Chemical Interactions Modulate λ6-85 Stability in Cells

Because steric crowding is most effective when the crowding agent is similar in size to the molecule that it acts upon and the average macromolecule inside cells is much larger than a small protein or peptide, steric crowding is not predicted to affect their folding inside cells. On the other hand, chemical interactions should perturb in-cell structure and stability because they arise from interactions between the surface of the small protein or peptide and its environment. Indeed, previous in vitro measurements of the λ-repressor fragment, λ_6-85 , in crowding matrices comprised of Ficoll or protein crowders support these predictions. Here we directly quantify the in-cell stability of λ_6-85 and distinguish the contribution of steric crowding and chemical interactions to its stability. Using a FRET-labeled λ_6-85 construct, we find that the fragment is stabilized by 5 °C in-cells compared to in vitro. We demonstrate that this stabilization cannot be explained by steric crowding because, as anticipated, Ficoll has no effect on λ_6-85 stability. We find that the in-cell stabilization arises from chemical interactions, mimicked in vitro by mammalian protein extraction reagent (M-PER^TM ). Comparison between FRET values in-cell and in Ficoll confirms that U-2 OS cytosolic crowding is reproduced at macromolecule concentrations of 15 %w/v. Our measurements validate the cytomimetic of 15% Ficoll and 20% M-PER^TM that we previously developed for protein and RNA folding studies. However, because the in-cell stability of λ_6-85 is reproduced by 20 %v/v M-PER^TM alone, we predict that this simplified mixture could be a useful tool to predict the in-cell behaviors of other small proteins and peptides. This article is protected by copyright. All rights reserved.

Protein Folding Stability Profiling of Colorectal Cancer Chemoresistance Identifies Functionally Relevant Biomarkers

Reported here is the application of three protein folding stability profiling techniques (including the stability of proteins from rates of oxidation, thermal protein profiling, and limited proteolysis approaches) to identify differentially stabilized proteins in six patient-derived colorectal cancer (CRC) cell lines with different oxaliplatin sensitivities and eight CRC patient-derived xenografts (PDXs) derived from two of the patient derived cell lines with different oxaliplatin sensitivities. Compared to conventional protein expression level analyses, which were also performed here, the stability profiling techniques identified both unique and novel proteins and cellular components that differentiated the sensitive and resistant samples including 36 proteins that were differentially stabilized in at least two techniques in both the cell line and PDX studies of oxaliplatin resistance. These 36 differentially stabilized proteins included 10 proteins previously connected to cancer chemoresistance. Two differentially stabilized proteins, fatty acid synthase and elongation factor 2, were functionally validated in vitro and found to be druggable protein targets with biological functions that can be modulated to improve the efficacy of CRC chemotherapy. These results add to our understanding of CRC oxaliplatin resistance, suggest biomarker candidates for predicting oxaliplatin sensitivity in CRC, and inform new strategies for overcoming chemoresistance in CRC.

Contribution of process-induced molten-globule state formation in duck liver protein to the enhanced binding ability of (E,E)-2,4-heptadienal

BACKGROUND

Extracted proteins of alternative animal origin tend to present strong off-flavor perception due to physicochemical interactions of coextracted off-flavor compounds with proteins. To investigate the relationship between absorption behaviors of volatile aromas and the processes-induced variations in protein microstructures and molecular conformations, duck liver protein isolate (DLp) was subjected to heating (65/100 °C, 15 min) and ultra-high pressure (UHP, 100-500 MPa/10 min, 28 °C) treatments to obtain differential unfolded protein states.

RESULTS

Heat and UHP treatments induced the unfolding of DLp to varied degrees, as revealed by fluorescence spectroscopy, ultraviolet-visible absorption, circular dichroism spectra and surface hydrophobicity measurements. Two types of heating-denatured states with varied unfolding degrees were obtained, while UHP at both levels of 100/500 MPa caused partial unfolding of DLp and the presence of a molten-globule state, which significantly enhanced the binding affinity between DLp and (E,E)-2,4-heptadienal. In particular, significantly modified secondary structures of DLp were observed in heating-denatured samples. Excessive denaturing and unfolding degrees resulted in no significant changes in the absorption behavior of the volatile ligand, as characterized by observations of fluorescence quenching and analysis of headspace concentrations.

CONCLUSION

Defining process-induced conformational transition behavior of matrix proteins could be a promising strategy to regulate food flavor attributes and, particularly, to produce DLp coextracted with limited off-flavor components by modifying their interaction during extraction processes. © 2023 Society of Chemical Industry.

Tear nanoDSF Denaturation Profile Is Predictive of Glaucoma

Primary open-angle glaucoma (POAG) is a frequent blindness-causing neurodegenerative disorder characterized by optic nerve and retinal ganglion cell damage most commonly due to a chronic increase in intraocular pressure. The preservation of visual function in patients critically depends on the timeliness of detection and treatment of the disease, which is challenging due to its asymptomatic course at early stages and lack of objective diagnostic approaches. Recent studies revealed that the pathophysiology of glaucoma includes complex metabolomic and proteomic alterations in the eye liquids, including tear fluid (TF). Although TF can be collected by a non-invasive procedure and may serve as a source of the appropriate biomarkers, its multi-omics analysis is technically sophisticated and unsuitable for clinical practice. In this study, we tested a novel concept of glaucoma diagnostics based on the rapid high-performance analysis of the TF proteome by differential scanning fluorimetry (nanoDSF). An examination of the thermal denaturation of TF proteins in a cohort of 311 ophthalmic patients revealed typical profiles, with two peaks exhibiting characteristic shifts in POAG. Clustering of the profiles according to peaks maxima allowed us to identify glaucoma in 70% of cases, while the employment of artificial intelligence (machine learning) algorithms reduced the amount of false-positive diagnoses to 13.5%. The POAG-associated alterations in the core TF proteins included an increase in the concentration of serum albumin, accompanied by a decrease in lysozyme C, lipocalin-1, and lactotransferrin contents. Unexpectedly, these changes were not the only factor affecting the observed denaturation profile shifts, which considerably depended on the presence of low-molecular-weight ligands of tear proteins, such as fatty acids and iron. Overall, we recognized the TF denaturation profile as a novel biomarker of glaucoma, which integrates proteomic, lipidomic, and metallomic alterations in tears, and monitoring of which could be adapted for rapid non-invasive screening of the disease in a clinical setting.

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.

Comparative Analysis of Protein Folding Stability-Based Profiling Methods for Characterization of Biological Phenotypes

Recently, a new suite of mass spectrometry-based proteomic methods has been developed that enables evaluation of protein folding stability on the proteomic scale. These methods utilize chemical and thermal denaturation approaches (SPROX and TPP, respectively) as well as proteolysis strategies (DARTS, LiP, and PP) to assess protein folding stability. The analytical capabilities of these technique have been well-established for protein target discovery applications. However, less is known about the relative advantages and disadvantages of using these different strategies to characterize biological phenotypes. Reported here is a comparative study of SPROX, TPP, LiP, and conventional protein expression level measurements using both a mouse model of aging and a mammalian cell culture model of breast cancer. Analyses on proteins in brain tissue cell lysates derived from 1- and 18-month-old mice (n = 4-5 at each time point) and on proteins in cell lysates derived from the MCF-7 and MCF-10A cell lines revealed a majority of the differentially stabilized protein hits in each phenotype analysis had unchanged expression levels. In both phenotype analyses, TPP generated the largest number and fraction of differentially stabilized protein hits. Only a quarter of all the protein hits identified in each phenotype analysis had a differential stability that was detected using multiple techniques. This work also reports the first peptide-level analysis of TPP data, which was required for the correct interpretation of the phenotype analyses performed here. Studies on selected protein stability hits also uncovered phenotype-related functional changes.

