Differences In Conformational Stability Research Articles

Enhanced Stability Differentiation of Therapeutic Polyclonal Antibodies with All Ion Unfolding-Ion Mobility-Mass Spectrometry.

Compared with monoclonal antibodies, polyclonal antibodies (pAbs) have rather significant characteristics, including lower cost, shorter production cycle, and higher affinity. Therefore, to facilitate their applications in clinic, it is equally critical to comprehensively characterize the conformational stabilities of pAb at the molecular weight-resolved scale, which is technically challenging due to the lack of an effective analytical tool capable of simultaneously providing both stability and molecular weight information within an acceptable error range. Ion mobility-mass spectrometry (IM-MS) has grown as an alternative to rapidly assess protein conformational stability with accurate molecular weight information maintained, especially when equipped with a collision-induced unfolding (CIU) regime. Dynamic and transient conformational intermediates can be captured with the CIU-IM-MS technique, adding to traditional static structural measurements with collisional cross section. Most CIU-IM-MS-centered protocols are focusing on the application to isolated, targeted protein ions, namely, analyzing one single charge state at one time, limiting its analytical throughput and speed. In this study, we employed an enhanced unfolding regime, all ion unfolding (AIU), capable of the simultaneous operation of numerous ions at a time during stepped unfolding processes to analyze pAb. Results show that AIU can quantitatively characterize the subtle differences in conformational stability among four structurally similar pAbs with improved resolving capability by around a 2-4-fold increment in both stability and structure differentiating parameters. Besides, AIU also benefits from considerably saved time cost and improved spectrum quality with an elevated signal-to-noise ratio.

Determining the Conformational Stability of a Protein from Urea and Thermal Unfolding Curves

This article contains protocols for determining the conformational stability of a globular protein from either urea or thermal unfolding curves. Circular dichroism is the optical spectroscopic technique most commonly used to monitor protein unfolding. These protocols describe how to analyze data from an unfolding curve to obtain the thermodynamic parameters necessary to calculate conformational stability, and how to determine differences in stability between protein variants. Curr. Protoc. Protein Sci. 71:28.4.1-28.4.14. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Determining protein conformational stability from urea-induced unfolding curves Support Protocol 1: Preparing a urea stock solution Support Protocol 2: Analyzing urea unfolding curves Basic Protocol 2: Determining the conformational stability of a protein from thermal unfolding curves Support Protocol 3: Analyzing thermal unfolding curves Support Protocol 4: Determining differences in conformational stability for protein variants.

Understanding how natural sequence variation in serum albumin proteins affects conformational stability and protein adsorption

Serum albumins are evolutionary conserved proteins that are found in many animal species, and purified forms are widely used in biotechnology applications, such as components within surface passivation coatings and drug delivery systems. As such, there has long been interest in studying how serum albumins adsorb onto solid supports, although existing studies are limited to one or two species. Herein, we comprehensively investigated three serum albumins of bovine (BSA), human (HSA), and rat (RSA) origin, and discovered striking differences in their conformational stabilities and adsorption properties. Together with bioinformatics analysis, dynamic light scattering (DLS) and circular dichroism (CD) spectroscopy measurements revealed that the proteins form different types of macromolecular assemblies in solution. BSA and HSA existed as individual monomers while RSA formed multimers, and each protein exhibited sequence-dependent variations in conformational stability as well. Quartz crystal microbalance-dissipation (QCM-D) and localized surface plasmon resonance (LSPR) experiments further showed that BSA and HSA proteins adsorb to form well-packed adlayers, and the extent of protein uptake and spreading depended on their unique conformational stabilities. Conversely, RSA adsorption resulted in sparse adlayers and appreciably less spreading of the adsorbed multimers, as confirmed by attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy experiments. Together, our findings demonstrate that significant differences in conformational stability and adsorption behavior exist even between evolutionary conserved serum albumins with high sequence and structural similarity and illustrate how rational engineering of protein structures and stabilities, guided by insights from nature, might be useful to design protein-based coatings for various biointerfacial science applications.

