Resonance assignments and secondary structure analysis of E. coli thioredoxin by magic angle spinning solid-state NMR spectroscopy

De novo site-specific 13C and 15N backbone and sidechain resonance assignments are presented for uniformly enriched E. coli thioredoxin, established using two-dimensional homo- and heteronuclear solid-state magic angle spinning NMR correlation spectroscopy. Backbone dihedral angles and secondary structure were derived from the statistical analysis of the secondary chemical shifts, and are in good agreement with solution values for the intact full-length thioredoxin, with the exception of a small number of residues located at the termini of the individual secondary structure elements. A large number of cross-peaks observed in the DARR spectra with long mixing times correspond to the pairs of carbon atoms separated by 4-6 angstroms, suggesting that DARR could be efficiently employed for observation of medium- and long-range correlations. The 108 amino acid residue E. coli thioredoxin is the largest uniformly enriched protein assigned to this degree of completeness by solid-state NMR spectroscopy to date. It is anticipated that with a combination of two-dimensional correlation experiments and high magnetic fields, resonance assignments and secondary structure can be generally derived for other noncrystalline proteins.     

Spectroscopic and computational investigation of the ground and low excited states of some symmetrical heterocyclic disulfides

The electronic absorption and emission spectra of some symmetrical heterocyclic disulfides are investigated. The reversible disulfide — thione transformation in water is discussed in view of the complex equilibrium processes present. UV irradiation and pH influence on the above transformation is also studied. The emission properties at room and low temperature are related to the computed molecular geometries of the ground and low excited states of the compounds.     

Assignments of carbon NMR resonances for microcrystalline ubiquitin

Solid-state NMR 2D spectroscopy was used to correlate carbon backbone and side-chain chemical shifts for uniformly (13)C,(15)N-enriched microcrystalline ubiquitin. High applied field strengths, 800 MHz for protons, moderate proton decoupling fields, 80-100 kHz, and high magic angle sample spinning frequencies, 20 kHz, were used to narrow the most of the carbon line widths to 0.5-0.8 ppm. Homonuclear magnetization transfer was effected by matching the proton RF field to the spinning frequency, the so-called dipolar-assisted rotational resonance (DARR) (Takegoshi, K.; Nakamura, S.; Terao, T. Chem. Phys. Lett. 2001, 344, 631-637), and a mixing time of 20 ms was used to maximize the intensity of one-bond transfers between carbon atoms. This polarization transfer sequence resulted in roughly 14% transfer efficiencies for directly bonded carbon pairs and 4% transfer efficiencies for carbons separated by a third carbon. With this simple procedure, the majority of the one-bond correlations was observed with moderate transfer efficiencies, and many two-bond correlations were also observed with weaker intensities. Spin systems could be identified for more than half of the amino acid side chains, and site-specific assignments were readily possible via comparison with 400 MHz (15)N-(13)C-(13)C correlation spectroscopy (described separately).     

Comparative study of photodynamic properties of 13,15-N-cycloimide derivatives of chlorin p6