Secondary structural analyses of histone H2A-H2B proteins extracted from heated cells

Histone proteins, building blocks of chromatins, participate in enzymatic reactions in cells heated at around 45°C though in vitro the denaturation of histones significantly proceeds at a similar temperature. It implies that unidentified mechanisms prevent thermal denaturation of histones in vivo. However, studies on the histone structures in the heated cells have been scarce. Here, we analyzed the secondary structures of histone H2A-H2B proteins originating from the heated cells using circular dichroism spectroscopy. The secondary structure contents of the H2A-H2B extracted from the heated cells differed from those of H2A-H2B both native and denatured in vitro but reverted to the native structures by incubating the heated cells at 37°C within 2 h. Such structural flexibility may play a role in protecting genomic functions governed by chromatin structures from heat stresses.

Probing the interaction of fisetin with human serum transferrin via spectroscopic and molecular docking approaches

The binding of fisetin to human serum transferrin (HST) was investigated by spectroscopic (steady-state fluorescence, synchronous fluorescence, Förster resonance energy transfer) and molecular docking approaches. HST fluorescence is quenched by fisetin by a static process. The binding takes place with a moderate affinity and it is driven by hydrogen bonding and van der Waals forces. Synchronous fluorescence study indicates that Trp is more involved in the fluorescent quenching of HST by fisetin than Tyr. The energy transfer between HST and fisetin occurs at a distance of 2.31 nm confirming the results obtained by fluorescence. The binding of fisetin to HST favors thermal denaturation of HST conformation. The transition temperature for HST was obtained at 53.81 °C while the presence of the fisetin led to its change to 49.06 °C. The molecular docking of fisetin to HST confirms the results obtained by the spectroscopic experiments showing a moderate affinity of fisetin for HST.Communicated by Ramaswamy H. Sarma.

Effect of SDS Micelles on Actinomycin D - DNA Complexes

DNA thermal denaturation was evaluated as a measure of the effect of antitumor drug actinomycin D on the stability of the double helix and also the effect of SDS micelles on actinomycin D - DNA complexes. The results indicated that the melting temperature of DNA was dependent on drug concentration, increasing with actinomycin D concentration. High thermal stabilization (about 10 °C) of the DNA helix after the association with actinomycin D clearly demonstrates the intercalative binding mode. The presence of SDS micelles leads to the release of intercalated actinomcyin D molecules from DNA double helix and their further relocation in surfactant micelles. These results highlighted that the drug release can be controlled in time and by varying the concentration and nature of surfactant.

Reverse Engineering Analysis of the High-Temperature Reversible Oligomerization and Amyloidogenicity of PSD95-PDZ3

PSD95-PDZ3, the third PDZ domain of the post-synaptic density-95 protein (MW 11 kDa), undergoes a peculiar three-state thermal denaturation (N ↔ In ↔ D) and is amyloidogenic. PSD95-PDZ3 in the intermediate state (I) is reversibly oligomerized (RO: Reversible oligomerization). We previously reported a point mutation (F340A) that inhibits both ROs and amyloidogenesis and constructed the PDZ3-F340A variant. Here, we “reverse engineered” PDZ3-F340A for inducing high-temperature RO and amyloidogenesis. We produced three variants (R309L, E310L, and N326L), where we individually mutated hydrophilic residues exposed at the surface of the monomeric PDZ3-F340A but buried in the tetrameric crystal structure to a hydrophobic leucine. Differential scanning calorimetry indicated that two of the designed variants (PDZ3-F340A/R309L and E310L) denatured according to the two-state model. On the other hand, PDZ3-F340A/N326L denatured according to a three-state model and produced high-temperature ROs. The secondary structures of PDZ3-F340A/N326L and PDZ3-wt in the RO state were unfolded according to circular dichroism and differential scanning calorimetry. Furthermore, PDZ3-F340A/N326L was amyloidogenic as assessed by Thioflavin T fluorescence. Altogether, these results demonstrate that a single amino acid mutation can trigger the formation of high-temperature RO and concurrent amyloidogenesis.

Elucidating the binding mechanism of an antimigraine agent with a model protein: insights from molecular spectroscopic, calorimetric and computational approaches

Sumatriptan (SUM), a serotonin activator used to treat migraines and cluster headaches. Molecular spectroscopic methods including fluorescence quenching, time dependent fluorescence, FRET, absorption, circular dichroism, differential scanning calorimetric and computational approaches were employed to unravel the interaction between sumatriptan and bovine serum albumin (BSA). The fluorescence quenching studies suggested the interaction between SUM and BSA with a moderate binding with the binding constant (K_b) in the order of 10⁴. The findings of temperature and time dependent fluorescence quenching studies confirmed the role of static quenching mechanism. Thermodynamic parameters suggested the key role of electrostatic force in the interaction of SUM with BSA. Absorption and CD spectral studies revealed the bioenvironmental changes around the Trp in BSA upon binding of SUM. Calorimetric based thermal denaturation results confirmed that the thermal stability of BSA was improved in the presence of SUM. resulted in the this decreased flexibility of protein chain. Site competitive studies indicated SUM was located in the hydrophobic cavity of site I which was further confirmed by the docking and dynamic simulation studies. Additionally, molecular dynamics simulations inferred the microenvironmental condition around the SUM and the amino acids and forces involved in the binding of SUM with BSA.Communicated by Ramaswamy H. Sarma.

Conformational Consequences for Compatible Osmolytes on Thermal Denaturation

Compatible osmolytes are a broad class of small organic molecules employed by living systems to combat environmental stress by enhancing the native protein structure. The molecular features that make for a superior biopreservation remain elusive. Through the use of time-resolved and steady-state spectroscopic techniques, in combination with molecular simulation, insight into what makes one molecule a more effective compatible osmolyte can be gained. Disaccharides differing only in their glycosidic bonds can exhibit different degrees of stabilization against thermal denaturation. The degree to which each sugar is preferentially excluded may explain these differences. The present work examines the biopreservation and hydration of trehalose, maltose, and gentiobiose.

Amidine- and Amidoxime-Substituted Heterocycles: Synthesis, Antiproliferative Evaluations and DNA Binding

The novel 1,2,3-triazolyl-appended N- and O-heterocycles containing amidine 4–11 and amidoxime 12–22 moiety were prepared and evaluated for their antiproliferative activities in vitro. Among the series of amidine-substituted heterocycles, aromatic diamidine 5 and coumarine amidine 11 had the most potent growth-inhibitory effect on cervical carcinoma (HeLa), hepatocellular carcinoma (HepG2) and colorectal adenocarcinoma (SW620), with IC₅₀ values in the nM range. Although compound 5 was toxic to non-tumor HFF cells, compound 11 showed certain selectivity. From the amidoxime series, quinoline amidoximes 18 and 20 showed antiproliferative effects on lung adenocarcinoma (A549), HeLa and SW620 cells emphasizing compound 20 that exhibited no cytostatic effect on normal HFF fibroblasts. Results of CD titrations and thermal melting experiments indicated that compounds 5 and 10 most likely bind inside the minor groove of AT-DNA and intercalate into AU-RNA. Compounds 6, 9 and 11 bind to AT-DNA with mixed binding mode, most probably minor groove binding accompanied with aggregate binding along the DNA backbone.

