Gd5-xYxTt4 (Tt = Si or Ge): effect of metal substitution on structure, bonding, and magnetism

A crystallographic study and theoretical assessment of the Gd/Y site preferences in the Gd 5- x Y x Tt 4 ( Tt = Si, Ge) series prepared by high-temperature methods is presented. All structures for the Gd 5- x Y x Si 4 system belong to the orthorhombic, Gd 5Si 4-type (space group Pnma). For the Gd 5- x Y x Ge 4 system, phases with x < 3.6 and x >or= 4.4 adopt the orthorhombic, Sm 5Ge 4-type structure. For the composition range of 3.6 相似文献   

Equilibration of tyrosyl radicals (Y356•, Y731•, Y730•) in the radical propagation pathway of the Escherichia coli class Ia ribonucleotide reductase

Escherichia coli ribonucleotide reductase is an α2β2 complex that catalyzes the conversion of nucleotides to deoxynucleotides using a diferric tyrosyl radical (Y(122)(?)) cofactor in β2 to initiate catalysis in α2. Each turnover requires reversible long-range proton-coupled electron transfer (PCET) over 35 ? between the two subunits by a specific pathway (Y(122)(?) ? [W(48)?] ? Y(356) within β to Y(731) ? Y(730) ? C(439) within α). Previously, we reported that a β2 mutant with 3-nitrotyrosyl radical (NO(2)Y(?); 1.2 radicals/β2) in place of Y(122)(?) in the presence of α2, CDP, and ATP catalyzes formation of 0.6 equiv of dCDP and accumulates 0.6 equiv of a new Y(?) proposed to be located on Y(356) in β2. We now report three independent methods that establish that Y(356) is the predominant location (85-90%) of the radical, with the remaining 10-15% delocalized onto Y(731) and Y(730) in α2. Pulsed electron-electron double-resonance spectroscopy on samples prepared by rapid freeze quench (RFQ) methods identified three distances: 30 ± 0.4 ? (88% ± 3%) and 33 ± 0.4 and 38 ± 0.5 ? (12% ± 3%) indicative of NO(2)Y(122)(?)-Y(356)(?), NO(2)Y(122)(?)-NO(2)Y(122)(?), and NO(2)Y(122)(?)-Y(731(730))(?), respectively. Radical distribution in α2 was supported by RFQ electron paramagnetic resonance (EPR) studies using Y(731)(3,5-F(2)Y) or Y(730)(3,5-F(2)Y)-α2, which revealed F(2)Y(?), studies using globally incorporated [β-(2)H(2)]Y-α2, and analysis using parameters obtained from 140 GHz EPR spectroscopy. The amount of Y(?) delocalized in α2 from these two studies varied from 6% to 15%. The studies together give the first insight into the relative redox potentials of the three transient Y(?) radicals in the PCET pathway and their conformations.     

Influence of fluoride on the reversible binding of NO by [Fe(II)(EDTA)(H2O)]2-. Inhibition of autoxidation of [Fe(II)(EDTA)(H2O)]2-

The promising BioDeNO(x) process for NO removal from gaseous effluents suffers from an unsolved problem that results from the oxygen sensitivity of the Fe(II)-aminopolycarboxylate complexes used in the absorber unit to bind NO(g). The utilized [Fe(II)(EDTA)(H2O)](2-) complex is extremely oxygen sensitive and easily oxidized to give a totally inactive [Fe(III)(EDTA)(H2O)](-) species toward the binding of NO(g). We found that an in situ formed, less-oxygen-sensitive mixed-ligand complex, [Fe(II)(EDTA)(F)](3-), still reacts quantitatively with NO(g). The formation constant for the mixed ligand complex was determined spectrophotometrically. For [Fe(III)(EDTA)(F)](2-) we found log K(MLF)(F) = 1.7 +/- 0.1. The [Fe(II)(EDTA)(F)](3-) complex has a smaller value of log K(MLF)(F) = 1.3 +/- 0.2. The presence of fluoride does not affect the reversible binding of NO(g). Even over extended periods of time and fluoride concentrations of up to 1.0 M, the nitrosyl complex does not undergo any significant decomposition. The [Fe(III)(EDTA)(NO(-))](2-) complex releases bound NO on passing nitrogen through the solution to form [Fe(II)(EDTA)(H2O)](2-) almost completely. A reaction cycle is feasible in which fluoride inhibits the autoxidation of [Fe(II)(EDTA)(H2O)](2-) during the reversible binding of NO(g).     

