New structural insights into the refolding of ribonuclease T1 as seen by time-resolved Fourier-transform infrared spectroscopy

Spectroscopic Investigation of Phosphorus Mineralization as Affected by the Calcite-Water Interfacial Chemistry

The mineralization and bioavailability of phytic acid, the predominant organic phosphorus (OP) species in many soils, have generally been rendered limited due to its interaction with soil minerals. In particularly calcareous and neutral to slightly alkaline soils, phytic acid is known to actively react with calcite, although how this interaction affects phytic acid mineralization is still unknown. This study, therefore, investigated the mechanisms regarding how the calcite-water interface influences phytic acid mineralization by phytase, at pHs 6 and 8 using in situ spectroscopic techniques including solution nuclear magnetic resonance and attenuated total reflection Fourier transform infrared spectroscopy. The findings indicated a pH-specific effect of the calcite-water interface. Inhibited phytase activity and thus impaired phytic acid mineralization were induced by calcite at pH 6, while the opposite effect was observed at pH 8. How the interaction between phytic acid and calcite and between phytase and calcite differed between the two pH values contributed to the pH-specific effect. The results demonstrate the importance of soil pH, enzyme-, and OP-clay mineral interactions in controlling the mineralization and transformation of OP and, consequently, the release of phosphate in soils. The findings can also provide implications for the management of calcite-rich and limed soils.

Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation

The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.

Structural insight on the liquid silk from the middle silk gland of non-mulberry silkworm Antheraea assamensis

This study highlights the preliminary characterization of liquid silk from the middle silk gland (MSG) along with the in-silico analysis of the sericin protein of a less explored non mulberry silkworm Antheraea assamensis which is endemic to the North Eastern region of India. Various biophysical methods have been applied to elucidate the conformational patterns of the liquid silk present inside the MSG without removing the sericin layer. This will help us to know the actual features of the in vivo transitional status of the silk in the MSG which travel towards the anterior silk gland (ASG) prior to spinning. The SDS PAGE analysis represented the existence of the both fibroin and sericin bands in the sample. The structural pattern of the MSG liquid silk as revealed by various methods denoted the occurrence of β-sheet component along with some random coil and β-turn components which in turn suggests the transitional state of the liquid silk attributed to the existence of both the crystalline and amorphous contents. The thermo gravimetric study and the aggregation behavior analysis results proposed the occurrence of intermolecular hydrogen bonding between the sericin and fibroin in the MSG. This study will sensitize the better understanding of the behavior of the liquid silk in the MSG of non-mulberry silkworm A. assamensis and will open avenues for various application-based studies of this silk.Communicated by Ramaswamy H. Sarma.

Structural changes of Bombyx mori fibroin from silk gland to fiber as evidenced by Terahertz spectroscopy and other methods

Here we investigated the structural changes of silk fibroin during Bombyx mori silkworm spinning and reconstitution process. X-ray diffraction, Fourier transform infrared spectroscopy, polarized optical microscopy, and terahertz (THz) spectroscopy were applied to monitor the structural features of silk fibroin from posterior, middle silk glands, to cocoons, and then to reconstituted silk. Results show that from silk gland to cocoon, fibroin experiences a significant transformation in crystal structure from a typical silk I, to a silk I-rich mixed structure, and finally to a typical silk II state, accompanied with a change in secondary structure from α-helix and random coil structures to preferential orientation β-sheets. Compared with natural silk fibroins, the reconstituted silk fibroin lacks β-sheet conformation and orientation crystallization. Terahertz spectroscopy readily follows these silk fibroin structural changes. Two characteristic peaks for silk fibroin is observed in 2-10 THz. Their strength ratio is strongly correlated with the β-sheet conformation. The absorbance properties in 0.2-2.0THz also significantly change as a function of changing their crystal structures caused by diverse sources. All of these observations will help in the study of overall structure in silk fibroin to understand more completely the fibroin assembly process in natural spinning and reconstitution process.

Regenerated silk materials for functionalized silk orthopedic devices by mimicking natural processing

Silk fibers spun by silkworms and spiders exhibit exceptional mechanical properties with a unique combination of strength, extensibility and toughness. In contrast, the mechanical properties of regenerated silk materials can be tuned through control of the fabrication process. Here we introduce a biomimetic, all-aqueous process, to obtain bulk regenerated silk-based materials for the fabrication of functionalized orthopedic devices. The silk materials generated in the process replicate the nano-scale structure of natural silk fibers and possess excellent mechanical properties. The biomimetic materials demonstrate excellent machinability, providing a path towards the fabrication of a new family of resorbable orthopedic devices where organic solvents are avoided, thus allowing functionalization with bioactive molecules to promote bone remodeling and integration.