Protein Unfolding: Denaturant vs. Force

While protein refolding has been studied for over 50 years since the pioneering work of Christian Anfinsen, there have been a limited number of studies correlating results between chemical, thermal, and mechanical unfolding. The limited knowledge of the relationship between these processes makes it challenging to compare results between studies if different refolding methods were applied. Our current work compares the energetic barriers and folding rates derived from chemical, thermal, and mechanical experiments using an immunoglobulin-like domain from the muscle protein titin as a model system. This domain, I83, has high solubility and low stability relative to other Ig domains in titin, though its stability can be modulated by calcium. Our experiments demonstrated that the free energy of refolding was equivalent with all three techniques, but the refolding rates exhibited differences, with mechanical refolding having slightly faster rates. This suggests that results from equilibrium-based measurements can be compared directly but care should be given comparing refolding kinetics derived from refolding experiments that used different unfolding methods.

Molecular Analytical Assessment of Thermally Precipitated α-Lactalbumin after Resolubilization

Selective thermal precipitation followed by a mechanical separation step is a well described method for fractionation of the main whey proteins, α-lactalbumin (α-la) and β-lactoglobulin (β-lg). By choosing appropriate environmental conditions the thermal precipitation of either α-la or β-lg can be induced. Whereas β-lg irreversibly aggregates, the precipitated α-la can be resolubilized by a subsequent adjustment of the solution’s pH and the ionic composition. This study reports on the analytical characterization of resolubilized α-la compared to its native counterpart as a reference in order to assess whether the resolubilized α-la can be considered close to ‘native’. Turbidity and quantification by RP-HPLC of the resolubilized α-la solutions were used as a measure of solubility in aqueous environment. RP-HPLC was also applied to determine the elution time as a measure for protein’s hydrophobicity. DSC measurement was performed to determine the denaturation peak temperature of resolubilized α-la. FTIR spectroscopy provided insights in the secondary structure. The refolding of α-la achieved best results using pH 8.0 and a 3-fold stoichiometric amount of Ca²⁺ per α-la molecule. The results showed that the mechanism of aggregation induced by gentle thermal treatment under acidic conditions with subsequent mechanical separation is reversible to a certain extent, however, the exact native conformation was not restored.

The reduced form of the antibody CH2 domain

Among the immunoglobulin domains, the CH2 domain has the lowest thermal stability, which also depends on amino acid sequence and buffer conditions. To further identify factors that influence CH2 folding and stability, we characterized the domain in the reduced form using differential scanning fluorimetry and nuclear magnetic resonance. We show that the CH2 domain can fold, similarly to the disulfide-bridged form, without forming a disulfide-bridge, even though the protein contains two Cys residues. Although the reduced form exhibits thermal stability more than 15°C lower than the disulfide-bridged form, it does not undergo immediate full oxidization. To explain this phenomenon, we compared CH2 oxidization at different conditions and demonstrate a need for significant fluctuation of the folded conformation to enhance CH2 disulfide-bridge formation. We conclude that, since CH2 can be purified as a folded, semi-stable, reduced protein that can coexist with the oxidized form, verification of the level of oxidization at each step is critical in CH2 engineering studies.

Physico-Chemical Characteristics and In Vitro Gastro-Small Intestinal Digestion of New Zealand Ryegrass Proteins

Being widely abundant, grass proteins could be a novel source of plant proteins for human foods. In this study, ryegrass proteins extracted using two different approaches-chemical and enzymatic extraction, were characterised for their physico-chemical and in vitro digestion properties. A New Zealand perennial ryegrass cultivar Trojan was chosen based on its higher protein and lower dry matter contents. Grass protein concentrate (GPC) with protein contents of approximately 55 and 44% were prepared using the chemical and enzymatic approach, respectively. The thermal denaturation temperature of the GPC extracted via acid precipitation and enzymatic treatment was found to be 68.0 ± 0.05 °C and 66.15 ± 0.03 °C, respectively, showing significant differences in protein’s thermal profile according to the method of extraction. The solubility of the GPC was highly variable, depending on the temperature, pH and salt concentration of the dispersion. The solubility of the GPC extracted via enzymatic extraction was significantly lower than the proteins extracted via the chemical method. Digestion of raw GPC was also studied via a gastro-small intestinal in vitro digestion model and was found to be significantly lower, in terms of free amino N release, for the GPC prepared through acid precipitation. These results suggest that the physico-chemical and digestion characteristics of grass proteins are affected by the extraction method employed to extract the proteins. This implies that selection of an appropriate extraction method is of utmost importance for achieving optimum protein functionality during its use for food applications.

Stability and refolding of Dihydrofolate reductase enhances with nano-conjugation

The nano-conjugation of proteins is an active area of research due to potential biomedical and nanotechnological applications. Many protein-nanoconjugates were designed for various applications, such as drug delivery, molecular imaging, and liquid biopsy etc. However, the challenges remain to ensure protein stability and to retain the conformational state of the protein intact upon nano-conjugation. In this communication we have reported the status of stability and refolding ability of Au-NP conjugated zDHFR protein. The effect of nano-conjugation of zDHFR on the thermal stability and it's refolding from thermally denatured state have been extensively studied. Zebrafish Dihydrofolate reductase (zDHFR) is an essential enzyme which acts as a crucial part in synthesis of purine, thymidylate and various amino acids in cells. We have nano-conjugated zDHFR protein with Au-nanoparticles and studies were conducted for thermally denatured Au-NP conjugated zDHFR and compared with the non-conjugated protein. Refolding experiment of heat denatured Au-NP conjugated zDHFR was carried out to check the status of refolding and the result was compared with the non-conjugated protein. Our observation reveals that nano-conjugation stabilises the zDHFR protein against thermal denaturation. Furthermore, the nano-conjugation promotes refolding process of thermally unfolded DHFR such that the yield of refolding substantially increases.

Corrigendum: "Incorporating quantum dots into polymer microspheres via a spray-drying and thermal-denaturizing approach". Nanotechnology 17 (2006) 1791-1796"

Corrigendum.

Effect of marinating ingredients on temperature-induced denaturation of hemoglobin and its relation to red blood spot formation in cooked chicken breast

Red blood spot (RBS) commonly found in cooked chicken breast has caused severe economic loss as it is perceived as a sign of undercooked product. The objectives of this study were to investigate the cause of RBS as related to common ingredients used in marination, based on both chicken breast and isolated chicken hemoglobin (Hb) models. The effect of sodium chloride (NaCl), sodium tripolyphosphate (STPP), and glucose on thermal denaturation of Hb was investigated along with the extent of RBS formation in cooked marinated chicken breast. After vacuum tumbling for 65 min and subsequent storage at 4 °C for 20 hr, STPP and glucose were not absorbed into the center of chicken breast. However, Na⁺ was absorbed after 12 hr storage. The denaturation temperature (T_d ) of isolated chicken Hb decreased to 65.8 °C in the presence of 1.5 M NaCl, while that of the control was 69.4 °C. STPP at pH 9 decreased T_d of Hb to 61.4 °C. The alkaline pH induced by STPP destabilized the Hb structure. RBSs were observed at 100% incidence when cooked to core temperatures of 50 and 70 °C for 1 min. RBSs were completely eliminated at core temperature of 85 °C. The ingredients used during marination appeared to have a minimal effect on RBS formation due to their limited absorption into the chicken breast. The cooking temperature is a major factor governing RBSs, as it directly affects the denaturation of Hb.

