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Active site hydrogen-bond (H-bond) networks represent a key component by which metalloenzymes control the formation and deployment of high-valent transition metal-oxo intermediates. We report a series of dinuclear cobalt complexes that serve as structural models for the nonheme diiron enzyme family and feature a Co(2)(μ–OH)(2) diamond core stabilized by intramolecular H-bond interactions. We define the conditions required for the kinetically controlled synthesis of these complexes: [Co(2)(μ–OH)(2)(μ-OAc)(κ(1)-OAc)(2)(py(R))(4)][PF(6)] (1(R)), where OAc = acetate and py(R) = pyridine with para-substituent R, and we describe a homologous series of 1(R) in which the para-R substituent on pyridine is modulated. The solid state X-ray diffraction (XRD) structures of 1(R) are similar across the series, but in solution, their (1)H NMR spectra reveal a linear free energy relationship (LFER) where, as R becomes increasingly electron-withdrawing, the intramolecular H-bond interaction between bridging μ–OH and κ(1)-acetate ligands results in increasingly “oxo-like” μ–OH bridges. Deprotonation of the bridging μ–OH results in the quantitative conversion to corresponding cubane complexes: [Co(4)(μ-O)(4))(μ(3)-OAc)(4)(py(R))(4)] (2(R)), which represent the thermodynamic sink of self-assembly. These reactions are unusually slow for rate-limiting deprotonation events, but rapid-mixing experiments reveal a 6000-fold rate acceleration on going from R = OMe to R = CN. These results suggest that we can tune reactivity by modulating the μ–OH pK(a) in the presence of intramolecular H-bond interactions to maintain stability as the octahedral d(6) centers become increasingly acidic. Nature may similarly employ dynamic carboxylate-mediated H-bond interactions to control the reactivity of acidic transition metal-oxo intermediates.

Tyrosinase (Ty) and catechol oxidase (CO) are members of type-3 copper enzymes. While Ty catalyzes both phenolase and catecholase reactions, CO catalyzes only the latter reaction. In the present study, Ty was found to catalyze the catecholase reaction, but hardly the phenolase reaction in the presence of the metallochaperon called "caddie protein (Cad)". The ability of the substrates to dissociate the motif shielding the active-site pocket seems to contribute critically to the substrate specificity of Ty. In addition, a mutation at the N191 residue, which forms a hydrogen bond with a water molecule near the active center, decreased the inherent ratio of phenolase versus catecholase activity. Unlike the wild-type complex, reaction intermediates were not observed when the catalytic reaction toward the Y98 residue of Cad was progressed in the crystalline state. The increased basicity of the water molecule may be necessary to inhibit the proton transfer from the conjugate acid to a hydroxide ion bridging the two copper ions. The deprotonation of the substrate hydroxyl by the bridging hydroxide seems to be significant for the efficient catalytic cycle of the phenolase reaction.

Light is utilized as energy or information by rhodopsins (membrane proteins that contain a retinal chromophore). Heliorhodopsins (HeRs) are a new class of rhodopsins with low sequence identity (

The crystal structures of two triclinic polymorphs of a new tetra­kis-substituted pyrazine carb­oxy­lic acid, 3,3′,3′′,3′′′-[(pyrazine-2,3,5,6-tetra­yltetra­kis­(methyl­ene))tetra­kis­(sulfanedi­yl)]tetra­propionic acid, are reported, together with the crystal structures of two potassium-organic frameworks., Two polymorphs of the title tetra­kis-substituted pyrazine carb­oxy­lic acid, 3,3′,3′′,3′′′-{[pyrazine-2,3,5,6-tetra­yltetra­kis­(methyl­ene))tetra­kis­(sulfanedi­yl]}tetra­propionic acid, C20H28N2O8S4, (H4L1), have been obtained, H4L1_A and H4L1_B. Each structure crystallized with half a mol­ecule in the asymmetric unit of a triclinic P unit cell. The whole mol­ecules are generated by inversion symmetry, with the pyrazine rings being located about inversion centers. The crystals of H4L1_B were of poor quality, but the X-ray diffraction analysis does show the change in conformation of the –CH2—S—CH2—CH2– side chains compared to those in polymorph H4L1_A. In the crystal of H4L1_A, mol­ecules are linked by two pairs of O—H⋯O hydrogen bonds, enclosing R 2 2(8) ring motifs forming layers parallel to plane (100), which are linked by C—H⋯O hydrogen bonds to form a supra­molecular framework. In the crystal of H4L1_B, mol­ecules are also linked by two pairs of O—H⋯O hydrogen bonds enclosing R 2 2(8) ring motifs, however here, chains are formed propagating in the [001] direction and stacking up the a-axis. Reaction of H4L1 with Hg(NO3)2 in the presence of a potassium acetate buffer did not produce the expected binuclear complex, instead crystals of a potassium–organic framework were obtained, poly[(μ-3-{[(3,5,6-tris­{[(2-carb­oxy­eth­yl)sulfan­yl]meth­yl}pyrazin-2-yl)meth­yl]sulfan­yl}propano­ato)potassium], [K(C20H27N2O8S4)]n (KH3L1). The organic mono-anion possesses inversion symmetry with the pyrazine ring being located about an inversion center. A carb­oxy H atom is disordered by symmetry and the charge is compensated for by a potassium ion. A similar reaction with Zn(NO3)2 resulted in the formation of crystals of a dipotassium-organic framework, poly[(μ-3,3′-{[(3,6-bis­{[(2-carb­oxy­eth­yl)sulfan­yl]meth­yl}pyrazine-2,5-di­yl)bis(methyl­ene)]bis­(sulfanedi­yl)}dipropionato)dipotassium], [K2(C20H26N2O8S4)]n (K2H2L1). Here, the organic di-anion possesses inversion symmetry with the pyrazine ring being located about an inversion center. Two symmetry-related acid groups are deprotonated and the charges are compensated for by two potassium ions.