Theoretical study on the mechanism of the CH2F + NO2 reaction

Despite the importance of the Fluoromethyl radicals in combustion chemistry, very little experimental information on their reactions toward stable molecules is available in the literature. Motivated by recent laboratory characterization about the reaction kinetics of Chloromethyl radicals with NO2, we carried out a detailed potential energy survey on the CH2F + NO2 reaction at the B3LYP/6-311G(d,p) and MC-QCISD (single-point) levels as an attempt toward understanding the CH2F + NO2 reaction mechanism. It is shown that the CH2F radical can react with NO2 to barrierlessly generate adduct a (H2FCNO2), followed by isomerization to b1 (H2FCONO-trans) which can easily interconvert to b2 (H2FCONO-cis). Subsequently, Starting from b (b1, b2), the most feasible pathway is the C--F and N--O1 bonds cleavage along with N--F bond formation of b (b1, b2) leading to P1 (CH2O + FNO), or the direct N--O1 weak-bond fission of b (b1, b2) to give P2 (CH2FO + NO), or the 1,3-H-shift associated with N--O1 bond rupture of b1 to form P3 (CHFO + HNO), all of which may have comparable contribution to the reaction CH2F + NO2. Much less competitively, b2 either take the 1,4-H-shift and O1--N bond cleavage to form product P4 (CHFO + HON) or undergo a concerted H-shift to isomer c2 (HFCONOH), followed by dissociation to P4. Because the rate-determining transition state (TSab1) in the most competitive channels is only 0.3 kcal/mol higher than the reactants in energy, the CH2F + NO2 reaction is expected to be rapid, and may thus be expected to significantly contribute to elimination of nitrogen dioxide pollutants. The similarities and discrepancies among the CH2X + NO2 (X = H, F, and Cl) reactions are discussed in terms of the electronegativity of halogen atom. The present article may assist in future experimental identification of the product distributions for the title reaction, and may be helpful for understanding the halogenated methyl chemistry.     

Fourier transform infrared characterization of a CuB-nitrosyl complex in cytochrome ba3 from Thermus thermophilus: relevance to NO reductase activity in heme-copper terminal oxidases

The two heme-copper terminal oxidases of Thermus thermophilus have been shown to catalyze the two-electron reduction of nitric oxide (NO) to nitrous oxide (N2O) [Giuffre, A.; Stubauer, G.; Sarti, P.; Brunori, M.; Zumft, W. G.; Buse, G.; Soulimane, T. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 14718-14723]. While it is well-established that NO binds to the reduced heme a3 to form a low-spin heme {FeNO}7 species, the role CuB plays in the binding of the second NO remains unclear. Here we present low-temperature FTIR photolysis experiments carried out on the NO complex formed by addition of NO to fully reduced cytochrome ba3. Low-temperature UV-vis, EPR, and RR spectroscopies confirm the binding of NO to the heme a3 and the efficiency of the photolysis at 30 K. The nu(NO) modes from the light-induced FTIR difference spectra are isolated from other perturbed vibrations using 15NO and 15N18O. The nu(N-O)a3 is observed at 1622 cm-1, and upon photolysis, it is replaced by a new nu(N-O) at 1589 cm-1 assigned to a CuB-nitrosyl complex. This N-O stretching frequency is more than 100 cm-1 lower than those reported for Cu-NO models with three N-ligands and for CuB+-NO in bovine aa3. Because the UV-vis and RR data do not support a bridging configuration between CuB and heme a3 for the photolyzed NO, we assign the exceptionally low nu(NO) to an O-bound (eta1-O) or a side-on (eta2-NO) CuB-nitrosyl complex. From this study, we propose that, after binding of a first NO molecule to the heme a3 of fully reduced Tt ba3, the formation of an N-bound {CuNO}11 is prevented, and the addition of a second NO produces an O-bond CuB-hyponitrite species bridging CuB and Fea3. In contrast, bovine cytochrome c oxidase is believed to form an N-bound CuB-NO species; the [{FeNO}7{CuNO}11] complex is suggested here to be an inhibitory complex.     

