Negative thermal expansibility change for dissociation of lysozyme variant amyloid protofibril

A disulfide‐deficient variant of hen lysozyme, 0SS, is known to form an amyloid protofibril spontaneously, and to dissociate into monomers at high hydrostatic pressure. We carried out native PAGE at various temperatures (20–35°C) and pressures (0.1–200 MPa), to characterize the dissociation equilibrium of disulfide‐deficient variant of hen lysozyme amyloid protofibril. Based on the density profiles, the partial molar volume and thermal expansibility changes for dissociation, Δv_D and Δe_D, were obtained to be ?74 cm³/mol at 25°C and ?2.3 cm³ mol^?1 K^?1, respectively. The dissociation of amyloid fibril destroys the cross β‐structure, and such conformational destruction in native protein fold rarely accompanies negative thermal expansibility change. We discussed the negative thermal expansibility change in terms of hydration and structural packing of the amyloid protofibril.     

Subtilisin-catalyzed religation of proteolyzed hen egg-white lysozyme: investigation of the role of disulfides

Background: The use of proteases to form, instead of break, peptide bonds has expanded the repertoire of techniques available for protein semisynthesis. Several groups have previously reported the use of proteases in aqueous-organic solvents to form single amide bonds within proteins, but low yields and lengthy reaction times make this an impractical approach to protein synthesis. We recently found that proteolyzed triose phosphate isomerase can be re-ligated rapidly and efficiently by subtilisin, in mixed aqueous-organic solvent systems.Results: We now report the use of subtilisin to resynthesize hen egg-white lysozyme from a mixture of its proteolyzed fragments in high yield and with rapid reaction times. This enzymatic religation can also be achieved after reduction of the four disulfide bonds present in lysozyme, with the same efficiency as that observed for the disulfide-containing proteolysis mixture.Conclusions: For egg-white lysozyme, the subtilisin religation reaction can be used to re-synthesize a proteolyzed protein even after reduction of disulfide bonds. The utility of this reaction in more generalized protein semisynthesis reactions is currently being explored.     

Conformational changes of lysozymes with different numbers of disulfide bridges in sodium dodecyl sulfate solutions

Four disulfide bridges of hen egg-white lysozyme were selectively reduced to obtain its derivatives with three, two, and zero disulfide bridges (designated as 3SS, 2SS, and 0SS lysozymes, respectively). The 3SS lysozyme maintained the native conformation at pH 7.0 and 3.0. Even upon the reduction of two disulfide bridges, the protein conformation still remained unchanged at pH 7.0. Upon the reduction of all four disulfide bridges, the helicity, [θ]₂₇₀, and tryptophan fluorescence changed at pH 3.0 as well as at pH 7.0. The helicity of each derivative increased in a solution of sodium dodecyl sulfate (SDS). The SDS-induced helicity of the 0SS lysozyme was lower at pH 7.0 and higher at pH 3.0 than that of the intact lysozyme with four disulfide bridges. The helix formation appears to occur in originally nonhelical parts in each derivative at pH 7.0. In the cases of the 2SS and 0SS lysozymes at pH 3.0, however, some of the helices appear to be reformed also at moieties where the original helices are disrupted upon the cleavage of disulfide bridges. Received: 17 September 2000/Accepted: 24 March 2000     

Efficient immobilization of silver nanoparticles on metal substrates through various thiol molecules to utilize a gap mode in surface enhanced Raman scattering

To utilize a gap mode in surface enhanced Raman scattering, we elucidated the interaction between adsorbed species and Ag nanoparticles (AgNPs). Various thiol molecules such as normal alkanethiols, thiols with a phenyl, cyclohexane or naphthalene ring on Ag films immobilized AgNPs through van der Waals force, and electrostatic interaction. Immobilized AgNPs provided enormous Raman enhancement by a factor of 10⁷–10¹⁰ for thiol molecules at a nanogap, in consistent with that anticipated by finite difference time domain calculations. Only alkanethiols with a tert-methyl group and those with a carboxylic group did not immobilize any AgNPs probably owing to steric hindrance. A gap mode is relevant for a variety of metals even with large damping like Pt and Fe, indicating a crucial role of electric multipoles in AgNPs generated by a localized surface plasmon and induced mirror images in metal substrates for markedly enhanced electric field at a nanogap.     

