Protein Conformation-Controlled Rebinding Barrier of NO and Its Binding Trajectories in Myoglobin and Hemoglobin at Room Temperature

Effect of Electron-donating Group on NO Photolysis of {RuNO}6 Ruthenium Nitrosyl Complexes with N2 O2 Lgands Bearing π-Extended Rings

In this study, we introduced the electron-donating group (-OH) to the aromatic rings of Ru(salophen)(NO)Cl (0) (salophenH2 =N,N'-(1,2-phenylene)bis(salicylideneimine)) to investigate the influence of the substitution on NO photolysis and NO-releasing dynamics. Three derivative complexes, Ru((o-OH)2 -salophen)(NO)Cl (1), Ru((m-OH)2 -salophen)(NO)Cl (2), and Ru((p-OH)2 -salophen)(NO)Cl (3) were developed and their NO photolysis was monitored by using UV/Vis, EPR, NMR, and IR spectroscopies under white room light. Spectroscopic results indicated that the complexes were diamagnetic Ru(II)-NO+ species which were converted to low-spin Ru(III) species (d5 , S=1/2) and released NO radicals by photons. The conversion was also confirmed by determining the single-crystal structure of the photoproduct of 1. The photochemical quantum yields (ΦNO s) of the photolysis were determined to be 0>1, 2, 3 at both the visible and UV excitations. Femtosecond (fs) time-resolved mid-IR spectroscopy was employed for studying NO-releasing dynamics. The geminate rebinding (GR) rates of the photoreleased NO to the photolyzed complexes were estimated to be 0≃1, 2, 3. DFT and TDDFT computations found that the introduction of the hydroxyl groups elevated the ligand π-bonding orbitals (π (salophen)), resulting in decrease of the HOMO-LUMO gaps in 1-3. The theoretical calculations suggested that the Ru-NNO bond dissociations of the complexes were mostly initiated by the ligand-to-ligand charge transfer (LLCT) of π(salophen)→π*(Ru-NO) with both the visible and UV excitations and the decreasing ΦNO s could be explained by the changes of the electronic structures in which the photoactivable bands of 1-3 have relatively less contribution of transitions related with Ru-NO bond than those of 0.

Dynamics of Irreversible NO Release from Photoexcited Molsidomine

Molsidomine (SIN-10), an orally administered NO-delivery drug for vasodilation, cannot be used to alleviate hypertensive crisis because it releases NO at a slow rate. SIN-10 may be used to treat sudden cardiac abnormalities if the rapid and immediate release of NO is achieved via photoactivation. The photodissociation dynamics associated with the NO release process from SIN-10 in CHCl₃ was investigated using time-resolved infrared spectroscopy. Approximately 41% of photoexcited SIN-10 at 360 nm decomposed into CO₂, CH₂CH₃ radical, and the remaining radical fragment [SIN-1A(-H)] with a time constant of 43 ps. All SIN-1A(-H) released NO spontaneously with a time constant of 68 ns, becoming N-morpholino-aminoacetonitrile, resulting in 41% for the quantum yield of immediate NO release from SIN-10. The results obtained can be used to realize the quantitative control of the NO administration at a specific time, and SIN-10 can be potentially used to address the phenomenon of hypertensive crisis.

Investigating the Photodissociation Dynamics of CF2BrCF2I in CCl4 through Femtosecond Time-Resolved Infrared Spectroscopy

The photodissociation dynamics of CF₂BrCF₂I in CCl₄ at 280 ± 2 K were investigated by probing the C-F stretching mode from 300 fs to 10 μs after excitation at 267 nm using time-resolved infrared spectroscopy. The excitation led to the dissociation of I or Br atoms within 300 fs, producing the CF₂BrCF₂ or CF₂ICF₂ radicals, respectively. All nascent CF₂ICF₂ underwent further dissociation of I, producing CF₂CF₂ with a time constant of 56 ± 5 ns. All nascent g-CF₂BrCF₂ isomerized into the more stable a-CF₂BrCF₂ with a time constant of 47 ± 5 ps. Furthermore, a-CF₂BrCF₂ underwent a bimolecular reaction with either itself (producing CF₂BrCF₂Br and CF₂CF₂) or Br in the CCl₄ solution (producing CF₂BrCF₂Br) at a diffusion-limited rate. The secondary dissociation of Br from a-CF₂BrCF₂ was significantly slow to compete with the bimolecular reactions. Overall, approximately half of the excited CF₂BrCF₂I at 267 nm produced CF₂BrCF₂Br, whereas the other half produced CF₂CF₂. The excess energies in the nascent radicals were thermalized much faster than the secondary dissociation of I from CF₂ICF₂ and the observed bimolecular reactions, implying that the secondary reactions proceeded under thermal conditions. This study further demonstrates that structure-sensitive time-resolved infrared spectroscopy can be used to study various reaction dynamics in solution in real time.