Differences in conformational stability of the two alpha domains of the disease-associated and non-disease-associated subtypes of HLA-B27

The MHC Class I molecule, HLA-B27, is strongly linked with development of the inflammatory arthritic disease, ankylosing spondylitis (AS); whereas the B*2705 subtype shows strong association, B*2709 is not associated with disease, even though the two subtypes differ in only a single residue at position 116. Currently, attention is focused on the misfolding propensities of these two subtypes, including studies of disulfide-linked dimers and non-covalently formed high molecular weight (HMW) aggregates. Using mutants retaining only a single cysteine at positions C67 or C164, and using a cysteine-reactive, environment-sensitive, fluorescence probe (acrylodan), we find that within the same overall population of identical single-cysteine HLA-B27 molecules, there exist sub-populations which (a) possess free cysteines which react with acrylodan, (b) form disulfide-linked dimers, and (c) form HMW aggregates. Further, using acrylodan fluorescence, we find (d) that the α1 and α2 domains unfold independently of each other in HMW aggregates, (e) that these two domains of B*2709 are less stable to chemical and thermal denaturation than the corresponding domains of B*2705, suggesting easier clearance of misfolded molecules in the former, and (f) C67 is much more exposed in B*2705 than in B*2709, which could potentially explain how B*2705 more easily forms C67-mediated disulfide-bonded dimers.

Conformational Stability of Mammalian Prion Protein Amyloid Fibrils Is Dictated by a Packing Polymorphism within the Core Region

Mammalian prion strains are believed to arise from the propagation of distinct conformations of the misfolded prion protein PrP(Sc). One key operational parameter used to define differences between strains has been conformational stability of PrP(Sc) as defined by resistance to thermal and/or chemical denaturation. However, the structural basis of these stability differences is unknown. To bridge this gap, we have generated two strains of recombinant human prion protein amyloid fibrils that show dramatic differences in conformational stability and have characterized them by a number of biophysical methods. Backbone amide hydrogen/deuterium exchange experiments revealed that, in sharp contrast to previously studied strains of infectious amyloid formed from the yeast prion protein Sup35, differences in β-sheet core size do not underlie differences in conformational stability between strains of mammalian prion protein amyloid. Instead, these stability differences appear to be dictated by distinct packing arrangements (i.e. steric zipper interfaces) within the amyloid core, as indicated by distinct x-ray fiber diffraction patterns and large strain-dependent differences in hydrogen/deuterium exchange kinetics for histidine side chains within the core region. Although this study was limited to synthetic prion protein amyloid fibrils, a similar structural basis for strain-dependent conformational stability may apply to brain-derived PrP(Sc), especially because large strain-specific differences in PrP(Sc) stability are often observed despite a similar size of the PrP(Sc) core region.

The challenge of improved secretory production of active pharmaceutical ingredients in Saccharomyces cerevisiae: A case study on human insulin analogs

The yeast Saccharomyces cerevisiae has widely been used as a host for the production of heterologous proteins. Great attention has been put on improved secretory production of active pharmaceutical ingredients, and the secretory pathway of this eukaryotic host has been the playground of diverse strain engineering studies, aiming at enhanced cellular capacities for folding and trafficking of the target proteins. However, the cellular quality assessment for secretory proteins remains mostly unpredictable, and different target proteins often do not picture similar secretion yields, underlining the dependency of efficient secretion on the physicochemical properties of the protein of interest. In this study, two human insulin analog precursors (IAPs) with minor differences in their amino acid sequences were used as model secretory proteins. No differences between cells expressing these two proteins were found in the IAP transcript levels, gene copy numbers, or intra-cellularly accumulated proteins, yet a more than sevenfold difference in their secretion yields was found. Physiological characterization of cells expressing these proteins in batch processes revealed no significant difference in their specific growth rate, but an altered overflow metabolism. Global transcriptome analysis carried out in chemostat experiments pinpointed distinct steps during the protein maturation pathway to be differentially regulated and indicated an increased degradation of the IAP with the low secretion yield. In silico protein structure modeling of the IAPs suggested a difference in conformational stability, induced by the amino acid substitution, which most likely resulted in disparity in trafficking through the secretory pathway and thus a large difference in secretion yields.