Substituent effects on CL···N, S···N, and P···N noncovalent bonds

Cl, S, and P atoms have previously been shown as capable of engaging in a noncovalent bond with the N atom on another molecule. The effects of substituents B on the former atoms on the strength of this bond are examined, and it is found that the binding energy climbs in the order B = CH(3) < NH(2) < CF(3) < OH < Cl < NO(2) < F. However, there is some variability in this pattern, particularly for the NO(2) group. The A···N bonds (A = Cl, S, P) can be quite strong, amounting to as much as 10 kcal/mol. The binding energy arises from approximately equal contributions from its induction and electrostatic components, although the former becomes more dominant for the stronger bonds. The induction energy is due in large measure to the transfer of charge from the N lone pair to a B-A σ* antibonding orbital of the electron-acceptor molecule containing Cl, S, or P. These A···N bonds typically represent the lowest-energy structure on each potential energy surface, stronger than H-bonds such as NH···F, CH···N, or SH···N.     

Acetate binding at the photosystem II oxygen evolving complex: an S(2)-state multiline signal ESEEM study

Previously, using acetate deuterated in the methyl hydrogen positions, we showed that acetate binds in close proximity to the Mn cluster/Y(.)(z) tyrosine dual spin complex in acetate-inhibited photosystem II (PSII) preparations exhibiting the "split" EPR signal arising from the S(2)-Y(.)(z) interaction [Force, D. A.; Randall, D. W.; Britt, R. D. Biochemistry 1997, 36, 12062-12070]. By using paramagnetic NO to quench the paramagnetism of Y(.)(z), we are able to observe the ESEEM spectrum of deuterated acetate interacting with only the Mn cluster. A good fit of the ESEEM data indicates two (2)H dipolar hyperfine couplings of 0.097 MHz and one of 0.190 MHz. Modeling of these dipolar interactions, using our "dangler" 3 + 1 model for the S(2)-state of the Mn cluster, reveals distances consistent with direct ligation of acetate to the Mn cluster. As acetate inhibition is competitive with the essential cofactor Cl(-), this suggests that Cl(-) ligates directly to the Mn cluster. The effect of acetate binding on the structure of the Mn cluster is investigated by comparing the Mn-histidine coupling in NO/acetate-treated PSII and untreated PSII using ESEEM. We find that the addition of acetate and NO does not affect the histidine ligation to the Mn cluster. We also investigate the ability of acetate to access Y(.)(z) in Mn-depleted PSII, a PSII preparation expected to be more solvent accessible than intact PSII. We detect no coupling between Y(.)(z) and acetate. We have previously shown that small alcohols such as methanol can ligate to the Mn cluster with ease, while larger alcohols such as 2-propanol, as well as DMSO, are excluded [Force, D. A.; Randall, D. W.; Lorigan, G. A.; Clemens, K. L.; Britt, R. D. J. Am. Chem. Soc. 1998, 120, 13321-13333]. We probe the effect of acetate binding on the ability of methanol and DMSO to bind to the Mn cluster. We find that methanol is able to bind to the Mn cluster in the presence of acetate. We detect no DMSO binding in the presence of acetate. Thus, acetate binding does not increase the affinity or accessibility for DMSO binding at the Mn cluster. We also explore the possibility that the acetate binding site is also a binding site for substrate water. By comparing the ratioed three-pulse ESEEM spectra of a control, untreated PSII sample in 50% D(2)O to an NO/acetate-treated PSII sample in 50% D(2)O, we find that the binding of acetate to the oxygen evolving complex of photosystem II displaces deuterons bound very closely to the Mn cluster.     

