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Recently, deuterium-labeled drugs, such as deutetrabenazine, have attracted considerable attention. Consequently, understanding the reaction mechanisms of deuterium-labeled drugs is crucial, both fundamentally and for real applications. To understand the mechanisms of H- and D-transfer reactions, in this study, we used deuterated anisole as a deutetrabenazine model and computationally considered the nuclear quantum effects of protons, deuterons, and electrons. We demonstrated that geometrical differences exist in the partially and fully deuterated methoxy groups and hydrogen-bonded structures of intermediates and transition states due to the H/D isotope effect. The observed geometrical features and electronic structures are ascribable to the different nuclear quantum effects of protons and deuterons. Primary and secondary kinetic isotope effects (KIEs) were calculated for H- and D-transfer reactions from deuterated and undeuterated anisole, with the calculated primary KIEs in good agreement with the corresponding experimental data. These results reveal that the nuclear quantum effects of protons and deuterons need to be considered when analyzing the reaction mechanisms of H- and D-transfer reactions and that a theoretical approach that directly includes nuclear quantum effects is a powerful tool for the analysis of H/D isotope effects in H- and D-transfer reactions.

Structure–function relationships in proteins have been one of the crucial scientific topics in recent research. Heme proteins have diverse and pivotal biological functions. Therefore, clarifying their structure–function correlation is significant to understand their functional mechanism and is informative for various fields of science. In this study, we constructed convolutional neural network models for predicting protein functions from the tertiary structures of heme-binding sites (active sites) of heme proteins to examine the structure–function correlation. As a result, we succeeded in the classification of oxygen-binding protein (OB), oxidoreductase (OR), proteins with both functions (OB–OR), and electron transport protein (ET) with high accuracy. Although the misclassification rate for OR and ET was high, the rates between OB and ET and between OB and OR were almost zero, indicating that the prediction model works well between protein groups with quite different functions. However, predicting the function of proteins modified with amino acid mutation(s) remains a challenge. Our findings indicate a structure–function correlation in the active site of heme proteins. This study is expected to be applied to the prediction of more detailed protein functions such as catalytic reactions.

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.

Heme proteins play diverse and important biological roles, from electron transfer and chemical catalysis, to oxygen transport and/or storage. Although the distortion of heme porphyrin correlates with the physical properties of heme, such as the redox potential and oxygen affinity, the relationship between heme distortion and the heme protein environment is unclear. We here tested the hypothesis that the protein environment of the heme-binding pocket determines heme distortion (conformation). We analyzed the correlations between the amino acid composition of the heme-binding pocket and the magnitude of heme distortion along 12 vibrational modes by using machine learning. A correlation was detected in the three lowest-vibrational modes. Analysis of heme distortions in nearly the same environments of the heme-binding pocket supported this notion. Our analyses indicate that the heme-binding pocket environment is a major factor impacting the distortion of heme porphyrin along the three lowest-vibrational modes. In addition, statistical analysis of the distortion of heme porphyrin revealed that the peaks of distributions of the ruffling and breathing distortions are shifted from 0 (the equilibrium structure). Both the ruffling and breathing distortions are correlated with the redox potential of heme, so that heme molecules with these distortions have a lower redox potential than planar molecules. These findings explain the structure–function relationship of heme and can inform protein function engineering.

Nitric oxide (NO) reductase from the fungus Fusarium oxysporum is a P450-type enzyme (P450nor) that catalyzes the reduction of NO to nitrous oxide (N(2)O) in the global nitrogen cycle. In this enzymatic reaction, the heme-bound NO is activated by the direct hydride transfer from NADH to generate a short-lived intermediate (I), a key state to promote N–N bond formation and N–O bond cleavage. This study applied time-resolved (TR) techniques in conjunction with photolabile-caged NO to gain direct experimental results for the characterization of the coordination and electronic structures of I. TR freeze-trap crystallography using an X-ray free electron laser (XFEL) reveals highly bent Fe–NO coordination in I, with an elongated Fe–NO bond length (Fe–NO = 1.91 Å, Fe–N–O = 138°) in the absence of NAD(+). TR-infrared (IR) spectroscopy detects the formation of I with an N–O stretching frequency of 1,290 cm(−1) upon hydride transfer from NADH to the Fe(3+)–NO enzyme via the dissociation of NAD(+) from a transient state, with an N–O stretching of 1,330 cm(−1) and a lifetime of ca. 16 ms. Quantum mechanics/molecular mechanics calculations, based on these crystallographic and IR spectroscopic results, demonstrate that the electronic structure of I is characterized by a singly protonated Fe(3+)–NHO(•−) radical. The current findings provide conclusive evidence for the N(2)O generation mechanism via a radical–radical coupling of the heme nitroxyl complex with the second NO molecule.