Structural basis for stabilization of human telomeric G-quadruplex [d-(TTAGGGT)]4 by anticancer drug adriamycin

Besides inhibiting DNA duplication, DNA dependent RNA synthesis and topoisomerase-II enzyme action, anticancer drug adriamycin is found to cause telomere dysfunction and shows multiple strategies of action on gene functioning. We present evidence of binding of adriamycin to parallel stranded intermolecular [d-(TTAGGGT)]₄ G-quadruplex DNA comprising human telomeric DNA by proton and phosphorus-31 nuclear magnetic resonance spectroscopy. Diffusion ordered spectroscopy shows formation of complex between the two molecules. Changes in chemical shift and line broadening of DNA and adriamycin protons suggest participation of specific chemical groups/moieties in interaction. Presence of sequential nuclear Overhauser enhancements at all base quartet steps and absence of large downfield shifts in ³¹P resonances give clear proof of absence of intercalation of adriamycin chromophore between base quartets. Restrained molecular dynamics simulations using observed 15 short intermolecular inter proton distance contacts depict stacking of ring D of adriamycin with terminal G6 quartet by displacing T7 base and external groove binding close to T1-T2-A3 bases. The disappearance of imino protons monitored as a function of temperature and differential scanning calorimetry experiments yield thermal stabilization of 24 °C, which is likely to come in the way of telomerase association with telomeres. The findings pave the way for design of alternate anthracycline based drugs with specific modifications at ring D to enhance induced thermal stabilization and use alternate mechanism of binding to G-quadruplex DNA for interference in functional pathway of telomere maintenance by telomerase enzyme besides their well known action on duplex DNA. Communicated by Ramaswamy H. Sarma.

N-Acetylaspartate Is an Important Brain Osmolyte

Most of the human diseases related to various proteopathies are confined to the brain, which leads to the development of various forms of neurological disorders. The human brain consists of several osmolytic compounds, such as N-Acetylaspartate (NAA), myo-inositol (mI), glutamate (Glu), glutamine (Gln), creatine (Cr), and choline-containing compounds (Cho). Among these osmolytes, the level of NAA drastically decreases under neurological conditions, and, hence, NAA is considered to be one of the most widely accepted neuronal biomarkers in several human brain disorders. To date, no data are available regarding the effect of NAA on protein stability, and, therefore, the possible effect of NAA under proteopathic conditions has not been fully uncovered. To gain an insight into the effect of NAA on protein stability, thermal denaturation and structural measurements were carried out using two model proteins at different pH values. The results indicate that NAA increases the protein stability with an enhancement of structure formation. We also observed that the stabilizing ability of NAA decreases in a pH-dependent manner. Our study indicates that NAA is an efficient protein stabilizer at a physiological pH.

Molecular dynamics studies of the protective and destructive effects of sodium dodecyl sulfate in thermal denaturation of hen egg-white lysozyme and bovine serum albumin

To investigate the protective and destructive effects of sodium dodecyl sulfate (SDS) in thermal denaturation of proteins, we carried out twelve independent atomistic molecular dynamics (MD) simulations of bovine serum albumin (BSA) and hen egg-white lysozyme (LYZ) in pure water and SDS solutions at 25 and 80 °C, using SDS concentrations of 0.01, 0.05, 0.1 and 1 M. In the case of the BSA in pure water and SDS solutions, it was found that its helicity decreased from 67.02% in reference structure to 35% in pure water at 80 °C due to thermal denaturation, whereas it increased to 49.34, 52.36 and 54% at 0.01, 0.05 and 0.1 M SDS, respectively, owing to the SDS protective effect. In 1 M SDS, however, the surfactant's protective effect was weak, and consequently the helicity of the BSA decreased to 47.01%. In contrast, no protection by SDS was observed for the LYZ in SDS solutions as the loss of its helices increased with SDS concentration from 0.01 to 1 M. In attempt to interpret the SDS effects molecularly, we calculated the diffusion coefficients of SDS in the protein solutions. The calculated values were found to decrease with increasing SDS concentration in the BSA solutions, but to increase with SDS concentration in the LYZ solutions. The decrease or increase in the diffusion coefficient of SDS was attributed to the net negative or positive charge on the proteins at neutral pH, indicating that electrostatic repulsions or attractions affect diffusivity significantly and can moderate SDS-proteins non-covalent interactions. Communicated by Ramaswamy H. Sarma.

Molecular dynamics studies of the protective and destructive effects of sodium dodecyl sulfate in thermal denaturation of hen egg-white lysozyme and bovine serum albumin

To investigate the protective and destructive effects of sodium dodecyl sulfate (SDS) in thermal denaturation of proteins, we carried out twelve independent atomistic molecular dynamics (MD) simulations of bovine serum albumin (BSA) and hen egg-white lysozyme (LYZ) in pure water and SDS solutions at 25 and 80 °C, using SDS concentrations of 0.01, 0.05, 0.1 and 1 M. In the case of the BSA in pure water and SDS solutions, it was found that its helicity decreased from 67.02% in reference structure to 35% in pure water at 80 °C due to thermal denaturation, whereas it increased to 49.34, 52.36 and 54% at 0.01, 0.05 and 0.1 M SDS, respectively, owing to the SDS protective effect. In 1 M SDS, however, the surfactant's protective effect was weak, and consequently the helicity of the BSA decreased to 47.01%. In contrast, no protection by SDS was observed for the LYZ in SDS solutions as the loss of its helices increased with SDS concentration from 0.01 to 1 M. In attempt to interpret the SDS effects molecularly, we calculated the diffusion coefficients of SDS in the protein solutions. The calculated values were found to decrease with increasing SDS concentration in the BSA solutions, but to increase with SDS concentration in the LYZ solutions. The decrease or increase in the diffusion coefficient of SDS was attributed to the net negative or positive charge on the proteins at neutral pH, indicating that electrostatic repulsions or attractions affect diffusivity significantly and can moderate SDS-proteins non-covalent interactions. Communicated by Ramaswamy H. Sarma.

An in vitro mimic of in-cell solvation for protein folding studies

Ficoll, an inert macromolecule, is a common in vitro crowder, but by itself it does not reproduce in-cell stability or kinetic trends for protein folding. Lysis buffer, which contains ions, glycerol as a simple kosmotrope, and mimics small crowders with hydrophilic/hydrophobic patches, can reproduce sticking trends observed in cells but not the crowding. We previously suggested that the proper combination of Ficoll and lysis buffer could reproduce the opposite in-cell folding stability trend of two proteins: variable major protein-like sequence expressed (VlsE) is destabilized in eukaryotic cells and phosphoglycerate kinase (PGK) is stabilized. Here, to discover a well-characterized solvation environment that mimics in-cell stabilities for these two very differently behaved proteins, we conduct a two-dimensional scan of Ficoll (0-250 mg/ml) and lysis buffer (0-75%) mixtures. Contrary to our previous expectation, we show that mixtures of Ficoll and lysis buffer have a significant nonadditive effect on the folding stability. Lysis buffer enhances the stabilizing effect of Ficoll on PGK and inhibits the stabilizing effect of Ficoll on VlsE. We demonstrate that a combination of 150 mg/ml Ficoll and 60% lysis buffer can be used as an in vitro mimic to account for both crowding and non-steric effects on PGK and VlsE stability and folding kinetics in the cell. Our results also suggest that this mixture is close to the point where phase separation will occur. The simple mixture proposed here, based on commercially available reagents, could be a useful tool to study a variety of cytoplasmic protein interactions, such as folding, binding and assembly, and enzymatic reactions. SIGNIFICANCE STATEMENT: The complexity of the in-cell environment is difficult to reproduce in the test tube. Here we validate a mimic of cellular crowding and sticking interactions in a test tube using two proteins that are differently impacted by the cell: one is stabilized and the other is destabilized. This mimic is a starting point to reproduce cellular effects on a variety of protein and biomolecular interactions, such as folding and binding.

