Subtle Structural Effects Research Articles

Allosteric regulation of the biotin-dependent enzyme pyruvate carboxylase by acetyl-CoA

The activity of the biotin-dependent enzyme pyruvate carboxylase from many organisms is highly regulated by the allosteric activator acetyl-CoA. A number of X-ray crystallographic structures of the native pyruvate carboxylase tetramer are now available for the enzyme from Rhizobium etli and Staphylococcus aureus. Although all of these structures show that intersubunit catalysis occurs, in the case of the R. etli enzyme, only two of the four subunits have the allosteric activator bound to them and are optimally configured for catalysis of the overall reaction. However, it is apparent that acetyl-CoA binding does not induce the observed asymmetrical tetramer conformation and it is likely that, under normal reaction conditions, all of the subunits have acetyl-CoA bound to them. Thus the activation of the enzyme by acetyl-CoA involves more subtle structural effects, one of which may be to facilitate the correct positioning of Arg353 and biotin in the biotin carboxylase domain active site, thereby promoting biotin carboxylation and, at the same time, preventing abortive decarboxylation of carboxybiotin. It is also apparent from the crystal structures that there are allosteric interactions induced by acetyl-CoA binding in the pair of subunits not optimally configured for catalysis of the overall reaction.

XPF-ERCC1: On the Bubble

In this issue of Structure, Das et al. report the structure of the helix-hairpin-helix dimerization domain of XPF bound to ssDNA. These results provide insight into the architecture of nucleotide excision repair machinery and how it interacts with damaged DNA substrates.

Structural Effects Behind the Low Temperature Nonconventional Relaxor Behavior of the Sr2NaNb5O15 Bronze

An exhaustive temperature dependent structural and dielectric study of the tetragonal tungsten bronze-type Sr(2)NaNb(5)O(15) (SNN) compound has been performed in the 300-100 K temperature range, by combining X-ray, neutron diffraction, and transmission electron microscopy with dielectric measurements, in order to clarify the structural effects responsible for the observed low temperature dielectric properties. Interestingly, a relevant second anomaly in the dielectric constant, in addition to the ferroelectric (FE) to paraelectric (PE) transition at T(C) = 518 K is found at T ≈ 240 K, revealing a relaxor-like behavior of the material at low temperature. This phenomenon has been previously observed in FE perovskite-type phases and referred to as the re-entrant phenomenon. However, FE polarization tends to vanish below this low temperature dielectric anomaly and this fact is not expected for a classical relaxor-ferroelectric phase. Although there is no structural transition from RT to 100 K, there is a change in the elastic properties of the material in the considered temperature range and the intense anomaly at ~240 K could be associated to a smeared-out phase transition to a frustrated FE/ferroelastic (FEL) low temperature state in correlation with subtle structural effects.

Structural, Dynamical, and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases

Among the distinct strategies proposed to expand the genetic alphabet, size-expanded nucleobases are promising for the development of modified DNA duplexes with improved biotechnological properties. In particular, duplexes built up by replacing canonical bases with the corresponding benzo-fused counterparts could be valuable as molecular nanowires. In this context, this study reports the results of classical molecular dynamics simulations carried out to examine the structural and dynamical features of size-expanded DNAs, including both hybrid duplexes containing mixed pairs of natural and benzo-fused bases (xDNA) and pure size-expanded (xxDNA) duplexes. Furthermore, the electronic structure of both natural and size-expanded duplexes is examined by means of density functional computations. The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. The most relevant differences are found in the enhanced size of the grooves, and the reduction in the twist. However, the analysis also reveals subtle structural effects related to the nature and sequence of benzo-fused bases in the duplex. On the other hand, electronic structure calculations performed for xxDNAs confirm the reduction in the HOMO-LUMO gap predicted from the analysis of the natural bases and their size-expanded counterparts, which suggests that pure size-expanded DNAs can be good conductors. A more complex situation is found for xDNAs, where fluctuations in the electrostatic interaction between base pairs exerts a decisive influence on the modulation of the energy gap.