Visible-light NO photolysis of ruthenium nitrosyl complexes with N2O2 ligands bearing π-extended rings and their photorelease dynamics

NO photorelease and its dynamics for two {RuNO}⁶ complexes, Ru(salophen)(NO)Cl (1) and Ru(naphophen)(NO)Cl (2), with salen-type ligands bearing π-extended systems (salophenH₂ = N,N'-(1,2-phenylene)-bis(salicylideneimine) and naphophenH₂ = N,N'-1,2-phenylene-bis(2-hydroxy-1-naphthylmethyleneimine)) were investigated. NO photolysis was performed under white room light and monitored by UV/Vis, EPR, and NMR spectroscopies. NO photolysis was also performed under 459 and 489 nm irradiation for 1 and 2, respectively. The photochemical quantum yields of the NO photolysis (Φ_NO) of both 1 and 2 were determined to be 9% at the irradiation wavelengths. The structural and spectroscopic characteristics of the complexes before and after the photolysis confirmed the conversion of diamagnetic Ru(II)(L)(Cl)-NO⁺ to paramagnetic S = ½ Ru(III)(L)(Cl)-solvent by photons (L = salophen^2- and naphophen^2-). The photoreleased NO radicals were detected by spin-trapping EPR. DFT and TDDFT calculations found that the photoactive bands are configured as mostly the ligand-to-ligand charge transfer (LLCT) of π(L) → π*(Ru-NO), suggesting that the NO photorelease was initiated by the LLCT. Dynamics of NO photorelease from the complexes in DMSO under 320 nm excitation were investigated by femtosecond (fs) time-resolved mid-IR spectroscopy. The primary photorelease of NO occurred for less than 0.32 ps after the excitation. The rate constants (k_-1) of the geminate rebinding of NO to the photolyzed 1 and 2 were determined to be (15 ps)^-1 and (13 ps)^-1, respectively. The photochemical quantum yields of NO photolysis (Φ_NO, λ = 320 nm) were estimated to be no higher than 14% for 1 and 11% for 2, based on the analysis of the fs time-resolved IR data. The results of fs time-resolved IR spectroscopy and theoretical calculations provided some insight into the overall kinetic reaction pathway, localized electron pathway or resonance pathway, of the NO photolysis of 1 and 2. Overall, our study found that the investigated {RuNO}⁶ complexes, 1 and 2, with planar N₂O₂ ligands bearing π-extended rings effectively released NO under visible light.

Photodissociation Dynamics of Nitric Oxide from N-Acetylcysteine- or N-Acetylpenicillamine-bound Roussin's Red Ester