Dynamic hydrogen-bonding network in the distal pocket of the nitrosyl complex of Pseudomonas aeruginosa cd1 nitrite reductase

cd(1) nitrite reductase (NIR) is a key enzyme in the denitrification process that reduces nitrite to nitric oxide (NO). It contains a specialized d(1)-heme cofactor, found only in this class of enzymes, where the substrate, nitrite, binds and is converted to NO. For a long time, it was believed that NO must be released from the ferric d(1)-heme to avoid enzyme inhibition by the formation of ferrous-nitroso complex, which was considered as a dead-end product. However, recently an enhanced rate of NO dissociation from the ferrous form, not observed in standard b-type hemes, has been reported and attributed to the unique d(1)-heme structure (Rinaldo, S.; Arcovito, A.; Brunori, M.; Cutruzzolà, F. J. Biol. Chem. 2007, 282, 14761-14767). Here, we report on a detailed study of the spatial and electronic structure of the ferrous d(1)-heme NO complex from Pseudomonas aeruginosa cd(1) NIR and two mutants Y10F and H369A/H327A in solution, searching for the unique properties that are responsible for the relatively fast release. There are three residues at the "distal" side of the heme (Tyr(10), His(327), and His(369)), and in this work we focus on the identification and characterization of possible H-bonds they can form with the NO, thereby affecting the stability of the complex. For this purpose, we have used high field pulse electron-nuclear double resonance (ENDOR) combined with density functional theory (DFT) calculations. The DFT calculations were essential for assigning and interpreting the ENDOR spectra in terms of geometric structure. We have shown that the NO in the nitrosyl d(1)-heme complex of cd(1) NIR forms H-bonds with Tyr(10) and His(369), whereas the second conserved histidine, His(327), appears to be less involved in NO H-bonding. This is in contrast to the crystal structure that shows that Tyr(10) is removed from the NO. We have also observed a larger solvent accessibility to the distal pocket in the mutants as compared to the wild-type. Moreover, it was shown that the H-bonding network within the active site is dynamic and that a change in the protonation state of one of the residues does affect the strength and position of the H-bonds formed by the others. In the Y10F mutant, His(369) is closer to the NO, whereas mutation of both distal histidines displaces Tyr(10), removing its H-bond. The implications of the H-bonding network found in terms of the complex stability and catalysis are discussed.     

Sulfur-rich zinc chemistry: new tris(thioimidazolyl)hydroborate ligands and their zinc complex chemistry related to the structure and function of alcohol dehydrogenase

The 1-substituted tris(2-thioimidazolyl)hydroborate ligands Tt(R) were prepared as the potassium salts from KBH(4) and the corresponding 1-R-2-thioimidazole for R = t-Bu and C(6)H(4)-p-CH(CH(3))(2) (Cum). Their reactions with zinc salts yielded the tetrahedral complexes Tt(R)Zn-X with X = F, Cl, ONO(2) and (Tt(t)()(-)(Bu))(2)Zn. With zinc perchlorate the labile perchlorate complexes Tt(R)Zn-OClO(3) were obtained. They served as starting materials for the incorporation of substrates which are relevant for the chemistry of horse liver alcohol dehydrogenase: Ethanol led to [Tt(t)()(-Bu)Zn.EtOH] ClO(4).EtOH, p-nitrophenol (NitOH) yielded Tt(Cum)Zn-ONit. Pyridine-2-carbaldehyde and salicylic aldehyde were incorporated as N(pyridine) and O(phenolate) coligands with possible additional O(aldehyde) coordination. Substituted pyridyl methanols (R-PyCH(2)OH) yielded the trinuclear complexes [(Tt(t)()(-Bu))(2)Zn(3)(R-PyCH(2)O)(2)] (ClO(4))(2) with bridging Tt and pyridylmethoxide ligands. Preliminary experiments on the functional modeling of alcohol dehydrogenase have shown that TtZn complexes promote both the dehydrogenation of 2-propanol and the hydrogenation of pentafluorobenzaldehyde.     

