Distinct cysteine sulfhydryl environments detected by analysis of Raman S-hh markers of Cys-->Ser mutant proteins

Monitoring of Propiolamide-Mediated Molecular Crosstalk between Ferroptosis and Apoptosis by Raman Spectroscopy

Inducing programmed cell death is an efficient strategy for cancer treatments, and a deep understanding of the molecular mechanisms underlying cell death pathways is of significance for the rational design of anticancer drugs. Herein, propiolamide-mediated crosstalk between ferroptosis and apoptosis is investigated. In situ monitoring of reactive oxygen species (ROS) formation and the structural changes of propiolamide compounds is achieved by Raman spectroscopy. The molecular mechanisms of propiolamides in inducing monooxygenase-mediated ROS generation and inhibiting GPX4 activities are revealed. Furthermore, the pro-ferroptotic and pro-apoptotic roles of the propiolamides containing terminal alkynes are verified. This study provides an in situ and label-free strategy for monitoring enzyme-drug interactions and their dynamics. It is a first attempt to study the structural basis of molecular crosstalk through two important enzymes in cell death. This study paves the way for designing novel drugs that are capable of triggering a synergistic contribution of multiple cell death forms to anticancer efficacy.

Phase-Regulated Active Hydrogen Behavior on Molybdenum Disulfide for Electrochemical Nitrate-to-Ammonia Conversion

Electrochemical reduction of nitrate waste is promising for environmental remediation and ammonia preparation. This process includes multiple hydrogenation steps, and thus the active hydrogen behavior on the surface of the catalyst is crucial. The crystal phase referred to the atomic arrangements in crystals has a great effect on active hydrogen, but the influence of the crystal phase on nitrate reduction is still unclear. Herein, enzyme-mimicking MoS2 in different crystal phases (1T and 2H) are used as models. The Faradaic efficiency of ammonia reaches ≈90 % over 1T-MoS2 , obviously outperforming that of 2H-MoS2 (27.31 %). In situ Raman spectra and theoretical calculations reveal that 1T-MoS2 produces more active hydrogen on edge S sites at a more positive potential and conducts an effortless pathway from nitrate to ammonia instead of multiple energetically demanding hydrogenation steps (such as *HNO to *HNOH) performed on 2H-MoS2 .

A molecular dynamics study of protein denaturation induced by sulfonate-based surfactants

Microsecond timescale explicit-solvent atomistic simulations were carried out to investigate how anionic surfactants modulate protein structure and dynamics. We found that lysozyme undergoes near-complete denaturation at the high concentration (> 0.1 M) of sodium pentadecyl sulfonate (SPDS), while only partial denaturation occurs at the concentration slightly below 0.1 M. In large part, protein denaturation is structurally manifested by disappearance of helical segments and loss of tertiary interactions. The computational prediction of the extent of burial of cysteine residues was experimentally validated by measuring the accessibility of the respective sulfhydryl groups. Overall, our work indicates an interesting synergy between electrostatic and hydrophobic contributions to lysozyme's denaturation process by anionic surfactants. In fact, first disulfide bridges and hydrogen bonds from protein surface to SPDS head groups loosen the protein globule followed by fuller denaturation via insertion of the surfactant's hydrophobic tails into the protein core.

Three asymmetric BODIPY derivatives as fluorescent probes for highly selective and sensitive detection of cysteine in living cells

Biothiols are widely involved in various important physiological activities and play a significant role in maintaining redox homeostasis in living organisms. Herein, we designed and synthesized three new asymmetric fluorescent probes (BDP-S-Ph, BDP-S-ENE and BDP-S-R) to discriminate Cys from Hcy/GSH. These probes reacted with Cys to form meso-amino-BODIPYs via SNAr substitution-rearrangement, thereby inducing a fluorescence turn-on effect. Moreover, they could selectively and sensitively detect Cys in solution with low detection limits (50 nM, 28 nM and 87 nM, respectively). Through comparing the response rates of the three probes to Cys, we concluded that the increase of conformational restrictions led to a decrease in probe reactivity. Besides, the sensing mechanism was demonstrated by mass spectrometry. Furthermore, cell experiments indicated that the probes were able to image exogenous and endogenous Cys through green or red channels in living cells.