Functional amyloids are abundant in living organisms from prokaryotes to eukaryotes playing diverse biological functions. In contrast to the irreversible aggregation of most known pathological amyloids, we postulate that naturally-occurring functional amyloids are reversible under the evolutionary pressure to be able to module the fibrillization process, reuse the composite peptides, or perform their biological functions. β-endorphin, an endogenous opioid peptide hormone, forms such kind of reversible amyloid fibrils in secretory granules for efficient storage and returns to the functional state of monomers upon release into the blood. The environment change between the low pH in secretory granules and the neutral pH in extracellular spaces is believed to drive the reversible fibrillization of β-endorphin. Here, we investigate the critical role of a buried glutamate, Glu8, in the pH-responsive disassembly of β-endorphin fibrils using all-atom molecular dynamics simulations along with structure-based pKa prediction. The fibril was stable at pH 5.5 or lower with all the buried Glu8 residues protonated and neutrally charged. After switching to the neutral pH, Glu8 residues of peptides at the outer layers of the ordered fibrils became deprotonated due to partial solvent exposure, causing sheet-to-coil conformational changes and subsequent exposure of adjacent Glu8 residues in the inner chains. Via iterative deprotonation of Glu8 and induced structural disruption, all Glu8 residues would be progressively deprotonated. Electrostatic repulsion between deprotonated Glu8 residues along with their high solvation tendency disrupted the hydrogen bonding between the β1 strands and increased the solvent exposure of those otherwise buried residues in the cross-β core. Overall, our computational study reveals that strategic positioning of ionizable residues into the cross-β core is a potential approach to design reversible amyloid fibrils as pH-responsive smart bio-nanomaterials.

The function of photoreceptors relies on efficient transfer of absorbed light energy from the chromophore to the protein to drive conformational changes that ultimately generate an output signal. In retinal-binding proteins, mainly two mechanisms exist to store the photon energy after photoisomerization: 1) conformational distortion of the prosthetic group retinal, and 2) charge separation between the protonated retinal Schiff base (RSBH(+)) and its counterion complex. Accordingly, energy transfer to the protein is achieved by chromophore relaxation and/or reduction of the charge separation in the RSBH(+)-counterion complex. Combining FTIR and UV-Vis spectroscopy along with molecular dynamics simulations, we show here for the widely used, red-activatable Volvox carteri channelrhodopsin-1 derivate ReaChR that energy storage and transfer into the protein depends on the protonation state of glutamic acid E163 (Ci1), one of the counterions of the RSBH(+). Ci1 retains a pK(a) of 7.6 so that both its protonated and deprotonated forms equilibrate at physiological conditions. Protonation of Ci1 leads to a rigid hydrogen-bonding network in the active-site region. This stabilizes the distorted conformation of the retinal after photoactivation and decelerates energy transfer into the protein by impairing the release of the strain energy. In contrast, with deprotonated Ci1 or removal of the Ci1 glutamate side chain, the hydrogen-bonded system is less rigid, and energy transfer by chromophore relaxation is accelerated. Based on the hydrogen out-of-plane (HOOP) band decay kinetics, we determined the activation energy for these processes in dependence of the Ci1 protonation state.

Phytochromes are biological photoswitches that interconvert between two parent states (Pr and Pfr). The transformation is initiated by photoisomerization of the tetrapyrrole chromophore, followed by a sequence of chromophore and protein structural changes. In the last step, a phytochrome-specific peptide segment (tongue) undergoes a secondary structure change, which in prokaryotic phytochromes is associated with the (de)activation of the output module. The focus of this work is the Pfr-to-Pr photoconversion of the bathy bacteriophytochrome Agp2 in which Pfr is the thermodynamically stable state. Using spectroscopic techniques, we studied the structural and functional consequences of substituting Arg211, Tyr165, His278, and Phe192 close to the biliverdin (BV) chromophore. In Pfr, substitutions of these residues do not affect the BV structure. The characteristic Pfr properties of bathy phytochromes, including the protonated propionic side chain of ring C (propC) of BV, are preserved. However, replacing Arg211 or Tyr165 blocks the photoconversion in the Meta-F state, prior to the secondary structure transition of the tongue and without deprotonation of propC. The Meta-F state of these variants displays low photochemical activity, but electronic excitation causes ultrafast alterations of the hydrogen bond network surrounding the chromophore. In all variants studied here, thermal back conversion from the photoproducts to Pfr is decelerated but substitution of His278 or Phe192 is not critical for the Pfr-to-Pr photoconversion. These variants do not impair deprotonation of propC or the α-helix/β-sheet transformation of the tongue during the Meta-F-to-Pr decay. Thus, we conclude that propC deprotonation is essential for restructuring of the tongue.

Because of its versatile coordination modes and strong coordination ability, the mercaptoacetic acid substituted 1,2,4-triazole 2-{[5-(pyridin-2-yl)-4H-1,2,4-triazol-3-yl]sulfanyl}acetic acid (H2L) was synthesized and characterized. Treatment of H2L with cobalt and nickel acetate afforded the dinuclear complexes {μ-3-[(carboxylatomethyl)sulfanyl]-5-(pyridin-2-yl)-4H-1,2,4-triazol-4-ido-κ2 N 1,N 5:N 2,O}bis[aqua(methanol-κO)cobalt(II)] methanol disolvate, [Co2(C9H6N4O2S)2(CH3OH)2(H2O)2]·2CH3OH (1), and {μ-3-[(carboxylatomethyl)sulfanyl]-5-(pyridin-2-yl)-4H-1,2,4-triazol-4-ido-κ2 N 1,N 5:N 2,O}bis[diaquanickel(II)] methanol disolvate dihydrate, [Ni2(C9H6N4O2S)2(H2O)4]·2CH3OH·2H2O (2), respectively. Complex 1 crystallized in the monoclinic space group P21/c, while 2 crystallized in the tetragonal space group I41/a. Single-crystal X-ray diffraction studies revealed that H2L is doubly deprotonated and acts as a tetradentate bridging ligand in complexes 1 and 2. For both of the obtained complexes, extensive hydrogen-bond interactions contribute to the formation of their three-dimensional supermolecular structures. Hirshfeld surface analysis was used to illustrate the intermolecular interactions. Additionally, the urease inhibitory activities of 1, 2 and H2L were investigated against jack bean urease, where the two complexes revealed strong urease inhibition activities.