Protein denaturation kinetic processes of a simple and a complex reaction mechanism analyzed by an iso-conversional method

The protein denaturation kinetic processes of a simple and a complex reaction mechanism represented by bovine serum albumin and hen egg-white lysozyme were analyzed by an iso-conversional method using differential scanning calorimetry. After differential scanning calorimetry using the iso-conversional method, the results were found to pose distinct contrasts between the two proteins. Bovine serum albumin showed an increasing peak temperature of the transition as the scan rate and protein concentration increased, whereas hen egg-white lysozyme exhibited almost constant peak temperature. The differential scanning calorimetry transition of bovine serum albumin was calorimetrically irreversible, while one part of hen egg-white lysozyme denaturation process was irreversible during which aggregation occurred and the other part was reversible. The iso-conversional method indicated that the value of bovine serum albumin apparent activation energy hardly varied with the degree of conversion, which showed that the denaturation kinetic process should conform to single reaction model. Using the master plots method, the most possible kinetic model for bovine serum albumin denaturation might be described by F _n kinetic model. On the contrary, the hen egg-white lysozyme value of apparent activation energy decreased with the increase of degree of conversion. It was not a process involving the two standard reversible states, and can be described by the simple Lumry–Eyring model. The iso-conversional method provides new opportunities in exploring a simple and a complex reaction mechanism of protein denaturation.     

溶液中金属盐对溶菌酶高级结构的影响

探索蛋白质结构稳定性及其淀粉样纤维化的环境条件具有重要意义.本文采用了荧光光谱法研究溶液中的金属盐对鸡卵清溶菌酶内源荧光和淀粉样纤维化的影响.结果表明,金属盐能够增加溶菌酶的热稳定性,减小淬灭剂对内源荧光的作用,对溶菌酶的高级结构具有一定的稳定作用.另一方面,在长时间热胁迫的情况下,金属盐可促进溶菌酶分子的聚集而纤维化.金属盐的这种双重作用分别与其阳离子和阴离子的性质有关.     

Surface-Enhanced Raman Spectroscopy (SERS) for characterization SARS-CoV-2

We used SERS with silver nanoparticles (AgNPs) as the active substrate to develop a, simple, quick, and accurate method for the detection and characterization SARS-CoV-2 without the need for RNA isolation and purification. Inactivated SARS-CoV-2 was used. The SERS signals were more than 10⁵ times enhanced than the normal Raman (NR) spectra. The SERS spectra of SARS-CoV-2 fingerprint revealed pronounced intensity signals of nucleic acids; aromatic amino acid side chains: 1007 cm^?1 (Phe marker), 1095 cm^?1 (CN and PO₂^? markers), 1580 cm^?1 (Tyr, Trp markers). Vibrations of the protein main chain: 1144 cm^?1 (CN and NH₂ markers), 1221 cm^?1 (CN and NH markers), 1270 cm^?1 (NH₂ marker), 1453 cm^?1 (CHCH₂ marker). All of these biomolecules could be adsorbed on the AgNPs surface's dense hot patches. The intensity of the SERS band varied with the concentration of SARS-CoV-2, with a virus detection limit of less than 10³ vp/mL and RSDs of 20 %.     

