Temperature-dependent studies of NO recombination to heme and heme proteins

The rebinding kinetics of NO to the heme iron of myoglobin (Mb) is investigated as a function of temperature. Below 200 K, the transition-state enthalpy barrier associated with the fastest (approximately 10 ps) recombination phase is found to be zero and a slower geminate phase (approximately 200 ps) reveals a small enthalpic barrier (approximately 3 +/- 1 kJ/mol). Both of the kinetic rates slow slightly in the myoglobin (Mb) samples above 200 K, suggesting that a small amount of protein relaxation takes place above the solvent glass transition. When the temperature dependence of the NO recombination in Mb is studied under conditions where the distal pocket is mutated (e.g., V68W), the rebinding kinetics lack the slow phase. This is consistent with a mechanism where the slower (approximately 200 ps) kinetic phase involves transitions of the NO ligand into the distal heme pocket from a more distant site (e.g., in or near the Xe4 cavity). Comparison of the temperature-dependent NO rebinding kinetics of native Mb with that of the bare heme (PPIX) in glycerol reveals that the fast (enthalpically barrierless) NO rebinding process observed below 200 K is independent of the presence or absence of the proximal histidine ligand. In contrast, the slowing of the kinetic rates above 200 K in MbNO disappears in the absence of the protein. Generally, the data indicate that, in contrast to CO, the NO ligand binds to the heme iron through a "harpoon" mechanism where the heme iron out-of-plane conformation presents a negligible enthalpic barrier to NO rebinding. These observations strongly support a previous analysis (Srajer et al. J. Am. Chem. Soc. 1988, 110, 6656-6670) that primarily attributes the low-temperature stretched exponential rebinding of MbCO to a quenched distribution of heme geometries. A simple model, consistent with this prior analysis, is presented that explains a variety of MbNO rebinding experiments, including the dependence of the kinetic amplitudes on the pump photon energy.     

Frozen density functional free energy simulations of redox proteins: computational studies of the reduction potential of plastocyanin and rusticyanin

The evaluation of reduction potentials of proteins by ab initio approaches presents a major challenge for computational chemistry. This is addressed in the present investigation by reporting detailed calculations of the reduction potentials of the blue copper proteins plastocyanin and rusticyanin using the QM/MM all-atom frozen density functional theory, FDFT, method. The relevant ab initio free energies are evaluated by using a classical reference potential. This approach appears to provide a general consistent and effective way for reproducing the configurational ensemble needed for consistent ab initio free energy calculations. The FDFT formulation allows us to treat a large part of the protein quantum mechanically by a consistently coupled QM/QM/MM embedding method while still retaining a proper configurational sampling. To establish the importance of proper configurational sampling and the need for a complete representation of the protein+solvent environment, we also consider several classical approaches. These include the semi-macroscopic PDLD/S-LRA method and classical all-atom simulations with and without a polarizable force field. The difference between the reduction potentials of the two blue copper proteins is reproduced in a reasonable way, and its origin is deduced from the different calculations. It is found that the protein permanent dipole tunes down the reduction potential for plastocyanin compared to the active site in regular water solvent, whereas in rusticyanin it is instead tuned up. This electrostatic environment, which is the major effect determining the reduction potential, is a property of the entire protein and solvent system and cannot be ascribed to any particular single interaction.     

Insight into the electronic structure, optical properties, and redox behavior of the hybrid phthalocyaninoclathrochelates from experimental and density functional theory approaches

An insight into the electronic structure of several hafnium(IV), zirconium(IV), and lutetium(III) phthalocyaninoclathrochelates has been discussed on the basis of experimental UV-vis, MCD, electro- and spectroelectrochemical data as well as density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. On the basis of UV-vis and MCD spectroscopy as well as theoretical predictions, it was concluded that the electronic structure of the phthalocyninoclathrochelates can be described in the first approximation as a superposition of the weakly interacting phthalocyanine and clathrochelate substituents. Spectroelectrochemical data and DFT calculations clearly confirm that the highest occupied molecular orbital (HOMO) in all tested complexes is localized on the phthalocyanine ligand. X-ray crystallography on zirconium(IV) and earlier reported hafnium(IV) phthalocyaninoclathrochelate complexes revealed a slightly distorted phthalocyanine conformation with seven-coordinated metal center positioned ～1 ? above macrocyclic cavity. The geometry of the encapsulated iron(II) ion in the clathrochelate fragment was found to be between trigonal-prismatic and trigonal-antiprismatic.     