Extraordinary stability of hemocyanins from L. polyphemus and E. californicum studied using infrared spectroscopy from 294 to 20 K

Infrared spectroscopic evidence of a high stability towards exposure to sub-zero temperatures for hemocyanins from the arthropods Limulus polyphemus and Eurypelma californicum.

FTIR spectral signature of anticancer drugs. Can drug mode of action be identified?

Infrared spectroscopy has brought invaluable information about proteins and about the mechanism of action of enzymes. These achievements are difficult to transpose to living organisms as all biological molecules absorb in the mid infrared, with usually a high degree of overlap. Deciphering the contribution of each enzyme is therefore almost impossible. On the other hand, small changes in the infrared spectra of cells induced by environmental conditions or drugs may provide an accurate signature of the metabolic shift experienced by the cell as a response to a change in the growth medium. The present paper aims at reviewing the contribution of infrared spectroscopy to the description of small chemical changes that occur in cells when they are exposed to a drug. In particular, this review will focus on cancer cells and anti-cancer drugs. Results accumulated so far tend to demonstrate that infrared spectroscopy could be a very accurate descriptor of the mode of action of anticancer drugs. If confirmed, such a segmentation of potential drugs according to their "mode of action" will be invaluable for the discovery of new therapeutic molecules. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.

FTIR characterization of protein-polysaccharide interactions in extruded blends

Soy protein-based blends were processed by double screw extrusion and the effects of different types and contents of polysaccharides were analyzed. Although extrusion has not been widely used for this type of blends, in this study it was observed that the increase in polysaccharide content in blends caused a decrease in specific mechanical energy (SME), facilitating extrusion process and showing the potential of this process, which is more cost effective at industrial scale. In order to explain this behavior, infrared spectroscopy analysis was carried out, mainly in the amide I and II regions. Moreover, curve fitting analysis showed the conformational changes produced in the blends due to the addition of polysaccharides, which affected protein denaturation. These changes also affected properties such as moisture content (MC) and total solubility matter (TSM). However, conformational changes did not show significant effects with respect to piece density (PD) or in the expansion ratio (ER) of the pellets. The quantitative analysis of the changes in the amide I and II regions provided novel information about the modifications produced in protein-based blends modified with polysaccharides. In this context, infrared spectroscopy provided a convenient and powerful means to monitor interactions between all ingredients used in the blend formulation, which is of great importance in order to explain changes in the functional properties of biodegradable materials used for industrial applications in food and pharmaceutical industries.

Infrared spectroscopy of proteins

This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.

Maximum entropy deconvolution of infrared spectra: use of a novel entropy expression without sign restriction

Absorbance and difference infrared spectra are often acquired aiming to characterize protein structure and structural changes of proteins upon ligand binding, as well as for many other chemical and biochemical studies. Their analysis requires as a first step the identification of the component bands (number, position, and area) and as a second step their assignment. The first step of the analysis is challenged by the habitually strong band overlap in infrared spectra. Therefore, it is useful to make use of a mathematical method able to narrow the component bands to the extent to eliminate, or at least reduce, the band overlap. Additionally, to be of general applicability this method should permit negative values for the solution. We present a maximum entropy deconvolution approach for the band-narrowing of absorbance and difference spectra showing the required characteristics, which uses the generalized negative Burg-entropy (Itakura-Saito discrepancy) generalized for difference spectra. We present results on synthetic noisy absorbance and difference spectra, as well as on experimental infrared spectra from the membrane protein bacteriorhodopsin.

Formation of critical oligomers is a key event during conformational transition of recombinant syrian hamster prion protein

We have investigated the conformational transition and aggregation process of recombinant Syrian hamster prion protein (SHaPrP90-232) by Fourier transform infrared spectroscopy, circular dichroism spectroscopy, light scattering, and electron microscopy under equilibrium and kinetic conditions. SHaPrP90-232 showed an infrared absorbance spectrum typical of proteins with a predominant alpha-helical structure both at pH 7.0 and at pH 4.2 in the absence of guanidine hydrochloride. At pH 4.2 and destabilizing conditions (0.3-2 m guanidine hydrochloride), the secondary structure of SHaPrP90-232 was transformed to a strongly hydrogen-bonded, most probably intermolecularly arranged antiparallel beta-sheet structure as indicated by dominant amide I band components at 1620 and 1691 cm-1. Kinetic analysis of the transition process showed that the decrease in alpha-helical structures and the increase in beta-sheet structures occurred concomitantly according to a bimolecular reaction. However, the concentration dependence of the corresponding rate constant pointed to an apparent third order reaction. No beta-sheet structure was formed within the dead time (190 ms) of the infrared experiments. Light scattering measurements revealed that the structural transition of SHaPrP90-232 was accompanied by formation of oligomers, whose size was linearly dependent on protein concentration. Extrapolation to zero protein concentration yielded octamers as the smallest oligomers, which are considered as "critical oligomers." The small oligomers showed spherical and annular shapes in electron micrographs. Critical oligomers seem to play a key role during the transition and aggregation process of SHaPrP90-232. A new model for the structural transition and aggregation process of the prion protein is described.