Design and synthesis of a novel "turn-on" long range measuring fluorescent probe for monitoring endogenous cysteine in living cells and Caenorhabditis elegans

Cysteine (Cys) is an indispensable small organic molecule containing sulfhydryl groups, which has essential regulatory effects on the physiological process of human body. In this work, a red emission fluorescent probe TCFQ-Cys was designed and exploited based on 2-(3-cyano-4,5,5-trimethylfuran-2(5H)-ylidene) malononitrile-derivatives. The probe could effectively monitor Cys through the typical acrylate cleavage. The detecting system showed a red emission at 633 nm and the fluorescence was stable within the pH range of 6-9. The detection could be completed in 30 min. TCFQ-Cys presented high sensitivity with a detection limit of 0.133 μM and high selectivity towards Cys from other biological mercaptans. The most important feature was that the system had a wide linear range of 0-300 μM, which covered the physiological requirements of Cys detection. Subsequently, we conducted the biological imaging of Cys in MCF-7 cells and Caenorhabditis elegans (C. elegans). Therefore, TCFQ-Cys had a practical application prospect for further investigating the physiological function of Cys.

Selective adsorption of palladium and platinum from secondary wastewater using Escherichia coli BL21 and Providencia vermicola

It is important to recover precious metals from secondary wastewater because of their low crustal abundance. The selective adsorption of palladium (Pd) and platinum (Pt) ions from secondary wastewater, which contains a large amount aluminium and sodium ions, was investigated using Escherichia coli BL21 (BL21), genetically modified E. coli BL21 (EC20) and Providencia vermicola (P. V.). The results demonstrated that P.V., BL21 and EC20 cells took 95.9%, 88.2% and 97.5% of Pd ions, and 64.8%, 93.2% and 100% of Pt ions form industrial wastewater, respectively. All three bacterial biomass could be reused for Pd adsorption with a second adsorption efficiency of > 85%, specifically, the EC20 cells could absorb 93.8% of Pd ions from wastewater. SEM-EDS and XPS analyses confirmed the occurrence of Pd and Pt on the surface of wastewater-absorbed biomass. The shift in FTIR spectrum implied that functional groups, such as hydroxyl, amino, carboxyl and phosphate groups, were involved in wastewater adsorption.

Simultaneous quantification of multiple endogenous biothiols in single living cells by plasmonic Raman probes

Three endogenous biothiols in single cells were simultaneously quantified by plasmonic Raman probes and quantitative principal component analysis (qPCA).

Intracellular biothiols mediate many important physiological and pathological processes. Due to their low content and competing thiol-reactivity, it is still an unmet challenge to quantify them within a complicated intracellular environment. Herein, we demonstrated a strategy to discriminate three biothiols, i.e. cysteine (Cys), homo-cysteine (Hcy) and glutathione (GSH), and quantify their concentrations within single living cells, using one platform of Raman probe. By monitoring the reaction kinetics of biothiols with Raman probes and discriminating their products with a quantitative principal component analysis (qPCA) method, these three biothiols could be simultaneously quantified in both cell lysis and single living cells. The concentrations of Cys, Hcy and GSH in single Hela cells were 158 ± 19 μM, 546 ± 67 μM and 5.07 ± 0.62 mM, respectively, which gives the precise concentrations of these three biothiols at a single cell level for the first time. This method provides a general strategy for discriminating each component from a mixed system and has potential for quantifying any biomolecules within an in vitro or in vivo biological environment.

Green and Sustainable Technology for High-Efficiency and Low-Damage Manipulation of Densely Crosslinked Proteins

A two-step technology using nontoxic and eco-friendly chemicals is developed for the durable setting of densely/highly crosslinked proteins, such as wool and hair. Currently, most technologies for morphological modification are effective only for materials from non-highly-crosslinked proteins and cellulose. Before their morphological change, only water is needed to interrupt hydrogen bonds and ionic linkages, which stabilize the relative positions of molecules in non-highly-crosslinked proteins and cellulose. However, highly crosslinked proteins contain disulfide crosslinks, which are insusceptible to water. Thus, the controlled cleavage of disulfide bonds is required for creating new morphologies of highly crosslinked protein materials, such as hair and wool. Herein, cysteine and citric acid (CA) were used for the two-step setting of highly crosslinked proteins. This recipe showed better morphological change and less mechanical loss than commercial hair styling products. A reaction between CA and keratin was proposed, and verified via NMR and Raman spectra and titration. This technology could be a prospective alternative to achieve durable hair setting, anticrease finishing of wool textiles, and other durable morphological changes needed for highly crosslinked proteins.