Transient tyrosine and tryptophan radicals play key roles in the electron transfer (ET) reactions of photosystem (PS) II, ribonucleotide reductase (RNR), photolyase, and many other proteins. However, Tyr and Trp are not functionally interchangeable, and the factors controlling their reactivity are often unclear. Cytochrome c peroxidase (CcP) employs a Trp191(•+) radical to oxidize reduced cytochrome c (Cc). Although a Tyr191 replacement also forms a stable radical, it does not support rapid ET from Cc. Here we probe the redox properties of CcP Y191 by non-natural amino acid substitution, altering the ET driving force and manipulating the protic environment of Y191. Higher potential fluorotyrosine residues increase ET rates marginally, but only addition of a hydrogen bond donor to Tyr191(•) (via Leu232His or Glu) substantially alters activity by increasing the ET rate by nearly 30-fold. ESR and ESEEM spectroscopies, crystallography, and pH-dependent ET kinetics provide strong evidence for hydrogen bond formation to Y191(•) by His232/Glu232. Rate measurements and rapid freeze quench ESR spectroscopy further reveal differences in radical propagation and Cc oxidation that support an increased Y191(•) formal potential of ~200 mV in the presence of E232. Hence, Y191 inactivity results from a potential drop owing to Y191(•+) deprotonation. Incorporation of a well-positioned base to accept and donate back a hydrogen bond upshifts the Tyr(•) potential into a range where it can effectively oxidize Cc. These findings have implications for the Y(Z)/Y(D) radicals of PS II, hole-hopping in RNR and cryptochrome, and engineering proteins for long-range ET reactions.

Thiotemplated pyrrole is a prevailing intermediate in the synthesis of numerous natural products where the pyrrole is tethered to a carrier protein (CP). Biosynthesis of the pyrrole requires oxidation of an L-proline side chain. Herein, we investigated the biocatalytic mechanism of proline-to-pyrrole synthesis using the recently reported (Thapa et al., Biochemistry, 2019, 58, 918) structure of a Type II non-ribosomal protein synthetase (NRPS) Bmp3-Bmp1 (Oxidase-CP) complex. The substrate (L-proline side chain) is attached to the Bmp1(CP) and the catalytic site is located inside the flavin-dependent oxidase (Bmp3). Interestingly, the FAD molecule is free (unbound) within the Bmp3 catalytic site. We show that the FAD isoalloxazine ring is stabilized in the catalytic site of Bmp3 by strong hydrogen bonding with Asn123, Ile125, Ser126, and Thr158. The stability of the dimeric Bmp3 system including one FAD molecule in our simulation suggests that the tetrameric Bmp3 assembly, as found in the crystal structure, is not functionally important. After the initial deprotonation followed by an enamine-imine tautomerization, oxidation of either the C2-C3 bond or the C2-N1 bond, through a hydride transfer (either from C3 or N1), is required for the pyrrole synthesis. Using molecular dynamics simulations, quantum mechanics/molecular mechanics simulations, and electronic structure calculations, we conclude that the hydride transfer is more likely to occur from C3 than N1. Additionally, we demonstrated the elasticity in the oxidase active site through enzymatic synthesis of proline derivatives.

Acetylcholinesterase (AChE) is the crucial enzyme in the central nervous system. It is the target of various organophosphorus nerve agents and pesticides, and the inhibition of AChE is a therapeutic strategy for the treatment of various neurological-related diseases. The Glu202 is a key residue adjacent to the catalytic His447 and plays important role in catalysis. Although the Glu202 has long been considered as negatively charged in many studies, more and more evidences support a protonated Glu202. However, Glu202 is freely accessible by solvent, and thus it seems more reasonable for Glu202 to majorly take the deprotonated state. In the present work, we carried out a series of molecular dynamics simulations with the Glu202 adopting different protonation states. Our results show that the protonated Glu202 is important in maintaining the key hydrogen bond network that supports the catalytic triad, whereas the deprotonated Glu202 results in the collapse of the key hydrogen bond network which consequently destabilizes the catalytic His447. We also notice that different protonation states of Glu202 merely alters the binding mode of ACh. However, since the catalytic His447 is disrupted if Glu202 is deprotonated, His447 can not facilitate the nucleophilic attack performed by Ser203. Therefore, the catalytic efficiency of ACh hydrolysis should be remarkably decreased if Glu202 is deprotonated. Our findings suggest that, when designing and developing highly active AChE inhibitors or proposing mechanistic hypotheses for AChE-catalyzed reactions, the protonated state of Glu202 should be considered.

Cyanobacteriochromes (CBCRs) are bilin-binding photosensors of the phytochrome superfamily that show remarkable spectral diversity. The green/red CBCR subfamily is important for regulating chromatic acclimation of photosynthetic antenna in cyanobacteria and is applied for optogenetic control of gene expression in synthetic biology. They are suggested to combine the bilin C15-Z/C15-E photoisomerization with a change in the bilin protonation state to drive their absorption changes. However, structural information and direct evidence of the bilin protonation state are lacking. Here we report a high-resolution (1.63Å) crystal structure of the bilin-binding domain of the chromatic acclimation sensor RcaE in the red-absorbing photoproduct state. The bilin is buried within a “pan” consisting of hydrophobic residues, where the bilin configuration/conformation is C5-Z,syn/C10-Z,syn/C15-E,syn with the A–C rings co-planar and the D-ring tilted. Three pyrrole nitrogens of the A–C rings are covered in the α-face with a hydrophobic lid of Leu249 influencing the bilin pKa, whereas they are directly hydrogen-bonded in the β-face with the carboxyl group of Glu217. Glu217 is further connected to a cluster of waters forming a hole in the pan, which are in exchange with solvent waters in molecular dynamics simulation. We propose that the “holey pan” structure functions as a proton-exit/influx pathway upon photoconversion. NMR analysis demonstrated that the four pyrrole nitrogen atoms are indeed fully protonated in the red-absorbing state, but one of them, most likely the B-ring nitrogen, is deprotonated in the green-absorbing state. These findings deepen our understanding of the diverse spectral tuning mechanisms present in CBCRs.Significance StatementGreen/red CBCRs are one of the most important CBCR subfamilies owing to their physiological roles in cyanobacteria phylum and optogenetic applications. They are known to utilize a change in the bilin protonation state to drive the marked change in green/red absorption, but the structural basis of the protochromic green/red photocycle are not well understood. Here, we have determined the crystal structure of the chromatic acclimation sensor RcaE of this subfamily in the photoproduct state, demonstrating a unique conformation of the bilin and its interacting residues. In addition, we provide direct evidence of the protonation state of the bilin via NMR analysis. These findings bring insight to our understanding of the molecular mechanisms underlying the spectral diversity of CBCRs.