Comparative study of 13,15-[N-(2-hydroxyethyl)]cycloimide chlorin p6 (2), 13,15-(N-acetoxy)cycloimide chlorin p6 (3), 13,15-(N-hydroxy)cycloimide chlorin p6 methyl ester (4) and 13,15-(N-methoxy)cycloimide chlorin p6 methyl ester (5) together with the previously investigated 13,15-[N-(3-hydroxypropyl)]cycloimide chlorin p6 (1) was performed. The dependence of the key photodynamic properties of 1-5 on the introduced substituents was analyzed. The photoinduced cell-killing activity of 4 is 100- and 280-fold higher than that of chlorin p6 and Photogem, respectively, as estimated on A549 human lung adenocarcinoma cells. The activity is reduced eight times in the order 4 > 5 > 1 > 2 > 3. The intracellular accumulation of 1-5 occurs in cytoplasm in a monomeric form bound to the lipids of cellular membranes. This form of 1, 2, 3, 4 and 5 is characterized by the high quantum yield of singlet oxygen generation, which depends on the introduced substituents, 0.66, 0.59, 0.35, 0.51 and 0.73, respectively. The photostability is two-fold less for 1 and four-fold less for 2, 3 and 5 than for 4. The rates of cellular uptake and efflux of 1-5 vary widely, thus providing the way to optimize the pharmacological properties of the photosensitizer (PS) using the respective substituents. Modifying the substituents, 1-5 were targeted to different cellular organelles. The enhanced accumulation in the Golgi apparatus and mitochondria complemented with diffuse staining of intracellular membranous structures is a property of 1-4. Compound 5 accumulates selectively in the lipid droplets and stains weakly perinuclear structures. Temperature-sensitive mechanisms of transport are responsible for the 1-4 uptake. Diffusion can play a role in the internalization of 5 but not of 1-4. Endocytosis via caveolae, clathrin-dependent and adenosine triphosphate-dependent pathways are not noticeably involved in the 1-5 internalization. Independently from their intracellular localization 1, 4 and 5 are highly efficient near-IR PS, which induce predominantly an apoptotic type of cell death under conditions providing ca 50% level of phototoxicity and necrosis at the 100% level of phototoxicity.     

Oxidation of formic acid and carbon monoxide on gold electrodes studied by surface-enhanced Raman spectroscopy and DFT.

The oxidation of formic acid and carbon monoxide was studied at a gold electrode by a combination of electrochemistry, in situ surface-enhanced Raman spectroscopy (SERS), differential electrochemical mass spectrometry, and first-principles DFT calculations. Comparison of the SERS results and the (field-dependent) DFT calculations strongly suggests that the relevant surface-bonded intermediate during oxidation of formic acid on gold is formate HCOO- ad*. Formate reacts to form carbon dioxide via two pathways: at low potentials, with a nearby water to produce carbon dioxide and a hydronium ion; at higher potentials, with surface-bonded hydroxyl (or oxide) to give carbon dioxide and water. In the former pathway, the rate-determining step is probably related to the reaction of surface-bonded formate with water, as measurements of the reaction order imply a surface almost completely saturated with adsorbate. The potential dependence of the rate of the low-potential pathway is presumably governed by the potential dependence of formate coverage. There is no evidence for CO formation on gold during oxidation of formic acid. The oxidation of carbon monoxide must involve the carboxyhydroxyl intermediate, but SERS measurements do not reveal this intermediate during CO oxidation, most likely because of its low surface coverage, as it is formed after the rate-determining step. Based on inconclusive spectroscopic evidence for the formation of surface-bonded OH at potentials substantially below the surface oxidation region, the question whether surface-bonded carbon monoxide reacts with surface hydroxyl or with water to form carboxyhydroxyl and carbon dioxide remains open. The SERS measurements show the existence of both atop and bridge-bonded CO on gold from two distinguishable low-frequency modes that agree very well with DFT calculations.     

Changes in calmodulin main-chain dynamics upon ligand binding revealed by cross-correlated NMR relaxation measurements

The fast dynamics of protein backbones are often investigated by nuclear magnetic relaxation experiments that report on the degree of spatial restriction of the amide bond vector. By comparing calmodulin in the peptide-bound and peptide-free states with these classical methods, we observe little difference in the dynamics of the polypeptide main chain (average order parameter decrease of 0.01 unit upon binding). However, when using NMR methods that monitor the mobility of the CO-Calpha bond vector, we reveal a significant reduction of dynamics of the protein main chain (average order parameter decrease of 0.048 units). Previous investigations have suggested that the side-chain dynamics is reduced by an average of 0.07 order parameter units upon ligand binding (Lee, A. L.; Kinnear, S. A.; Wand, A. J. Nat. Struct. Biol. 2000, 7, 72-77). The current findings suggest that the change of the CO-Calpha bond vector dynamics is intermediate between the changes in NH and side-chain dynamics and report a previously undetected loss of main-chain entropy. Weak site-to-site correlations between the different motional indicators are also observed.     