神经红蛋白突变体(F28Y,F106Y)的构建、 表达与表征

构建了神经红蛋白F28Y, F106Y的两种突变体, 并进行了表达、 纯化和谱学表征. 电喷雾质谱表明突变体蛋白的分子量与理论值一致. 氧化型和还原型F28Y及F106Y的紫外 可见吸收光谱与野生型相似, 仅氧化型F28Y的Soret 带有2 nm的蓝移, 说明这两种突变体蛋白仍保持六配位形式. F28Y的荧光最大发射峰明显红移(340 nm→347 nm), 表明其荧光基团更加暴露于极性环境中. 圆二色光谱表明, 突变体蛋白的α 螺旋含量降低且F28Y产生了β 折叠, 这是由于F28相对于F106则位于疏水腔外部且更加接近于溶剂表面所致. 热稳定性顺序为NGB>F28Y>F106Y, F106Y最不稳定, 是因为其与血红素间存在着较强的疏水作用, 突变使F106与血红素间的作用力减弱, 从而导致血红素在热变性条件下更容易从蛋白中解离出来.     

Hydrogen impurity effects. A(5)Tt(3)Z intermetallic compounds between A = Ca, Sr, Ba, Eu, Yb and Tt = Sn, Pb with Cr(5)B(3)-like structures that are stabilized by hydride or fluoride (Z)

The binary systems Ca-Sn, Ba-Sn, Eu-Sn, Yb-Sn, Sr-Pb, Ba-Pb, and Eu-Pb do not contain Cr(5)B(3)-like A(5)Tt(3) phases when care is taken to exclude hydrogen from the reactions (Tt = tetrel, Si-Pb). All form ternary A(5)Tt(3)H(x)() phases (x < or = 1) with "stuffed" Cr(5)B(3)-like structures instead, and all of those tested, Ca-Sn, Ba-Sn, Sr-Pb, and Ba-Pb, also yield the isostructural A(5)Tt(3)F. The structures and compositions of Ca(5)Sn(3)H(x), Ca(5)Sn(3)F(0.89), Eu(5)Sn(3)H(x), and Sr(5)Pb(3)F have been refined from single-crystal X-ray diffraction data and of Ca(5)Sn(3)D from powder neutron data. The interstitial H, F atoms are bound in a tetrahedral (A(2+))(4) cavity in a Cr(5)B(3)-type metal atom structure. Nine previous reports of binary "Ba(5)Sn(3)", "Yb(5)Sn(3)", "Sr(5)Pb(3)", and "Ba(5)Pb(3)" compounds were wrong and presumably concerned the hydrides. The new ternary phases are generally Pauli-paramagnetic, evidently with pi electrons from the characteristic tetrelide dimers in this structure type at least partially delocalized into the conduction band. The Sn-Sn bonds appear correspondingly shortened on oxidation. Other new phases reported are CaSn (CrB type), Yb(5)Sn(4)H(x) (Sm(5)Ge(4)), YbSn ( approximately TlTe), Ba(5)Pb(3) ( approximately W(5)Si(3)), and Yb(31)Pb(20) (Ca(31)Sn(20)).     