Green Fluorescent Protein (GFP) is known to undergo excited-state proton transfer (ESPT). Formation of a short H-bond favors ultrafast ESPT in GFP-like proteins, such as the GFP S65T/H148D mutant, but the detailed mechanism and its quantum nature remain to be resolved. Here we study in vacuo, light-induced proton transfer from the GFP chromophore in hydrogen-bonded complexes with two anionic proton acceptors, I− and deprotonated trichloroacetic acid (TCA−). We address the role of the strong H-bond and the quantum mechanical proton-density distribution in the excited state, which determines the proton-transfer probability. Our study shows that chemical modifications to the molecular network drastically change the proton-transfer probability and it can become strongly wavelength dependent. The proton-transfer branching ratio is found to be 60 % for the TCA complex and 10 % for the iodide complex, being highly dependent on the photon energy in the latter case. Using high-level ab initio calculations, we show that light-induced proton transfer takes place in S1, revealing intrinsic photoacid properties of the isolated GFP chromophore in strongly bound H-bonded complexes. ESPT is found to be very sensitive to the topography of the highly anharmonic potential in S1, depending on the quantum-density distribution upon vibrational excitation. We also show that the S1 potential-energy surface, and hence excited-state proton transfer, can be controlled by altering the chromophore microenvironment.

We report on the motional and proton transfer dynamics of the super photobase FR0-SB in the series of normal alcohols C1 (methanol) through C8 (n-octanol) and ethylene glycol. Steady-state and time-resolved fluorescence data reveal that the proton abstraction dynamics of excited FR0-SB depend on the identity of the solvent and that the transfer of the proton from solvent to FR0-SB*, forming FR0-HSB+*, fundamentally alters the nature of interactions between the excited molecule and its surroundings. In its unprotonated state, solvent interactions with FR0-SB* are consistent with slip limit behavior, and in its protonated form, intermolecular interactions are consistent with a much stronger interaction of FR0-HSB+* with the deprotonated solvent RO–. We understand the excited-state population dynamics in the context of a kinetic model involving a transition state wherein FR0-HSB+* is still bound to the negatively charged alkoxide, prior to solvation of the two charged species. Data acquired in ethylene glyco...

The hydrogen bond (HB) between 4‐hydroxycinnamic acid (HC4) and glutamic acid E46 of photoactive yellow protein is exceptionally strong. In the 0.82‐å resolution X‐ray structure for this protein (PDB ID: 1NWZ), the O—H…O distance is only 2.57 å. The position of the H atom between these two O atoms has not been determined in that structure, and in the absence of that information, it is impossible to determine whether or not this HB is a low‐barrier HB (LBHB), as was proposed recently based on neutron structures of this protein (Yamaguchi et al., Proceedings of the National Academy of Sciences of the United States of America, 2009, 106: 440–444). Residual electron density maps computed using the 1NWZ data reveal that this H atom is 0.92 å from the O(ε2) atom of E46 and 1.67 å from the O(4)′ of HC4, and that the O—H…O bond angle is 167°. These observations indicate that E46 is protonated, and HC4 is deprotonated, as was originally suggested, and that the HB in question is not an LBHB.

Recently, several artificial nucleobases, such as B, S, J, V, X, K, P, and Z, have been proposed to help in the expansion of the genetic information system and diagnosis of diseases. Among these bases, P and Z were identified to form stable DNA and to participate in the replication. However, the stabilities of P:Z and other artificial base pairs are not fully understood. The abilities of these unnatural nucleobases in mispairing with themselves and with natural bases are also not known. Here, the ωB97X-D dispersion-corrected density functional theoretical and complete basis set (CBS-QB3) methods are used to obtain accurate structural and energetic data related to base pair interactions involving these unnatural nucleobases. The roles of protonation and deprotonation of certain artificial bases in inducing mutations are also studied. It is found that each artificial purine has a complementary artificial pyrimidine, the base pair interactions between which are similar to those of the natural Watson-Crick base pairs. Hence, these base pairs will function naturally and would not impart mutagenicity. Among these base pairs, the J:V complex is found to be the most stable and promising artificial base pair. Remarkably, the noncomplementary artificial nucleobases are found to form stable mispairs, which may generate mutagenic products in DNA. Similarly, the misinsertions of natural bases opposite artificial bases are also found to be mutagenic. The mechanisms of these mutations are explained in detail. These results are in agreement with earlier biochemical studies. It is thus expected that this study would aid in the advancement of the synthetic biology to design more robust artificial nucleotides.

Photoactive yellow protein (PYP) is a small photoreceptor protein that has two unusually short hydrogen bonds between the deprotonated p-coumaric acid chromophore and two amino acids, a tyrosine and a glutamic acid. This has led to considerable debate as to whether the glutamic acid-chromophore hydrogen bond is a low barrier hydrogen bond, with conflicting results in the literature. We have modified the pK(a) of the tyrosine by amber suppression and of the chromophore by chemical substitution. X-ray crystal structures of these modified proteins are nearly identical to the wild-type protein, so the heavy atom distance between proton donor and acceptor is maintained, even though these modifications change the relative proton affinity between donor and acceptor. Despite a considerable change in relative proton affinity, the NMR chemical shifts of the hydrogen-bonded protons are only moderately affected. QM/MM calculations were used to explore the protons’ potential energy surface and connect the calculated proton position with empirically measured proton chemical shifts. The results are inconsistent with a low barrier hydrogen bond but in all cases are consistent with a localized proton, suggesting an ionic hydrogen bond rather than a low barrier hydrogen bond.