TAT-Modified Gold Nanoparticle Carrier with Enhanced Anticancer Activity and Size Effect on Overcoming Multidrug Resistance

Highly efficient targeted delivery is crucial for successful anticancer chemotherapy. In this study, we developed a drug delivery system ANS-TAT-AuNP that loads anticancer molecule 2-(9-anthracenylmethylene)-hydrazinecarbothioamide (ANS) via conjugation with cell-penetrating peptide TAT modified AuNPs. The in vitro study showed that the IC₅₀ value of ANS-TAT-AuNPs_3.8 nm reduced by 11.28- (24 h) and 12.64-fold (48 h) after incubation with liver hepatocellular carcinoma HepG₂ cells compared to that of free ANS, suggesting that TAT modified AuNPs could enhance the antiproliferative activity of ANS. Also, ANS-TAT-AuNPs showed a size effect on overcoming multidrug resistance (MDR). The potential of ANS-TAT-AuNPs in overcoming MDR was assessed with MCF-7/ADR drug-resistant cell line, the drug resistance index (DRI) of which was extremely high (>190). The DRI of ANS-TAT-AuNPs_22.1 nm decreased dramatically to 1.48 (24 h) and 2.20 (48 h), while that of ANS-TAT-AuNPs_3.8 nm decreased to 7.64 (24 h) and 7.77 (48 h), indicating that ANS-TAT-AuNPs_22.1 nm could treat extremely resistant MCF-7/ADR cancer cells as drug sensitive ones. The data suggest that the larger AuNPs had more profound effect on overcoming MDR, which could effectively prevent drug efflux due to their size being much larger than that of the p-glycoprotein channel (9-25 Å).

Resonance Raman Probes for Organelle-Specific Labeling in Live Cells

Raman microspectroscopy provides for high-resolution non-invasive molecular analysis of biological samples and has a breakthrough potential for dissection of cellular molecular composition at a single organelle level. However, the potential of Raman microspectroscopy can be fully realized only when novel types of molecular probes distinguishable in the Raman spectroscopy modality are developed for labeling of specific cellular domains to guide spectrochemical spatial imaging. Here we report on the design of a next generation Raman probe, based on BlackBerry Quencher 650 compound, which provides unprecedentedly high signal intensity through the Resonance Raman (RR) enhancement mechanism. Remarkably, RR enhancement occurs with low-toxic red light, which is close to maximum transparency in the biological optical window. The utility of proposed RR probes was validated for targeting lysosomes in live cultured cells, which enabled identification and subsequent monitoring of dynamic changes in this organelle by Raman imaging.

Filamentous virus decoration with gold nanoparticles: global fingerprints of bionanocomposites acquired with SERS

A bioconjugation reaction is used to obtain fd viruses with one gold nanoparticle at the tip and gold nanowire-like structures.

Multimolecular salivary mucin complex is altered in saliva of cigarette smokers: detection of disulfide bridges by Raman spectroscopy

Saliva contains mucins, which protect epithelial cells. We showed a smaller amount of salivary mucin, both MG1 and MG2, in the premenopausal female smokers than in their nonsmoking counterparts. Smokers' MG1, which contains almost 2% cysteine/half cystine in its amino acid residues, turned out to be chemically altered in the nonsmoker's saliva. The smaller acidic glycoprotein bands were detectable only in smoker's saliva in the range of 20–25 kDa and at 45 kDa, suggesting that degradation, at least in part, caused the reduction of MG1 mucin. This is in agreement with the previous finding that free radicals in cigarette smoke modify mucins in both sugar and protein moieties. Moreover, proteins such as amylase and albumin are bound to other proteins through disulfide bonds and are identifiable only after reduction with DTT. Confocal laser Raman microspectroscopy identified a disulfide stretch band of significantly stronger intensity per protein in the stimulated saliva of smokers alone. We conclude that the saliva of smokers, especially stimulated saliva, contains significantly more oxidized form of proteins with increased disulfide bridges, that reduces protection for oral epithelium. Raman microspectroscopy can be used for an easy detection of the damaged salivary proteins.

