Dehydration of main-chain amides in the final folding step of single-chain monellin revealed by time-resolved infrared spectroscopy

Kinetic IR spectroscopy was used to reveal β-sheet formation and water expulsion in the folding of single-chain monellin (SMN) composed of a five-stranded β-sheet and an α-helix. The time-resolved IR spectra between 100 μs and 10 s were analyzed based on two consecutive intermediates, I1 and I2, appearing within 100 μs and with a time constant of ≈100 ms, respectively. The initial unfolded state showed broad amide I′ corresponded to a fluctuating conformation. In contrast, I1 possessed a feature at 1,636 cm−1 for solvated helix and weak features assignable to turns, demonstrating the rapid formation of helix and turns. I2 possessed a line for solvated helix at 1,637 cm−1 and major and minor lines for β-sheet at 1,625 and 1,680 cm−1, respectively. The splitting of the major and minor lines is smaller than that of the native state, implying an incomplete formation of the β-sheet. Furthermore, both major and minor lines demonstrated a low-frequency shift compared to those of the native state, which was interpreted to be caused by hydration of the C=O group in the β-sheet. Together with the identification of solvated helix, the core domain of I2 was interpreted as being hydrated. Finally, slow conversion of the water-penetrated core of I2 to the dehydrated core of the native state was observed. We propose that both the expulsion of water, hydrogen-bonded to main-chain amides, and the completion of the secondary structure formation contribute to the energetic barrier of the rate-limiting step in SMN folding

Probing the cytochrome c′ folding landscape

The folding kinetics of R. palustris cytochrome c′ (cyt c′) have been monitored by heme absorption and native Trp72 fluorescence at pH 5. The Trp72 fluorescence burst signal suggests early compaction of the polypeptide ensemble. Analysis of heme transient absorption spectra reveals deviations from two-state behavior, including a prominent slow phase that is accelerated by the prolyl isomerase cyclophilin. A nonnative proline configuration (Pro21) likely interferes with the formation of the helical bundle surrounding the heme

New Insights into Metal Ion-Crown Ether Complexes Revealed by SEIRA Spectroscopy

We demonstrate a powerful spectroscopic technique, surface-enhanced infrared absorption (SEIRA) spectroscopy, not only for detecting host-guest complexes in solution but for examining the relationship between the guest selectivity, complex structure, and solvent effect. We synthesize thiol derivatives of 15-crown-5 and 18-crown-6 [2-(6-mercaptohexyloxy)methyl-15-crown-5 (15C5-C1OC6-SH) and 2-(6-mercaptohexyloxy)methyl-18-crown-6 (18C6-C1OC6-SH)] and adsorb them on gold surfaces through S–Au bonds. The IR difference spectra of the M+•15C5-C1OC6 (M = Li, Na, K, Rb, and Cs) complexes on gold are observed using aqueous solutions of MCl by SEIRA spectroscopy. The spectra show noticeable change in the C–O stretching vibration around 1100 cm–1. The spectral patterns of M+•15C5-C1OC6 are similar for Li+ and Na+, and for K+, Rb+, and Cs+; the interaction between the metal ions and 15C5-C1OC6 changes drastically between Na+ and K+ in the series of alkali metal ions. On the other hand, the equilibrium constant of the complex formation determined by the IR intensity shows clear preference for Na+ ion. We also observe the IR difference spectra of M+•18C6-C1OC6 in methanol and compare them with those in water. The spectral patterns in methanol are almost the same as those in water, but the equilibrium constant in methanol does not show preference for any ion, different from the K+ preference in water. From these findings we attribute the origin of the ion selectivity of 15C5 and 18C6 in solution to the interaction between the metal ions and the crown ethers in the complexes or the solvation energy of free ions. In the case of 15C5-C1OC6 in water, the preference of Na+ over K+, Rb+, and Cs+ can be attributed to the strength of the interaction or the size matching between the metal ions and 15C5-C1OC6; the Na+ selectivity over Li+ ion is dominated by the solvation energy of free ions. For 18C6-C1OC6 in methanol, the equilibrium constant for the complex formation becomes much bigger in methanol than that in water and loses the selectivity in methanol, because the solvation energy in methanol is fairly smaller than that in water, predominating the contribution from the strength of the interaction between the metal ions and 18C6-C1OC6. The IR spectra measured by SEIRA spectroscopy are quite sensitive to the property of host-guest complexes such as the intermolecular interaction, the structure, and the orientation against the gold surface. However, the evidence of the guest selectivity emerges primarily in the intensity of the spectra, rather than band positions or spectral patterns in the IR spectra.This work was partly supported by grants from JSPS to YF (22247024 and 24650203)

An oxyl/oxo mechanism for dioxygen bond formation in PSII revealed by X-ray free electron lasers

Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S0 to S4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S1, S2, and S3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S2, but flipping of D1 Glu189 upon transition to S3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn4CaO6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation

Capturing structural changes of the S-1 to S-2 transition of photosystem II using time-resolved serial femtosecond crystallography

Photosystem II (PSII) catalyzes light-induced water oxidation through an S-i-state cycle, leading to the generation of di-oxygen, protons and electrons. Pumpprobe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S-1-to-S-2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S-2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S-1-to-S-2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed

Oxygen-evolving photosystem II structures during S1–S2–S3 transitions

Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0–4) at the Mn4CaO5 cluster1,2,3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4,5,6,7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O–O bond formation