Excipient exchange in the comparison of preparations of the same biologic made by different manufacturing processes: An exploratory study with recombinant human growth hormone (rhGH)

Demonstrations of bio-similarity between subsequent entry (follow-on) biologics and innovator’s formulated drug products may depend upon methods that either remove excipients completely or allow the exchange of excipients to give equivalent formulations. Excipient exchange through dialysis is perhaps the simplest of such methods but its use has been hotly debated. This debate, in the absence of published data, has relied largely on theoretical considerations. This study presents data that indicate that excipient exchange can allow comparisons of different formulations of the same therapeutic protein. The use of excipient exchange to and from one concentration of mannitol to another or to a mixture of glycine and mannitol was reproducibly demonstrated for recombinant human growth hormone (rhGH). We show that marketed rhGH products from several different manufacturers exhibit differences in conformational stability when compared directly. These differences, however, are shown to be the result of differences in formulation rather than in the drug substance itself and were removed through excipient exchange. The data presented, therefore, also indicate that failure to assure a common excipient background can lead to erroneous conclusions about the similarities and differences in the physico-chemical properties of two preparations of the same therapeutic protein made by different manufacturing processes.

Effects of Fish Heme Protein Structure and Lipid Substrate Composition on Hemoglobin-Mediated Lipid Oxidation

Hemoglobin (Hb) promoted lipid oxidation more effectively in washed tilapia as compared to washed cod in spite of a 2.8-fold higher polyenoic index in the washed cod. This suggested that increasing the fatty acid unsaturation of the substrate did not accelerate the onset of lipid oxidation. Substantial phospholipid hydrolysis in the washed cod was observed, which has the potential to inhibit lipid oxidation. MetHb formation and lipid oxidation occurred more rapidly at pH 6.3 as compared to pH 7.4. Trout Hb autoxidized faster and was a better promoter of lipid oxidation as compared to tilapia Hb. The greater ability of trout Hb to promote lipid oxidation was attributed in part to its lower conformational and structural stability based on secondary and tertiary structure, acid-induced unfolding, and thermal aggregation measurements. It is suggested that the structural instability and lipid oxidation capacity of trout Hb were at least partly due to low hemin affinity. Trout and tilapia Hb were equivalent in their ability to cause lipid oxidation in washed cod muscle heated to 80 degrees C. Apparently, these high temperatures denature both trout and tilapia Hb to such an extent that any differences in conformational stability observed at lower temperatures were negated.

Site-specific Conformational Studies of Prion Protein (PrP) Amyloid Fibrils Revealed Two Cooperative Folding Domains within Amyloid Structure

Despite the ability of most proteins to form amyloid, very little is know about amyloid fibril structures and the factors that govern their stability. Using amyloid fibrils produced from full-length prion protein (PrP), we describe a reliable approach for determining both site-specific and global conformational stability of the fibrillar form. To measure site-specific stability, we produced six variants of PrP by replacing the residues at positions 88, 98, 127, 144, 196, and 230 with cysteine, labeled the new cysteines with the fluorescent dye acrylodan, and investigated their conformational status within the amyloid form in guanidine hydrochloride-induced denaturation experiments. We found that the fibrils labeled at positions 127, 144, 196, and 230 displayed cooperative unfolding and showed a very high C1/2 value similar to that observed for the global unfolding of the amyloid structure. The unfolding at residue 98 was also cooperative; however, it showed a C1/2 value substantially lower than that of global unfolding, whereas the unfolding of fibrils labeled at residue 88 was non-cooperative. These data illustrate that there are at least two independent cooperative folding domains within the amyloid structure of the full-length PrP. In addition, kinetic experiments revealed only a partial overlap between the region that constituted the fibrillar cross-beta core and the regions that were involved in nucleation. This result illustrates that separate PrP regions accounted for the nucleation and for the formation of the conformationally most stable fibrillar core.