Homocysteine thiolactone and protein homocysteinylation: mechanistic studies with model peptides and proteins

In vitro incubations were performed to show that homocysteine thiolactone could generate covalent adducts with model peptides and proteins. MS and MS/MS data suggest that the thiolactone reacts with the side-chain amino group of lysine residues as well as with the N-terminal amino group or C-terminal carboxy group. For larger peptides and proteins, the contribution from the in-amino groups of lysine residues should be predominant. These data could help explain the detrimental effects of elevated levels of homocysteine and homocysteine thiolactone.     

A density functional theory investigation of Fe-N-O bonding in heme proteins and model systems

We report the results of a series of density functional theory (DFT) calculations of the M?ssbauer quadrupole splittings and isomer shifts in NO heme model compounds, together with the results of calculations of the M?ssbauer quadrupole splittings, isomer shifts, and electron paramagnetic resonance hyperfine coupling constants in a model Fe(II)(NO)(imidazole) complex as a function of Fe-NO bond length and Fe-N-O bond angle. The results of the M?ssbauer quadrupole splitting and isomer shift calculations on the NO heme model compounds show good accord between theory and experiment, with the largest errors being observed for structures having the largest crystallographic R(1) values. The results of the property surface calculations were then used to calculate Fe-NO bond length and Fe-N-O bond angle probability surfaces (Z-surfaces) for a nitrosyl hemoglobin, using, in addition, an energy filter. The results obtained yielded a most probable Fe-NO bond length (r) of 1.79 A and an Fe-N-O bond angle (beta) of 136 degrees -137 degrees. This bond length is somewhat longer than those observed in most model compounds but may be due, at least in part, to hydrogen bond formation with the distal His residue. Bond elongation was also observed in a geometry optimized Fe(II)(NO)(imidazole) complex hydrogen bonded to an imidazole residue, in which we find r = 1.76-1.78 A and beta = 137 degrees -138 degrees. The computed bond angles are close to the canonical approximately 140 degrees value found in most model systems. Highly bent Fe-N-O bond angles or very long Fe-NO bond lengths seem unlikely to occur in proteins, due to their high energies. We also investigated the molecular orbitals and spin densities in each of the six coordinate systems investigated and found the orbitals and spin densities to be generally similar those described previously for five coordinate systems. Taken together, these results show that M?ssbauer quadrupole splittings and isomer shifts, in addition to electron paramagnetic resonance hyperfine coupling constants, can now be calculated for nitrosyl heme systems with relatively good accuracy and that the results so obtained can be used to determine Fe-N-O geometries in metalloproteins. The Z-surface approach is thus applicable to both diamagnetic (CO) and paramagnetic (NO) heme proteins with in both cases the metal-ligand binding geometries found in the proteins being very close to those seen in model systems.     

Homology-free prediction of functional class of proteins and peptides by support vector machines

Protein and peptide sequences contain clues for functional prediction. A challenge is to predict sequences that show low or no homology to proteins or peptides of known function. A machine learning method, support vector machines (SVM), has recently been explored for predicting functional class of proteins and peptides from sequence-derived properties irrespective of sequence similarity, which has shown impressive performance for predicting a wide range of protein and peptide classes including certain low- and non- homologous sequences. This method serves as a new and valuable addition to complement the extensively-used alignment-based, clustering-based, and structure-based functional prediction methods. This article evaluates the strategies, current progresses, reported prediction performances, available software tools, and underlying difficulties in using SVM for predicting the functional class of proteins and peptides.     

Control of cytochrome C redox potential: axial ligation and protein environment effects

