Quantitative, Diffusion NMR Based Analytical Tool To Distinguish Folded, Disordered, and Denatured Biomolecules

Translational Diffusion and Self-Association of an Intrinsically Disordered Protein κ-Casein Using NMR with Ultra-High Pulsed-Field Gradient and Time-Resolved FRET

Much attention has been given to studying the translational diffusion of globular proteins, whereas the translational diffusion of intrinsically disordered proteins (IDPs) is less studied. In this study, we investigate the translational diffusion and how it is affected by the self-association of an IDP, κ-casein, using pulsed-field gradient nuclear magnetic resonance and time-resolved Förster resonance energy transfer. Using the analysis of the shape of diffusion attenuation and the concentration dependence of κ-casein diffusion coefficients and intermolecular interactions, we demonstrate that κ-casein exhibits continuous self-association. When the volume fraction of κ-casein is below 0.08, we observe that κ-casein self-association results in a macroscopic phase separation upon storage at 4 °C. At κ-casein volume fractions above 0.08, self-association leads to the formation of labile gel-like networks without subsequent macroscopic phase separation. Unlike α-casein, which shows a strong concentration dependence and extensive gel-like network formation, only one-third of κ-casein molecules participate in the gel network at a time, resulting in a more dynamic and less extensive structure. These findings highlight the unique association properties of κ-casein, contributing to a better understanding of its behavior under various conditions and its potential role in casein micelle formation.

The Potent PHL4 Transcription Factor Effector Domain Contains Significant Disorder

The phosphate-starvation response transcription-factor protein family is essential to plant response to low-levels of phosphate. Proteins in this transcription factor (TF) family act by altering various gene expression levels, such as increasing levels of the acid phosphatase proteins which catalyze the conversion of inorganic phosphates to bio-available compounds. There are few structural characterizations of proteins in this TF family, none of which address the potent TF activation domains. The phosphate-starvation response-like protein-4 (PHL4) protein from this family has garnered interest due to the unusually high TF activation activity of the N-terminal domain. Here, we demonstrate using solution nuclear magnetic resonance (NMR) measurements that the PHL4 N-terminal activating TF effector domain is mainly an intrinsically disordered domain of over 200 residues, and that the C-terminal region of PHL4 is also disordered. Additionally, we present evidence from size-exclusion chromatography, diffusion NMR measurements, and a cross-linking assay suggesting full-length PHL4 forms a tetrameric assembly. Together, the data indicate the N- and C-terminal disordered domains in PHL4 flank a central folded region that likely forms the ordered oligomer of PHL4. This work provides a foundation for future studies detailing how the conformations and molecular motions of PHL4 change as it acts as a potent activator of gene expression in phosphate metabolism. Such a detailed mechanistic understanding of TF function will benefit genetic engineering efforts that take advantage of this activity to boost transcriptional activation of genes across different organisms.

Quantitative at-line monitoring of enzymatic hydrolysis using benchtop diffusion nuclear magnetic resonance spectroscopy

Benchtop diffusion nuclear magnetic resonance (NMR) spectroscopy was used to perform quantitative monitoring of enzymatic hydrolysis. The study aimed to test the feasibility of the technology to characterize enzymatic hydrolysis processes in real time. Diffusion ordered spectroscopy (DOSY) was used to measure the signal intensity and apparent self-diffusion constant of solubilized protein in hydrolysate. The NMR technique was tested on an enzymatic hydrolysis reaction of red cod, a lean white fish, by the endopeptidase alcalase at 50°C. Hydrolysate samples were manually transferred from the reaction vessel to the NMR equipment. Measurement time was approximately 3 min per time point. The signal intensity from the DOSY experiment was used to measure protein concentration and the apparent self-diffusion constant was converted into an average molecular weight and an estimated degree of hydrolysis. These values were plotted as a function of time and both the rate of solubilization and the rate of protein breakdown could be calculated. In addition to being rapid and noninvasive, DOSY using benchtop NMR spectroscopy has an advantage compared with other enzymatic hydrolysis characterization methods as it gives a direct measure of average protein size; many functional properties of proteins are strongly influenced by protein size. Therefore, a method to give protein concentration and average size in real time will allow operators to more tightly control production from enzymatic hydrolysis. Although only one type of material was tested, it is anticipated that the method should be applicable to a broad variety of enzymatic hydrolysis feedstocks.