Amino-terminal Domain Stability Mediates Apolipoprotein E Aggregation into Neurotoxic Fibrils

The three isoforms of apolipoprotein (apo) E are strongly associated with different risks for Alzheimer's disease: apoE4 > apoE3 > apoE2. Here, we show at physiological salt concentrations and pH that native tetramers of apoE form soluble aggregates in vitro that bind the amyloid dyes thioflavin T and Congo red. However, unlike classic amyloid fibrils, the aggregates adopt an irregular protofilament-like morphology and are seemingly highly α-helical. The aggregates formed at substantially different rates (apoE4 > apoE3 > apoE2) and were significantly more toxic to cultured neuronal cells than the tetramer. Since the three isoforms have large differences in conformational stability that can influence aggregation and amyloid pathways, we tested the effects of mutations that increased or decreased stability. Decreasing the conformational stability of the amino-terminal domain of apoE increased aggregation rates and vice versa. Our findings provide a new perspective for an isoform-specific pathogenic role for apoE aggregation in which differences in the conformational stability of the amino-terminal domain mediate neurodegeneration.

Differences in conformational stability of barley alpha-amylase isozymes 1 and 2. Role of charged groups and isozyme 2 specific salt-bridges

Abstract Barley alpha-amylase isozymes 1 (AMY1) and 2 (AMY2) have 80% sequence identity but possess different physico-chemical properties. By incubation in the range 37–85 °C T50 is 75.2 °C of AMY1 and 79.2 °C of AMY2. While AMY2 is also most stable in urea at pH 6.7, [urea]50 being 8.2 M compared to 7.9 M for AMY1, AMY1 has highest stability in urea below pH 6 or in the presence of NaCl. Moreover AMY1 is most stable in guanidinium chloride. Charge screening thus destabilises AMY2 but stabilises AMY1. Isozyme sequence comparison suggests that AMY1 lacks four of the 20 salt-bridges identified in the crystal structure of AMY2. The four residues that differ comprise Lys67AMY2 and Asp267AMY2, forming salt-bridges on the surface of the catalytic (β/α)8-barrel (domain A), and Glu96AMY2 and His344AMY2 that participate in charged networks between domain A and the small domain B and the C-terminal domain, respectively. Four corresponding AMY2 mimics A68K; D97E; Q269D; N346H were made in AMY1 by site-directed mutagenesis. While D97E and Q269D have slightly improved stability compared to AMY1 wild-type, N346H and, under certain conditions, A68K are destabilised. The four mutants show 22–176% activity (kcat/Km) toward 2-chloro-4-nitrophenol β- d -maltoheptaoside and amylose DP17 and 43–117% activity for insoluble starch.

Role of entropy in protein thermostability: folding kinetics of a hyperthermophilic cold shock protein at high temperatures using 19F NMR.

We used (19)F NMR to extend the temperature range accessible to detailed kinetic and equilibrium studies of a hyperthermophilic protein. Employing an optimized incorporation strategy, the small cold shock protein from the bacterium Thermotoga maritima (TmCsp) was labeled with 5-fluorotryptophan. Although chaotropically induced unfolding transitions revealed a significant decrease in the stabilization free energy upon fluorine labeling, the protein's kinetic folding mechanism is conserved. Temperature- and guanidinium chloride-dependent equilibrium unfolding transitions monitored by (19)F NMR agree well with the results from optical spectroscopy, and provide a stringent test of the two-state folding character of TmCsp. Folding and unfolding rate constants at high temperatures were determined from the (19)F NMR spectra close to the midpoint of thermal unfolding by global line shape analysis. In combination with results from stopped-flow experiments at lower temperatures, they show that the folding rate constant of TmCsp and its temperature dependence closely resemble those of its mesophilic homologue from Bacillus subtilis, BsCspB. However, the unfolding rate constant of TmCsp is two orders of magnitude lower over the entire temperature range that was investigated. Consequently, the difference in conformational stability between the two proteins is solely due to the unfolding rate constant over a wide temperature range. A thermodynamic analysis points to an important role of entropic factors in the stabilization of TmCsp relative to its mesophilic homologues.

Fatty acid-binding proteins of nervous tissue.