Comparative Analysis of Mass-Spectrometry-Based Proteomic Methods for Protein Target Discovery Using a One-Pot Approach

Recently, several mass-spectrometry- and protein-denaturation-based proteomic methods have been developed to facilitate protein target discovery efforts in drug mode-of-action studies. These methods, which include the stability of proteins from rates of oxidation (SPROX), pulse proteolysis (PP), chemical denaturation and protein precipitation (CPP), and thermal proteome profiling (TPP) techniques, have been used in an increasing number of applications in recent years. However, while the advantages and disadvantages to using these different techniques have been reviewed, the analytical characteristics of these methods have not been directly compared. Reported here is such a direct comparison using the well-studied immunosuppressive drug, cyclosporine A (CsA), and the proteins in a yeast cell lysate. Also described is a one-pot strategy that can be utilized with each technique to streamline data acquisition and analysis. We find that there are benefits to utilizing all four strategies for protein target discovery including increased proteomic coverage and reduced false positive rates that approach 0%. Moreover, the one-pot strategy described here makes such an experiment feasible, because of the 10-fold reduction in reagent costs and instrument time it affords.

Calcium ion induced thermodynamic stability, bisubstrate specificity, and differential organic solvent tolerance of a predominantly β-sheet serine protease from Bacillus aquimaris VITP4

The present study was aimed to get insights on the role of calcium ions on the thermodynamic stability, substrate specificity, and organic solvent compatibility of the extracellular protease produced by Bacillus aquimaris VITP4. Presence of Ca²⁺ enhanced the activity of the enzyme in the temperature range of 30-60 °C and increased the half-life from 164 to 234 Min. Circular dichroism experiments indicated that the temperature of half-denaturation (T_m ) of the protease increased from 76 to 86 °C. As judged by fluorescence emission profiles, the overall fold of the enzyme around the tryptophan residues could be similar. Further, thermal inactivation experiments revealed that the enzyme followed first order kinetics, with increase in energy for inactivation (E_ai ) by 24.2 ± 1.2 kJ mol ^-1 in the presence of Ca²⁺ . Studies with synthetic peptides as well as with bovine serum albumin signified preferential hydrolysis of the peptide bonds at the C-terminus of alanine residues (with a k_cat /K_M of 141,400 M^-1  Sec^-1 ) and at the C-terminus of arginine residues with a lower specificity (72,400 M^-1  Sec^-1 ), indicating bisubstrate specificity of the enzyme. The enzyme was found to be compatible with organic solvents (50%, v/v) such as acetonitrile and butanol, indicating possible application under demanding nonaqueous conditions.

A simple model for determining affinity from irreversible thermal shifts

Thermal denaturation (Tm) data are easy to obtain; it is a technique that is used by both small labs and large‐scale industrial organizations. The link between ligand affinity (K_D) and ΔTm is understood for reversible denaturation; however, there is a gap in our understanding of how to quantitatively interpret ΔTm for the many proteins that irreversibly denature. To better understand the origin, and extent of applicability, of a K_D to ΔTm correlate, we define equations relating K_D and ΔTm for irreversible protein unfolding, which we test with computational models and experimental data. These results suggest a general relationship exists between K_D and ΔTm for irreversible denaturation.

The application of artificial neural networks (ANN) for the denaturation of meat proteins – the kinetic analysis method

BACKGROUND

Artificial neural networks (ANN) are a common mathematical tool widely used in many research fields. Since they are applicable to non-linear relationships and do not require preliminary assumptions, they are a particularly promising tool in relation to meat processing. Thermal denaturation contains    a lot of information concerning the quality of meats. The aim was to create a methodology of kinetic analysis to obtain a quick and accurate tool for meat protein denaturation in non-isothermal conditions based on   The Coats-Redfern equation with the use of ANN.

METHODS

The analyses were carried out on samples of minced samples of Longissimus dorsi (pork). Thermal properties were determined using the differential scanning calorimetry (DSC) method with a Q100 TA Instruments apparatus. The data obtained was processed using the artificial neural network module in Statistica 13.0 software.

RESULTS

The following models fit well with experimental data: F1 and F2 (r = 0.99, F Snedecor’s F statistics 836943.20 and 971947.41 respectively). Deviations from experimental conversion degrees were higher for model F2, while for F1, good conformity was obtained across the whole range of α(T).

CONCLUSIONS

This preliminary study confirmed that methods of traditional kinetics of processes in non-isothermal conditions based on the Coats-Redfern equation can be successfully applied to meat protein denaturation. The method of kinetic analysis allows a high level of accuracy to be achieved and meets the requirements of an efficient engineering tool. &nbsp.

The Effect of High-Pressure Microfluidization Treatment on the Foaming Properties of Pea Albumin Aggregates

The effect of dynamic high-pressure treatment, also named microfluidization, on the surface properties of thermal pea albumin aggregates (AA) and their foaming ability was investigated at pH 3, 5, and 7. The solubility of albumin particles was not affected by the increase in microfluidization pressure from 70 to 130 MPa. Particle charge depended only on the pH, whereas protein surface hydrophobicity was stable at pH 5, decreased at pH 3, but increased at pH 7 after microfluidization treatment and with the applied pressure. Surface tension of AA measured at air/water interface was favorably affected by the microfluidization treatment at each pH preferentially due to size reduction and increased flexibility of protein particles. The foaming capacity and stability of AA depended on the pH conditions and the microfluidization treatment. The high-pressure treatment had little influence in foaming properties at acidic pHs, probably related to a more compact form of AA at these pHs. At neutral pH, the foaming properties of pea AA were strongly influenced by their surface properties and size associated with significant modifications in AA structure with microfluidization. Changes in albumin aggregate characteristics with pH and microfluidization pressure are also expected to modulate other techno-functional properties, such as emulsifying property. PRACTICAL APPLICATION: Albumins are known for their interesting nutritional values because they are rich in essential amino acids. This fraction is not currently marketed as a protein isolate for human consumption, but can be considered as a potential new vegetable protein ingredient. This document demonstrated that heat treatment or dynamic high-pressure technology can control the foaming properties of this protein for possible use in expanded foods.

Studies on the Interaction of [SnMe2Cl2(bu2bpy)] Complex with ct-DNA Using Multispectroscopic, Atomic Force Microscopy (AFM) and Molecular Docking

The interaction of SnMe₂Cl₂(bu₂bpy)complex with calf thymus DNA (ct-DNA) has been explored following, using spectroscopic methods, viscosity measurements, Atomic force microscopy, Thermal denaturation and Molecular docking. It was found that Sn(IV) complex could bind with DNA via intercalation mode as evidenced by hyperchromism and bathochromic in UV-Vis spectrum; these spectral characteristics suggest that the Sn(IV) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of SnMe₂Cl₂(bu₂bpy) represented a significant increase of MB intensity as to release MB from MB-DNA system. Positive values of ΔH and ΔS imply that the complex is bound to ct-DNA mainly via the hydrophobic attraction. Large complexes contain the DNA chains with an average size of 859 nm were observed by using AFM for Sn(IV) Complex-DNA. The Fourier transform infrared study showed a major interaction of Sn(IV) complex with G-C and A-T base pairs and a minor perturbation of the backbone PO₂ group. Addition of the Sn(IV)complex results in a noticeable rise in the Tm of DNA. In addition, the results of viscosity measurements suggest that SnMe₂Cl₂(bu₂bpy) complex may bind with the classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that Sn(IV)complex interacts with DNA by intercalation mode. Optimized docked model of DNA-complex mixture confirmed the experimental results.