Case Study on a Rare Effect: The Experimental and Theoretical Analysis of a Manganese(III) Spin-Crossover System

The six-coordinated mononuclear manganese(III) complex [Mn(5-Br-sal-N-1,5,8,12)]ClO(4) has been synthesized and isolated in crystalline form. Magnetic measurements and variable-temperature single-crystal X-ray crystallography corroborated with theoretical analysis provided firm evidence for the spin-crossover effects of this system. The monomeric complex cations are made by a hexadentate mixed-donor Schiff base ligand imposing a distorted octahedral geometry and subtle structural effects determining the manifestation of the variable spin properties of the manganese(III) centers. The spin crossover in [Mn(5-Br-sal-N-1,5,8,12)]ClO(4) has resulted in an unprecedented crystallographic observation of the coexistence of high-spin (HS; S = 2) and low-spin (LS; S = 1) manganese(III) complex cations in equal proportions around 100 K. At room temperature, the two crystallographically distinct manganese centers are both HS. Only one of the two slightly different units undergoes spin crossover in the temperature range ∼250-50 K, whereas the other remains in the HS state down to 50 K. The density functional theory calculations, performed as relevant numerical experiments designed to identify the role of orbital and interelectron effects, revealed unedited aspects of the manganese(III) spin-conversion mechanisms, developed in the conceptual frame of ligand-field models.

High-precision Penning-trap mass measurements of heavy xenon isotopes for nuclear structure studies

With the double Penning-trap mass spectrometer ISOLTRAP at ISOLDE/CERN the masses of the neutron-rich isotopes $^{136\ensuremath{-}146}\mathrm{Xe}$ were measured with a relative uncertainty of the order of ${10}^{\ensuremath{-}8}$ to ${10}^{\ensuremath{-}7}$. In particular, the masses of $^{144\ensuremath{-}146}\mathrm{Xe}$ were measured for the first time. These new mass values allow one to extend calculations of the mass surface in this region. Proton-Neutron interaction strength, obtained from double differences of binding energies, relate to subtle structural effects, such as the onset of octupole correlations, the growth of collectivity, and its relation to the underlying shell model levels. In addition, they provide a test of density functional calculations.

Structural Investigation of Carbosilane Liquid Crystalline Dendrimers

X-ray and neutron scattering investigations have been made on two series of liquid crystal dendrimers. The low generations (first to fourth) predominantly show smectic phases. The fifth generation shows a tendency to form columnar phases and two different types have been observed. The transition from smectic to columnar has been explained in terms of the distance between the dendritic core and the mesogenic units. As the generation number is increased, the distance increases until it becomes greater than the maximum length of the flexible spacers causing a change in molecular shape and the formation of columnar phases. Although the materials are nearly monodisperse, the small variation in the number of mesogens per molecule gives rise to some subtle structural effects. Two coexisting structures have been observed over large temperature ranges in some materials and small angle neutron scattering indicates that there is some microphase segregation which is a reversible function of temperature.

Antitumour bis(cyclopentadienyl) metal complexes: titanocene and molybdocene dichloride and derivatives

This Perspective will focus on recent developments in the field of antitumour metallocenes structurally related to titanocene dichloride. Despite extensive testing of titanocene dichloride which culminated in phase I and II clinical trials, further trials have been abandoned. While DNA has been implicated as the major target related to anticancer activity, identification of the active species and mechanism of action has been poorly understood and hence the design of second generation titanocene derivatives has not been possible. Recent mechanistic studies have provided a plausible mechanism for delivery of Ti to cancer cells via transferrin mediated endocytosis. This mechanism requires the presence of labile Cp-Ti bonds that hydrolyse on a time scale to deliver Ti to transferrin. A large range of titanocene derivatives in which the cyclopentadienyl rings have been substituted by both electron withdrawing and donating groups, including aromatic, alkyl and cyclic amines, have been prepared and tested for activity in the last 5 years. These results have shown that subtle structural effects can have a significant effect on biological activity and that biological activity is highly cell line dependent. However, the biological chemistry and cellular studies required to determine the mechanism of action of these new titanocenes have not been reported. In contrast, the bioorganometallic chemistry and cellular studies of molybdocene dichloride have implicated interaction with cellular thiols as the key reaction related to biological activity. Tailoring of the pseudohalide ligands by tuning the strength of the Mo-S bonds provides the opportunity to enhance cell uptake. Further research is required to establish the origin of antitumour activity.