Inhibitory effect of safranal and crocin,two principle compounds of <Emphasis Type="Italic">Crocus sativus</Emphasis>, on fibrillation of lysozyme

A key feature in more than twenty amyloid-related diseases is the aggregation of intra-and/or extracellular misfolded proteins as amyloid fibrils. Therefore, preventing or reversing amyloid aggregation by using of small molecules is considered as useful approaches to the treatment of these diseases. We have evaluated the ability of safranal and crocin, to inhibit amyloid self-assembly of hen egg white lysozyme (HEWL), as an in vitro model system. Structural properties of HEWL in the presence of these compounds were investigated individually using thioflavin T, anilinonaphthalene-8-sulfonic acid fluorescence assays, far-UV circular dichroism and scanning electron microscopy as well as docking method. Our results showed that incubation of HEWL with either crocin or safranal at various concentrations leads a significant inhibition in the rate of amyloid formation. Docking analysis revealed crocin and safranal interact with the central hydrophobic region of lysozyme through van der Waals interaction. Hydroxyl group in crocin through hydrogen bonds connected to the several hydrophilic amino acids of lysozyme, while in safranal there are just one aldehyde group that through hydrogen bonds connected to aspartic acid in lysozyme. It can be concluded that both hydrophobic and hydrophilic groups contribute to lower lysozyme fibril accumulation.     

Dynamic redox environment-intensified disulfide bond shuffling for protein refolding in vitro: molecular simulation and experimental validation

One challenge in protein refolding is to dissociate the non-native disulfide bonds and promote the formation of native ones. In this study, we present a coarse-grained off-lattice model protein containing disulfide bonds and simulate disulfide bond shuffling during the folding of this model protein. Introduction of disulfide bonds in the model protein led to enhanced conformational stability but reduced foldability in comparison to counterpart protein without disulfide bonds. The folding trajectory suggested that the model protein retained the two-step folding mechanism in terms of hydrophobic collapse and structural rearrangement. The disulfide bonds located in the hydrophobic core were formed before the collapsing step, while the bonds located on the protein surface were formed during the rearrangement step. While a reductive environment at the initial stage of folding favored the formation of native disulfide bonds in the hydrophobic core, an oxidative environment at a later stage of folding was required for the formation of disulfide bonds at protein surface. Appling a dynamic redox environment, that is, one that changes from reductive to oxidative, intensified disulfide bond shuffling and thus resulted in improved recovery of the native conformation. The above-mentioned simulation was experimentally validated by refolding hen-egg lysozyme at different urea concentrations and oxidized glutathione/reduced glutathione (GSSG/GSH) ratios, and an optimal redox environment, in terms of the GSSG to GSH ratio, was identified. The implementation of a dynamic redox environment by tuning the GSSG/GSH ratio further improved the refolding yield of lysozyme, as predicted by molecular simulation.     

Improved detection limits for electrospray ionization on a magnetic sector mass spectrometer by using an array detector

Array detection was compared with point detection for solutions of hen egg-white lysozyme, equine myoglobin, and ubiquitin analyzed by electrospray ionization with a magnetic sector mass spectrometer. The detection limits for samples analyzed by using the array detector system were at least 10 times lower than could be achieved by using a point detector on the same mass spectrometer. The minimum detectable quantity of protein corresponded to a signal-to-background ratio of approximately 2∶1 for a 500 amol/μL solution of hen egg-white lysozyme. However, the ultimate practical sample concentrations appeared to be in the 10–100 fmol/μL range for the analysis of dilute solutions of relatively pure proteins or simple mixtures.     

EFFECTS OF PHOTODYNAMIC PROCESSES AND ULTRAVIOLET LIGHT ON DUCK AND HEN EGG-WHITE LYSOZYMES

Abstract— The photochemical yields for inactivation and amino acid destruction in hen and duck egg-white lysozyme are presented. Duck lysozyme II is devoid of histidine but it has two more tyrosine residues than does hen lysozyme. The data indicate that sensitized oxidation of the single histidine residue of hen lysozyme is of no significance for the inactivation of this lysozyme. The ultraviolet destruction of tryptophan and cystine residues appears to be equally related with the loss in enzymatic activity of hen lysozyme. In the case of duck lysozyme, however, the ultraviolet inactivation appears to be predominantly governed by the destruction of cystine residues.     