Identification of a redox-sensitive switch within the JAK2 catalytic domain

Four cysteine residues (Cys866, Cys917, Cys1094, and Cys1105) have direct roles in cooperatively regulating Janus kinase 2 (JAK2) catalytic activity. Additional site-directed mutagenesis experiments now provide evidence that two of these residues (Cys866 and Cys917) act together as a redox-sensitive switch, allowing JAK2's catalytic activity to be directly regulated by the redox state of the cell. We created several variants of the truncated JAK2 (GST/(NΔ661)rJAK2), which incorporated cysteine-to-serine or cysteine-to-alanine mutations. The catalytic activities of these mutant enzymes were evaluated by in vitro autokinase assays and by in situ autophosphorylation and transphosphorylation assays. Cysteine-to-alanine mutagenesis revealed that the mechanistic role of Cys866 and Cys917 is functionally distinct from that of Cys1094 and Cys1105. Most notable is the observation that the robust activity of the CC866,917AA mutant is unaltered by pretreatment with dithiothreitol or o-iodosobenzoate, unlike all other JAK2 variants previously examined. This work provides the first direct evidence for a cysteine-based redox-sensitive switch that regulates JAK2 catalytic activity. The presence of this redox-sensitive switch predicts that reactive oxygen species can impair the cell's response to JAK-coupled cytokines under conditions of oxidative stress, which we confirm in a murine pancreatic β-islet cell line.

Intra- and inter-subunit disulfide bond formation is nonessential in adeno-associated viral capsids

The capsid proteins of adeno-associated viruses (AAV) have five conserved cysteine residues. Structural analysis of AAV serotype 2 reveals that Cys289 and Cys361 are located adjacent to each other within each monomer, while Cys230 and Cys394 are located on opposite edges of each subunit and juxtaposed at the pentamer interface. The Cys482 residue is located at the base of a surface loop within the trimer region. Although plausible based on molecular dynamics simulations, intra- or inter-subunit disulfides have not been observed in structural studies. In the current study, we generated a panel of Cys-to-Ser mutants to interrogate the potential for disulfide bond formation in AAV capsids. The C289S, C361S and C482S mutants were similar to wild type AAV with regard to titer and transduction efficiency. However, AAV capsid protein subunits with C230S or C394S mutations were prone to proteasomal degradation within the host cells. Proteasomal inhibition partially blocked degradation of mutant capsid proteins, but failed to rescue infectious virions. While these results suggest that the Cys230/394 pair is critical, a C394V mutant was found viable, but not the corresponding C230V mutant. Although the exact nature of the structural contribution(s) of Cys230 and Cys394 residues to AAV capsid formation remains to be determined, these results support the notion that disulfide bond formation within the Cys289/361 or Cys230/394 pair appears to be nonessential. These studies represent an important step towards understanding the role of inter-subunit interactions that drive AAV capsid assembly.

The C-terminal cysteine annulus participates in auto-chaperone function for Salmonella phage P22 tailspike folding and assembly

Elongated trimeric adhesins are a distinct class of proteins employed by phages and viruses to recognize and bind to their host cells, and by bacteria to bind to their target cells and tissues. The tailspikes of E. coli phage K1F and Bacillus phage Ø29 exhibit auto-chaperone activity in their trimeric C-terminal domains. The P22 tailspike is structurally homologous to those adhesins. Though there are no disulfide bonds or reactive cysteines in the native P22 tailspikes, a set of C-terminal cysteines are very reactive in partially folded intermediates, implying an unusual local conformation in the domain. This is likely to be involved in the auto-chaperone function. We examined the unusual reactivity of C-terminal tailspike cysteines during folding and assembly as a potential reporter of auto-chaperone function. Reaction with IAA blocked productive refolding in vitro, but not off-pathway aggregation. Two-dimensional PAGE revealed that the predominant intermediate exhibiting reactive cysteine side chains was a partially folded monomer. Treatment with reducing reagent promoted native trimer formation from these species, consistent with transient disulfide bonds in the auto-chaperone domain. Limited enzymatic digestion and mass spectrometry of folding and assembly intermediates indicated that the C-terminal domain was compact in the protrimer species. These results indicate that the C-terminal domain of the P22 tailspike folds itself and associates prior to formation of the protrimer intermediate, and not after, as previously proposed. The C-terminal cysteines and triple β-helix domains apparently provide the staging for the correct auto-chaperone domain formation, needed for alignment of P22 tailspike native trimer.