Atropisomeric Discrimination in New RuII Complexes Containing the C2‐Symmetric Didentate Chiral Phenyl‐1,2‐bisoxazolinic Ligand

A new family of Ru(II) complexes containing the tridentate meridional 2,2':6',2''-terpyridine (trpy) ligand, a C(2)-symmetric didentate chiral oxazolinic ligand 1,2-bis[4'-alkyl-4',5'-dihydro-2'-oxazolyl]benzene (Phbox-R, R = Et or iPr), and a monodentate ligand, of general formula [Ru(Y)(trpy)(Phbox-R)](n+) (Y = Cl, H(2)O, py, MeCN, or 2-OH-py (2-hydroxypyridine)) have been prepared and thoroughly characterized. In the solid state the complexes have been characterized by IR spectroscopy and by X-ray diffraction analysis in two cases. In solution, UV/Vis, cyclic voltammetry (CV), and one-dimensional (1D) and two-dimensional (2D) NMR spectroscopy techniques have been used. We have also performed density functional theory (DFT) calculations with these complexes to interpret and complement experimental results. The oxazolinic ligand Phbox-R exhibits free rotation along the phenyloxazoline axes. Upon coordination this rotation is restricted by an energy barrier of 26.0 kcal mol(-1) for the case of [Ru(trpy)(Phbox-iPr)(MeCN)](2+) thus preventing its potential interconversion. Furthermore due to steric effects the two atropisomers differ in energy by 5.7 kcal mol(-1) and as a consequence only one of them is obtained in the synthesis. Subtle but important structural effects occur upon changing the monodentate ligands that are detected by NMR spectroscopy in solution and interpreted by using their calculated DFT structures.

Synthesis, Structure and Reactivity of Sulfur‐Rich [Fe(L1)(L2)(‘tpS4’)] Complexes with Rigid [Fe(‘tpS4’] Cores and σ−π Co‐Ligands (‘tpS4’2− = 1,2‐Bis(2‐mercaptophenylthio)phenylene(2−); L1, L2 = CO, PR3, NO)

AbstractOptimisation of synthesis and purification steps has made the new ligand ‘tpS4’2− available in preparative amounts. Treatment of FeCl2·4H2O with ‘tpS4’‐Li2 or ‘tpS4’‐Na2 yielded [Fe(‘tpS4’)] (1), which in the solid state and in the absence of co‐ligands probably trimerises to give paramagnetic [Fe(‘tpS4’)]3. The [Fe(‘tpS4’)] fragment displays helical coordination of the ‘tpS4’2− ligand and binds σ−π ligands such as CO, NO and phosphanes to give diamagnetic 18‐valence‐electron complexes of general formula [Fe(L1)(L2)(‘tpS4’)]. The cis‐dicarbonyl complex [Fe(CO)2(‘tpS4’)] (2) is labile and readily dissociates CO to give dinuclear [Fe(CO)(‘tpS4’)]2 (3). Simultaneous coordination of CO and phosphanes yielded [Fe(CO)(PR3)(‘tpS4’)] with R = Me (4), Et (5), Pr (6) and Bu (7), but it proved impossible to obtain analogous complexes with bulky PPh3 or PCy3 ligands. Bis(phosphane) complexes could be obtained only with PMe3 and the bidentate dppe, which yielded [Fe(PMe3)2(‘tpS4’)] (8) and [Fe(dppe)(‘tpS4’)] (11). Alkylphosphanes with longer alkyl substituents, such as PnPr3 and PnBu3, gave the labile derivatives [Fe(PR3)2(‘tpS4’)] with R = nPr (9) and nBu (10). Complexes 9 and 10 reversibly dissociate one PR3 ligand, yielding diamagnetic [Fe(PR3)(‘tpS4’)] fragments. These findings explain the decisive and hitherto inexplicable influence of PPr3 and PBu3 ligands upon the stabilisation of N2H2 in the diazene complexes [μ‐N2H2{Fe(PR3)(‘tpS4’)}2] with R = Pr, Bu. Treatment of [Fe(‘tpS4’)] (1) or [Fe(CO)(‘tpS4’)]2 (3) with NO or NO+ yielded [Fe(NO)2(‘tpS4’)] (12). The molecular structures of 3, 4, 7 and 8 were determined by X‐ray structure analysis. Spectroscopic and structural results indicate that the differences in reactivity between [Fe(L1)(L2)(‘tpS4’)] and homologous [Fe(L1)(L2)(‘S4’)] complexes can be traced back to subtle electronic and structural effects. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)