Determination of configurational isomers in cyclic polysulfides by Raman spectroscopy

Cyclic polysulfides such as trithiolanes, tetrathianes and their derivatives are found in natural sources like archaea, mushrooms and vegetables. They gained interest for research and industrial applications because of their pronounced flavors and biological activity. This study compares Raman spectra of reference compounds and cyclic polysulfides which were synthesized in-house and separated by preparative gas chromatography. The data show that the positions of the Raman bands due to SS stretching vibrations in the wavenumber region from 550 to 450 cm⁻¹ can determine the relative stereochemistry of 2,5-dialkyl trithiolanes and 4,6-dialkyl tetrathianes. Configurational cis isomers were distinguished from their corresponding trans isomers. In addition, 4,6-dialkyl-1,2,4,5-tetrathiane with disulfide bonds were distinguished from the constitutive isomer 3,6-dialkyl-1,2,3,5-tetrathiane with trisulfide bonds.     

2D correlation deep UV resonance raman spectroscopy of early events of lysozyme fibrillation: kinetic mechanism and potential interpretation pitfalls

The early stages of hen egg white lysozyme (HEWL) fibrillation were quantitatively characterized by two-dimensional correlation deep UV resonance Raman spectroscopy (2D-DUVRR) in terms of the sequential order of events and their characteristic times. The evolution of individual secondary structural elements was established through the correlation between Amide I, Amide III, and Calpha-H bending Raman bands. The temporal order of tertiary and individual secondary structural changes was probed through the cross-correlation of phenylalanine and Amide Raman bands. Both the sequential order and the characteristic times of tertiary and secondary structural changes allowed for reconstructing the molecular mechanism of lysozyme structural changes at the early stages of fibrillation. The 2D-DUVRR analysis of our data indicated that melting of the alpha-helix happened after the formation of the disordered structure, which was termed as apparent inverse order of secondary structural changes. We demonstrated that this apparent inverse order of events is typical for all chemical reactions involving the formation of intermediate(s), which may lead to the serious misinterpretation of 2D correlation results. We proposed a new simulation-aided approach for reconstructing and quantitatively characterizing the reaction mechanism of a (bio)chemical reaction that accounts for the apparent inverse order of events.     

The raman spectrum of biosynthetic human growth hormone. Its deconvolution,bandfitting, and interpretation

The Raman spectrum of amorphous biosynthetic human growth hormone, somatotropin, has been measured at high signal-to-noise ratios, using a CW argon ion laser and single channel detection. The rms signal-to-noise ratio varies from 1800:1 in the Amide I region near 1650 cm⁻¹ region, to 500:1 in the disulfide stretch region near 500 cm⁻¹.Component Raman bands have been extracted from the entire spectral envelope from 1800-400 cm⁻¹, by an interactive process involving both partial deconvolution and band-fitting. Interconsistency of all bands has been achieved by multiple overlapping of adjacent regions that had been isolated for the band-fitting programs.The resulting areas of the Raman component bands have been interpreted to show the ratios of peptide conformations in the hormone: 64% α-helix, 24% β-sheet, 8% β-turns and 4% γ-turns. Analysis of the tyrosine region, usually described as a Fermi resonance doublet near ∼830–850 cm⁻¹, shows four bands, at 825, 833, 853, and 859 cm⁻¹ in this macromolecule. Integrated intensities of these bands (2:2:2:2) are interpreted to show that only half of the eight tyrosine residues function as hydrogen-bond bridges via the acceptance of protons.Both disulfide bridges fall within the frequency ranges for normal, unstressed SS bonds: The 511 and 529 cm⁻¹ bands are indicative of the gauche-gauche-gauche and trans-gauche-gauche conformations, respectively.     