In situ captured antibacterial action of membrane-incising peptide lamellae

Developing unique mechanisms of action are essential to combat the growing issue of antimicrobial resistance. Supramolecular assemblies combining the improved biostability of non-natural compounds with the complex membrane-attacking mechanisms of natural peptides are promising alternatives to conventional antibiotics. However, for such compounds the direct visual insight on antibacterial action is still lacking. Here we employ a design strategy focusing on an inducible assembly mechanism and utilized electron microscopy (EM) to follow the formation of supramolecular structures of lysine-rich heterochiral β3-peptides, termed lamellin-2K and lamellin-3K, triggered by bacterial cell surface lipopolysaccharides. Combined molecular dynamics simulations, EM and bacterial assays confirmed that the phosphate-induced conformational change on these lamellins led to the formation of striped lamellae capable of incising the cell envelope of Gram-negative bacteria thereby exerting antibacterial activity. Our findings also provide a mechanistic link for membrane-targeting agents depicting the antibiotic mechanism derived from the in-situ formation of active supramolecules.

Direct Assessment of Oligomerization of Chemically Modified Peptides and Proteins in Formulations using DLS and DOSY-NMR

PURPOSE

Protein higher order structure (HOS) including the oligomer distribution can be critical for efficacy, safety and stability of drug products (DP). Oligomerization is particularly relevant to chemically modified protein therapeutics that have an extended pharmacokinetics profile. Therefore, the direct assessment of protein oligomerization in drug formulation is desired for quality assurance and control.

METHODS

Here, two non-invasive methods, dynamic light scattering (DLS) and diffusion ordered spectroscopy (DOSY) NMR, were applied to measure translational diffusion coefficients (Ddls and Dnmr) of proteins in formulated drug products. The hydrodynamic molecular weights (MWhd), similar to hydrodynamic size, of protein therapeutics were derived based on a log(Ddls) vs log(MWhd) correlation model established using protein standards.

RESULTS

An exponent value of -0.40 ± 0.01 was established for DLS measured log(D) vs. log(MWhd) using protein standards and a theoretical exponent value of -0.6 was used for unstructured polyethylene glycol (PEG) chains. The analysis of DLS derived MWhd of the primary species showed the fatty acid linked glucagon-like peptide 1 (GLP-1) was in different oligomer states, but the fatty acid linked insulin and PEG linked proteins were in monomer states. Nevertheless, equilibrium and exchange between oligomers in formulations were universal and clearly evidenced from DOSY-NMR for all drugs except peginterferon alfa-2a.

CONCLUSION

The correlation models of log(D) vs. log(MWhd) could be a quick and efficient way to predict MWhd of protein, which directly informs on the state of protein folding and oligomerization in formulation.

Structural studies of protein-nucleic acid complexes: A brief overview of the selected techniques

Protein-nucleic acid complexes are involved in all vital processes, including replication, transcription, translation, regulation of gene expression and cell metabolism. Knowledge of the biological functions and molecular mechanisms beyond the activity of the macromolecular complexes can be determined from their tertiary structures. Undoubtably, performing structural studies of protein-nucleic acid complexes is challenging, mainly because these types of complexes are often unstable. In addition, their individual components may display extremely different surface charges, causing the complexes to precipitate at higher concentrations used in many structural studies. Due to the variety of protein-nucleic acid complexes and their different biophysical properties, no simple and universal guideline exists that helps scientists chose a method to successfully determine the structure of a specific protein-nucleic acid complex. In this review, we provide a summary of the following experimental methods, which can be applied to study the structures of protein-nucleic acid complexes: X-ray and neutron crystallography, nuclear magnetic resonance (NMR) spectroscopy, cryogenic electron microscopy (cryo-EM), atomic force microscopy (AFM), small angle scattering (SAS) methods, circular dichroism (CD) and infrared (IR) spectroscopy. Each method is discussed regarding its historical context, advancements over the past decades and recent years, and weaknesses and strengths. When a single method does not provide satisfactory data on the selected protein-nucleic acid complex, a combination of several methods should be considered as a hybrid approach; thus, specific structural problems can be solved when studying protein-nucleic acid complexes.