[The Role of Calcium in the Conformational Changes of the Recombinant S100A8/S100A9]

Calprotectin is a member of the EF-hand proteins, composed of two subunits, S100A8 (MRP8) and S100A9 (MRP14). These proteins are involved in important processes including cell signaling, regulation of inflammatory responses, cell cycle control, differentiation, regulation of ion channel activity and defense against microbial agents in a calcium dependent manner. In the present study, recombinant S100A8 and S100A9 were expressed in E. coli BL21 and then purified using Ni-NTA affinity chromatography. The structure of the S100A8/A9 complex in the presence and absence of calcium was assessed by circular dichroism and fluorescence spectroscopy. The intrinsic fluorescence emission spectra of the S100A8/A9 complex in the presence of calcium showed a reduction in fluorescence intensity, reflecting conformational changes within the protein with the exposure of aromatic residues to the protein surface. The far ultraviolet-circular dichroism spectra of the complex in the presence of calcium revealed minor changes in the regular secondary structure of the complex. Also, increased thermal stability of the S100A8/A9 complex in the presence of calcium was indicated.

Genotyping based on thermal denaturation of amplification products identifies species of the Mycobacterium tuberculosis complex

PURPOSE

To develop a fast and inexpensive genotyping assay to identify the Mycobacterium tuberculosis complex (MTC) species most prevalent in human tuberculosis (TB), based on the thermal denaturation profiles of PCR products from mycobacterial 16S rDNA and three MTC genomic regions of difference (RD).

METHODOLOGY

Genotypes were determined by the presence and thermal denaturation profiles of the amplicons generated in the 'preliminary' PCR mixture (16S rDNA), followed by those of the simultaneous D1 (RD9+, RD1-) and D2 (RD4+, RD4-) PCR mixtures. The 16S rDNA profile identifies the genus Mycobacterium; the absence of any additional RD profile identifies Mycobacterium non-tuberculous (MNT) strains; additional RD4+ and RD9+ profiles without RD1- identify M. tuberculosis; an additional RD4+ profile per se identifies M. africanum; an additional RD4- profile per se identifies Mycobaterium bovis; additional RD1- and RD4- profiles identify M. bovis BCG.

RESULTS

Genotypes of a panel with 44 mycobacterial strains coincided in 16 MB and five non-MTC strains; in the remaining 23 MTC strains, 17 MTB and five MA concordant genotypes and one discordant MB genotype were resolved. The genotypes of 13 human and bovine MTC isolates coincided in all four MB and eight of the nine MTB isolates.

CONCLUSION

Sensitivity, specificity and positive and negative predictive values of the method are 100 % for the genus Mycobacterium, which resolves MB, MTB and MA genotypes. Species/genotype agreement is 97.7 % for the panel and 92.3 % for the MTC isolates. This method may be advantageously used to identify the most prevalent MTC species in humans.

Noncovalent Interaction of Tilmicosin with Bovine Serum Albumin

Tilmicosin is a widely used antibiotic in veterinary applications. Its antimicrobial activity is ranged from Gram-positive and some Gram-negative bacteria towards activities against Mycoplasma and Chlamydia. Adsorption affinity of tilmicosin antibiotics towards bovine serum albumin was investigated by both spectroscopic (UV-vis, Photoluminescence) and calorimetric methods. The interaction was determined on the basis of quenching of albumin by tilmicosin. Results confirm noncovalent binding of tilmicosin on bovine serum albumin with 1:1 stoichiometry associated with pK = 4.5, highlighting possible removal of tilmicosin molecules from the albumin surface through exchange reactions by known competitor molecules. Calorimetric measurements have confirmed the weak interaction between tilmicosin and albumin and reflect enhanced denaturation of the albumin in the presence of tilmicosin antibiotic. This process is associated with the decreased activation energy of conformational transition of the albumin. It opens a new, very quick reaction pathway without any significant effect on the product by noncovalent binding the tilmicosin molecules to the protein molecules. Results highlight the medical importance of these investigations by considerable docking of the selected antibiotic molecules on serum albumins. Although the binding may cause toxic effects in living bodies, the strength of the binding is weak enough to find competitor molecules for effective removals from their surface.

Spectroscopic and calorimetric characterization of spermine oxidase and its association forms

Spermine oxidase (SMOX) is a flavin-containing enzyme that oxidizes spermine to produce spermidine, 3-aminopropanaldehyde, and hydrogen peroxide. SMOX has been shown to play key roles in inflammation and carcinogenesis; indeed, it is differentially expressed in several human cancer types. Our previous investigation has revealed that SMOX purified after heterologous expression in Escherichia coli actually consists of monomers, covalent homodimers, and other higher-order forms. All association forms oxidize spermine and, after treatment with dithiothreitol, revert to SMOX monomer. Here, we report a detailed investigation on the thermal denaturation of SMOX and its association forms in native and reducing conditions. By combining spectroscopic methods (circular dichroism, fluorescence) and thermal methods (differential scanning calorimetry), we provide new insights into the structure, the transformation, and the stability of SMOX. While the crystal structure of this protein is not available yet, experimental results are interpreted also on the basis of a novel SMOX structural model, obtained in silico exploiting the recently solved acetylspermine oxidase crystal structure. We conclude that while at least one specific intermolecular disulfide bond links two SMOX molecules to form the homodimer, the thermal denaturation profiles can be justified by the presence of at least one intramolecular disulfide bond, which also plays a critical role in the stabilization of the overall three-dimensional SMOX structure, and in particular of its flavin adenine dinucleotide-containing active site.

Evaluation of compound selectivity of aldo-keto reductases using differential scanning fluorimetry

Inhibitors of AKR1B10 belonging to the aldo-keto reductase (AKR) superfamily are considered promising candidates for anti-cancer drugs. AKR1B1, a structurally similar isoform of AKR1B10, is involved in glucose metabolism. Thus, selective inhibition of AKR1B10 is required for the development of anti-cancer drugs. In this study, we first compared correlations between melting temperature and the 50% inhibition concentration obtained from differential scanning fluorimetry (DSF) and an enzyme inhibitory experiment, respectively, and a good correlation was found, except for compounds with low solubility. This result indicates that the DSF method is useful for drug screening for the AKR superfamily. We then evaluated their selectivity as inhibitors against all seven major human AKR1 family proteins and found that C18 is most specific for AKR1B10.

Effects of protein and phosphate buffer concentrations on thermal denaturation of lysozyme analyzed by isoconversional method

Thermal denaturation of lysozymes was studied as a function of protein concentration, phosphate buffer concentration, and scan rate using differential scanning calorimetry (DSC), which was then analyzed by the isoconversional method. The results showed that lysozyme thermal denaturation was only slightly affected by the protein concentration and scan rate. When the protein concentration and scan rate increased, the denaturation temperature (Tm) also increased accordingly. On the contrary, the Tm decreased with the increase of phosphate buffer concentration. The denaturation process of lysozymes was accelatated and the thermal stability was reduced with the increase of phosphate concentration. One part of degeneration process was not reversible where the aggregation occurred. The other part was reversible. The apparent activation energy (Ea) was computed by the isoconversional method. It decreased with the increase of the conversion ratio (α). The observed denaturation process could not be described by a simple reaction mechanism. It was not a process involving 2 standard reversible states, but a multi-step process. The new opportunities for investigating the kinetics process of protein denaturation can be supplied by this novel isoconversional method.