Axial iron ligation and protein encapsulation of the heme cofactor have been investigated as effectors of the reduction potential (E degrees ') of cytochrome c through direct electrochemistry experiments. Our approach was that of partitioning the E degrees ' changes resulting from binding of imidazole, 2-methyl-imidazole, ammonia, and azide to both cytochrome c and microperoxidase-11 (MP11), into the enthalpic and entropic contributions. N-Acetylmethionine binding to MP11 was also investigated. These ligands replace Met80 and a water molecule axially coordinated to the heme iron in cytochrome c and MP11, respectively. This factorization was achieved through variable temperature E degrees ' measurements. In this way, we have found that (i) the decrease in E degrees ' of cytochrome c due to Met80 substitution by a nitrogen-donor ligand is almost totally enthalpic in origin, as a result of the stronger electron donor properties of the exogenous ligand which selectively stabilize the ferric state; (ii) on the contrary, the binding of the same ligands and N-acetylmethionine to MP11 results in an enthalpic stabilization of the reduced state, whereas the entropic effect invariably decreases E degrees ' (the former effect prevails for the methionine ligand and the latter for the nitrogenous ligands). A comparison of the reduction thermodynamics of cytochrome c and the MP11 adducts offers insight on the effect of changing axial heme ligation and heme insertion into the folded polypeptide chain. Principally, we have found that the overall E degrees ' increase of approximately 400 mV, comparing MP11 and native cytochrome c, consists of two opposite enthalpic and entropic terms of approximately +680 and -280 mV, respectively. The enthalpic term includes contributions from both axial methionine binding (+300 mV) and protein encapsulation of the heme (+380 mV), whereas the entropic term is almost entirely manifest at the stage of axial ligand binding. Both terms are dominated by the effects of water exclusion from the heme environment.     

Cyclic voltammetry and voltabsorptometry studies of redox proteins immobilised on nanocrystalline tin dioxide electrodes

Protein film cyclic voltammetry is a well-established technique for the study of redox proteins immobilised on electrode surfaces. In this paper, we use nanostructured SnO(2) electrodes to demonstrate that cyclic voltabsorptometry is an effective, complimentary approach to such studies of protein redox function. We exemplify this approach using two different redox systems: microperoxidase-11 (MP-11) and flavodoxin Desulfovibrio vulgaris Hildenborough (Fld). Both systems were immobilised on nanocrystalline SnO(2) electrodes and the resulting films investigated by simultaneous cyclic voltammetry and voltabsorptometry. We demonstrate that cyclic voltabsorptometry allows the unambiguous and background free observation of redox reactions for both systems studied.     

Synthetic metal-binding protein surface domains for metal ion-dependent interaction chromatography. II. Immobilization of synthetic metal-binding peptides from metal ion transport proteins as model bioactive protein surface domains.

This preliminary investigation tests the premise that biologically relevant (1) peptide-metal ion interactions, and (2) metal ion-dependent macromolecular recognition events (e.g., peptide-peptide interactions) may be modeled by biomimetic affinity chromatography. Divinylsulfone-activated agarose (6%) was used to immobilize three different synthetic peptides representing metal-binding protein surface domains from the human plasma metal transport protein histidine-rich glycoprotein (HRG). The synthetic peptides represented 1-3 multiple repeat units of the 5-residue sequence (Gly-His-His-Pro-His) found in the C-terminal of HRG. By frontal analyses, immobilized HRG peptides of the type (GHHPH)nG, where n = 1-3, were each found to have a similar binding capacity for both Cu(II) ions and Zn(II) ions (31-38 mumol/ml gel). The metal ion-dependent interaction of a variety of model peptides with each of the immobilized HRG peptide affinity columns demonstrated differences in selectivity despite the similar internal sequence homology and metal ion binding capacity. The immobilized 11-residue HRG peptide was loaded with Cu(II) ions and used to demonstrate selective adsorption and isolation of proteins from human plasma. These results suggest that immobilized metal-binding peptides selected from known solvent-exposed protein surface metal-binding domains may be useful model systems to evaluate the specificity of biologically relevant metal ion-dependent interaction and transfer events in vitro.     

Efficient photodissociation of O2 from synthetic heme and heme/M (M = Fe, Cu) complexes

Single wavelength excitation (lambdaex = 355 or 532 nm) of low-temperature stabilized (198 K) synthetic heme-dioxygen and heme-dioxygen/M complexes, where M = copper or iron in a non-heme environment, results in the dissociation of dioxygen as indicated by the generation of the ferrous heme (Soret band, 427 nm) and the bleaching of the ferric-superoxide (FeIII(O2-)) 410-nm Soret band in the transient absorption difference spectrum. Dioxygen rebinds to the four heme complexes studied with comparable rate constants ( approximately 6-9 x 105 M-1 s-1). However, the quantum yield for complete dissociation of O2 from our simplest heme-O2 complex (F8)FeIII(O2-) (phi = 0.60) is higher than the other complexes measured (phi = approximately 0.2-0.3) as well as that for oxy-myoglobin (phi = 0.3).     