The photochemical release of nitric oxide (NO) from a NO precursor is advantageous in terms of spatial, temporal, and dosage control of NO delivery to target sites. To realize full control of the quantitative NO administration from photoactivated NO precursors, it is necessary to have detailed dynamical information on the photodissociation of NO from NO precursors. We synthesized two new water-soluble Roussin's red esters (RREs), [Fe₂(μ-N-acetylcysteine)₂(NO)₄] and [Fe₂(μ-N-acetylpenicillamine)₂(NO)₄], which have five times longer lifetime than the well-known [Fe₂(μ-cysteine)₂(NO)₄]. The photodissociation dynamics of NO from these RREs in water were investigated over a broad time range from 0.3 ps to 10 μs after excitation at 310 and 400 nm using femtosecond time-resolved infrared (IR) spectroscopy. When these RREs are excited, they either release one NO, producing a radical species deficient in one NO (R), [Fe₂(μ-RS)₂(NO)₃], or relax into the ground state without photodeligation via an electronically excited intermediate state (M). R appears immediately after photoexcitation, suggesting that one NO is photodissociated faster than 0.3 ps. A certain fraction of R undergoes geminate recombination (GR) with NO with a time constant of 7-9 ps, while the remaining R competitively binds to the solvent. Solvent-bound R eventually bimolecularly recombines with NO with a rate constant of (1.3-1.6) × 10⁸ M^-1 s^-1. For a given RRE molecule, the fractional yield of M (0.62-0.76) depends on the excitation wavelength (λ_ex); however, the relaxation time of M (6 ± 1 ns) is independent of λ_ex. Although the primary quantum yield of NO photodissociation (Φ₁) was found to be 0.24-0.38, the final yield of NO suitable for other reactions (Φ₂) was reduced to 0.14-0.29 due to the picosecond GR of the dissociated NO with R. Detailed photoexcitation dynamics of RRE can be utilized in the quantitative control of NO administration at a specific site and time, promoting pin-point usage of NO in chemistry and biology. We demonstrate that femtosecond IR spectroscopy combined with quantum chemical calculations is a powerful method for obtaining detailed dynamic information on photoactivated NO precursors such as Φ₁ and Φ₂, the GR yield, and secondary reactions of the nascent photoproducts, which are essential information for the design of efficient photoactivated NO precursors and their quantitative utilization.

Effect of Single-Point Mutations on Nitric Oxide Rebinding and the Thermodynamic Stability of Myoglobin

The effect of single amino acid mutations on the rebinding dynamics of nitrogen monoxide (NO) to myoglobin is investigated using reactive molecular dynamics simulations. In particular, mutations of residues surrounding the heme-active site (Leu29, His64, Val68) were considered. Consistent with experiments, all mutations studied here have a significant effect on the kinetics of the NO-rebinding process, which consists of a rapid (several 10 ps) and a slow (100s of ps) time scale. For all modifications considered, the time scales and rebinding fractions agree to within a few percents with results from experiments by adjusting one single, physically meaningful, conformationally averaged quantity: the asymptotic energy separation between the NO-bound (²A) and photodissociated (⁴A) states. It is furthermore shown that the thermodynamic stability of wild-type versus mutant Mb for the ligand-free and ligand-bound variants of the protein can be described by the same computational model. Therefore, ligand kinetics and thermodynamics are related in a direct fashion akin to Φ-value analysis, which establishes a relationship between protein folding rates and thermal stability of proteins.

Photodissociation dynamics of nitric oxide from roussin’s red ester probed by time-resolved infrared spectroscopy

To explore nitric oxide (NO)-donating capability of Roussin’s red ester [Fe2(μ-RS)2(NO)4] (RRE), photodissociation of NO from RRE and its subsequent reaction dynamics were probed by monitoring the N–O stretching mode after excitation with a 400-nm photon. As a result of the experiment, the NO generation quantum yield was obtained.

Rebinding dynamics of NO to microperoxidase-8 probed by time-resolved vibrational spectroscopy

Femtosecond vibrational spectroscopy was used to probe the rebinding kinetics of NO to microperoxidase-8 (Mp), an ideal model system for the active site of ligand-binding heme proteins, including myoglobin and hemoglobin, after the photodeligation of MpNO in glycerol/water (G/W) solutions at 294 K. The geminate rebinding (GR) of NO to Mp in viscous solutions was highly efficient and ultrafast and negligibly dependent on the solution viscosity, which was adjusted by changing the glycerol content from 65% to 90% by volume in G/W mixtures. The kinetics of the GR of NO to Mp in viscous solutions was well represented by an exponential function with a time constant of ca. 11 ps. Although the kinetic traces of the GR of NO to Mp in solutions with three different viscosities (18, 81, and 252 cP) almost overlap, they show a slight difference early in the decay process. The kinetic traces were also described by the diffusion-controlled reaction theory with a Coulomb potential. Since the ligand is deligated in a neutral form, an ionic pair of NO(-) and Mp(+) may be produced before forming the Mp-NO bond by an electron transfer from Mp to NO as the deligated NO is sufficiently near to the Fe atom of Mp. The strong reactivity between NO and ferrous heme may arise from the Coulomb interaction between the reacting pair, which is consistent with the harpooning mechanism for NO binding to heme.