We studied the effects of heme distortions on the chemical properties in two protein classes, oxidoreductases and oxygen carrier proteins, in the Protein Data Bank by a combination of statistics and quantum chemistry. A statistical analysis of heme distortion provided the characteristic distortions. They were reasonably correlated with the redox potentials and oxygen affinities evaluated by quantum chemical calculations, implying that heme proteins utilize these distortions to enhance their functions. The combination of statistical analysis and quantum chemical calculations is useful for the elucidation of the structure-function relationships.

To understand detailed geometrical changes and electronic structures of the adsorbed water molecules (H2O, D2O, and HDO) and H2O- and D2O-ice Ih(0 0 0 1) basal surfaces induced by the H/D isotope effect, nuclear quantum effects of the proton and deuteron in the first-principles calculations should be considered. We applied our developed combined plane wave and localized basis set (CPLB) method, which can directly treat the electronic structures of the surface and the localized adsorbed region with the nuclear quantum effect, to analyze the H/D isotope effect of adsorbed water molecules on ice. We demonstrated the geometrical change in the adsorbed water and H2O-ice surface due to the H/D isotope effect because the hydrogen bonds involving D (D2O and HDO) were longer than those involving H. Hence, the adsorption energies of D2O and HDO molecules were smaller than those of H2O because of the geometrical changes induced by the H/D isotope effect. The H/D isotope effect led to weaker adsorption energy and longer hydrogen bonds on the D2O-ice surface than those on the H2O-ice surface. We successfully described the H/D isotope effect of water adsorption on the ice Ih(0 0 0 1) surface by directly considering the quantum effect of the proton and deuteron.

We theoretically investigated a significant contraction of the hydrogen-bonding O⋯O distance upon H/D substitution in our recently developed purely organic crystals, κ-H3(Cat-EDT-ST)2 (H-ST) and its isotopologue κ-D3(Cat-EDT-ST)2 (D-ST), having π-electron systems coupled with hydrogen-bonding fluctuation. The origin of this geometrical H/D isotope effect was elucidated by using the multicomponent DFT method, which takes the H/D nuclear quantum effect into account. The optimized O⋯O distance in H-ST was found to be longer than that in D-ST due to the anharmonicity of the potential energy curve along the O H bond direction, which was in reasonable agreement with the experimental trend.

κ-H3(Cat-EDT-TTF)2 (H-TTF) is a hydrogen-bonded π-electron system which was found to reveal C2/c symmetry at 50–293 K, while its isotopologue, κ-D3(Cat-EDT-TTF)2 (D-TTF), showed the phase transition at 185 K from C2/c to P. To elucidate the origin of such a difference, we calculated the potential energy curves (PECs) for the hydrogen transfer along the H-bonds in these conductors. We found that both the π-stacking and the hydrogen nuclear quantum effect drastically affected the hydrogen transfer energy. By taking account of both effects, we obtained a symmetric single-well effective PEC for H-TTF, which indicated that the hydrogen was always located at the center of the H-bond. By contrast, the effective PEC of D-TTF was a low-barrier double-well, indicating that the position of the H-bonded deuterium would change according to the temperature. We concluded that the π-stacking and the nuclear quantum effect were the key factors for the appearance of phase transition only in D-TTF.

Photoactive yellow protein (PYP) has a characteristic hydrogen bond (H bond) between p-coumaric acid chromophore and Glu46, whose OH bond length has been observed to be 1.21Å by the neutron diffraction technique [Proc. Natl. Acad. Sci. 106, 440–4]. Although it has been expected that such a drastic elongation of the OH bond could be caused by the quantum effect of the hydrogen nucleus, previous theoretical computations including the nuclear quantum effect have so far underestimated the bond length by more than 0.07Å. To elucidate the origin of the difference, we performed a vibrational analysis of the H bond on potential energy curve with O…O distance of 2.47Å on the equilibrium structure, and that with O…O distance of 2.56Å on the experimental crystal structure. While the vibrationally averaged OH bond length for equilibrium structure was underestimated, the corresponding value for crystal structure was in reasonable agreement with the corresponding experimental values. The elongation of the O…O distance by the quantum mechanical or thermal fluctuation would be indispensable for the formation of a low-barrier hydrogen bond in PYP.