Recent advances in microfluidics-based bioNMR analysis

Nuclear magnetic resonance (NMR) has been used in a variety of fields due to its powerful analytical capability. To facilitate biochemical NMR (bioNMR) analysis for samples with a limited mass, a number of integrated systems have been developed by coupling microfluidics and NMR. However, there are few review papers that summarize the recent advances in the development of microfluidics-based NMR (μNMR) systems. Herein, we review the advancements in μNMR systems built on high-field commercial instruments and low-field compact platforms. Specifically, μNMR platforms with three types of typical microcoils settled in the high-field NMR instruments will be discussed, followed by summarizing compact NMR systems and their applications in biomedical point-of-care testing. Finally, a conclusion and future prospects in the field of μNMR were given.

Quantitative Interpretation of Protein Diffusion Coefficients in Mixed Protiated-Deuteriated Aqueous Solvents

Diffusion-ordered nuclear magnetic resonance (NMR) spectroscopy is widely used for the analysis of mixtures, dispersing the signals of different species in a two-dimensional spectrum according to their diffusion coefficients. However, interpretation of these diffusion coefficients is typically purely qualitative, for example, to deduce which species are bigger or smaller. In studies of proteins in solution, important questions concern the molecular weight of the proteins, the presence or absence of aggregation, and the degree of folding. The Stokes–Einstein Gierer–Wirtz estimation (SEGWE) method has been previously developed to simplify the complex relationship between diffusion coefficient and molecular mass, allowing the prediction of a species’ diffusion coefficient in a pure solvent based on its molecular weight. Here, we show that SEGWE can be extended to successfully predict both peptide and protein diffusion coefficients in mixed protiated–deuteriated water samples and, hence, distinguish effectively between globular and disordered proteins.

Monitoring Protein Global and Local Parameters in Unfolding and Binding Studies: The Extended Applicability of the Diffusion Coefficient─Molecular Size Empirical Relations

Protein unfolding and denaturation are main issues in biochemical and pharmaceutical research. Using a global parameter, the translational diffusion coefficient D, folded, unfolded, and intrinsically disordered proteins of a given molar mass M can be distinguished based on their distinct hydrodynamic properties. For broader applications, we provide generalized, PFG-NMR-based empirical D-M relations validated at different temperatures and ready to use with the corresponding corrections in different media. We demonstrate that these relations enable a more accurate molecular mass determination and show fewer potential errors than those of the common methods based on small-molecular diffusion standards. We monitor unfolding of three model proteins using 8 M urea and dimethyl sulfoxide (DMSO)-water mixtures as denaturing agents, highlighting the effect of disulfide bonds. Denaturation in 8 M urea is pH-dependent; in addition, for proteins with highly stable disulfide bonds, a reducing agent (TCEP) is required to achieve complete unfolding. Regarding the effect of local parameters, we show that at low DMSO concentrations─common conditions in pharmaceutical binding studies─the PFG-NMR-derived global parameters are not significantly affected. Still, the atomic environments can change, and the bound solvent molecule can inhibit the binding of a partner molecule. Using proteins with natural isotopic abundance, this effect can be proven by fast ¹H-¹⁵N 2D correlation spectra. Our results enable fast and easy estimation of protein molecular mass and the degree of folding in various media; moreover, the effect of the cosolvent on the atomic-level structure can be traced without the need of isotope labeling.