The Mechanism of Biochemical NO-Sensing: Insights from Computational Chemistry

The binding of small gas molecules such as NO and CO plays a major role in the signaling routes of the human body. The sole NO-receptor in humans is soluble guanylyl cyclase (sGC) – a histidine-ligated heme protein, which, upon NO binding, activates a downstream signaling cascade. Impairment of NO-signaling is linked, among others, to cardiovascular and inflammatory diseases. In the present work, we use a combination of theoretical tools such as MD simulations, high-level quantum chemical calculations and hybrid QM/MM methods to address various aspects of NO binding and to elucidate the most likely reaction paths and the potential intermediates of the reaction. As a model system, the H-NOX protein from Shewanella oneidensis (So H-NOX) homologous to the NO-binding domain of sGC is used. The signaling route is predicted to involve NO binding to form a six-coordinate intermediate heme-NO complex, followed by relatively facile His decoordination yielding a five-coordinate adduct with NO on the distal side with possible isomerization to the proximal side through binding of a second NO and release of the first one. MD simulations show that the His sidechain can quite easily rotate outward into solvent, with this motion being accompanied in our simulations by shifts in helix positions that are consistent with this decoordination leading to significant conformational change in the protein.     

Synthesis, characterization and DNA interaction studies of complexes of lanthanide nitrates with tris(2-[(3,4-dihydroxybenzylidene)imino]ethyl)amine

A new tripodal, hydroxyl-rich ligand, tris{2-[(3,4-dihydroxybenzylidene)imino]ethyl}amine (L), and its complexes with lanthanide nitrates were synthesized. These complexes which are stable in air with the general formula of [LnL(NO(3))(2)]NO(3).H(2)O (Ln=La, Sm, Eu, Gd, Y) were characterized by molar conductivity, elemental analysis, IR spectra and thermal analysis. The NO(3)(-) groups coordinated to lanthanide mono-dentately, and the coordination number in these complexes may be 8. The interaction of complexes with DNA were investigated by ultraviolet and fluorescent spectra, which showed that the binding mode of complexes with DNA was intercalation, and the binding affinity with DNA were La(III) complex>Sm(III) complex>Eu(III) complex>Gd(III) complex>Y(III) complex. Based on these results, it can be shown that the La(III)complex is promising candidate for therapeutic reagents and DNA probes.     

Tertiary contact formation in alpha-synuclein probed by electron transfer

To explore tertiary contact formation in alpha-synuclein, a natively unfolded protein implicated in Parkinson's disease, we have measured the rates of reaction between a powerful electron donor, the tryptophan (W) triplet excited state, and an acceptor, 3-nitro-tyrosine (Y(NO2)) in six different variants, probing loop sizes between 15 and 132 residues. Electron transfer rates decrease with loop size with the fastest contact time of 140 ns for the N-terminal pair and the slowest of 1.2 mus for the N- to C-terminal pair. Diffusion coefficients ranging from approximately 2 x 10-6 to approximately 10-5 cm2 s-1 were extracted from simultaneous fits of the W to Y(NO2) electron (triplet excited state) and energy transfer (singlet excited state) kinetics.     

电喷雾质谱法研究细胞色素Tb5及其F35Y突变体蛋白 肽链和辅基的相互作用

本文通过牛肝线粒体细胞色素Tb5和它的F35Y突变体蛋白相对分子质量的外标法测定,得到细胞色素Tb5全蛋白的相对分子质量为10077.5脱辅基蛋白的相对分子质量为9461.4F35Y突变体蛋白的相对分子质量为10093.6,它的脱辅基蛋白的相对分子质量为9477.5,不同nozzle电压下的电喷雾质谱结果表明,该电压的大小明显影响蛋白肽链与血红素辅基之间的非共价结合,随着电压的降低,全蛋白谱峰的强度逐渐增大,然而,过低的电压导致了Na^+,K^+离子加合峰相对强度的增加,而不利于谱图分析。同时,考察到细胞色素Tb5在甲醇溶液和酸性溶液中的变性行为,因此选择nozzle电压70V,10%的甲醇水溶液和pH=7为得到全蛋白质谱峰的最佳条件。相同实验条件下得到的野生型CytTb5和F35Y突变体全蛋白的质谱峰相比较,其相对丰度有悬殊的差异,表明F35Y突变体蛋白的血红素结合能力明显低于野生型蛋白。通过解离出的Hemeb的分子离子峰进行解析,证明铁仍以三价离子存在于血红素辅基中。     