Fatty acid-binding proteins (FABPs) are cytosolic 14-15 kDa proteins, which are supposed to be involved in fatty acid (FA) uptake, transport, and targeting. They may modulate FA concentration and in this way influence function of enzymes, membranes, ion channels and receptors, and gene expression and cellular growth and differentiation. Nine FABP types can be discerned with a specific tissue distribution. In spite of 30-70% amino acid sequence identity, they have a similar tertiary, beta-clam structure in which the FA is bound. Nervous tissue contains four FABP types with a distinct spatio-temporal distribution. Myelin (M)-FABP is only present in the peripheral nerves, brain (B)-FABP and epidermal (E)-FABP mainly in glial cells and neurons, respectively of pre- and perinatal brain, and heart (H)-FABP in adult brain. Possible functions of FABPs in the nervous system are discussed. Binding studies with a range of physiological FA showed no large differences between recombinant proteins of the four human FABP types in binding specificity and affinity, also not for polyunsaturated FA (PUFA). The transfer of FA from fixed liposomes to mitochondria was similarly promoted by the four types. A marked difference in conformational stability was observed with H-FABP > B-FABP > M-FABP > E-FABP. Surface epitopes of H-FABP showed reaction with anti-B-FABP antibodies, but no other cross-reactivity of FABP type and heterologous antibodies was observed. The functional significance of the distinct spatio-temporal pattern of the four FABP types remains to be elucidated.

Energetic Implications for Protein Phosphorylation: CONFORMATIONAL STABILITY OF HPr VARIANTS THAT MIMIC PHOSPHORYLATED FORMS

The HPr protein from Bacillus subtilis is a key protein in the phosphoenolpyruvate-sugar transport system. HPr has two biological phosphorylation sites. The active site histidine is transiently phosphorylated in the phosphotransferase reaction while phosphorylation of serine 46 diminishes the activity of HPr. Here, we use protein engineering and equilibrium protein folding experiments to determine if the two phosphorylation events are energetically coupled. Our approach is to use structural mimics of the two phosphorylated forms of HPr, where histidine 15 is replaced by a negatively charged glutamate and serine 46 is changed to an aspartate, both alone and in combination. The thermodynamic analysis of the differences in conformational stability between the single and double mutants shows that the two phosphorylation sites are not energetically coupled in the HPr protein. We also show that single mutants of the active site histidine residue can have dramatic effects on the conformational stability of HPr. Combined with structural information, the method employed here will be of general use in unraveling the biological effects of phosphorylation on protein activity.

The thermal stability of the tryptic fragment of bovine microsomal cytochrome b5 and a variant containing six additional residues

Thermally induced denaturation has been measured for both oxidised and reduced forms of the tryptic fragment or bovine microsomal cytochrome b 5 using spectrophotometric methods. In the oxidised state, the tryptic fragment of cytochrome b 5 (Ala 7-Lys 90) denatures in a single cooperative transition with a midpoint temperature ( T m) of ∼ 67°C (pH 7.0). The reduced form of the tryptic fragment of cytochrome b 5 shows a higher transition temperature of ∼ 73°C at pH 7.0 and this is reflected in the values of Δ H m, Δ S m, and Δ(Δ G) of ∼ 310kJ · mol −1, 900J · mol −1 · K −1 and 5 kJ · mol −1. Increased thermal stability is demonstrated for a variant protein that contains the first 90 amino acid residues of cytochrome b 5. These novel increases in stability are observed in both redox states and result from the presence of six additional residues at the amino-terminus. The two forms of cytochrome b 5 do not differ significantly in structure with the results suggesting that the reorganisation energy (λ) of the variant protein, as measured indirectly from redox-linked differences in conformational stability, is small. Consequently the reported subtle differences in reactivity between variants of cytochrome b 5 may result from the presence of additional N-terminal residues on the surface of the protein.

Differences in conformational stability between native and phosphorylated acetylcholinesterase as evidenced by a monoclonal antibody

Monoclonal antibody 25B1 generated against diisopropyl phosphorofluoridate inhibited fetal bovine serum acetylcholinesterase has been extensively characterized with respect to its anticholinesterase properties. This antibody demonstrated considerably different properties from previously reported inhibitory antibodies raised against acetylcholinesterase in terms of the degree of inhibition (greater than 98%), the high degree of specificity, and the stability of the antigen-antibody complex. Monoclonal antibody 25B1 appears to be directed against a conformational epitope located in close proximity to the catalytic center of the enzyme and was found to be most suitable for studying the stabilization of the active site of acetylcholinesterase against denaturation by heat or guanidine following phosphorylation by organophosphorus anticholinesterase compounds. This approach allowed the determination of stability rank order of various phosphorylated acetylcholinesterases. Among all the organophosphates tested, the combination of a methyl group and a negatively charged oxygen attached to the P atom, CH3P(O)(O-)-AChE, conferred the greatest protection to the active site of aged or nonaged organophosphoryl conjugates of acetylcholinesterase.