Time-resolved events on the reaction pathway of transcript initiation by a single-subunit RNA polymerase: Raman crystallographic evidence

The nucleotidyl transfer reaction leading to formation of the first phosphodiester bond has been followed in real time by Raman microscopy, as it proceeds in single crystals of the N4 phage virion RNA polymerase (RNAP). The reaction is initiated by soaking nucleoside triphosphate (NTP) substrates and divalent cations into the RNAP and promoter DNA complex crystal, where the phosphodiester bond formation is completed in about 40 min. This slow reaction allowed us to monitor the changes of the RNAP and DNA conformations as well as bindings of substrate and metal through Raman spectra taken every 5 min. Recently published snapshot X-ray crystal structures along the same reaction pathway assisted the spectroscopic assignments of changes in the enzyme and DNA, while isotopically labeled NTP substrates allowed differentiation of the Raman spectra of bases in substrates and DNA. We observed that substrates are bound at 2-7 min after soaking is commenced, the O-helix completes its conformational change, and binding of both divalent metals required for catalysis in the active site changes the conformation of the ribose triphosphate at position +1. These are followed by a slower decrease of NTP triphosphate groups due to phosphodiester bond formation that reaches completion at about 15 min and even slower complete release of the divalent metals at about 40 min. We have also shown that the O-helix movement can be driven by substrate binding only. The kinetics of the in crystallo nucleotidyl transfer reaction revealed in this study suggest that soaking the substrate and metal into the RNAP-DNA complex crystal for a few minutes generates novel and uncharacterized intermediates for future X-ray and spectroscopic analysis.

Evidence for the presence of a critical disulfide bond in the mouse EP3γ receptor

To determine the contribution of cysteines to the function of the mouse E-prostanoid subtype 3 gamma (mEP3γ), we tested a series of cysteine-to-alanine mutants. Two of these mutants, C107A and C184A, showed no agonist-dependent activation in a cell-based reporter assay for mEP3γ, whereas none of the other cysteine-to-alanine mutations disrupted mEP3γ signal transduction. Total cell membranes prepared from HEK293 cells transfected with mEP3γ C107A or C184A had no detectable radioligand binding. Other mutant mEP3γ receptors had radioligand affinities and receptor densities similar to wild-type. Cell-surface ELISA against the N-terminal HA-tag of C107A and C184A demonstrated 40% and 47% reductions respectively in receptor protein expression at the cell surface, and no radioligand binding was detected as assessed by intact cell radioligand binding experiments. These data suggest a key role for C107 and C184 in both receptor structure/stability and function and is consistent with the presence of a conserved disulfide bond between C107 and C184 in mouse EP3 that is required for normal receptor expression and function. Our results also indicate that if a second disulfide bond is present in the native receptor it is non-essential for receptor assembly or function.

Differences in the molecular structure of beta(2)-microglobulin between two morphologically different amyloid fibrils

Differences in the molecular structures of beta(2)-microglobulin between the two morphologically different amyloid fibrils having a needlelike [long-straight (LS)] and flexible [wormlike (WL)] character were investigated by infrared, Raman, and vacuum-ultraviolet circular dichroism spectroscopy. It turned out that although the beta-sheet content was comparable between the two kinds of fibrils (53 +/- 6% for the LS fibril and 47 +/- 6% for the WL fibril), the protonation states of the carboxyl side chains were distinctly different; the deprotonated (COO(-)) and protonated (COOH) forms were dominant in the LS and WL fibrils at pH 2.5, respectively, meaning that the pK(a) is specifically lowered in the LS fibril. Such a difference was not observed for the fibrils of the core fragments. Since site-specific interactions generally cause variation in the pK(a) of carboxyl side chains in proteins, these results suggest that "hook"-like interactions generated by hydrogen bonding and the formation of a salt bridge are present in the LS fibril, providing enthalpic stabilization. Presumably, the carboxyl groups fix the spatial arrangement of beta-strands and beta-sheets, bringing about the needlelike morphology. The absence of this regulation would result in the flexible morphology of the WL fibril, providing entropic stabilization.