77Se NMR chemical shifts of 9-(arylselanyl)triptycenes: new standard for planar structures of ArSeR and applications to determine the structures in solutions

A set of new delta(Se) parameters is proposed as a standard for the planar (pl) orientational effect of p-YC(6)H(4) (Ar) in ArSeR, employing 9-(arylselanyl)triptycenes (1: p-YC(6)H(4)SeTpc). The Se-C(R) bond in ArSeR is placed on the Ar plane in pl and it is perpendicular to the plane in pd. Large upfield shifts are observed for Y = NMe(2), OMe, and Me (-22 to -6 ppm) and large downfield shifts for Y = COOEt, CN, and NO(2) (19-37 ppm), relative to Y = H, with small upfield and moderate downfield shifts by Y of halogens (-1 ppm for Y = F and 4 ppm for Y = Cl and Br). This must be the result of the p(Se)-pi(C(6)H(4))-p(Y) conjugation in 1 (pl). While the character of delta(Se) in 1 (pl) is very similar to that in 9-(arylselanyl)anthracenes (2 (pl)), it is very different from that of 1-(arylselanyl)anthraquinones (3 (pd)). Sets of delta(Se) of 1 and 2 must serve as the standard for pl and that of 3 does for pd in solutions. Structures of various ArSeR in solutions are determined from the viewpoint of the orientational effect based on the standard delta(Se) of 1-3. While the structure of 2-methyl-1-(arylselanyl)naphthalenes is concluded to be all pl in solutions, those of 8-chloro- and 8-bromo-1-(arylselanyl)naphthalenes are all pd, except for Y = COOEt, CN, and NO(2): The equilibrium between pd and pl contributes to those with Y = COOEt, CN, and NO(2). The structure of 1-(arylselanyl)naphthalenes changes depending on Y. The structures of ArSeMe and ArSeCOPh are shown to be pl and pd, respectively, in solutions. Those of ArSePh and ArSeAr seem to change depending on Y. delta(Se) of 1-3 are demonstrated to serve as the standard to determine the structures in solutions. The rules of thumb derived from the characters in delta(Se) for 1-3 are very useful to determine the structures of ArSeR in solutions, in addition to the analysis based on the plots.     

Substituent cross-interaction effects on the electronic character of the C=N bridging group in substituted benzylidene anilines--models for molecular cores of mesogenic compounds. A 13C NMR study and comparison with theoretical results

13C NMR chemical shifts delta(C)(C=N) were measured in CDCl3 for a wide set of mesogenic molecule model compounds, viz. the substituted benzylidene anilines p-X-C6H4CH=NC6H4-p-Y (X = NO2, CN, CF3, F, Cl, H, Me, MeO, or NMe2; Y = NO2, CN, F, Cl, H, Me, MeO, or NMe2). The substituent dependence of delta(C)(C=N) was used as a tool to study electronic substituent effects on the azomethine unit. The benzylidene substituents X have a reverse effect on delta(C)(C=N): electron-withdrawing substituents cause shielding, while electron-donating ones behave oppositely, the inductive effects clearly predominating over the resonance effects. In contrast, the aniline substituents Y exert normal effects: electron-withdrawing substituents cause deshielding, while electron-donating ones cause shielding of the C=N carbon, the strengths of the inductive and resonance effects being closely similar. Additionally, the presence of a specific cross-interaction between X and Y could be verified. The electronic effects of the neighboring aromatic ring substituents systematically modify the sensitivity of the C=N group to the electronic effects of the benzylidene or aniline ring substituents. Electron-withdrawing substituents on the aniline ring decrease the sensitivity of delta(C)(C=N) to the substitution on the benzylidine ring, while electron-donating substituents have the opposite effect. In contrast, electron-withdrawing substituents on the benzylidene ring increase the sensitivity of delta(C)(C=N) to the substituent on the aniline ring, while electron-donating substituents act in the opposite way. These results can be rationalized in terms of the substituent-sensitive balance of the electron delocalization (mesomeric effects). The present NMR characteristics are discussed as regards the computational literature data. Valuable information has been obtained on the effects of the substituents on the molecular core of the mesogenic model compounds.     