Pulse-field gradient nuclear magnetic resonance of protein translational diffusion from native to non-native states

Hydrodynamic radii (R_h -values) calculated from diffusion coefficients measured by pulse-field-gradient nuclear magnetic resonance are compared for folded and unfolded proteins. For native globular proteins, the R_h -values increase as a power of 0.35 with molecular size, close to the scaling factor of 0.33 predicted from polymer theory. Unfolded proteins were studied under four sets of conditions: in the absence of denaturants, in the presence of 6 M urea, in 95% dimethyl sulfoxide (DMSO), and in 40% hexafluoroisopropanol (HFIP). Scaling factors under all four unfolding conditions are similar (0.49-0.53) approaching the theoretical value of 0.60 for a fully unfolded random coil. Persistence lengths are also similar, except smaller in 95% DMSO, suggesting that the polypeptides are more disordered on a local scale with this solvent. Three of the proteins in our unfolded set have an asymmetric sequence-distribution of charged residues. While these proteins behave normally in water and 6 M urea, they give atypically low R_h -values in 40% HFIP and 95% DMSO suggesting they are forming electrostatic hairpins, favored by their asymmetric sequence charge distribution and the low dielectric constants of DMSO and HFIP. While diffusion-ordered NMR spectroscopy can separate small molecules, we show a number of factors combine to make protein-sized molecules much more difficult to resolve in mixtures. Finally, we look at the temperature dependence of apparent diffusion coefficients. Small molecules show a linear temperature response, while large proteins show abnormally large apparent diffusion coefficients at high temperatures due to convection, suggesting diffusion reference standards are only useful near 25°C.

Characterization of Polymer Molecular Weight Distribution by NMR Diffusometry: Experimental Criteria and Findings

NMR diffusometry finds useful applications in characterizing molecular weight (M) and molecular weight distribution (MWD) for polymers due to its unique advantages in generic detection, chemical selectivity, and quantitation. Here, we present a fundamental study to explore how the condition of diffusion measurement impacts the determined MWD. We use the critical dilute concentration C_dilute^* to explicitly delineate the boundary of the sufficiently dilute condition, below which chain interactions have a negligible impact on polymer diffusion. We present solid evidence to validate the postulated theory that links C_dilute^* to molecular weight, polydispersity, and chain conformation. Quantitative analysis reveals the consequence of violating the sufficiently dilute condition with M/MWD characterization. These findings provide useful guidance for M/MWD characterization by NMR diffusion and help to rationalize the data disparity that exists in the literature. The results further provide new insights into the interplay between chain conformations and diffusion for globular structure, such as proteins, and provide a different approach toward characterizing polymer architecture and molecular weight.

Investigating thermal stability based on the structural changes of lactase enzyme by several orthogonal methods

Thermal stability of lactase (β-galactosidase) enzyme has been studied by a variety of physico-chemical methods. β-galactosidase is the main active ingredient of medications for lactose intolerance. It is typically produced industrially by the Aspergillus oryzae filamentous fungus. Lactase was used as a model to help understand thermal stability of enzyme-type biopharmaceuticals. Enzyme activity (hydrolyzation of lactose) of β-galactosidase was determined after storing the solid enzyme substance at various temperatures. For a better understanding of the relationship between structure and activity changes we determined the mass and size of the molecules with gel electrophoresis and dynamic light scattering and detected aggregation processes. A bottom-up proteomic procedure was used to determine the primary amino acid sequence and to investigate changes in the N-glycosylation pattern of the protein. NMR and CD spectroscopic methods were used to observe changes in higher order structures and to reveal relationships between structural and functional changes.

Molar mass effect in food and health

It is demanded to supply foods with good quality for all the humans. With the advent of aging society, palatable and healthy foods are required to improve the quality of life and reduce the burden of finance for medical expenditure. Food hydrocolloids can contribute to this demand by versatile functions such as thickening, gelling, stabilising, and emulsifying, controlling texture and flavour release in food processing. Molar mass effects on viscosity and diffusion in liquid foods, and on mechanical and other physical properties of solid and semi-solid foods and films are overviewed. In these functions, the molar mass is one of the key factors, and therefore, the effects of molar mass on various health problems related to noncommunicable diseases or symptoms such as cancer, hyperlipidemia, hyperglycemia, constipation, high blood pressure, knee pain, osteoporosis, cystic fibrosis and dysphagia are described. Understanding these problems only from the viewpoint of molar mass is limited since other structural characteristics, conformation, branching, blockiness in copolymers such as pectin and alginate, degree of substitution as well as the position of the substituents are sometimes the determining factor rather than the molar mass. Nevertheless, comparison of different behaviours and functions in different polymers from the viewpoint of molar mass is expected to be useful to find a common characteristics, which may be helpful to understand the mechanism in other problems.

