2D Correlation Analysis: Sequential Order Judging

Simultaneous bio-reduction of nitrate and Cr(VI) by mechanical milling activated corn straw

Abundant lignocellulose waste is an ideal energy source for environmental bioremediation, but its recalcitrance to bioavailability makes this a challenging prospect. We hypothesized that the disruption of straw's recalcitrant structure by mechanochemical ball milling would enhance its availability for the simultaneous bioreduction of nitrate and Cr(VI). The results showed that the ball-milling process increased the quantity of water-soluble organic matter released from corn straw and changed the composition of organic matter by strongly disrupting its lignocellulose structure. The increase in ball-milling time increased the specific surface area of the straw and favored the adhesion of microorganisms on the straw surface, which enhanced the bioavailability of the energy in the straw. Substantially increased removal of NO₃^--N (206.47 ± 0.67 mg/g) and Cr(VI) (37.62 ± 0.09 mg/g) was achieved by using straw that was ball milled for 240 min, which validated that ball milling can improve the utilization efficiency of straw by microorganisms. Cellular and molecular biological analyses showed that ball-milled straw increased microbial energy metabolism and cellular activity related to the electron transport chain. This work offers a potential way to achieve the win-win goal of utilizing agricultural wastes and remediating environmental pollution.

Monitoring Deuterium Uptake in Single Bacterial Cells via Two-Dimensional Raman Correlation Spectroscopy

Raman-stable isotope labeling using heavy water (Raman-D₂O) is attracting great interest as a fast technique with various applications ranging from the identification of pathogens in medical samples to the determination of microbial activity in the environment. Despite its widespread applications, little is known about the fundamental processes of hydrogen-deuterium (H/D) exchange, which are crucial for understanding molecular interactions in microorganisms. By combining two-dimensional (2D) correlation spectroscopy and Raman deuterium labeling, we have investigated H/D exchange in bacterial cells under time dependence. Most C-H stretching signals decreased in intensity over time, prior to the formation of the C-D stretching vibration signals. The intensity of the C-D signal gradually increased over time, and the shape of the C-D signal was more uniform after longer incubation times. Deuterium uptake showed high variability between the bacterial genera and mainly led to an observable labeling of methylene and methyl groups. Thus, the C-D signal encompassed a combination of symmetric and antisymmetric CD₂ and CD₃ stretching vibrations, depending on the bacterial genera. The present study allowed for the determination of the sequential order of deuterium incorporation into the functional groups of proteins, lipids, and nucleic acids and hence understanding the process of biomolecule synthesis and the growth strategies of different bacterial taxa. We present the combination of Raman-D₂O labeling and 2D correlation spectroscopy as a promising approach to gain a fundamental understanding of molecular interactions in biological systems.

Structural properties of an engineered outer membrane protein G mutant, OmpG-16SL, investigated with infrared spectroscopy

The structural and functional differences between wild type (WT) outer membrane protein G and its two mutants are investigated with Fourier transform infrared spectroscopy. Both mutants have a long extension to the primary sequence to increase the number of β-strands from 14 (wild type) to 16 in an attempt to enlarge the pore diameter. The comparison among proteins is made in terms of pH-dependent conformational changes and thermal stability. Results show that all proteins respond to pH change but at different degrees. At acidic environment, all proteins contain the same number of residues participated in β-sheet structure. However, at neutral pH, the mutants have less ordered structure compared to WT porin. Thermal stability tests show that mutants differ significantly from WT porin at neutral pH. Although the transition temperature is directly proportional with the amount of β-sheet content, the changes in the pre-transition phase that pave the way to structural breakdown are shown to involve interactions among charged residues by two-dimensional correlation spectroscopy analysis. Results of the analysis show that side chain interactions play an active role under increasing temperature. Both mutants have more unordered secondary structure but they respond to pH change in tertiary structure level. Findings of this study provided deeper insight on the active players in structural stability of the WT porin.Communicated by Ramaswamy H. Sarma [Formula: see text].

Generalized Two-dimensional Correlation Analysis for Unimodal Waveforms Modeled by Quadratic Polynomials

We describe further potential of generalized 2D correlation analysis, aiming to realize the automation of the sequential order determination of signal variations. By modeling unimodal waveforms using quadratic functions, we can analytically express 2D correlation functions to yield an index to determine the sequential order. Based on the obtained results, we find an exception for determining the sequential order of signal variations. To resolve the exception, we suggest an extended way of interpreting the sequential order of signal intensity changes.

Sequential Order of the Secondary Structure Transitions of Proteins under External Perturbations: Regenerated Silk Fibroin under Thermal Treatment

Whether the process of protein folding/unfolding is fully cooperative or it contains sequential elements has long been a fundamental issue in protein science. This issue seemingly became straightforward since the appearance of generalized two-dimensional (2D) correlation spectroscopy in 1990s, because 2D correlation analysis has been considered as a convenient and powerful analytical tool to determine the sequential order of events under external physical or chemical perturbations. In this work, the sequential order of the secondary structure transitions of regenerated silk fibroin under thermal treatment from 130 to 220 °C was first studied using generalized 2D correlation spectroscopy, but an apparently doubtful sequential order was obtained; β-sheet was the first one to change at low temperature, then the random coil, followed by the nonamide C═O and, finally, the α-helix. A subsequent detailed in situ infrared spectral analysis showed that the main secondary structures of silk fibroin, including α-helix, β-turn, random coil and β-sheet (high-wavenumber component), all changed with a fully cooperative manner at a relatively low temperature of 150 °C. But the low-wavenumber component of β-sheet started to change at a higher temperature of 180 °C. Besides, it has also been found that, before 200 °C, the loss of α-helix and random coil was transformed into β-turn, β-sheet, and nonamide C═O. After 200 °C, some β-turn structure was also disruptured and transformed into β-sheet and nonamide C═O.