Reactions of gaseous organic compounds on silica surface. Spectral studies and synthetic aspects

The results of infrared spectroscopic and mass-spectrometric studies on reactions of vapor phase carboxylic acids, polyazamacrocyclic ligands, pyrimidine bases, acetylacetonates and related compounds with hydroxylic, chlorosilylated, halo- and aminoalkylsilylated silica surfaces are analyzed. Application of various reactions for the gasphase derivatization of silica materials and for the gassolid-phase synthesis of 2,5-dioxoperazines is discussed.     

Analysis of HIV-1 fusion peptide inhibition by synthetic peptides from E1 protein of GB virus C

The aim of this study was to identify proteins that could inhibit the activity of the peptide sequence representing the N-terminal of the surface protein gp41 of HIV, corresponding to the fusion peptide of the virus (HIV-1 FP). To do this we synthesized and studied 58 peptides corresponding to the envelope protein E1 of the hepatitis G virus (GBV-C). Five of the E1 synthetic peptides: NCCAPEDIGFCLEGGCLV (P7), APEDIGFCLEGGCLVALG (P8), FCLEGGCLVALGCTICTD (P10), QAGLAVRPGKSAAQLVGE (P18) and AQLVGELGSLYGPLSVSA (P22) were capable of inhibiting the leakage of vesicular contents caused by HIV-1 FP. A series of experiments were carried out to determine how these E1 peptides interact with HIV-1 FP. Our studies analyzed the interactions with and without the presence of lipid membranes. Isothermal titration calorimetry revealed that the binding of P7, P18 and P22 peptides to HIV-1 FP is strongly endothermic, and that binding is entropy-driven. Gibbs energy for the process indicates a spontaneous binding between E1 peptides and HIV-1 FP. Moreover, confocal microscopy of Giant Unilamellar Vesicles revealed that the disruption of the lipid bilayer by HIV-1 FP alone was inhibited by the presence of any of the five selected peptides. Our results highlight that these E1 synthetic peptides could be involved in preventing the entry of HIV-1 by binding to the HIV-1 FP. Therefore, the continued study into the interaction between GBV-C peptides and HIV-1 FP could lead to the development of new therapeutic agents for the treatment of AIDS.     

Insight into the structural characteristics of core-links and flat-aluminum tridecamers: a density functional theory study

The structures of core-links Al(13) (C-Al(13)) and flat-Al(13) (F-Al(13)) complexes in aqueous solution have been investigated using density functional theory (DFT) at the level of B3LYP/6-31G(d). The present work focuses on the following three aspects: (1) C-Al(13)(9+) was optimized with the consideration of solvent effect and the (27)Al NMR chemical shifts using Hartree Fock GIAO and B3LYP GIAO methods were computed respectively; (2) the optimization of F-Al(13)(15+) was also performed and the (27)Al NMR chemical shifts were obtained using the same methods as above; (3) the structural parameters of a series of typical aluminum species (Al(3+), AlOH(2+), AlF(2+), Al(2)(4+), Al(6)(6+), K-Al(13)(7+), C-Al(13)(9+) and F-Al(13)(15+)) were compared.     

Impact of proximal and distal pocket site-directed mutations on the ferric/ferrous heme redox potential of yeast cytochrome c peroxidase