Pullulanase is a starch-debranching enzyme that is generally employed to efficiently break down starch for the production of high-glucose syrup. Acidic adaptation of pullulanases is of special interest. In this study, we conducted protein engineering to improve the acidic adaptation of Bacillus acidopullulyticus pullulanase (BaPul) and used a hydrogen-bond-based approach to identify promising residues that may change the deprotonation constants (pKa) of the catalytic residues. A total of 19 amino acids were selected for mutation according to the crystal structure of BaPul. The pH optimum of the L627R mutant shifted from 5.0 to 4.0, and its relative activity at pH 4.0 was 117% that of the wide-type enzyme. The improved efficacy of the L627R mutant at pH 4.0 was confirmed by kinetic parameters and pKa prediction. Moreover, the L627R mutant exhibited increased tolerance against acid-mediated denaturation, and its maximum d -glucose content (97.4%) was obtained after 40 h incubation, which is shorter by 10 h compared with the time required by the wide-type enzyme to produce a comparable amount of the monosaccharide. The L627R mutant may be suitable for industrial application because its shortened reaction time translates to reduced energy consumption.

We conducted a comprehensive time-resolved resonance Raman spectroscopy study of the structures of the retinal chromophore during the photocycle of the sodium-ion pump Krokinobacter rhodopsin 2 (KR2). We succeeded in determining the structure of the chromophore in the unphotolyzed state and in the K, L, M, and O intermediates, by overcoming the problem that only a small fraction of the M intermediate is accumulated in the KR2 photocycle. The Schiff base in the retinal chromophore forms a strong hydrogen bond in the unphotolyzed state and in the K, L, and O intermediates and is deprotonated in the M intermediate. Formation of this strong hydrogen bond facilitates deprotonation of the Schiff base, which is necessary for the sodium ion to move past the Schiff base. The polyene chain in the chromophore of KR2 is twisted in all of the states of the photocycle: the portion near the Schiff base is largely twisted in the unphotolyzed state and in the K intermediate, whereas the middle portion of the polyene chain becomes largely twisted in the L, M, and O intermediates. During the photocycle, the twisted structure of the polyene chain and strong hydrogen bond at the Schiff base are advantageous for transient relocation of the Schiff base proton. The obtained resonance Raman data clarified the unique structural features of the KR2 chromophore, which are not accessible by other methods.

Radical cations of nucleobases are key intermediates causing genome mutation, among which cytosine C•+ is of growing importance because the ensuing cytosine oxidation causes GC → AT transversions in DNA replication. Although the chemistry and biology of steady-state C oxidation products have been characterized, time-resolved study of initial degradation pathways of C•+ is still at the preliminary stage. Herein, we choose i-motif, a unique C-quadruplex structure composed of hemiprotonated base pairs C(H)+:C, to examine C•+ degradation in a DNA surrounding without interference of G bases. Comprehensive time-resolved spectroscopy were performed to track C•+ dynamics in i-motif and in free base dC. The competing pathways of deprotonation (1.4 × 107 s–1), tautomerization (8.8 × 104 s–1), and hydration (5.3 × 103 s–1) are differentiated, and their rate constants are determined for the first time, underlining the strong reactivity of C•+. Distinct pathway is observed in i-motif compared with dC, showing the prom...

Channelrhodopsins (ChR) are cation channels that can be expressed heterologously in various living tissues, including cardiac and neuronal cells. To tune spatial and temporal control of potentials across ChR-enriched cell membranes, it is essential to understand how pore hydration impacts the ChR photocycle kinetics. Here, we measure channel opening and closing rates of channelrhodopsin chimera and selected variants (C1C2 wild type, C1C2-N297D, C1C2-N297V, and C1C2-V125L) and correlate them with changes in chemical interactions among functionally important residues in both closed and open states. Kinetic results substantiate that replacement of helices I and II in ChR2 with corresponding residues from ChR1, to make the chimera C1C2, affects the kinetics of channelrhodopsin pore gating significantly, making C1C2 a unique channel. As a prerequisite for studies of ion transport, detailed understanding of the water pathway within a ChR channel is important. Our atomistic simulations confirm that opening of the channel and initial hydration of the previously dry gating regions between helices I, II, III, and VII of the channel occurs with 1) the presence of 13-cis retinal; 2) deprotonation of a glutamic acid gating residue, E129; and 3) subsequent weakening of the central gate hydrogen bond between the same glutamic acid E129 and asparagine N282 in the central region of the pore. Also, an aspartate (D292) is the unambiguous primary proton acceptor for the retinal Schiff base in the hydrated channel.SIGNIFICANCEChannelrhodopsins (ChR) are light-sensitive ion channels used in optogenetics, a technique that applies light to selectively and non-invasively control cells (e.g., neurons) that have been modified genetically to express those channels. Using electrophysiology, we measured the opening and closing rates of a ChR chimera, and several variants, and correlated those rates with changes in chemical interactions determined from atomistic simulations. Significant new insights include correlation of single-point-mutations with four factors associated with pore hydration and cation conductance. Additionally, our work unambiguously identifies the primary proton acceptor for the retinal chromophore in the channel open state. These new insights add to mechanistic understanding of light-gated membrane transport and should facilitate future efforts to control membrane potentials spatially and temporally in optogenetics.

The design of biomimetic models of metalloenzymes needs to take into account many factors and is therefore a challenging task. We propose in this work an original strategy to control the second coordination sphere of a metal centre and its distal environment. A biomimetic complex, reproducing the first coordination sphere, is encapsulated in a self-assembled hydrogen-bonded capsule. The cationic complex is co-encapsulated with its counter-anion or with solvent molecules. The capsule is dynamic, allowing a fast in/out exchange of the co-encapsulated species. It also provides both a hydrogen-bonding site in the second coordination sphere and a source of proton as it can be deprotonated in the presence of the complex, providing a globally neutral host-guest assembly. This simple and broad scope strategy is unprecedented in biomimetic studies. The approach appears to be a very promising method for the stabilisation of reactive species and for the study of their reactivity.

