Solution conformation of DNA

Optical observations on linear B-form DNA by the method of electric linear dichroism show that the value of the limiting reduced dichroism is molecular weight-dependent, increasing with molecular weight to a limit of about ?1.41 ± 0.02 in aqueous solution. These data and the rotational relaxation times obtained from the decay of the dichroism when the orienting field is instantaneously removed, imply the existence of a non-linear tertiary equilibrium structure for DNA. The data indicate that the essential B-form parameters of the double-stranded DNA are retained in this tertiary structure, and are not consistent with a DNA structure in which the base-pairs have a 34 ° propeller-like twist (Hogan et al., 1978). The interpretation of the dichroism data is supported by a clear demonstration that the magnitude of dichroism change in ethanol corresponds to that expected for the B to A-form structural transition as determined from X-ray diffraction. We propose that the tertiary structure of B-DNA is a helical coil and suggest the limits of the structural parameters of the coil consistent with the observations.     

Theoretical π-π* absorption and circular dichroic spectra of polypeptide β-structures

Absorption and circular dichroic (CD) spectra of the π-π* transition near 200 nm are calculated for poly(Gly), poly(Ala), poly(Abu), and poly(Val) in the β_P (paralle) and β_A (antiparallel) pleated-sheet structures using the dipole interaction model and including interactions among all atoms; optical parameters were obtained from previous studies of related molecules. Most of the calculations are for structures with one or three chains of six residues each. The oscillator strength and splitting of the π-π* modes are found to be affected only to a small extent by variations in side-chain structure and conformation, whereas the CD spectrum is very sensitive to these variations. Poly(Gly) and poly(Ala) β-structures in uniform, planar lattices do not show sufficient rotational strength to account for observed CD spectra. Poly(Abu) and poly(Val) β-structures in uniform, planar lattices show rotational strengths comparable to experiment when χ¹ is near ?60° for β_A-structures or in a broad range near 140° for β_P-structures. Poly(Ala) in uniformly twisted β_A- and β_P-structures or in irregular β_A-structures corresponding to regions of the crystal structure of concanavalin A also show enhanced rotational strengths in the principal π-π* CD band. Absorption and CD spectra calculated for poly(Abu) in uniform β_A- and β_P-structures are compared with experimental data on poly(Lys) in the β-form, assuming side-chain conformations in Abu that maximize the intensity of the principal CD band. The calculations for the β_A-form show the better agreement with experiment for both types of spectra.     

Indole- and caffeine-resistant mutations of Schizophyllum commune are involved in the behavior of a class III B mating-type factor in trp1 cells

We have reported that a parental strain of Schizophyllun commune T11 (trp1) is fully compatible with a strain T37 (Bα1′β4, trp1), but indole- and caffeine-resistant mutants (In^R-13 and Caf^R-9 respectively) derived from the T11 are semicompatible with the same T37. The compound-resistant mutations, ind1 and cfn1, were linked to neither A nor B mating-type factors. In^R-13, Caf^R-9, and all of indole- and caffeine-resistant progenies (ind1, trp1; cfn1, trp1) were semicompatible with the T37, and compatible with a strain T40 (Bα1′β4, TRP1) although the T40 contained the same class III B mating-type factor as the T37. The In^R-13 and Caf^R-9 were also semicompatible with any tester strains (Bα1′β4, trp1) developed, and the resulting heterokaryons produced non-aggregated and semiaggregated masses of hyphae, respectively. In the mutant heterokaryons, nuclei were distributed irregularly especially in case of [trp1/trp1] background; anucleate, uninucleate, binucleate and multinucleate cells were found with modified hyphae which contained a different type of septation (pseudoclamps and simple septa other than true clamps). We concluded that the ind1 and cfn1 mutations alter the normal behavior of one of class III B mating-type factors in Trp⁻ cells.     

An analysis of the influence of age and school-attendance status on the spread of variola minor.