Cytochrome c peroxidase (CCP) contains a five-coordinate heme active site. The reduction potential for the ferric to ferrous couple in CCP is anomalously low and pH dependent (Eo?=?~?180?mV vs. S.H.E. at pH 7). The contribution of the protein environment to the tuning of the redox potential of this couple is evaluated using site-directed mutants of several amino acid residues in the environment of the heme. These include proximal pocket mutation of residues Asp-235, Trp-191, Phe-202, and His-175, distal pocket mutation of residues Trp-51, His-52, and Arg-48; and a heme edge mutation of Ala-147. Where unknown, the structural changes resulting from the amino acid substitution have been studied by X-ray crystallography. In most cases, ostensibly polar or charged residues are replaced by large hydrophobic groups or alternatively by Ala or Gly. These latter have been shown to generate large, solvent-filled cavities. Reduction potentials are measured as a function of pH by spectroelectrochemistry. Starting with the X-ray-derived structures of CCP and the mutants, or with predicted structures generated by molecular dynamics (MD), predictions of redox potential changes are modeled using the protein dipoles Langevin dipoles (PDLD) method. These calculations serve to model an electrostatic assessment of the redox potential change with simplified assumptions about heme iron chemistry, with the balance of the experimentally observed shifts in redox potential being thence attributed to changes in the ligand set and heme coordination chemistry, and/or other changes in the structure not directly evident in the X-ray structures (e.g., ionization states, specific roles played by solvent species, or conformationally flexible portions of the protein). Agreement between theory and experiment is good for all mutant proteins with the exception of the mutation Arg 48 to Ala, and His 52 to Ala. In the former case, the influence of phosphate buffer is adduced to account for the discrepancy, with evidence for phosphate binding in the distal pocket, and measurements made in a bis?Ctris propane/2-(N-morpholino)ethanesulfonic acid buffer system agree well with theory. For the latter case, an unknown structural element relevant to His-52 and/or solvent influence in the mutant akin to anion binding in the distal pocket (though lacking proof that it is, and in this case lacking a phosphate effect) manifests in this mutant. The use of exogenous (sixth) ligands in dissecting the contributions to control of redox potential is also explored as a pathway for model building.     

Mechanistic Insight into Hydroboration of Imines from Combined Computational and Experimental Studies

Boron Lewis acid-catalyzed and catalyst-free hydroboration reactions of imines are attractive due to the mild reaction conditions. In this work, the mechanistic details of the hydroboration reactions of two different kinds of imines with pinacolborane (HBpin) are investigated by combining density functional theory calculations and some experimental studies. For the hydroboration reaction of N-(α-methylbenzylidene)aniline catalyzed by tris[3,5-bis(trifluoromethyl)phenyl]borane (BAr^F₃), our calculations show that the reaction proceeds through a boron Lewis acid-promoted hydride transfer mechanism rather than the classical Lewis acid activation mechanism. For the catalyst- and solvent-free hydroboration reaction of imine, N-benzylideneaniline, our calculations and experimental studies indicate that this reaction is difficult to occur under the reaction conditions reported previously. With a combination of computational and experimental studies, we have established that the commercially available BH₃ ⋅ SMe₂ can serve as an efficient catalyst for the hydroboration reactions of N-benzylideneaniline and similar imines. The hydroboration reactions catalyzed by BH₃ ⋅ SMe₂ are most likely to proceed through a hydroboration/B−H/B−N σ-bond metathesis pathway, which is very different from that of the reaction catalyzed by BAr^F₃.     

Insight into the extraction and characterization of cellulose nanocrystals from date pits

This study aims to extract and characterize cellulose nanocrystals (CNCs) from date pits (DP), an agricultural solid waste. Two methods were used and optimized for the cellulose nanocrystals (CNCs) extraction, namely the mechanical stirrer method (CNCs₁) and the Soxhlet apparatus method (CNCs₂) in terms of chemical used, cost, and energy consumption. The results showed that scanning electron microscopy revealed the difference in the morphology as they exhibit rough surfaces with irregular morphologies due to the strong chemical treatments during the delignification and bleaching process. Moreover, transmission electron microscopy analysis for CNCs reveals the true modification that was made through sulfuric acid hydrolysis as it presents cellulose microfibrils with a packed structure. Fourier transform infrared proved that the CNCs were successfully extracted using the two methods since most of the lignin and hemicellulose components were removed. The crystallinity index of CNCs₁ and CNCs₂ was 69.99%, and 67.79%, respectively, and both presented a high yield of CNCs (≥10%). Ultimately, both techniques were successful at extracting CNCs. Based on their cost-effectiveness and time consumption, it was concluded that method 1 was less expensive than method 2 based on the breakdown of the cost of each step for CNCs production.     

Density functional study of organocatalytic mannich‐type reactions: Insight into reverse diastereoselectivities arising from catalysts with different scaffolds

Density functional study have been carried out to investigate the stereoselectivities in the Mannich‐type reactions promoted by five typical amino acid catalysts with different scaffolds. The reverse diastereoselectivities in the cyclic and acyclic α‐ and β‐amino acids‐promoted Mannich reactions have been satisfactorily explained by the density functional theory (DFT) methods at the SMD/M06‐2X/6‐31G** computational level. The activation strain analysis has been used to account for the selectivity‐switching for these selected bifunctional catalysts. © 2015 Wiley Periodicals, Inc.