The cataract-associated R14C mutant of human gamma D-crystallin shows a variety of intermolecular disulfide cross-links: a Raman spectroscopic study

The Arg14 to Cys (R14C) mutation in the human gammaD-crystallin (HGD) gene has been associated with a juvenile-onset hereditary cataract. We showed previously [Pande, A., et al. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 1993-1998] that rapid oxidation of Cys14 in the mutant leads to the formation of intermolecular, disulfide-cross-linked aggregates at physiological pH. Here we present a Raman spectroscopic analysis of R14C and HGD and show that R14C forms such aggregates even at pH 4.5. The lower pH enabled us to monitor the evolution of a variety of disulfide cross-links with distinct conformations around the CC-SS-CC dihedral angles. At least three cysteine residues are involved, forming protein-protein cross-links through disulfide-exchange reactions. From the pattern of the S-S and Trp Raman bands, we infer that Cys32 is likely to be involved in the cross-linking. The data suggest that protein precipitation in the mutant may not be the direct result of disulfide cross-linking, although such cross-linking is the initiating event. Thus, our Raman data not only enhance the understanding of the reactivity of Cys14 in the R14C mutant and the mechanism of opacity, but also shed light on the mechanism of oxidative degradation during long-term storage of thiol-containing pharmaceuticals.

Phase transitions in the crystals of L- and DL-cysteine on cooling: the role of the hydrogen-bond distortions and the side-chain motions. 2. DL-cysteine

Structural strain and a first-order phase transition in the crystalline DL-cysteine on cooling and on reverse heating were followed by Raman spectroscopy and X-ray diffraction. The transition is reversible and has a large hysteresis (over 100 K). The temperature at which the transition is observed depends strongly on the cooling/heating rate. The phase transition is accompanied by crystal fragmentation. The low-temperature phase could be obtained not only as a result of the solid-state transformation in situ as a polycrystalline sample (with strong preferred orientation, or without it, depending on the preparative technique), but also (using an original crystallization technique) as a single crystal of the quality suitable for structural analysis. For the first time, the crystal structure of the low-temperature phase was solved independently by powder and by single-crystal diffraction techniques. The spectral changes were correlated with the precise diffraction data on the intramolecular conformations and the intermolecular hydrogen bonding before and after the phase transition. The role of the distortion of the intermolecular hydrogen bonds and of the motions of the -CH(2)SH side chains in the phase transition is discussed in a comparison with the low-temperature phase transition in L-cysteine, which is of a different type and preserves the single crystals intact (Kolesov et al. J. Phys. Chem. B, 2008, 112 (40), 12827-12839).

Raman tweezers provide the fingerprint of cells supporting the late stages of KSHV reactivation

Kaposi's sarcoma-associated herpesvirus (KSHV) has both latent and lytic phases of replication. The molecular switch that triggers a reactivation is still unclear. Cells from the S phase of the cell cycle provide apt conditions for an active reactivation. In order to specifically delineate the Raman spectra of cells supporting KSHV reactivation, we followed a novel approach where cells were sorted based on the state of infection (latent versus lytic) by a flow cytometer and then analysed by the Raman tweezers. The Raman bands at 785, 813, 830, 1095 and 1128 cm(-1) are specifically altered in cells supporting KSHV reactivation. These five peaks make up the Raman fingerprint of cells supporting KSHV reactivation. The physiological relevance of the changes in these peaks with respect to KSHV reactivation is discussed in the following report.