Definitions are proposed for the independent and joint contributions that the chemical groups A and B make to the free energy of association of the ligand A?B with a receptor. The definitions are independent of the choice of the standard state and are consistent with the basic thermodynamic cycle relating the association of the ligands A?B, A?Y and X?B to the receptor Rappaport 1976. The basic idea is the use of the excess free energy of association of the ligand A?Y over the free energy of association of the reference ligand X?Y as the measure of the “independent” contribution of the group A to the binding. This definition allows the free energy of association of the ligand A?B to be written as the sum of the independent contributions of the groups A and B, their joint contribution, and an invariant free energy of association of the reference ligand with any receptor. With the appropriate definition of the receptor-reference ligand complex, water can be chosen as the reference ligand. Using ΔG(A?OH)?AG(HOH), ΔG(H?B?H)?ΔG(HOH) and ΔG(HO?C)?ΔG(HOH) as the definitions of the “independent” contributions of the chemical groups A, B and C to the binding of the ligand A?B?C, the joint contribution of the groups A and C to the binding is ΔG(A?B?C) ? ΔG(A?B?H) ? ΔG(H-B-C) + ΔG(H?B?H).     

Affinity chromatography without immobilized ligands; A new method for studying macromolecular interactions using high-performance liquid chromatography

A new method for studying macromolecular interactions was devised. The principle is based on affinity chromatography with a mobile zone of affinity ligand instead of a column with immobilized ligand. In this method, the difference in migration velocities between the moving zone of affinity ligand and a sample in a conventional gel-permeation column is utilized. The fast migrating zone (A zone), which is later injected into the column, and the slow migrating zone (B zone), which is injected beforehand, interfere with each other at the passing point in the column if A and B interact such as A + B ? AB. The zone interference deforms each elution profile of A and B, because the complex AB has a migration velocity different from the others. The elution profiles in zone-interference chromatography are calculated by computer simulation in the framework of the plate theory. The binding constant is calculated from the peak shift of elution volume of B in the zone-interference chromatogram. The interaction between single-strand DNA (A zone) and ribonuclease A (B zone) was studied.     

Random coil conformations of polynucleotides: a study incorporating long-range correlations due to dynamics of the sugar residue

A novel virtual bond scheme joining the atoms P-C4′ and C4′-P of a nucleotide repeat, consistent with the stereochemistry of polynucleotide chains, has been developed. The scheme, with its inherent feature to account for all the major sources of flexibility, could also consider effectively the short range and long range interactions, thereby simplifying the analysis of random coil and ordered structures. Using this scheme, unperturbed end-to-end dimensions and persistence lengths of polynucleotide chains have been computed incorporating the dynamical aspects of the sugar ring as well as the C4′ C5′ bond and the correlated changes in phosphodiester conformations. Calculated unperturbed dimensions are in excellent agreement with experimental values. Results show that the random coil is characterized by a large proportion of helical segments of the A-form.     

Development of novel adenosine receptor ligands based on the 3-amidocoumarin scaffold

With the aim of finding new adenosine receptor (AR) ligands presenting the 3-amidocoumarin scaffold, a study focusing on the discovery of new chemical entities was carried out. The synthesized compounds 1–8 were evaluated in radioligand binding (A₁, A_2A and A₃) and adenylyl cyclase activity (A_2B) assays in order to determine their affinity for human AR subtypes. The 3-benzamide derivative 4 showed the highest affinity of the whole series and was more than 30-fold selective for the A₃ AR (K_i = 3.24 μM). The current study supported that small structural changes in this scaffold allowed modulating the affinity resulting in novel promising classes of A₁, A_2A, and/or A₃ AR ligands. We also performed docking calculations in hA_2A and hA₃ to identify the hypothetical binding mode for the most active compounds. In addition, some ADME properties were calculated in order to better understand the potential of these compounds as drug candidates.     

Fatty acid derivatives and dammarane triterpenes from the glandular trichome exudates of Ibicella lutea and Proboscidea louisiana