Experimental and Modelling Study of the Denaturation of Milk Protein by Heat Treatment

Heat treatment of milk aims to inhibit the growth of microbes, extend the shelf-life of products and improve the quality of the products. Heat treatment also leads to denaturation of whey protein and the formation of whey protein-casein polymer, which has negative effects on milk product. Hence the milk heat treatment conditions should be controlled in milk processing. In this study, the denaturation degree of whey protein and the combination degree of whey protein and casein when undergoing heat treatment were also determined by using the Native-PAGE and SDS-PAGE analysis. The results showed that the denaturation degree of whey protein and the combination degree of whey protein with casein extended with the increase of the heat-treated temperature and time. The effects of the heat-treated temperature and heat-treated time on the denaturation degree of whey protein and on the combination degree of whey protein and casein were well described using the quadratic regression equation. The analysis strategy used in this study reveals an intuitive and effective measure of the denaturation degree of whey protein, and the changes of milk protein under different heat treatment conditions efficiently and accurately in the dairy industry. It can be of great significance for dairy product proteins following processing treatments applied for dairy product manufacturing.

Characterization of Chemically and Thermally Treated Oil-in-Water Heteroaggregates and Comparison to Conventional Emulsions

Heteroaggregated oil-in-water (O/W) emulsions formed by targeted combination of oppositely charged emulsion droplets were proposed to be used for the modulation of physical properties of food systems, ideally achieving the formation of a particulate 3-dimensional network at comparably low-fat content. In this study, rheological properties of Quillaja saponins (QS), sugar beet pectin (SBP), and whey protein isolate (WPI) stabilized conventional and heteroaggregated O/W emulsions at oil contents of 10% to 60% (w/w) were investigated. Selected systems having an oil content of 30% (w/w) and different particle sizes (d₄₃ ≤ 1.1 or ≥16.7 μm) were additionally subjected to chemical (genipin or glutaraldehyde) and thermal treatments, aiming to increase network stability. Subsequently, their rheological properties and stability were assessed. Yield stresses (τ₀ ) of both conventional and heteroaggregated O/W emulsions were found to depend on emulsifier type, oil content, and initial droplet size. For conventional emulsions, high yield stresses were only observed for SBP-based emulsions (τ₀ ,_SBP approximately 157 Pa). Highest yield stresses of heteroaggregates were observed when using small droplets stabilized by SBP/WPI (approximately 15.4 Pa), being higher than those of QS/WPI (approximately 1.6 Pa). Subsequent treatments led to significant alterations in rheological properties for SBP/WPI systems, with yield stresses increasing 29-fold (glutaraldehyde) and 2-fold (thermal treatment) compared to untreated heteroaggregates, thereby surpassing yield stresses of similarly treated conventional SBP emulsions. Genipin-driven treatments proved to be ineffective. Results should be of interest to food manufacturers wishing to design viscoelastic food emulsion based systems at lower oil droplet contents.

Dodine as a transparent protein denaturant for circular dichroism and infrared studies

The fungicide dodine combines the cooperative denaturation properties of guanidine with the mM denaturation activity of SDS. It was previously tested only on two small model proteins. Here we show that it can be used as a chemical denaturant for phosphoglycerate kinase (PGK), a much larger two-domain enzyme. In addition to its properties as a chemical denaturant, dodine facilitates thermal denaturation of PGK, and we show for the first time that it also facilitates pressure denaturation of a protein. Much higher quality circular dichroism and amide I' infrared spectra of PGK can be obtained in dodine than in guanidine, opening the possibility for use of dodine as a denaturant when UV or IR detection is desirable. One caution is that dodine denaturation, like other detergent-based denaturants, is less reversible than guanidine denaturation.

Processed Meat Protein and Heat-Stable Peptide Marker Identification Using Microwave-Assisted Tryptic Digestion

New approaches to rapid examination of proteins and peptides in complex food matrices are of great interest to the community of food scientists. The aim of the study is to examine the influence of microwave irradiation on the acceleration of enzymatic cleavage and enzymatic digestion of denatured proteins in cooked meat of five species (cattle, horse, pig, chicken and turkey) and processed meat products (coarsely minced, smoked, cooked and semi-dried sausages). Severe protein aggregation occurred not only in heated meat under harsh treatment at 190 °C but also in processed meat products. All the protein aggregates were thoroughly hydrolyzed after 1 h of trypsin treatment with short exposure times of 40 and 20 s to microwave irradiation at 138 and 303 W. There were much more missed cleavage sites observed in all microwave-assisted digestions. Despite the incompleteness of microwave-assisted digestion, six unique peptide markers were detected, which allowed unambiguous identification of processed meat derived from the examined species. Although the microwave-assisted tryptic digestion can serve as a tool for rapid and high-throughput protein identification, great caution and pre-evaluation of individual samples is recommended in protein quantitation.

Robust and convenient analysis of protein thermal and chemical stability

We present the software CDpal that is used to analyze thermal and chemical denaturation data to obtain information on protein stability. The software uses standard assumptions and equations applied to two-state and various types of three-state denaturation models in order to determine thermodynamic parameters. It can analyze denaturation monitored by both circular dichroism and fluorescence spectroscopy and is extremely flexible in terms of input format. Furthermore, it is intuitive and easy to use because of the graphical user interface and extensive documentation. As illustrated by the examples herein, CDpal should be a valuable tool for analysis of protein stability.

Physicochemical origin of high correlation between thermal stability of a protein and its packing efficiency: a theoretical study for staphylococcal nuclease mutants

There is an empirical rule that the thermal stability of a protein is related to the packing efficiency or core volume of the folded state and the protein tends to exhibit higher stability as the backbone and side chains are more closely packed. Previously, the wild type and its nine mutants of staphylococcal nuclease were compared by examining their folded structures. The results obtained were as follows: The stability was not correlated with the number of intramolecular hydrogen bonds, intramolecular electrostatic interaction energy, or degree of burial of the hydrophobic surface; though the empirical rule mentioned above held, it was not the proximate cause of higher stability; and the number of van der Waals contacts N vdW, or equivalently, the intramolecular van der Waals interaction energy was an important factor governing the stability. Here we revisit the wild type and its nine mutants of staphylococcal nuclease using our statistical-mechanical theory for hydration of a protein. A molecular model is employed for water. We show that the pivotal factor is the magnitude of the water-entropy gain upon folding. The gain originates from an increase in the total volume available to the translational displacement of water molecules coexisting with the protein in the system. The magnitude is highly correlated with the denaturation temperature T m. Moreover, the apparent correlation between N vdW and T m as well as the empirical rule is interpretable (i.e., their physicochemical meanings can be clarified) on the basis of the water-entropy effect.

