reaction is mainly entropic in nature. For phenylalanine and leucine, solubility measurements at different concentrations of supporting electrolyte allowed to determine total and specific solubility values, then used to obtain the Setschenow and the activity coefficients of all the species involved in the protonation equilibria. The values of the first protonation constant in (CH3)4NCl are lower than the corresponding values in NaCl, due to the weak interaction between the deprotonated amino group and (CH3)4N(+). In this light, differences between the protonation functions in NaCl and (CH3)4NCl were used for the quantification of the stability of the weak [(CH3)4N(+)-L(-)] complexes that resulted log K = -0.38 ± 0.07 as an average value for the six amino acids.

Pharmaceutical salts and cocrystals involving amino acids: a brief structural overview of the state-of-art

Salification of new drug substances in order to improve physico-chemical or solid-state properties (e.g. dissolution rate or solubility, appropriate workup process, storage for further industrial and marketing development) is a well-accepted procedure. Amino acids, like aspartic acid, lysine or arginine take a great part in this process and are implicated in several different formulations of therapeutic agent families, including antibiotics (amoxicillin from beta lactam class or cephalexin from cephalosporin class), NSAIDs (ketoprofen, ibuprofen and naproxen from profen family, acetylsalicylic acid) or antiarrhythmic agents (e.g. ajmaline). Even if more than a half of known pharmaceutical molecules possess a salifiable moiety, what can be done for new potential drug entity that cannot be improved by transformation into a salt? In this context, after a brief review of pharmaceutical salts on the market and the implication of amino acids in these formulations, we focus on the advantage of using amino acids even when the target compound is not salifiable by exploiting their zwitterionic potentialities for cocrystal edification. We summarize here a series of new examples coming from literature to support the advantages of broadening the application of amino acids in formulation for new drug substances improvement research for non-salifiable molecules.

Amino acids as promoieties in prodrug design and development

Prodrugs are biologically inactive agents that upon biotransformation in vivo result in active drug molecules. Since prodrugs might alter the tissue distribution, efficacy and the toxicity of the parent drug, prodrug design should be considered at the early stages of preclinical development. In this regard, natural and synthetic amino acids offer wide structural diversity and physicochemical properties. This review covers the use of amino acid prodrugs to improve poor solubility, poor permeability, sustained release, intravenous delivery, drug targeting, and metabolic stability of the parent drug. In addition, practical considerations and challenges associated with the development of amino acid prodrugs are also covered.

The energetics of organic synthesis inside and outside the cell

Thermodynamic modelling of organic synthesis has largely been focused on deep-sea hydrothermal systems. When seawater mixes with hydrothermal fluids, redox gradients are established that serve as potential energy sources for the formation of organic compounds and biomolecules from inorganic starting materials. This energetic drive, which varies substantially depending on the type of host rock, is present and available both for abiotic (outside the cell) and biotic (inside the cell) processes. Here, we review and interpret a library of theoretical studies that target organic synthesis energetics. The biogeochemical scenarios evaluated include those in present-day hydrothermal systems and in putative early Earth environments. It is consistently and repeatedly shown in these studies that the formation of relatively simple organic compounds and biomolecules can be energy-yielding (exergonic) at conditions that occur in hydrothermal systems. Expanding on our ability to calculate biomass synthesis energetics, we also present here a new approach for estimating the energetics of polymerization reactions, specifically those associated with polypeptide formation from the requisite amino acids.

The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins

A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a series of publications dedicated to the roles that different amino acid residues play in defining the phenomenon of protein intrinsic disorder. We start with proline because data suggests that of the 20 common amino acid residues, this one is the most disorder-promoting.