Time-resolved FTIR difference spectroscopy as tool for investigating refolding reactions of ribonuclease T1 synchronized with trans --> cis prolyl isomerization

The structurally well-characterized enzyme ribonuclease T1 was used as a model protein to further evaluate time-resolved Fourier transform IR difference spectroscopy in conjunction with temperature-jump techniques as a useful detection technique for protein folding studies. Compared to the wild-type protein, it was confirmed that the lack of one cis-proline bond at position 55 of the S54G/P55N variant is sufficient to significantly simplify and accelerate the refolding process. This result was sustained by the characterization of the early refolding events that occurred within the experimental dead time.

Impact of four (13)C-proline isotope labels on the infrared spectra of ribonuclease T1

Ribonuclease T1 was biosynthesized, with all four prolines (13)C-labeled in the peptide C[double bond]O bond, using a proline auxotrophic yeast strain of Saccharomyces cerevisiae. The (13)C- and (12)C-proline isotopomers of ribonuclease T1 were investigated by infrared spectroscopy in the thermally unfolded and natively folded state at 80 and 20 degrees C, respectively. In the thermally unfolded state, both proteins established almost indistinguishable spectral features in the secondary structure sensitive amide I region. In contrast, the spectra measured at 20 degrees C revealed substantial qualitative and quantitative differences, though parallel analysis by circular dichroism suggested identical native folds for both isotopomers. Major spectral differences in the infrared spectra were detected at 1626 and 1679 cm(-1), which are diagnostic marker bands for antiparallel beta-sheets in ribonuclease T1 and at 1645 cm(-1), a region that is characteristic for the infrared absorption of irregular structures. Starting with the known three-dimensional structure of ribonuclease T1, the observed effects of the isotope labeling are discussed on the basis of transition dipole coupling between the (12)C[double bond]O and (13)C[double bond]O groups. The experimental results were confirmed by transition dipole coupling calculations of the amide I manifold of the labeled and unlabeled variant.

The infrared absorption of amino acid side chains

Amino acid side chains play fundamental roles in stabilising protein structures and in catalysing enzymatic reactions. These fields are increasingly investigated by infrared spectroscopy at the molecular level. To help the interpretation of the spectra, a review of the infrared absorption of amino acid side chains in H(2)O and 2H(2)O is given. The spectral region of 2600-900cm(-1) is covered.

Hydrogen peroxide-induced structural alterations of RNAse A

Proteins exposed to oxidative stress are degraded via proteolytic pathways. In the present study, we undertook a series of in vitro experiments to establish a correlation between the structural changes induced by mild oxidation of the model protein RNase A and the proteolytic rate found upon exposure of the modified protein toward the isolated 20 S proteasome. Fourier transform infrared spectroscopy was used as a structure-sensitive probe. We report here strong experimental evidence for oxidation-induced conformational rearrangements of the model protein RNase A and, at the same time, for covalent modifications of amino acid side chains. Oxidation-related conformational changes, induced by H(2)O(2) exposure of the protein may be monitored in the amide I region, which is sensitive to changes in protein secondary structure. A comparison of the time- and H(2)O(2) concentration-dependent changes in the amide I region demonstrates a high degree of similarity to spectral alterations typical for temperature-induced unfolding of RNase A. In addition, spectral parameters of amino acid side chain marker bands (Tyr, Asp) revealed evidence for covalent modifications. Proteasome digestion measurements on oxidized RNase A revealed a specific time and H(2)O(2) concentration dependence; at low initial concentration of the oxidant, the RNase A turnover rate increases with incubation time and concentration. Based on these experimental findings, a correlation between structural alterations detected upon RNase A oxidation and proteolytic rates of RNase A is established, and possible mechanisms of the proteasome recognition process of oxidatively damaged proteins are discussed.