Polymorphism of paracetamol

The thermodynamic relationship between crystal modifications of paracetamol was studied by alternative methods. Temperature dependence of saturated vapor pressure for polymorphic modifications of the drug paracetamol (acetaminophen) was mea sured and thermodynamic functions of the sublimation process calculated. Solution calorimetry was carried out for the two modifications in the same solvent. Thermodynamic parameters for sublimation for form I (monoclinic) were found: ΔG _sub²⁹⁸=60.0 kJ mol⁻¹; ΔH _sub²⁹⁸=117.9±0.7 kJ mol⁻¹; ΔS _sub²⁹⁸=190±2 J mol⁻¹ K⁻¹. For the orthorhombic modification (form II), the saturated vapor pressure could only be studied at 391 K. Phase transition enthalpy at 298 K, ΔH _tr²⁹⁸(I→II)=2.0±0.4 kJ mol⁻¹, was derived as the difference between the solution enthalpies of the noted polymorphs in the same solution (methanol). Based on ΔH _tr²⁹⁸ (I→II), differences between temperature dependencies of heat capacities of both modifications and the vapor pressure value of form II at 391 K, the temperature dependence of saturated vapor pressure and thermodynamic sublimation parameters for modification II were also estimated (ΔG _sub²⁹⁸=56.1 kJ mol⁻¹; ΔH _sub²⁹⁸=115.9±0.9 kJ mol⁻¹; ΔS _sub²⁹⁸=200±3 J mol⁻¹ K⁻¹). The results indicate that the modifications are monotropically related, which is in contrast to findings recently reported found by classical thermochemical methods.     

Synthesis, structure, and X-band (9.5 GHz) EPR characterization of the new series of pH-sensitive spin probes: N,N-disubstituted 4-amino-2,2,5,5-tetramethyl-3-imidazoline 1-oxyls

[reaction: see text] An approach to the synthesis of new imidazoline nitroxides bearing an N',N'-disubstituted amidine group is reported. The approach is based on the alkylation of diamagnetic 4-R-amino-1,2,2,5,5-pentamethyl-3-imidazolines with bromoacetic acid ethyl ester; the products of alkylation are further oxidized to the corresponding nitroxides. The approach allows a variety of functional groups to be introduced into the nitroxide molecule structure. Alkylation with bromoacetic acid ethyl ester was found to proceed with high regioselectivity and afford the products of exo-alkylation. The regiochemical assignment is made on the basis of 13C NMR spectra and confirmed by X-ray diffraction study. All of the nitroxides synthesized here were shown to have pH-dependent EPR spectra with pKa ranging from 3.5 to 6.2. For nitroxides 13 bearing the carboxylic group remote to the nitroxide moiety, the changes in isotropic magnetic parameters of EPR spectra due to reversible deprotonation of the carboxylic group were found to be small. For these nitroxides, we demonstrate an alternative approach for pKa determination that is based on measuring the peak-to-peak line width of the EPR spectrum in the presence of the paramagnetic broadening agent potassium ferricyanide. The partition coefficients of nitroxides in octanol/H2O and octanol/phosphate buffer solution mixtures were measured to reveal a range of their lipophilicities.     

Hydrolytic metal-mediated coupling of dialkylcyanamides at a Pt(IV) center giving a new family of diimino ligands