High selectivity and sensitivity detection of fluoride anions (F−) in an organic solution by the naked eye has always been a challenge. In this investigation, a simple compound based on aminobenzodifuranone (ABDF) was designed and synthesized. Deprotonation of the amino moiety caused by F− is responsible for a color change from dark blue to various colors (colorless, yellow, orange, and red) in different common organic solvents due to a blue shift over 200 nm in the UV/Vis spectrum. The color change is quite visible to the naked eye under ambient light. The detection limit for F− can reach a concentration of as low as 5.0 × 10−7 M with high selectivity, even in a solution containing multiple anions.

One-electron oxidation of adenine (A) leads initially to the formation of adenine radical cation (A•+). Subsequent deprotonation of A•+ can provoke deoxyribonucleic acid (DNA) damage, which further causes senescence, cancer formation, and even cell death. However, compared with considerable reports on A•+ reactions in free deoxyadenosine (dA) and duplex DNA, studies in non-B-form DNA that play critical biological roles are rare at present. It is thus of vital importance to explore non-B-form DNA, among which the triplex is an emerging topic. Herein, we investigate the deprotonation behavior of A•+ in the TAT triplex with continuous A bases by time-resolved laser flash photolysis. The rate constants for the one-oxidation of triplex 8.4 × 108 M−1 s−1 and A•+ deprotonation 1.3 × 107 s−1 are obtained. The kinetic isotope effect of A•+ deprotonation in the TAT triplex is 1.8, which is characteristic of a direct release of the proton into the solvent similar to free base dA. It is thus elucidated that the A•+ proton bound with the third strand is most likely to be released into the solvent because of the weaker Hoogsteen H-bonding interaction and the presence of the highly mobile hydration waters within the third strand. Additionally, it is confirmed through Fourier transform infrared spectroscopy that the deprotonation of A•+ results in the dissociation of the third strand and disruption of the secondary structure of the triplex. These results provide valuable kinetic data and in-depth mechanistic insights for understanding the adenine oxidative DNA damage in the triplex.One-electron oxidation of adenine (A) leads initially to the formation of adenine radical cation (A•+). Subsequent deprotonation of A•+ can provoke deoxyribonucleic acid (DNA) damage, which further causes senescence, cancer formation, and even cell death. However, compared with considerable reports on A•+ reactions in free deoxyadenosine (dA) and duplex DNA, studies in non-B-form DNA that play critical biological roles are rare at present. It is thus of vital importance to explore non-B-form DNA, among which the triplex is an emerging topic. Herein, we investigate the deprotonation behavior of A•+ in the TAT triplex with continuous A bases by time-resolved laser flash photolysis. The rate constants for the one-oxidation of triplex 8.4 × 108 M−1 s−1 and A•+ deprotonation 1.3 × 107 s−1 are obtained. The kinetic isotope effect of A•+ deprotonation in the TAT triplex is 1.8, which is characteristic of a direct release of the proton into the solvent similar to free base dA. It is thus elucidated that the A•+ p...

The synthetic model complex [Cu(4)S(dppa)(4)](2+) (1, dppa = (Ph(2)P)(2)NH) was found to have N(2)O reductase activity in methanol solvent, mediating the 2H(+)/2e(−) reduction of N(2)O to N(2) + H(2)O in the presence of an exogenous electron donor (CoCp(2)). A stoichiometric product featuring two deprotonated dppa ligands was characterized, indicating a key role of second-sphere N–H residues as proton donors during N(2)O reduction. The activity of 1 towards N(2)O was suppressed in solvents that are unable to provide hydrogen bonding to the second-sphere N–H groups. Structural and computational data indicated that second-sphere hydrogen bonding induces structural distortion of the [Cu(4)S] active site, accessing a strained geometry with enhanced reactivity due to localization of electron density along a dicopper edge site. The behavior of 1 mimics several aspects of the Cu(Z) catalytic site of nitrous oxide reductase: activity in the 4Cu(I):1S redox state, use of a second-sphere proton donor, and reactivity dependence on both primary and secondary sphere effects.

Both deprotonated and neutral achiral title dipeptides assume similar structures of two conformations, which are related by a unit-cell inversion centre. Two molecules of both conformations of the metal-free neutral dipeptide are linked by two hydrogen bonds, while two molecules of both conformations of the ionized form coordinate a calcium ion in calcium(II) bis[2-(2-{[(benzyloxy)carbonyl]amino}acetamido)-2-methylpropanoate] monohydrate, 0.5Ca2+·C14H17N2O5 −·0.5H2O, which lies on an inversion centre and forms a distorted octahedral complex with the metal ion. These CaII complexes are connected in the crystal via hydrogen bonds in the b- and c-axis directions, whereas in the a-axis direction, they stack via apolar contacts. In the metal-free crystal, namely 2-(2-{[(benzyloxy)carbonyl]amino}acetamido)-2-methylpropanoic acid, C14H18N2O5, molecules are hydrogen bonded in the a- and c-axis directions, and stack in the b–axis direction via apolar contacts.

The title compound, [Ni(C14H12BrN2O)2][Ni(C14H13BrN2O)2](ClO4)2·CH3OH consists of two mononuclear ([Ni(HL)2]2+ and [NiL 2]) complex molecules linked by strong hydrogen bonding [O...O separations of only 2.430 (5) Å], which is the shortest reported to date for such species. In one of the complexes, both the coordinated phenoxy groups retain their protons and thus this is the cationic equivalent species of the other complex where both coordinated phenoxy groups are deprotonated. In addition, perchlorate anions are present for charge balance, as well as methanol solvate molecules. For the neutral NiL 2 complex, each 2-ethylaminepyridine arm is disordered over two equivalent conformations with occupancies of 0.750 (8):0.250 (8). The perchlorate anion is disordered over two equivalent conformations with occupancies of 0.602 (8):0.398 (8). The perchlorate ions also link to the H atoms on the methanol methyl and hydroxyl groups. These interactions link the moieties into a complex three-dimensional array. The crystal studied was refined as a two-component twin.