Aerobic oxidation of hydrocarbons catalyzed by electronegative iron salen complexes

A number of salen derivatives bearing electronegative substitutents and their corresponding iron(III) chloro complexes have been prepared. Several of the complexes catalyze aerobic oxidation of cyclohexene, primarily to allylic oxidation products. Evidence supports a radical chain autoxidation mechanism, with the complex functioning to decompose intermediate alkyl hydroperoxides. Activity is observed only for complexes with relatively high Fe( III II ) reduction potentials, but the incomplete correlation of activity with potential indicates that more subtle structural and electronic effects also play an important role in determining the rates of the catalytic reactions.

Active-Site Topologies of Human CYP2D6 and Its Aspartate-301 → Glutamate, Asparagine, and Glycine Mutants

Cytochrome P450 2D6 (CYP2D6) catalyzes the oxidation of substrates with a positively charged nitrogen atom 5–7 Å from the site of the oxidation. The active-site topology of CYP2D6 is examined here with phenyl-, 2-naphthyl-, andp-biphenyldiazene, which react with P450 enzymes to form σ-bonded aryl–iron (Fe–Ar) complexes. Ferricyanide-mediated migration of the aryl group from the iron to the porphyrin nitrogens produces theN-arylprotoporphyrin IX regioisomers (NB:NA:NC:ND, in which the aryl group is bound to the nitrogen of pyrrole rings B, A, C, and D, respectively) in the following ratios (zero means <5%): phenyl, 10:90:00:00; 2-naphthyl, 09:91:00:00; andp-biphenyl, 16:84:00:00. These results suggest that the CYP2D6 active site is open above pyrrole ring A and to a small extent above pyrrole ring B but is closed above pyrrole rings C and D. This geometry differs from those determined by the same method for P450s for which crystal structures are available. Replacement of Asp-301 by a Glu, which preserves the carboxylate side chain, causes no detectable change in theN-aryl porphyrin regioisomer patterns and only minor changes in the catalytic activity. Replacement of Asp-301 by an Asn or Gly, which eliminates the negatively charged side chain, suppresses migration of the aryl groups to pyrrole ring B without impairing migration to pyrrole ring A and virtually abolishes catalytic activity. These results provide a refined model of the active site of CYP2D6. They confirm, furthermore, that the loss of activity observed when Asp-301 is replaced by a neutral residue is due to loss of the charge-pairing interaction with the substrate positive charge and/or subtle structural effects in the vicinity of pyrrole ring B, but not to major structural reorganization of the active site.

The three-dimensional structure of peptide-MHC complexes.

The ability of MHC molecules to present a broad spectrum of peptide antigens for T cell recognition requires a compromise between high affinity and broad specificity. Three-dimensional atomic structures of several class I and class II MHC molecules reveal a unique structural solution to this problem: Tight binding to the peptide main chain is supplemented by more or less restrictive interactions with peptide side chains. In spite of these contacts, peptide side-chain and conformational variability ensures that the resulting peptide-MHC complex presents an antigenically unique surface to T cell receptors. Extension of this understanding to other peptide-MHC complexes, including agonist/antagonist peptides and the identification of antigenic peptides within protein sequences, however, requires a detailed analysis of the interactions that determine both peptide-MHC binding affinity and the conformations of bound peptides. While many of these interactions can be modeled by homology with known structures, their specificity can depend sensitively on subtle and long-range structural effects. Structurally and immunologically important distinctions are also found between the class I and class II peptide-binding strategies. Taken together, these interactions ultimately determine the ability of an individual to respond successfully to immune challenges.

