Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a crystallographic method to track enzymatic reactions. Here we demonstrate the application of this method using fungal NO reductase, a heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, we identify a NO-bound form of the enzyme, which is an initial intermediate with a slightly bent Fe-N-O coordination geometry at a resolution of 2.1 Å. The NO geometry is compatible with those analyzed by XFEL-based cryo-crystallography and QM/MM calculations, indicating that we obtain an intact Fe3+-NO coordination structure that is free of X-ray radiation damage. The slightly bent NO geometry is appropriate to prevent immediate NO dissociation and thus accept H− from NADH. The combination of using XFEL and a caged-compound is a powerful tool for determining functional enzyme structures during catalytic reactions at the atomic level.

Multicomponent quantum mechanical (MC_QM) calculation has been extended with ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) scheme [ONIOM(MC_QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated the first implementation and application of ONIOM(MC_QM:MM) method for the analysis of the geometry and the isotope shift in hydrogen-bonding center of photoactive yellow protein. ONIOM(MC_QM:MM) calculation for a model with deprotonated Arg52 reproduced the elongation of O-H bond of Glu46 observed by neutron diffraction crystallography. Among the unique isotope shifts in different conditions, the model with protonated Arg52 with solvent effect reasonably provided the best agreement with the corresponding experimental values from liquid NMR measurement. Our results implied the availability of ONIOM(MC_QM:MM) to distinguish the local environment around hydrogen bonds in a biomolecule.

Hydrogen-bonding heterogeneous bilayers on substrates have been studied as a base for new functions of molecular adlayers by means of atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRAS), and density functional theory (DFT) calculations. Here, we report the formation of the catechol-fused bis(methylthio)tetrathiafulvalene (HCat-BMT-TTF) adlayer hydrogen bonding with an imidazole-terminated alkanethiolate self-assembled monolayer (Im-SAM) on Au(111). The heterogeneous bilayer is realized by sequential two-step immersions in solutions for the individual Im-SAM and HCat-BMT-TTF adlayer formations. In the measurements by AFM, a grained HCat-BMT-TTF adlayer on Im-SAM is revealed. The coverage and the chemical states of HCat-BMT-TTF on Im-SAM are specified by XPS. On the vibrational spectrum measured by IRAS, the strong hydrogen bonds between HCat-BMT-TTF and Im-SAM are characterized by the remarkably red-shifted OH stretching mode at 3140 cm, which is much lower than that for hydrogen-bonding water (typically ∼3300 cm). The OH stretching mode frequency and the adsorption strength for the HCat-BMT-TTF molecule hydrogen bonding with imidazole groups are quantitatively examined on the basis of DFT calculations.

The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-form and the filamentous F-form, which drive organelle transport and cell motility. This mechanical work is driven by the ATPase activity at the catalytic site in the F-form. For deeper understanding of the actin cellular functions, the reaction mechanism must be elucidated. Here, we show that a single actin molecule is trapped in the F-form by fragmin domain-1 binding and present their crystal structures in the ATP analog-, ADP-Pi-, and ADP-bound forms, at 1.15-Å resolutions. The G-to-F conformational transition shifts the side chains of Gln137 and His161, which relocate four water molecules including W1 (attacking water) and W2 (helping water) to facilitate the hydrolysis. By applying quantum mechanics/molecular mechanics calculations to the structures, we have revealed a consistent and comprehensive reaction path of ATP hydrolysis by the F-form actin. The reaction path consists of four steps: 1) W1 and W2 rotations; 2) P G –O 3B bond cleavage; 3) four concomitant events: W1–PO 3 − formation, OH − and proton cleavage, nucleophilic attack by the OH − against P G , and the abstracted proton transfer; and 4) proton relocation that stabilizes the ADP-Pi–bound F-form actin. The mechanism explains the slow rate of ATP hydrolysis by actin and the irreversibility of the hydrolysis reaction. While the catalytic strategy of actin ATP hydrolysis is essentially the same as those of motor proteins like myosin, the process after the hydrolysis is distinct and discussed in terms of Pi release, F-form destabilization, and global conformational changes.