On the structure, infrared and Raman spectra of the 2:1 cysteine–Zn complex

A recent study on the Raman spectrum of the cysteine zwitterion and anion, and the 2:1 (Cys)₂Zn complex was reanalyzed employing B3LYP/6-311++G(3df,2pd) calculations in a simulated water environment. The spectra were rediscussed in light of the apparent incorrect structure determined in the original paper for this complex. The complex turns out to be tetrahedral and tetracoordinated instead of octahedral hexacoordinated, as initially proposed. The calculated Raman spectrum of the complex agrees very well with the experimental data, showing that both the geometrical and electronic structures are well represented. Three metal–ligand bands are found, two of them involving mostly the symmetrical and asymmetrical stretching of the Zn–N and Zn–S bonds. They were measured at 334 and 296 cm^?1 and calculated at 319 and 249 cm^?1, respectively. The third band involves the stretching of Zn–S bonds but also skeletal vibrations of the ligand. This band, measured at 399 cm^?1 and calculated at 444 cm^?1, has been previously assigned incorrectly to a Zn–O bond which does not actually exists since the CO ₂ ^?1 fragments are located away from the Zn ion.     

Production,Purification and Characterization of the Hen Egg-White Lysozyme Inhibitor from Enterobacter cloacae M-1002

Three hen egg-white lysozyme inhibitor producing strains, Enterobacter cloacae M-1002, E. sakazakii M-1204, and Erwinia rhapontici H-55, were isolated from the soils of Taiwan. E. cloacae M-1002 appeared to be a promising inhibitor producing strain. One inhibitor was isolated from the culture broth of this strain. Maximum lysozyme inhibitory activity was obtained when the bacterium was grown aerobically in a medium consisting of 0.75% glucose, 0.25% beef extract, 1.0% polypeptone, and 0.25% sodium L-glutamate (pH 70) at 37 °C after 36–48 hrs. A hen egg-white lysozyme inhibitor was isolated from the culture broth of this strain. The inhibitor was purified from the culture supernatant of E. cloacae M-1002 by ammonium sulfate fractionation, DEAE-Sepharose CL-6B column chromatography and Fractogel TSK HW-55 (S) gel chromatography. Molecular weight of the purified lysozyme inhibitor was estimated to be 18, 000–20, 000 by SDS-PAGE and HPLC, and was composed of 71% amino acid and 23% total sugar. Serine, glycine, and alanine in a 3:2:1 molar ratio were the major amino acids, calculated to be 32.8, 20.3, and 11.4% (mol%), respectively. Glucose and mannose were the major sugar components of the inhibitor. The inhibitor was stable at pH 5 to 8 and was stable under 50 °C. Only hen egg-white lysozyme was inhibited by the purified inhibitor but not the other tested enzymes such as lysozyme of celery, turnip; lytic enzyme of Pseudomonas aeruginosa M-1001; chitinase/lysozyme of P. aeruginosa K-187; or cellulase and xylanase of Streptomyces actuosus A-151 and Aspergillus sp. G-393. The inhibition of lysozyme to the bacterial cell lytic activity by the purified inhibitor was 100%.     

Characterization of 11-mercaptoundecanoic and 3-mercaptopropionic acids adsorbed on silver by surface-enhanced Raman scattering

Functionalized n-alkanethiols such as 11-mercaptoundecanoic (MUA) and 3-mercaptopropionic (MPA) acids are likely to adsorb in silver nanoparticles (AgNPs) solely through the thiol group (-SH) or also involving the carboxylate group (−COO⁻) in their structures. The relative tendency is closely related to pH conditions, solvent or the surface potential of the metallic nanoparticles. The SERS effect (Surface Enhancement Raman Scattering) was used for improving the understanding of MUA and MPA group interaction as well as the orientation of these organic compounds adsorbed on AgNPs and the influence of Cu(II) in solution. When analyzing the MPA SERS spectrum, it was verified that the thiol moiety was preferred to adsorb on the AgNPs surface in the thiolate form, presenting both anti and gauche conformations in both acidic and basic media. MUA SERS spectrum however, indicated that solely an anti conformation for the thiol moiety adsorbed on the AgNPs surface in both acidic and basic media. Adding Cu²⁺ ion resulted in coordination to the carboxyl or carboxylate moieties was confirmed by the downshift of the band assigned to OCO stretching. The presence of Cu(II) increased the tendency of gauche conformation for MPA; the coordination of MUA to Cu(II) resulted in a more upright conformation of the carboxylic/carboxylate moieties in both acidic and basic media, respectively.     