NO binding kinetics in myoglobin investigated by picosecond Fe K-edge absorption spectroscopy

Diatomic ligands in hemoproteins and the way they bind to the active center are central to the protein's function. Using picosecond Fe K-edge X-ray absorption spectroscopy, we probe the NO-heme recombination kinetics with direct sensitivity to the Fe-NO binding after 532-nm photoexcitation of nitrosylmyoglobin (MbNO) in physiological solutions. The transients at 70 and 300 ps are identical, but they deviate from the difference between the static spectra of deoxymyoglobin and MbNO, showing the formation of an intermediate species. We propose the latter to be a six-coordinated domed species that is populated on a timescale of ∼ 200 ps by recombination with NO ligands. This work shows the feasibility of ultrafast pump-probe X-ray spectroscopic studies of proteins in physiological media, delivering insight into the electronic and geometric structure of the active center.

Influence of reactive species on the modification of biomolecules generated from the soft plasma

Plasma medicine is an upcoming research area that has attracted the scientists to explore more deeply the utility of plasma. So, apart from the treating biomaterials and tissues with plasma, we have studied the effect of soft plasma with different feeding gases such as Air, N2 and Ar on modification of biomolecules. Hence, in this work we have used the soft plasma on biomolecules such as proteins ((Hemoglobin (Hb) and Myoglobin (Mb)), calf thymus DNA and amino acids. The structural changes or structural modification of proteins and DNA have been studied using circular dichroism (CD), fluorescence spectroscopy, protein oxidation test, gel electrophoresis, UV-vis spectroscopy, dynamic light scattering (DLS) and 1D NMR, while Liquid Chromatograph/Capillary Electrophoresis-Mass Spectrometer (LC/CE-MS) based on qualitative and quantitative bio-analysis have been used to study the modification of amino acids. Further, the thermal analysis of the protein has been studied with differential scanning calorimetry (DSC) and CD. Additionally, we have performed docking studies of H2O2 with Hb and Mb, which reveals that H2O2 molecules preferably attack the amino acids near heme group. We have also shown that N2 gas plasma has strong deformation action on biomolecules and compared to other gases plasma.

Time-resolved infrared spectroscopic studies of ligand dynamics in the active site from cytochrome c oxidase

The catalytic site of heme-copper oxidases encompasses two close-lying ligand binding sites: the heme, where oxygen is bound and reduced and the CuB atom, which acts as ligand entry and release port. Diatomic gaseous ligands with a dipole moment, such as the signaling molecules carbon monoxide (CO) and nitric oxide (NO), carry clear infrared spectroscopic signatures in the different states that allow characterization of the dynamics of ligand transfer within, into and out of the active site using time-resolved infrared spectroscopy. We review the nature and diversity of these processes that have in particular been characterized with CO as ligand and which take place on time scales ranging from femtoseconds to milliseconds. These studies have advanced our understanding of the functional ligand pathways and reactivity in enzymes and more globally represent intriguing model systems for mechanisms of ligand motion in a confined protein environment. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

Geminate rebinding dynamics of nitric oxide to ferric hemoglobin in D2O solution

Femtosecond mid-infrared (mid-IR) spectroscopy was used to probe geminate rebinding (GR) dynamics of photo-released nitric oxide (NO) to ferric hemoglobin (Hb(III)) in D2O solution at room temperature. Time-resolved vibrational spectra exhibit two overlapping NO bands for NO-bound Hb(III) (Hb(III)NO), a major band at 1925 cm(-1) (89%) and a minor one at 1905 cm(-1) (11%), suggesting that Hb(III)NO has at least two conformational substates. Both bands decay nonexponentially, each with a different time scale, and the decays are described by a stretched exponential function; the major band's decay is described by 0.96 exp(-t/40 ps)(0.86) + 0.04 and the minor band's decay is described by exp(-t/85 ps)(0.75). These decays arise mainly from the GR of the photo-released NO to Hb(III), indicating that the bound state's conformer influences the NO binding. In particular, the His64 residue, known to have inward conformation in the major band and outward conformation in the minor band, plays a significant role in controlling the binding of NO to Hb(III). The GR of NO to ferric Hb is slower than that to ferrous Hb, which shows fast and efficient GR due to the high reactivity of NO to the heme Fe(ii). The slower GR of NO to Hb(III) may be caused by the lower reactivity of NO to the heme Fe(iii).