In photosystem II (PSII), redox-active tyrosine Z (TyrZ) forms a low-barrier H-bond with Ne of D1-His190. The PSII crystal structures show that Nδ of D1-His190 donates an H-bond to the carbonyl O of D1-Asn298. However, at a level of ∼2 A resolution, a clear discrimination between the −NH2 and −C═O groups of the asparagine side chain may not be possible based on the electron density map. Using quantum mechanical/molecular mechanical calculations, we investigated the energetics of the D1-Asn298 conformations. In the D1-Asn298-rotated conformation, where the amide N group donates an H-bond to deprotonated Nδ of D1-His190, oxidation of S2 resulted in formation of a neutral radical, either TyrZ• or D1-His190•. This suggests that in the D1-Asn298-rotated conformation, the redox potential (Em) values of TyrZ/D1-His190 are lower than the Em of the Mn4CaO5 cluster due to deprotonated D1-His190. The large disorder of a water molecule (water 1117A) at D1-Asn298 in the crystal structure as well as the absence of wate...

5-Fluorouracil (5FU), a common anti-cancer drug, occurs in four tautomeric forms and possesses two potential sites of both protonation and deprotonation. Tautomeric and resonance structures of the ionized forms of 5FU create the systems of connected equilibriums. Since there are contradictory reports on the ionized forms of 5FU in the literature, complex theoretical studies on neutral, protonated and deprotonated forms of 5FU, based on the broad spectrum of DFT methods, are presented. These indicate that the O4 oxygen is more willingly protonated than the O2 oxygen and the N1 nitrogen is more willingly deprotonated than the N3 nitrogen in a gas phase. Such preferences are due to advantageous charge delocalization of the respective ions, which is demonstrated by the NBO and ESP analyses. In an aqueous phase, stability differences between respective protonated and deprotonated forms of 5FU are significantly diminished due to the competition between the mesomeric effect and solvation. The calculated pKa values of the protonated, neutral and singly deprotonated 5FU indicate that 5FU does not exist in the protonated and double-deprotonated forms in the pH range of 0&ndash, 14. The neutral form dominates below pH 8 and the N1 deprotonated form dominates above pH 8.

As previously shown for lutetium and yttrium, 1,2,3,4,5-pentamethylcyclopentadienyl (C5Me5 = Cp*)-bearing rare-earth metal dimethyl half-sandwich complexes [Cp*LnMe2]3 are now also accessible for holmium, dysprosium, and terbium via tetramethylaluminato cleavage of [Cp*Ln(AlMe4)2] with diethyl ether (Ho, Dy) and tert-butyl methyl ether (TBME) (Tb). C&ndash, H-bond activation and ligand redistribution reactions are observed in case of terbium and are dominant for the next larger-sized gadolinium, as evidenced by the formation of mixed methyl/methylidene clusters [(Cp*Ln)5(CH2)(Me)8] and metallocene dimers [Cp*2Ln(AlMe4)]2 (Ln = Tb, Gd). Applying TBME as a &ldquo, cleaving&rdquo, reagent can result in both TBME deprotonation and ether cleavage, as shown for the formation of the 24-membered macrocycle [(Cp*Gd)2(Me)(CH2OtBu)2(AlMe4)]4 or monolanthanum complex [Cp*La(AlMe4){Me3Al(CH2)OtBu}] and monoyttrium complex [Cp*Y(AlMe4)(Me3AlOtBu)], respectively. Complexes [Cp*Ln(AlMe4)2] (Ln = Ho, Dy, Tb, Gd) and [Cp*LnMe2]3 (Ln = Ho, Dy) are applied in isoprene and 1,3-butadiene polymerization, upon activation with borates [Ph3C][B(C6F5)4] and [PhNHMe2][B(C6F5)4], as well as borane B(C6F5)3. The trans-directing effect of AlMe3 in the binary systems [Cp*Ln(AlMe4)2]/borate is revealed and further corroborated by the fabrication of high-cis-1,4 polybutadiene (97%) with &ldquo, aluminum-free&rdquo, [Cp*DyMe2]3/[Ph3C][B(C6F5)4]. The formation of multimetallic active species is supported by the polymerization activity of pre-isolated cluster [(Cp*Ho)3Me4(CH2)(thf)2].

Crystals of a supramolecular lithium complex with a calix[4]arene derivative, namely tetramethanollithium 5,11,17,23-tetra-tert-butyl-25,26,27-trihydroxy-28-oxidocalix[4]arene methanol monosolvate, [Li(CH3OH)4](C44H55O4)·CH3OH or [Li(CH3OH)4]+·(calix[4]arene−)]·CH3OH (where calix[4]arene− represents a mono-anion species because of deprotonation of one H atom of the calixarene hydroxy groups), were obtained from p-tert-butylcalix[4]arene reacted with LiH in tetrahydrofuran, followed by recrystallization from methanol. The asymmetric unit comprises one mono-anionic calixarene molecule, one Li+ cation coordinated to four methanol molecules, and one methanol molecule included in the calixarene cavity. The calixarene molecule maintains a cone conformation by intramolecular hydrogen bonding between one phenoxide (–O−) and three pendent calixarene hydroxy groups (–OH). The coordinated methanol molecules around the metal cation play a significant role in forming the supramolecular assembly. The crystal structure of this assembly is stabilized by three sets of intermolecular interactions: (i) hydrogen bonds involving the –OH and –O− moieties of the calixarene molecules, the –OH groups of the coordinated methanol molecules, and the –OH group of the methanol molecule included in the calixarene cavity; (ii) C—H...π interactions between the calixarene molecules and/or the coordinated methanol molecules; (iii) O—H...π interactions between the calixarene molecule and the included methanol molecule.

The physicochemical properties of [Trpn–H]− and [Trpn⋯Cl]− (n = 1, 2) have been investigated in a combined computational and experimental infrared multiple dissociation (IRMPD) study. IRMPD spectra within the 850–1900 cm−1 region indicate that deprotonation is localized on the carboxylic acid moiety in [Trpn–H]− clusters. A combination of hydrogen bonding and higher order charge–quadrupole interactions appear to influence cluster geometries for all investigated systems. Calculated global minimum and low energy geometries of [Trp⋯Cl]− and [Trp2⋯Cl]− clusters favour coordination of the halide by the indole NH. [Trp2–H]− and [Trp2⋯Cl]− exhibit additional π–π interactions between the heterocyclic side chains.