Addition of excess R(2)NCN to an aqueous solution of K(2)[PtCl(4)] led to the precipitation of [PtCl(2)(NCNR(2))(2)] (R(2) = Me(2) 1; Et(2) 2; C(5)H(10) 3; C(4)H(8)O, 4) in a cis/trans isomeric ratio which depends on temperature. Pure isomers cis-1-3 and trans-1-3 were separated by column chromatography on SiO(2), while trans-4 was obtained by recrystallization. Complexes cis-1-3 isomerize to trans-1-3 on heating in the solid phase at 110 degrees C; trans-1 has been characterized by X-ray crystallography. Chlorination of the platinum(II) complexes cis-1-3 and trans-1-4 gives the appropriate platinum(IV) complexes [PtCl(4)(NCNR(2))(2)] (cis-5-7 and trans-5-8). The compound cis-6 was also obtained by treatment of [PtCl(4)(NCMe)(2)] with neat Et(2)NCN. The platinum(IV) complex trans-[PtCl(4)(NCNMe(2))(2)] (trans-5) in a mixture of undried Et(2)O and CH(2)Cl(2) undergoes facile hydrolysis to give trans-[PtCl(4)[(H)=C(NMe(2))OH](2)] (9; X-ray structure has been determined). The hydrolysis went to another direction with the cis-[PtCl(4)(NCNR(2))(2)] (cis-5-7) which were converted to the metallacycles [PtCl(4)[NH=C(NR(2))OC(NR(2))=NH]] (11-13) due to the unprecedented hydrolytic coupling of the two adjacent dialkylcyanamide ligands giving a novel (for both coordination and organic chemistry) diimino linkage. Compounds 11-13 and also 14 (R(2) = C(4)H(8)O) were alternatively obtained by the reaction between cis-[PtCl(4)(MeCN)(2)] and neat undried NCNR(2). The structures of complexes 11, 13, and 14 were determined by X-ray single-crystal diffraction. All the platinum compounds were additionally characterized by elemental analyses, FAB mass-spectrometry, and IR and (1)H and (13)C[(1)H] NMR spectroscopies.     

Nitrile-amidine coupling at Pt(IV) and Pt(II) centers. An easy entry to imidoylamidine complexes

Treatment of trans-[PtCl4(RCN)2] (R = Me, Et, Ph, NEt2) with 2 equiv of the amidine PhC(=NH)NHPh in a suspension of MeCN (R = Me), CHCl3 (R = Et, Ph), or in CHCl3 solution (R = NEt2) results in the formation of the imidoylamidine complexes trans-[PtCl4{NH=C(R)N=C(Ph)NHPh}2] (1-4) isolated in good yields (66-84%). The reaction of soluble complexes 3 and 4 with 2 equiv of Ph3P=CHCO2Me in CH2Cl2 (40 degrees C, 5 h) leads to dehydrochlorination resulting in a chelate ring closure to furnish the platinum(IV) chelates [PtCl2{NH=C(R)NC(Ph)=NPh}2] (R = Ph, 5; R = NEt2, 6), accordingly, and the phosphonium salt [Ph3PCH2CO2Me]Cl. Treatment of 5 with 3 equiv of Ph3P=CHCO2Me at 50 degrees C for 5 d resulted in only a 30% conversion to the corresponding Pt(II) complex [Pt{NH=C(NEt2)NC(Ph)=NPh}2] (15). The reduction can be achieved within several minutes, when Ph2PCH2CH2PPh2 in CDCl3 is used. When the platinum(II) complex trans-[PtCl2(RCN)2] is reacted with 2 equiv of the amidine, the imidoylamidinato complexes [PtCl(RCN){NH=C(R)NC(Ph)=NHPh}] (8-11) and [PhC(=NH)NHPh] x HCl (7) are formed. The reaction of trans-[PtCl2(RCN)2] with 4 equiv of the amidine under a prolonged reaction time or treatment of [PtCl(RCN){NH=C(R)NC(Ph)=NHPh}] (8-11) with 2 more equiv of the amidine yields the complex bearing two chelate rings [Pt{NH=C(R)NC(Ph)=NHPh}2] (12-15). The treatment of cis-[PtCl2(RCN)2] (R = Me, Et) with the amidine gives ca. 50-60% yield of [PtCl2{NH=C(R)NHC(Ph)=NHPh}] (16 and 17). All of the platinum compounds were characterized by elemental analyses; FAB mass spectrometry; IR spectroscopy; 1H, 13C{1H}, and 195Pt NMR spectroscopies, and four of them (4, 6, 8, and 15) were also characterized by X-ray crystallography. The coupling of the Pt-bound nitriles and the amidine is metal-mediated insofar as RCN and PhC(=NH)NHPh do not react in the absence of the metal centers in conditions more drastic than those of the observed reactions. The nitrile-amidine coupling reported in this work constitutes a route to the synthesis of imidoylamidine complexes, some of them exhibiting luminescent properties.