NMR studies of a complex of deuterated calmodulin with melittin.

Completely deuterated calmodulin ([2H]CaM) has been prepared by expressing the chicken gene for CaM in Escherichia coli grown in 2H2O on a deuterated medium. The structural and dynamic properties of a 1:1 CaM/melittin (Mel) complex have been investigated by proton NMR. The spectrum of bound Mel is obtained directly from the spectrum of the [2H]CaM X Mel complex and is found to resemble strongly the spectrum of the helical species in methanol rather than that of the random coil species in water. The spectrum of bound CaM is obtained indirectly from the difference spectrum between [1H]CaM X Mel and [2H]CaM X Mel. Many changes are observed between free and bound CaM and they are distributed in both halves of the molecule, indicating that the binding of Mel affects the structure in both parts of the molecule. The rates of exchange of the amide protons of [2H]CaM with 2H2O were compared to those of [2H]CaM X Mel. The results showed that most, but not all, of the protons exchanged more slowly in the complex; after 40 hr, the residual peaks number 7 in CaM and greater than 20 in the complex. Again, changes in rates in CaM due to binding of Mel occurred in both halves of the molecule. The relative rates of amide proton exchange in CaM and its complex with Mel prove to be a sensitive criterion of differences in conformational stability and/or structure.

Strain differences in kinetic and thermal stability of two mouse brain tryptophan hydroxylase activities

Levels of forebrain serotonin (5-HT), tryptophan, 5-hydroxyindoleacetic acid (5-HIAA) and hydroxylase cofactor (BH4) were comparable in two experimental mouse strains (A/J and C57Bl/6J) despite 2-3-fold differences in vitro in the relative activities of forebrain and midbrain tryptophan-5-monooxygenase (TPOH; EC 1.14.16.4). The enzyme activities did not differ with respect to Km for cofactor at saturating levels, but manifested different degrees of cooperativity with respect to cofactor when examined with BH4 concentrations within a physiological range. They differed also in the frequency and amplitude of kinetic variation around comparable mean velocity slopes across cofactor and time; in resistance to pre-incubation inactivation and responsiveness to its facilitation by calcium; in molecular weight heterogeneity as reflected in the distribution of molecular weight forms by gel diffusion chromatography; and in the number of peaks in power spectral analysis of kinetic variation patterns. Although the potential roles of small-molecule ligand and/or regulator proteins have not been ruled out, we hypothesize that differences in conformational stability underlie the differences in regulatory properties and make one enzyme activity more vulnerable to occlusive influences in vivo.

Conformational stability of lactate dehydrogenase from Bacillus thermus-aquaticus [proceedings

Proteins are synthesized and enzymes can function at surprisingly high temperatures in thermophilic micro-organisms. This temperature is about 90°C in the case of Bacillus thermus-aquaticus (A.T.C.C. 25104). Lactate dehydrogenase (EC 1.1.1.27) was isolated from this micro-organism, and the temperature dependence of the rate of pyruvate reduction and thermodynamic parameters of heat inactivation were comparedwith those of a mesophilic counterpart, namely pig skeletal muscle M4 lactate dehydrogenase, to reveal the difference in conformational stability and to obtain information about the nature of the forces responsible for the enhanced thermostability.

Analogies in protein pattern and conformation among ribosomes from different classes of vertebrates

1. 1. Ribosomal proteins from different vertebrates were compared by disc electrophoresis. Great similarities were observed within two main groups of rapidly migrating proteins, while a slowly moving group showed a marked difference between poikilothermal and homeothermal species. 2. 2. The difference was mainly associated with a protein in the large subunit, which in lower vertebrates was replaced by a related, but smaller molecule. 3. 3. Using these proteins as structural markers, a difference in conformational stability between the two types of ribosomes was observed at increased temperature and ionic strength. 4. 4. Two-dimensional electrophoresis was used for characterizing the various proteins, and determining their approximate molecular weights.