Multicomponent quantum mechanical (MC_QM) calculations with polarizable continuum model (PCM) have been tested against liquid (1)H NMR chemical shifts for a test set of 80 molecules. Improvement from conventional quantum mechanical calculations was achieved for MC_QM calculations. The advantage of the multicomponent scheme could be attributed to the geometrical change from the equilibrium geometry by the incorporation of the hydrogen nuclear quantum effect, while that of PCM can be attributed to the change of the electronic structure according to the polarization by solvent effects.

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 (H2Cat-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 H2Cat-BMT-TTF adlayer formations. In the measurements by AFM, a grained H2Cat-BMT-TTF adlayer on Im-SAM is revealed. The coverage and the chemical states of H2Cat-BMT-TTF on Im-SAM are specified by XPS. On the vibrational spectrum measured by IRAS, the strong hydrogen bonds between H2Cat-BMT-TTF and Im-SAM are characterized by the remarkably red-shifted OH stretching mode at 3140 cm-1, which is much lower than that for hydrogen-bonding water (typically ∼3300 cm-1). The OH stretching mode frequency and the adsorption strength for the H2Cat-BMT-TTF molecule hydrogen bonding with imidazole groups are quantitatively examined on the basis of DFT calculations.

In general, transferases undergo large structural changes and sequester substrate molecules, to shield them from water. By contrast, hydrolases exhibit only small structural changes, and expose substrate molecules to water. However, some hydrolases deeply bury their substrates within the proteins. To clarify the relationship between substrate-shielding and enzymatic functions, we investigated 70 representative hydrolase structures, and examined the relative accessible surface areas of their substrates. As compared to the hydrolases employing the single displacement reaction, the hydrolases employing the double displacement reaction bury the substrate within the proteins. The exo hydrolases display significantly more substrate-shielding from water than the endo hydrolases. It suggests that the substrate-shielding is related to the chemical reaction mechanism of the hydrolases and the substrate specificity. Proteins 2013; © 2012 Wiley Periodicals, Inc.

κ-H

The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5′-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an SN1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

H/D isotope effect on the circular dichroism spectrum of methyl α-D-glucopyranoside in aqueous solution has been analyzed by multicomponent density functional theory calculations using the polarizable continuum model. By comparing the computational spectra with the corresponding experimental spectrum obtained with a vacuum-ultraviolet circular dichroism spectrophotometer, it was demonstrated that the isotope effect provides insights not only into the isotopic difference of the intramolecular interactions of the solutes, but also into that of the solute–solvent intermolecular interaction.

Applicability of self-consistent-charge density-functional tight-binding method with dispersion correction (SCC-DFTB-D) was tested to the graphene adsorption of medium-sized molecules. We computed adsorbed structures of transition-metal complexes of porphyrin and porphycene on graphene, and evaluated the adsorption energies. The energies reasonably corresponded to the reference values evaluated by density functional theory (DFT) calculations. Furthermore, we confirmed the model size dependence of energy less than 1 kcal mol−1 by expanding the graphene size. SCC-DFTB-D can be an alternative choice for the computation of graphene adsorption of large molecules that are out of scope for typical DFT in terms of the computational cost.

In general, transferases undergo large structural changes and sequester substrate molecules, to shield them from water. By contrast, hydrolases exhibit only small structural changes, and expose substrate molecules to water. However, some hydrolases deeply bury their substrates within the proteins. To clarify the relationship between substrate-shielding and enzymatic functions, we investigated 70 representative hydrolase structures, and examined the relative accessible surface areas of their substrates. As compared to the hydrolases employing the single displacement reaction, the hydrolases employing the double displacement reaction bury the substrate within the proteins. The exo hydrolases display significantly more substrate-shielding from water than the endo hydrolases. It suggests that the substrate-shielding is related to the chemical reaction mechanism of the hydrolases and the substrate specificity.