Fluorescence-quenched solid phase combinatorial libraries in the characterization of cysteine protease substrate specificity

To map the substrate specificity of cysteine proteases, two combinatorial peptide libraries were synthesized and screened using the archetypal protease, papain. The use of PEGA resin as the solid support for library synthesis facilitated the application of an on-resin fluorescence-quenched assay. Results from the screening of library 2 indicated a preference for Pro or Val in the S3 subsite and hydrophobic residues in S2; the most prevalent residue not being Phe but Val. The S1 subsite exhibited a dual specificity for both small, nonpolar residues, Ala or Gly, as well as larger, Gln, and charged residues, Arg. Small residues predominated in the S1'-S4' subsites. Active peptides from the libraries and variations thereof were resynthesized and their kinetics of hydrolysis by papain assessed in solution phase assays. Generally, there was a good correlation between the extent of substrate cleavage on solid phase and the kcat/KM's obtained in solution phase assays. Several good substrates for papain were obtained, the best substrates being Y(NO2)PMPPLCTSMK(Abz) (kcat/KM = 2109 (mM s)-1), Y(NO2)PYAVQSPQK(Abz) (kcat/KM = 1524 (mM s)-1), and Y(NO2)PVLRQQRSK(Abz) (kcat/KM = 1450 (mM s)-1). These results were interpreted in structural terms by the use of molecular dynamics (MD). These MD calculations indicated two different modes for the binding of substrates in the narrow enzyme cleft.     

Broadening deoxysugar glycodiversity: natural and engineered transaldolases unlock a complementary substrate space

The majority of prokaryotic drugs are produced in glycosylated form, with the deoxygenation level in the sugar moiety having a profound influence on the drug's bioprofile. Chemical deoxygenation is challenging due to the need for tedious protective group manipulations. For a direct biocatalytic de novo generation of deoxysugars by carboligation, with regiocontrol over deoxygenation sites determined by the choice of enzyme and aldol components, we have investigated the substrate scope of the F178Y mutant of transaldolase B, TalB(F178Y), and fructose 6-phosphate aldolase, FSA, from E. coli against a panel of variously deoxygenated aldehydes and ketones as aldol acceptors and donors, respectively. Independent of substrate structure, both enzymes catalyze a stereospecific carboligation resulting in the D-threo configuration. In combination, these enzymes have allowed the preparation of a total of 22 out of 24 deoxygenated ketose-type products, many of which are inaccessible by available enzymes, from a [3×8] substrate matrix. Although aliphatic and hydroxylated aliphatic aldehydes were good substrates, D-lactaldehyde was found to be an inhibitor possibly as a consequence of inactive substrate binding to the catalytic Lys residue. A 1-hydroxy-2-alkanone moiety was identified as a common requirement for the donor substrate, whereas propanone and butanone were inactive. For reactions involving dihydroxypropanone, TalB(F178Y) proved to be the superior catalyst, whereas for reactions involving 1-hydroxybutanone, FSA is the only choice; for conversions using hydroxypropanone, both TalB(F178Y) and FSA are suitable. Structure-guided mutagenesis of Ser176 to Ala in the distant binding pocket of TalB(F178Y), in analogy with the FSA active site, further improved the acceptance of hydroxypropanone. Together, these catalysts are valuable new entries to an expanding toolbox of biocatalytic carboligation and complement each other well in their addressable constitutional space for the stereospecific preparation of deoxysugars.