Conformation and Side Chains Environments of Recombinant Human Interleukin-1 Receptor Antagonist (rh-IL-1ra) Probed by Raman, Raman Optical Activity, and UV-Resonance Raman Spectroscopy

The conformation and local environments of the side chains cysteines and aromatics of recombinant human interleukin-1 receptor antagonist (rh-IL-1ra) have been studied by visible Raman, Raman optical activity (ROA) and UVRR spectroscopy. The results reveal that the secondary structure of rh-IL-1ra is predominantly beta-sheet, which is consistent with conclusions from multinuclear NMR in solutions and X-ray diffraction analysis of crystals. It confirms that all four cysteines are in reduced state. Three cysteines are not hydrogen bonded and exposed. One cysteine is moderately hydrogen bonded and buried. This explains the earlier observation that only three cysteines were detectable using DTNB titration. No characteristic Raman band of disulfide bond was observed in the Raman spectra of rh-IL-1ra in both solution and in crystals. It rules out the supposition that there is one disulfide bond in rh-IL-1ra crystals based on X-ray diffraction. Raman and UVRR spectra of rh-IL-1ra exhibit canonical marker bands of tryptophan. They do not support the proposal that there is cation-pi interaction involving tryptophans in solutions and crystals. These results demonstrate that Raman spectroscopy offers certain advantages over X-ray diffraction for studies of detailed local environment and intermolecular interactions of side chains of proteins in solution and in crystals.

Raman spectroscopy of protein pharmaceuticals

Recent advances in optical and spectroscopic technologies have enabled a plethora of Raman spectrometers that are suitable for studies of protein pharmaceuticals. Highly sensitive Raman spectrometers have overcome the handicap of the fundamentally weak Raman effect that hampered their applications to protein pharmaceuticals in the past. These Raman spectrometers can now routinely measure protein therapeutics at the low concentration of 1 mg/mL, which is on par with other spectroscopic methods such as CD, fluorescence and FTIR spectroscopies. In this article, various Raman techniques that can be used for protein pharmaceutical studies are reviewed. Novel Raman marker of proteins discovered from fundamental studies of protein complexes are examined along with established Raman spectra and structure correlations. Examples of Raman spectroscopic studies of protein pharmaceuticals are demonstrated. Future applications of Raman spectroscopy to protein pharmaceuticals are discussed.

Mechanism of interaction of Pb(II) with milk proteins: a case study of alpha-casein

Alpha-casein is the major casein protein fraction from bovine milk and is responsible for binding to many ligands. This paper reports the results on the interaction of Pb(II) with alpha-casein. The interaction studies by spectroscopic titration indicate that Pb(II) has two binding sites with an association constant (ka) of (2.3 +/- 0.2) x 10 (5) M(-1). Raman spectra of the alpha-casein-Pb(II) complex show reduction in the amide I region as well as minor perturbations in the sulfhydryl region of alpha-casein. Stopped-flow studies show that the reaction mechanism of Pb(II) follows a pseudo-first-order reaction with a rate of 25 +/- 6 s(-1). The stopped-flow time-resolved spectra show peaks at 330 and 360 nm, correlating to Pb(II)-thiolate bands in the UV absorption spectra. Modification of cysteines present in alpha-casein does not result in binding of lead, indicating that cysteines could be one of the Pb(II) binding sites.

Impact of in vitro assembly defects on in vivo function of the phage P22 portal

The podovirus P22, which infects O-antigen strains of Salmonella, incorporates a dsDNA translocating channel (portal dodecamer) at a unique vertex of the icosahedral capsid. The portal subunit (gp1, 82.7 kDa) exhibits multiple S-Hcdots, three dots, centeredX hydrogen bonding states for cysteines 153, 173, 283 and 516 and these interactions are strongly perturbed by portal ring formation. Here, we analyze in vivo activities of wild type (wt) and Cys-->Ser mutant portals, demonstrate that in vivo activity is correlated with in vitro assembly kinetics, and suggest mechanistic bases for the observed assembly defects. The C283S portal protein, which assembles into rings at about half the rate of wt, exhibits significantly diminished infectivity ( approximately 50% of wt) and manifests its defect prior to DNA packaging, most likely at the stage of procapsid assembly. Conversely, the C516S mutant, which assembles at twice the rate of wt, is more severely deficient in vivo ( approximately 20% of wt) and manifests its defect subsequent to capsid maturation and DNA packaging. Both C153S and C173S portals function at levels close to wt. The results suggest that C283S and C516S mutations may be exploited for improved characterization of the folding and assembly pathway of P22 portal protein.