Linalool dehydratase/isomerase (LinD) from Castellaniella defragrans is a bifunctional enzyme that catalyzes the hydration of β-myrcene to (S)-linalool and the isomerization of (S)-linalool to geraniol. In this paper, on the basis of recently obtained crystal structures, the catalytic mechanism of LinD has been explored by a combined quantum mechanics and molecular mechanics (QM/MM) approach. Two computational models have been constructed. Model I (LinD-linalool) was derived from the crystal structure of the selenomethionine derivative of LinD (Semet-LinD) in complex with the natural substrate geraniol, whereas model II (LinD-β-myrcene) was constructed from the crystal structure of LinD in complex with β-myrcene. In addition to a minor conformational difference of the active sites, the two models also differ in the protonation state of key residues. In model I, the pocket residue Asp39' was set to be deprotonated and His129 was protonated on ND1, whereas in model II, Asp38' was set to be deprotonated and His128 was protonated on NE2. Our calculations reveal model II as the active one, which implies that hydration and dehydration are sensitive to the protonation state and fine structure of the active site. On the basis of model II, the conversion details from β-myrcene to geraniol can be obtained. Firstly, β-myrcene is hydrated by a crystal water (W14) and is converted into the stable intermediate (S)-linalool, then linalool is isomerized to geraniol with an overall energy barrier of 24.6 kcal mol-1. Besides, linalool can also reversibly convert into the reactant with an energy barrier of 24.1 kcal mol-1. It is also found that the intermediate IM1 can directly transform to geraniol without first converting to (S)-linalool. His128 and Tyr65 form hydrogen bonds to stabilize the structure of the active site, but they do not act as general acid/base catalysts during the catalytic reactions.

A 4-nitro-L-phenylalanine scaffold was used to construct effective ion pair receptors capable of binding anions in an enhanced manner with the assistance of alkali metal cations. A benzocrown ether was linked to a receptor platform via the amide function so as to support the squaramide function in anion binding and to allow all three NHs to act simultaneously. The binding properties of the receptors were determined using UV-vis, 1H NMR, 2D NMR, and DOSY spectroscopy in MeCN and in the solid state by X-ray measurements. Ion pair receptor 2 was found to interact with the most strongly with salts, and the removal of its key structural elements was shown to hinder the receptor action. The amide proton was recognized to switch from having involvement in an intramolecular hydrogen bond to interacting with anions upon complexation. Apart from carboxylates, which promote deprotonation, and other monovalent salts creating 1:1 complexes with the receptor, more complex equilibria were established upon the complexation of 2 with sulfates. Receptor 2 was shown to be capable of the extraction of ion pairs from the aqueous to organic phase and of the cation-enhanced transport chloride and sulfate anions across a bulk chloroform membrane. These features may open the door for its use in regulating ion concertation under interfacial conditions and acting as a potential drug to treat channelopathies.

The title compounds were obtained by deprotonation of 1,2,4-tri­hydroxy­anthra­quinone (purpurin) using sodium hydride followed by reaction with either 1-bromo­propane or 1-bromo­butane. The compounds were characterized by 1H and 13C NMR and the structures determined using single-crystal X-ray diffraction., The title compounds were obtained by deprotonation of 1,2,4-tri­hydroxy­anthra­quinone (purpurin) using sodium hydride followed by reaction with either 1-bromo­propane or 1-bromo­butane. 1,4-Dihy­droxy-2-propoxyanthra­quinone crystallizes as a 1:1 solvate from aceto­nitrile, C17H14O5·CH3CN. The anthra­quinone core of the mol­ecule is essentially planar and both hy­droxy groups participate in intra­molecular O—H⋯O (carbon­yl) hydrogen bonds. The propyl chain is angled slightly above the plane of the anthra­quinone moiety with a maximum deviation of 0.247 (2) Å above the plane for the terminal carbon atom. In contrast, 2-but­oxy-1,4-di­hydroxy­anthra­quinone, C18H16O5, crystallizes from nitro­methane with two independent mol­ecules in the asymmetric unit. The anthra­quinone core of each independent mol­ecule is essentially planar and both hy­droxy groups on both mol­ecules participate in intra­molecular O—H⋯O(carbon­yl) hydrogen bonds. The butyl chain in one mol­ecule is also angled slightly above the plane of the anthra­quinone moiety, with a maximum deviation of 0.833 (5) Å above the plane for the terminal carbon atom. In contrast, the butyl group on the second mol­ecule is twisted out of the plane of the anthra­quinone core with a torsion angle of 65.1 (3)°, resulting in a maximum deviation of 1.631 (5) Å above the plane for the terminal carbon atom.

The Escherichia coli uracil/H + symporter UraA, known as the representative nucleobase/cation symporter 2(NCS2) protein, gets involved in several crucial physiological processes for most living organisms on Earth, such as the uptake of nucleobases and transport of vitamin C. Some experiments proposed a working model to explain proton-coupling and uracil transporting process of UraA on the basis of the crystal structure of NCS2 protein, but the details of conformational changes remained unknown. Thus, in order to make clear conformational changes caused by the protonation and deprotonation process of some conserved proton-coupled residues, the molecular dynamics simulation was used to study the conformation of UraA complexes in different protonation states. The results demonstrated that the protonation of residue Glu241 and Glu290 resulted in the whole conformational transition from the inward-open to the outward-open state. It can be concluded that Glu290 was crucial in a network of hydrogen-bonds in the middle of the core domain involving another essential residue, mainly including tyr288 in TM8, Tyr342, Ser338 in TM12, and the network of hydrogen-bonds was the key to maintain the stability of conformation. Protonation of Glu290 affects the stability of network of H-bond and changed the domains TM3 TM10 TM12. Thus, Glu290 may play a vital role as a 'proton trigger' that affects spatial structural of amino and residues near substrate binding side leading to an outward-open conformation transition.