Curing Behaviors of Alkynyl-Terminated Copolyether with Glycidyl Azide Polymer in Energetic Plasticizers

Alkynyl-terminated polyethylene oxide−tetrahydrofuran (ATPET) and glycidyl azide polymer (GAP) could be linked through click-chemistry between the alkynyl and azide, and the product may serve a binder for solid propellants. The effects of the energetic plasticizers A3 [1:1 mixture of bis-(2,2-dinitropropy) acetal (BDNPA) and bis-(2,2-dinitropropyl) formal(BDNPN)] and Bu-NENA [N-butyl-N-(2nitroxyethyl) nitramine] on the curing reaction between ATPET and GAP have been studied. A diffusion-ordered nuclear magnetic resonance spectroscopy (DOSY-NMR) approach has been used to monitor the change in the diffusion coefficient of cross-linked polytriazole polyethylene oxide−tetrahydrofuran (PTPET). The change in the diffusion coefficient of PTPET with A3 plasticizer is significantly higher than that of PTPET with Bu-NENA. Viscosity analysis further highlighted the difference between A3 and Bu-NENA in the curing process—the curing curve of PTPET (A3) with time can be divided into two stages, with an inflection point being observed on the fourth day. For PTPET (Bu-NENA), in contrast, only one stage is seen. The above methods, together with gel permeation chromatography (GPC) analysis, revealed distinct effects of A3 and Bu-NENA on the curing process of PTPET. X-ray Photoelectron Spectroscopy (XPS) analysis showed that Bu-NENA has little effect on the valence oxidation of copper in the catalyst. Thermogravimetric (TG) analysis indicated that Bu-NENA helps to improve the thermal stability of the catalyst. After analysis of several possible factors by means of XPS, modeling with Material Studio and TG, the formation of molecular cages between Bu-NENA and copper is considered to be the reason for the above differences. In this article, GAP (Mn = 4000 g/mol) was used to replace GAP (Mn = 427 g/mol) to successfully synthesize the PTPET elastomer with Bu-NENA plasticizer. Mechanical data measured for the PTPET (Bu-NENA) sample included ε = 34.26 ± 2.98%, and σ = 0.198 ± 0.015 MPa.

The interpretation of small molecule diffusion coefficients: Quantitative use of diffusion-ordered NMR spectroscopy

Measuring accurate molecular self-diffusion coefficients, D, by nuclear magnetic resonance (NMR) techniques has become routine as hardware, software and experimental methodologies have all improved. However, the quantitative interpretation of such data remains difficult, particularly for small molecules. This review article first provides a description of, and explanation for, the failure of the Stokes-Einstein equation to accurately predict small molecule diffusion coefficients, before moving on to three broadly complementary methods for their quantitative interpretation. Two are based on power laws, but differ in the nature of the reference molecules used. The third addresses the uncertainties in the Stokes-Einstein equation directly. For all three methods, a wide range of examples are used to show the range of chemistry to which diffusion NMR can be applied, and how best to implement the different methods to obtain quantitative information from the chemical systems studied.