Ibicella lutea and Proboscidea louisiana, both of the Martyniaceae family, are known for rich glandular trichomes on their leaves and stems. Chemical investigations of the glandular trichome exudates on leaves of the two plants furnished three types of secondary metabolites, glycosylated fatty acids, glycerides (2-O-(3,6-diacetyloxyfattyacyl)glycerols and 2-O-(3-acetyloxyfattyacyl)glycerols) and dammarane triterpenes. The glycosylated fatty acids from I. lutea were determined to be 6(S)-(6-O-acetyl-β-d-glucopyranosyloxy)-octadecanoic acid (1A), -eicosanoic acid (1B) and -docosanoic acid (1C), as well as their respective deacetyl congeners (2A, 2B and 2C), whereas P. louisiana furnished 8(S)-(6-O-acetyl-β-d-glucopyranosyloxy)-eicosanoic acid (3A) and -docosanoic acid (3B) and their respective deacetyl congeners (4A and 4B), together with 2B. Both plants contained 12 identical 2-O-[(3R,6S)-3,6-diacetyloxyfattyacyl]glycerols (5A-L), in which the fatty acyl moieties contained between 17 and 21 carbon atoms. The corresponding mono-acetyloxy compounds, 2-O-[(3R)-3-acetyloxyfattyacyl]glycerols (6A–L) were detected in both plants. Among these glycerides, ten compounds (5A, 5C, 5F, 5H, 5K, 6A, 6C, 6F, 6H and 6K) had iso-fattyacyl structures and four (5E, 5J, 6E and 6J) had anteiso-fattyacyl structures. A previously unknown dammarane triterpene, betulatriterpene C 3-acetate (7), was isolated together with three known dammarane triterpenes, 24-epi-polacandrin 1,3-diacetate (8), betulatriterpene C (9) and 24-epi-polacandrin 3-acetate (10) from I. lutea, whereas 12 dammarane triterpenes, named probosciderols A–L (12–23), and the known compound betulafolienetriol (11) were isolated from P. louisiana. The structures of these compounds were elucidated by spectroscopic analysis including 2D-NMR techniques and chemical transformations. The 6-O-acetylglucosyloxy-fatty acids 1A–C (42%) and the dammarane triterpenes 7–10 (31%) were the two most abundant constituents in the glandular trichome exudate of I. lutea, whereas the dammarane triterpenes 11–23 (47%) and the glucosyloxy-fatty acids (4A, 4B and 2B) (38%) were the most abundant constituents in the glandular trichome exudate of P. louisiana.     

Automated prediction of 15N, 13Cα, 13Cβ and 13C′ chemical shifts in proteins using a density functional database

A database of peptide chemical shifts, computed at the density functional level, has been used to develop an algorithm for prediction of ¹⁵N and ¹³C shifts in proteins from their structure; the method is incorporated into a program called SHIFTS (version 4.0). The database was built from the calculated chemical shift patterns of 1335 peptides whose backbone torsion angles are limited to areas of the Ramachandran map around helical and sheet configurations. For each tripeptide in these regions of regular secondary structure (which constitute about 40% of residues in globular proteins) SHIFTS also consults the database for information about sidechain torsion angle effects for the residue of interest and for the preceding residue, and estimates hydrogen bonding effects through an empirical formula that is also based on density functional calculations on peptides. The program optionally searches for alternate side-chain torsion angles that could significantly improve agreement between calculated and observed shifts. The application of the program on 20 proteins shows good consistency with experimental data, with correlation coefficients of 0.92, 0.98, 0.99 and 0.90 and r.m.s. deviations of 1.94, 0.97, 1.05, and 1.08 ppm for ¹⁵N, ¹³C, ¹³C and ¹³C, respectively. Reference shifts fit to protein data are in good agreement with `random-coil' values derived from experimental measurements on peptides. This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement.     

Evidence that histidine forms a coordination bond to the A0A and A0B chlorophylls and a second H-bond to the A1A and A1B phylloquinones in M688HPsaA and M668HPsaB variants of Synechocystis sp. PCC 6803

The axial ligands of the acceptor chlorophylls, A_0A and A_0B, in Photosystem I are the Met sulfur atoms of M688_PsaA and M668_PsaB. To determine the role of the Met, His variants were generated in Synechocystis sp. PCC 6803. Molecular dynamics simulations on M688H_PsaA show that there exist low energy conformations with the His coordinated to A_0A and possibly H-bonded to A_1A. Transient EPR studies on M688H_PsaA indicate a more symmetrical electron spin distribution in the A_1A phyllosemiquinone ring consistent with the presence of an H-bond to the C1 carbonyl. Ultrafast optical studies on the variants show that the 150 fs charge separation between P₇₀₀ and A₀ remains unaffected. Studies on the ns timescale show that 57% of the electrons are transferred from A_0A⁻ to A_1A in M688H_PsaA and 48% from A_0B⁻ to A_1B in M668H_PsaB; the remainder recombine with P₇₀₀⁺ with 1/e times of 25 ns and 37 ns, respectively. Those electrons that reach A_1A and A_1B in the branch carrying the mutation are not transferred to F_X, but recombine with P₇₀₀⁺ with 1/e times of ~ 15 μs and ~ 5 μs, respectively. Hence, the His is coordinated to A₀ in all populations, but in a second population, the His may be additionally H-bonded to A₁. Electron transfer from A₀ to A₁ occurs only in the latter, but the higher redox potentials of A₀ and A₁ as a result of the stronger coordination bond to A₀ and the proposed second H-bond to A₁ preclude electron transfer to the Fe/S clusters.     