Natural rubber nanocomposites with SiC nanoparticles and carbon nanotubes

Single-walled carbon nanotubes (SWNTs) and SiC nanoparticles were dispersed in natural rubber (NR) polymer solution and subsequently evaporated the solvent to prepare NR nanocomposites. Using this technique, nanoparticles can be better dispersed in the NR matrix. The influence of nano-fillers on the mechanical properties of the resulting nanocomposites was quantified.Mechanical test results show an increase in the initial modulus with nanoscale reinforcements for up to 50% strain compared to pure NR. The modulus and strength of natural rubber with 1.5% SiC nanoparticles appear to be superior to those of SWNTs with the same filler content. In addition to mechanical testing, these nanocomposites were studied using the SEM and Raman spectroscopy techniques in order to understand the morphology of the resulting system and the load transfer mechanism, respectively. The Raman spectrum of the SWNT/NR system is characterized by a strong band at 1595 cm⁻¹ (G mode—C-C stretching) and other two bands at 1300 cm⁻¹ (D mode-disorder induced) and 2590 cm⁻¹ (D* band). A shift of the 2590 cm⁻¹ Raman band to the lower wavenumber was observed after subjecting SWNT/NR sample to cyclic stress testing. Ageing SWNT/NR specimen in distilled water for 30 days also provided a similar result. The Raman shift in aged samples indicates internal stress transfer from the natural rubber matrix to the SWNTs implying the existence of bonding at the interface.     

Derivative analysis of Raman spectra of liquid water in the OH (D) stretching region

Second derivative analysis of Raman spectra of H₂O, D₂O and HOD in liquid phase at room temperature for parallel and perpendicular polarized modes in the OH and OD stretching regions is reported. Five components obtained at approximately 3215, 3375, 3455, 3535 and 3640 cm⁻¹ for the second derivative plots of Raman spectra of liquid water are explained as due to the presence of three types of associated water species with (i) both OH bonds involved in moderately strong hydrogen bonds (SS), (ii) both OH bonds involved in weak hydrogen bonds (WW), and (iii) one OH bond involved in strong and one in weak hydrogen bonds (SW) respectively. The derivative plots obtained for Raman spectra of D₂O and HOD also contain features expected to be present on the basis of this model.     

A fast and low‐cost spray method for prototyping and depositing surface‐enhanced Raman scattering arrays on microfluidic paper based device

In this study, a fast, low‐cost, and facile spray method was proposed. This method deposits highly sensitive surface‐enhanced Raman scattering (SERS) silver nanoparticles (AgNPs) on the paper‐microfluidic scheme. The procedures for substrate preparation were studied including different strategies to synthesize AgNPs and the optimization of spray cycles. In addition, the morphologies of the different kinds of paper substrates were characterized by SEM and investigated by their SERS signals. The established method was found to be favorable for obtaining good sensitivity and reproducible results. The RSDs of Raman intensity of randomly analyzing 20 spots on the same paper or different filter papers depositing AgNPs are both below 15%. The SERS enhancement factor is approximately 2 × 10⁷. The whole fabrication is very rapid, robust, and does not require specific instruments. Furthermore, the total cost for 1000 pieces of chip is less than $20. These advantages demonstrated the potential for growing SERS applications in the area of environmental monitoring, food safety, and bioanalysis in the future.