Mapping fast protein folding with multiple-site fluorescent probes

Fast protein folding involves complex dynamics in many degrees of freedom, yet microsecond folding experiments provide only low-resolution structural information. We enhance the structural resolution of the five-helix bundle protein λ6-85 by engineering into it three fluorescent tryptophan-tyrosine contact probes. The probes report on distances between three different helix pairs: 1-2, 1-3, and 3-2. Temperature jump relaxation experiments on these three mutants reveal two different kinetic timescales: a slower timescale for 1-3 and a faster one for the two contacts involving helix 2. We hypothesize that these differences arise from a single folding mechanism that forms contacts on different timescales, and not from changes of mechanism due to adding the probes. To test this hypothesis, we analyzed the corresponding three distances in one published single-trajectory all-atom molecular-dynamics simulation of a similar mutant. Autocorrelation analysis of the trajectory reveals the same "slow" and "fast" distance change as does experiment, but on a faster timescale; smoothing the trajectory in time shows that this ordering is robust and persists into the microsecond folding timescale. Structural investigation of the all-atom computational data suggests that helix 2 misfolds to produce a short-lived off-pathway trap, in agreement with the experimental finding that the 1-2 and 3-2 distances involving helix 2 contacts form a kinetic grouping distinct from 1 to 3. Our work demonstrates that comparison between experiment and simulation can be extended to several order parameters, providing a stronger mechanistic test.

Kinetic and thermodynamic parameters for thermal denaturation of ovine milk lactoferrin determined by its loss of immunoreactivity

Lactoferrin is a protein with important biological functions that can be obtained from milk and by-products derived from the dairy industry, such as whey. Although bovine lactoferrin has been extensively studied, ovine lactoferrin is not quite as well known. In the present study, the effect of several heat treatments in 3 different media, over a temperature range from 66 to 75°C, has been studied on lactoferrin isolated from sheep milk. Denaturation of lactoferrin was determined by measuring its immunoreactivity with specific polyclonal antibodies. Kinetic and thermodynamic parameters obtained indicate that lactoferrin denatures by heat more rapidly in whey than in phosphate buffer or milk. The value of activation energy found for the denaturation process of lactoferrin when treated in whey is higher (390kJ/mol) than that obtained in milk (194kJ/mol) or phosphate buffer (179kJ/mol). This indicates that a great amount of energy is necessary to start denaturation of ovine lactoferrin, probably due to the interaction of this protein with other whey proteins. The changes in the hydrophobicity of lactoferrin after heat treatments were determined by fluorescence measurement using acrylamide. The decrease in the hydrophobicity constant was very small for the treatments from 66 to 75°C, up to 20min, which indicates that lactoferrin conformation did not experienced a great change. The results obtained in this study permit the prediction of behavior of ovine lactoferrin under several heat treatments and show that high-temperature, short-time pasteurization (72°C, 15 s) does not cause loss of its immunoreactivity and, consequently, would not affect its conformation and biological activity.

Thermal denaturation behavior of collagen fibrils in wet and dry environment

We have developed a new minimally invasive technique--integrated low-level energy adhesion technique (ILEAT)--which uses heat, pressure, and low-frequency vibrations for binding living tissues. Because the adhesion mechanism of the living tissues is not fully understood, we investigated the effect of thermal energy on the collagen structure in living tissues using ILEAT. To study the effect of thermal energy and heating time on the structure of the collagen fibril, samples were divided in two categories-wet and dry. Further, atomic force microscopy was used to analyze the collagen fibril structure before and after heating. Results showed that collagen fibrils in water denatured after 1 minute at temperatures higher than 80 °C, while partial denaturation was observed at temperatures of 80 °C and a heating time of 1 min. Furthermore, complete denaturation was achieved after 90 min, suggesting that the denaturation rate is temperature and time dependent. Moreover, the collagen fibrils in dry condition maintained their native structure even after being heated to 120 °C for 90 min in the absence of water, which specifically suppressed denaturation. However, partial denaturation of collagen fibrils could not be prevented, because this determines the adhesion between the collagen molecules, and stabilizes tissue bonding.

Analysis of protein stability and ligand interactions by thermal shift assay

Purification of recombinant proteins for biochemical assays and structural studies is time-consuming and presents inherent difficulties that depend on the optimization of protein stability. The use of dyes to monitor thermal denaturation of proteins with sensitive fluorescence detection enables rapid and inexpensive determination of protein stability using real-time PCR instruments. By screening a wide range of solution conditions and additives in a 96-well format, the thermal shift assay easily identifies conditions that significantly enhance the stability of recombinant proteins. The same approach can be used as an initial low-cost screen to discover new protein-ligand interactions by capitalizing on increases in protein stability that typically occur upon ligand binding. This unit presents a methodological workflow for small-scale, high-throughput thermal denaturation of recombinant proteins in the presence of SYPRO Orange dye.

Structural and protein interaction effects of hypertrophic and dilated cardiomyopathic mutations in alpha-tropomyosin

The potential alterations to structure and associations with thin filament proteins caused by the dilated cardiomyopathy (DCM) associated tropomyosin (Tm) mutants E40K and E54K, and the hypertrophic cardiomyopathy (HCM) associated Tm mutants E62Q and L185R, were investigated. In order to ascertain what the cause of the known functional effects may be, structural and protein-protein interaction studies were conducted utilizing actomyosin ATPase activity measurements and spectroscopy. In actomyosin ATPase measurements, both HCM mutants and the DCM mutant E54K caused increases in Ca²⁺-induced maximal ATPase activities, while E40K caused a decrease. Investigation of Tm's ability to inhibit actomyosin ATPase in the absence of troponin showed that HCM-associated mutant Tms did not inhibit as well as wildtype, whereas the DCM associated mutant E40K inhibited better. E54K did not inhibit the actomyosin ATPase activity at any concentration of Tm tested. Thermal denaturation studies by circular dichroism and molecular modeling of the mutations in Tm showed that in general, the DCM mutants caused localized destabilization of the Tm dimers, while the HCM mutants resulted in increased stability. These findings demonstrate that the structural alterations in Tm observed here may affect the regulatory function of Tm on actin, thereby directly altering the ATPase rates of myosin.

A neutral pH thermal hydrolysis method for quantification of structured RNAs

Riboswitch aptamers adopt diverse and complex tertiary structural folds that contain both single-stranded and double-stranded regions. We observe that this high degree of secondary structure leads to an appreciable hypochromicity that is not accounted for in the standard method to calculate extinction coefficients using nearest-neighbor effects, which results in a systematic underestimation of RNA concentrations. Here we present a practical method for quantifying riboswitch RNAs using thermal hydrolysis to generate the corresponding pool of mononucleotides, for which precise extinction coefficients have been measured. Thermal hydrolysis can be performed at neutral pH without reaction quenching, avoids the use of nucleases or expensive fluorescent dyes, and does not require generation of calibration curves. The accuracy of this method for determining RNA concentrations has been validated using quantitative (31)P-NMR calibrated to an external standard. We expect that this simple procedure will be generally useful for the accurate quantification of any sequence-defined RNA sample, which is often a critical parameter for in vitro binding and kinetic assays.

Protein analysis using real-time PCR instrumentation: incorporation in an integrated, inquiry-based project

Instrumentation for real-time PCR is used primarily for amplification and quantitation of nucleic acids. The capability to measure fluorescence while controlling temperature in multiple samples can also be applied to the analysis of proteins. Conformational stability and changes in stability due to ligand binding are easily assessed. Protein structure studies possible with a real-time PCR instrument address core topics in biochemistry and have valuable high-throughput applications in the fields of drug discovery and protein engineering. Protein analysis using real-time PCR instrumentation has been incorporated in an undergraduate laboratory project based on previously described projects. Students express, purify, and characterize a protein. Based on literature research and analysis using bioinformatics tools, they select a specific mutation to investigate. They then attempt to express, purify, and characterize their mutated protein. Thermal denaturation using a real-time PCR instrument is the primary tool used to compare the wild-type and mutated proteins. Alternative means for incorporation of protein analysis by real-time PCR instrumentation into laboratory experiences and additional modes of analysis are also described.