Four free cysteine residues found in human IgG1 of healthy donors

Modifications with different thiol reagents demonstrated that 28 of 32 cysteine residues of human IgG1 are involved in the formation of disulfide bonds, and four cysteines remain free. So IgG1 is a protein possessing both free SH-groups and disulfide bonds. Only one of the four SH-groups is accessible for silver or mercury ions and hydrophobic reagents, whereas the remaining three SH-groups are masked and can be revealed only after deep denaturation of the protein. Detection of the masked cysteine residues was shown to depend on the kinetics of intramolecular changes occurring during denaturation of the protein and on the method of the assay of the SH-groups.

Stalled folding mutants in the triple beta-helix domain of the phage P22 tailspike adhesin

The trimeric bacteriophage P22 tailspike adhesin exhibits a domain in which three extended strands intertwine, forming a single turn of a triple beta-helix. This domain contains a single hydrophobic core composed of residues contributed by each of the three sister polypeptide chains. The triple beta-helix functions as a molecular clamp, increasing the stability of this elongated structural protein. During folding of the tailspike protein, the last precursor before the native state is a partially folded trimeric intermediate called the protrimer. The transition from the protrimer to the native state results in a structure that is resistant to denaturation by heat, chemical denaturants, and proteases. Random mutations were made in the region encoding residues 540-548, where the sister chains begin to wrap around each other. From a set of 26 unique single amino acid substitutions, we characterized mutations at G546, N547, and I548 that retarded or blocked the protrimer to native trimer transition. In contrast, many non-conservative substitutions were tolerated at residues 540-544. Sucrose gradient analysis showed that protrimer-like mutants had reduced sedimentation, 8.0 S to 8.3 S versus 9.3 S for the native trimer. Mutants affected in the protrimer to native trimer transition were also destabilized in their native state. These data suggest that the folding of the triple beta-helix domain drives transition of the protrimer to the native state and is accompanied by a major rearrangement of polypeptide chains.

Identification by Site-directed Mutagenesis and Chemical Modification of Three Vicinal Cysteine Residues in Rat Mitochondrial Carnitine/Acylcarnitine Transporter

The proximity of the Cys residues present in the mitochondrial rat carnitine/acylcarnitine carrier (CAC) primary structure was studied by using site-directed mutagenesis in combination with chemical modification. CAC mutants, in which one or more Cys residues had been replaced with Ser, were overexpressed in Escherichia coli and reconstituted into liposomes. The effect of SH oxidizing, cross-linking, and coordinating reagents was evaluated on the carnitine/carnitine exchange catalyzed by the recombinant reconstituted CAC proteins. All the tested reagents efficiently inhibited the wild-type CAC. The inhibitory effect of diamide, Cu(2+)-phenanthroline, or phenylarsine oxide was largely reduced or abolished by the double substitutions C136S/C155S, C58S/C136S, and C58S/C155S. The decrease in sensitivity to these reagents was much lower in double mutants in which Cys(23) was substituted with Cys(136) or Cys(155). No decrease in inhibition was found when Cys(89) and/or Cys(283) were replaced with Ser. Sb(3+), which coordinates three cysteines, inhibited only the Cys replacement mutants containing cysteines 58, 136, and 155 of the six native cysteines. In addition, the mutant C23S/C89S/C155S/C283S, in which double tandem fXa recognition sites were inserted in positions 65-72, i.e. between Cys(58) and Cys(136), was not cleaved into two fragments by fXa protease after treatment with diamide. These results are interpreted in light of the homology model of CAC based on the available x-ray structure of the ADP/ATP carrier. They indicate that Cys(58), Cys(136), and Cys(155) become close in the tertiary structure of the CAC during its catalytic cycle.

Characterization of amino acids using Raman spectroscopy

A key process in the development of new drugs is elucidation of the interaction between the drug molecule and the target protein. Such knowledge then makes it possible to make systematic structural modifications of the drug molecule to optimize the interaction. Many analytical techniques can be applied to proteins in solution such as circular dichroism, ultraviolet, and fluorescence spectroscopy but these all have limitations. In this paper, we investigate the feasibility of using relatively simple, visible light Raman spectroscopic methods to investigate amino acids and related biopolymers.