Anionic food color tartrazine enhances antibacterial efficacy of histatin-derived peptide DHVAR4 by fine-tuning its membrane activity

Here it is demonstrated how some anionic food additives commonly used in our diet, such as tartrazine (TZ), bind to DHVAR4, an antimicrobial peptide (AMP) derived from oral host defense peptides, resulting in significantly fostered toxic activity against both Gram-positive and Gram-negative bacteria, but not against mammalian cells. Biophysical studies on the DHVAR4-TZ interaction indicate that initially large, positively charged aggregates are formed, but in the presence of lipid bilayers, they rather associate with the membrane surface. In contrast to synergistic effects observed for mixed antibacterial compounds, this is a principally different mechanism, where TZ directly acts on the membrane-associated AMP promoting its biologically active helical conformation. Model vesicle studies show that compared to dye-free DHVAR4, peptide-TZ complexes are more prone to form H-bonds with the phosphate ester moiety of the bilayer head-group region resulting in more controlled bilayer fusion mechanism and concerted severe cell damage. AMPs are considered as promising compounds to combat formidable antibiotic-resistant bacterial infections; however, we know very little on their in vivo actions, especially on how they interact with other chemical agents. The current example illustrates how food dyes can modulate AMP activity, which is hoped to inspire improved therapies against microbial infections in the alimentary tract. Results also imply that the structure and function of natural AMPs could be manipulated by small compounds, which may also offer a new strategic concept for the future design of peptide-based antimicrobials.

Peptide-bicelle interaction: Following variations in size and morphology by a combined NMR-SAXS approach

Changes in membrane properties occurring upon protein interaction are key questions in understanding membrane protein function. To report on the occurring size and shape variation we present here a combined NMR-SAXS method performed under physiological conditions using the same samples, enabling determination of a global parameter, the hydration radius (r_H) and estimating the bicelle shape. We use zwitterionic (DMPC/DHPC) and negatively charged (DMPC/DHPC/DMPG) bicelles and investigate the interaction with model transmembrane and surface active peptides (KALP23 and melittin). ¹H NMR measurements based mostly on the translational diffusion coefficient D determination are used to characterize cmc values of DHPC micelles under the investigated conditions, to describe DHPC distribution with exact determination of the q (long chain/short chain) lipid ratio, to estimate aggregation numbers and effective r_H values. The scattering curve is used to fit a lenticular core-shell model enabling us to describe the bicelle shape in terms of ellipsoidal axis length parameters. For all studied systems formation of oblate ellipsoids is found. Even though the r_G/r_H ratio would be an elegant way to characterize shape variations, we show that changes occurring upon peptide-bicelle interaction in the "effective" size and in the measure on the anisometry - morphology - of the objects can be described by using r_H and the simplistic ellipsoidal core-shell model. While the influence of the transmembrane KALP peptide is significant, effects upon addition of surface active melittin peptide seem negligible. This synergy of techniques under controlled conditions can provide information about bicellar shape modulation occurring during peptide-bicelle interactions.

Quo Vadis qNMR?

The quantification of a drug, its impurities, and e.g. components of a mixture has become routine in NMR laboratories and many applications have been described in the literature. However, besides simply using 1D ¹H or ¹³C NMR, a number of more advanced methods has been developed and used in the past. Here, we want to describe the applicability of nuclei beyond the classical ones ¹H and ¹³C. Mixtures can be characterized much better by applying various chemometric methods and separating the signals of mixture components can be achieved by DOSY experiments. All these methods contribute to the platform of qNMR methods and extend the possibilities of NMR for quantification and quality evaluation of drugs, excipients, polymers, and plant extracts. However, for quantification purposes, validation is always an issue and it is necessary to think about taking NMR related measures which might be different from the ones considered for chromatographic methods.

Translational diffusion of unfolded and intrinsically disordered proteins

Translational (or self-diffusion) coefficient in dilute solution is inversely proportional to the size of a diffusing molecule, and hence self-diffusion coefficient measurements have been applied to determine the effective hydrodynamic radii for a range of native and nonnative protein conformations. In particular, translational diffusion coefficient measurements are useful to estimate the hydrodynamic radius of natively (or intrinsically) disordered proteins in solution, and, thereby, probe the compactness of a protein as well as its change when environmental parameters such as temperature, solution pH, or protein concentration are varied. The situation becomes more complicated in concentrated solutions. In this review, we discuss the translational diffusion of disordered proteins in dilute and crowded solutions, focusing primarily on the information provided by pulsed-field gradient NMR technique, and draw analogies to well-structured globular proteins and synthetic polymers.