The Three-Dimensional Structure of Peptide-MHC Complexes

The ability of MHC molecules to present a broad spectrum of peptide antigens for T cell recognition requires a compromise between high affinity and broad specificity. Three-dimensional atomic structures of several class I and class II MHC molecules reveal a unique structural solution to this problem: Tight binding to the peptide main chain is supplemented by more or less restrictive interactions with peptide side chains. In spite of these contacts, peptide side-chain and conformational variability ensures that the resulting peptide-MHC complex presents an antigenically unique surface to T cell receptors. Extension of this understanding to other peptide-MHC complexes, including agonist/antagonist peptides and the identification of antigenic peptides within protein sequences, however, requires a detailed analysis of the interactions that determine both peptide-MHC binding affinity and the conformations of bound peptides. While many of these interactions can be modeled by homology with known structures, their specificity can depend sensitively on subtle and long range structural effects. Structurally and immunologically important distinctions are also found between the class I and class II peptide-binding strategies. Taken together, these interactions ultimately determine the ability of an individual to respond successfully to immune challenges.

High-resolution study of conductivity and cell potential versus doping concentration in potassium-doped polyacetylene: Correlation with structural transitions.

A high-resolution quasiequilibrium {ital in} {ital situ} study of parallel conductivity {sigma}{sub {parallel}} and open-circuit voltage {ital V}{sub OC} during potassium doping and dedoping of an oriented (CH){sub {ital x}} electrode is presented. Features in {ital dV}{sub OC}/{ital dy} and {ital d}{sigma}{sub {parallel}}/{ital dy} ({ital y}=K mole fraction) found previously at {ital y}=0.06, 0.12, and 0.15 are confirmed and correlated with recent x-ray and ESR results and with a model of staging via intercalation channels. We also find new features during dedoping at {ital y}=0.03 and 0.08 in {ital d}{sigma}{sub {parallel}}/{ital dy} but not in {ital dV}{sub OC}/{ital dy}, the former coinciding with a similar ESR feature. We propose that these are signatures of subtle structural effects that do not involve major changes in lattice constants or unit-cell symmetries. We tentatively assign the {ital y}=0.03 feature to a metastable dilute stage-2'' phase, by analogy to graphite intercalates. Similarly, three phases with the same stage-1 channel structure are inferred from the observation of three plateaus in {ital V}{sub OC}({ital y}) in the range 0.10{lt}{ital y}{lt}0.17 upon dedoping. A maximum {sigma}{sub {parallel}}=17 500 S/cm is found near {ital y}=0.12 during the first doping cycle. With successive cycles {sigma}{sub {parallel}}(max) decreases, the maximummore » attainable {ital y} also decreases, and {ital V}{sub OC}({ital y}) approaches the ideal behavior of an intercalation electrode exhibiting first-order phase transitions.« less

Vibrational circular dichroism in amino acids and peptides. 7. Amide stretching vibrations in polypeptides.

AbstractVibrational circular dichroism (VCD) spectra for the principal amide stretching vibrations, amide A (NH stretch) and amide I (predominantly CO stretch), are presented and analyzed for a variety of polypeptides dissolved in chloroform, as well as for two examples in D2O. Our results for poly(γ‐benzyl‐L‐glutamate) confirm the first and only previous report of VCD in polypeptides carried out by Singh and Keiderling [(1981) Biopolymers 20, 237–240]. Collectively, our spectra show that the sense of the bisignate VCD in these two regions depends on the sense of α‐helicity and not on the absolute configuration of the constituent amino acids. This conclusion is established by obtaining VCD for the two polypeptides, poly(β‐benzyl‐L‐asparate) and poly(im‐benzyl‐L‐histidine), that form left‐handed as opposed to right‐handed α‐helices. A new amide band having significant VCD intensity owing to its Fermi resonance interaction with the NH stretching mode has been identified as a weak shoulder on the low‐frequency side of the amide A band near 3200 cm−1 and is assigned as a combination band of the amide I and amide II vibrations. VCD spectra of polypeptides in D2O solution, although weak, have been successfully measured in the amide I region, where spectra appear to be more complicated due to the presence of solvated and internally hydrogen‐bonded amide groups. Strong monosignate contributions to the VCD in the amide A and amide I regions for some of the polypeptides indicate coupling of an electronic nature between these two regions and is deduced by an application of the concept of local sum rules of rotational strength. It appears that a detailed understanding of the VCD obtained for polypeptides will not only be diagnostic of secondary structure, but also of more subtle structural and vibrational effects that give rise to local, intrinsic chirality in the amide vibrations.