Eliminating tyrosine sequence variants in CHO cell lines producing recombinant monoclonal antibodies

Amino acid sequence variants are defined as unintended amino acid sequence changes that contribute to product variation with potential impact to product safety, immunogenicity, and efficacy. Therefore, it is important to understand the propensity for sequence variant (SV) formation during the production of recombinant proteins for therapeutic use. During the development of clinical therapeutic products, several monoclonal antibodies (mAbs) produced from Chinese Hamster Ovary (CHO) cells exhibited SVs at low levels (≤3%) in multiple locations throughout the mAbs. In these examples, the cell culture process depleted tyrosine, and the tyrosine residues in the recombinant mAbs were replaced with phenylalanine or histidine. In this work, it is demonstrated that tyrosine supplementation eliminated the tyrosine SVs, while early tyrosine starvation significantly increased the SV level in all mAbs tested. Additionally, it was determined that phenylalanine is the amino acid preferentially misincorporated in the absence of tyrosine over histidine, with no other amino acid misincorporated in the absence of tyrosine, phenylalanine, and histidine. The data support that the tyrosine SVs are due to mistranslation and not DNA mutation, most likely due to tRNA(Tyr) mischarging due to the structural similarities between tyrosine and phenylalanine.

On transversal hydrophobicity of some proteins and their modules

Hydrophobicity of proteins encoded in the genomes of diverse organisms was quantified using two novel concepts: (A) amino acid (AA) bulkiness-dependent hydrophobicity profiles and (B) spatial context of hydrophobicity distribution in AA triads. Both concepts were introduced into an algorithm that was used for extracting protein clusters from diverse genomic databases whose sequence attributes were similar to those in the multiple sequence alignment (MSA) of a given family of proteins. The sequences of the G protein-coupled receptors (GPCRs) encoded in different genomes were used as templates for testing the above concepts. The following sequence attributes were used for protein clustering: (A) sequence similarity scores (IDs); (B) amino acid composition (AAC); (C) hydrophobicity; (D) AA-bulkiness; and (E) alpha-helical propensity potentials. Diverse GPCRs display variable distributions of AA bulkiness-dependent buildups and declines in the hydrophobicity profiles that may be related to their function-dependent way of packing and allostery in the membrane. It is shown that intramolecular transversal nonbonded interactions between the TM segments in diverse GPCRs involve about 50% of hydrophobic atoms. Similar interaction networks exist between alpha-helices of tetratricopeptide (TPR) motifs-containing immunophilins and other proteins containing alpha-helical bundles.

Mutation of His465 alters the pH-dependent spectroscopic properties of Escherichia coli glutamate decarboxylase and broadens the range of its activity toward more alkaline pH

Glutamate decarboxylase (GadB) from Escherichia coli is a hexameric, pyridoxal 5'-phosphate-dependent enzyme catalyzing CO(2) release from the alpha-carboxyl group of L-glutamate to yield gamma-aminobutyrate. GadB exhibits an acidic pH optimum and undergoes a spectroscopically detectable and strongly cooperative pH-dependent conformational change involving at least six protons. Crystallographic studies showed that at mildly alkaline pH GadB is inactive because all active sites are locked by the C termini and that the 340 nm absorbance is an aldamine formed by the pyridoxal 5'-phosphate-Lys(276) Schiff base with the distal nitrogen of His(465), the penultimate residue in the GadB sequence. Herein we show that His(465) has a massive influence on the equilibrium between active and inactive forms, the former being favored when this residue is absent. His(465) contributes with n approximately 2.5 to the overall cooperativity of the system. The residual cooperativity (n approximately 3) is associated with the conformational changes still occurring at the N-terminal ends regardless of the mutation. His(465), dispensable for the cooperativity that affects enzyme activity, is essential to include the conformational change of the N termini into the cooperativity of the whole system. In the absence of His(465), a 330-nm absorbing species appears, with fluorescence emission spectra more complex than model compounds and consisting of two maxima at 390 and 510 nm. Because His(465) mutants are active at pH well above 5.7, they appear to be suitable for biotechnological applications.

Calculation of the aqueous thermodynamic properties of citric acid cycle intermediates and precursors and the estimation of high temperature and pressure equation of state parameters

The citric acid cycle (CAC) is the central pathway of energy transfer for many organisms, and understanding the origin of this pathway may provide insight into the origins of metabolism. In order to assess the thermodynamics of this key pathway for microorganisms that inhabit a wide variety of environments, especially those found in high temperature environments, we have calculated the properties and parameters for the revised Helgeson-Kirkham-Flowers equation of state for the major components of the CAC. While a significant amount of data is not available for many of the constituents of this fundamental pathway, methods exist that allow estimation of these missing data.