Effects of Syndepositional Structures on Lower Vicksburg (Oligocene) Fluvial-Deltaic Sedimentation, McAllen Ranch Field Area, Hidalgo County, South Texas: ABSTRACT

The lower Vicksburg sandstones of the McAllen Ranch field area (including McAllen Ranch, Santa Anita, and Guadalupe fields) in south Texas have been significant gas producers for almost 4 decades. However, the relationship of syndepositional structures to the type and distribution of depositional systems is still not fully understood. The importance of growth faults, especially major regional faults, has long been recognized. Further detailed studies concentrating on deeper sandstones of the Vicksburg Formation indicate that these faults in the lower Vicksburg are characterized by low-angle fault-planes and greatly expanded stratigraphic intervals with plunging rollover structures on the downthrown fault blocks. Greatest stratigraphic expansion is associated with channel- outh bar or delta-front facies. Extensive drilling and acquisition of high-resolution seismic data in this area have provided the necessary stratigraphic control to determine the significance of more subtle structural effects on sedimentation. The present study is based on the analysis of 142 well logs, 10 cores, and several seismic lines. The information from cores, characteristic log patterns, and net-sandstone maps of discrete genetic subunits strongly suggests a high-constructive deltaic origin for the reservoir facies. The maps show areas of rapid subsidence associated with large-scale mud movements. These movements result in the formation of sediment-withdrawal basins and fringing syndepositional anticlinal ridges. The localized basins have a profound effect on the style of deltaic sedimentation. Most significant is the exceptional thickening of the distal delta-plain facies characterized by interdistributary bay mud and crevasse splay sands. The splay sands contain abundant macerated plant material. Individual splays have a limited lateral extent, are stacked vertically, and form complex imbricated sand bodies wh ch are gas-prone stratigraphic traps. Such an area presents an ideal target for explorationists and a complex set of problems for the production staffs comtemplating secondary recovery projects. End_of_Article - Last_Page 1431------------

On the structure of chemisorbed acetylene and ethylene on Ni, Pd and Pt surfaces

Filtered He II ( hv = 40.8 eV) photoemission spectra for acetylene and ethylene molecularly chemisorbed at T ∼ 100 K on Ni(111), Ni(110), Pd(111) and Pt(111) have been obtained. The resulting vertical ionization potentials are presented and used within the framework of an approximate model to obtain information of the geometric structure of these molecules. Two initial state effects are discussed which are found to be important in deducing the molecular structures. These include an initial state shift of the lowest lying carbon-2s derived orbital and a metal atom induced shift of the σ CC valence orbital for strongly distorted species. The magnitudes of both effects are estimated — the latter using Hartree — Fock LCAO calculations of Be interacting with acetylene or ethylene. The deduced geometries of chemisorbed ethylene are found to differ only slightly from those determined without considering these effects, but for acetylene two classes of structures are found. One class of structures is weakly distorted while the other is strongly distorted (∼sp 2.5 hybridization). The latter structure is consistent with recent vibrational loss studies of chemisorbed acetylene on Ni(111) and Pt(111). In contrast to chemisorbed acetylene, chemisorbed ethylene on Ni shows relatively weak distortions. More subtle crystallographic and structural effects for acetylene and ethylene on (111), (100) and (110) Ni surfaces are also discussed.