1,3-Dialkyl-8-N-substituted benzyloxycarbonylamino-9-deazaxanthines as potent adenosine receptor ligands: Design,synthesis, structure–affinity and structure–selectivity relationships

A number of 1,3-dialkyl-9-deazaxanthines (9-dAXs), bearing a variety of N-substituted benzyloxycarbonylamino substituents at position 8, were prepared and evaluated for their binding affinity to the recombinant human adenosine receptors (hARs), chiefly to the hA_2B and hA_2A AR subtypes. Several ligands endowed with excellent binding affinity to the hA_2B receptors, but low selectivity versus hA_2A and hA₁ were identified. Among these, 1,3-dimethyl-N-3′-thienyl carbamate 15 resulted as the most potent ligand at hA_2B (K_i = 0.8 nM), with a low selectivity versus hA_2A (hA_2A/hA_2B = 12.6) and hA₁ (hA₁/hA_2B = 12.5) and a higher selectivity versus hA₃ (hA₃/hA_2B = 454). When tested in functional assays in vitro, compound 15 exhibited high antagonist activities and efficacies versus both the A_2A and A_2B receptor subtypes, with pA₂ values close to the corresponding pK_is. A comparative analysis of structure–affinity and structure–selectivity relationships of the similar analogues 8-N-substituted benzyloxycarbonylamino- and 8-N-substituted phenoxyacetamido-9-dAXs suggested that their binding modes at the hA_2B and hA_2A ARs may strongly differ. Computational studies help to clarify this striking difference arising from a simple, albeit crucial, structural change, from CH₂OCON to OCH₂CON, in the para-position of the 8-phenyl ring.     

Mechanism of primary and secondary ion-radical pair formation in photosystem I complexes

The mechanisms of the ultrafast charge separation in reaction centers of photosystem I (PS I) complexes are discussed. A kinetic model of the primary reactions in PS I complexes is presented. The model takes into account previously calculated values of redox potentials of cofactors, reorganization energies of the primary P700⁺A ₀ ^- and secondary P700⁺A ₁ ^- ion-radical pairs formation, and the possibility of electron transfer via both symmetric branches A and B of redox-cofactors. The model assumes that the primary electron acceptor A₀ in PS I is represented by a dimer of chlorophyll molecules Chl2A/Chl3A and Chl2B/Chl3B in branches A and B of the cofactors. The characteristic times of formation of P700⁺A ₀ ^- and P700⁺A ₁ ^- calculated on the basis of the model are close to the experimental values obtained by pump-probe femtosecond absorption spectroscopy. It is demonstrated that a small difference in the values of redox potentials between the primary electron acceptors A_0A and A_0B in branches A and B leads to asymmetry of the electron transfer in a ratio of 70: 30 in favor of branch A. The secondary charge separation is thermodynamically irreversible in the submicrosecond range and is accompanied by additional increase in asymmetry between the branches of cofactors of PS I.     

An informational analysis of the inter-male behaviour of the grasshopper chortophaga viridifasciata

Communication among male grasshoppers spaces individuals and prevents ipsi-sexual courtship (without fighting). Information theory measures applied to data from 2169 interactions elucidate the system making this possible. These measures demonstrate the communicatory nature of twelve categories of behaviour and enable these categories to be ranked in order of relative strength. Strong signals of initiator (A) and responder (B) differ. Uncertainties of both A and B increase as interactions proceed, and the former starts and remains higher than the latter, reflecting the higher gross activity of A. Normalized transmissions make possible meaningful comparisons with other arthropod groups and show that A's actions have a stronger effect on B than do B's on A.     

NMR and NQR parameters of the SiC-doped on the (4,4) <Emphasis Type="Italic">armchair</Emphasis> single-walled BPNT: a computational study

The structural properties, NMR and NQR parameters in the pristine and silicon carbide (SiC) doped boron phosphide nanotubes (BPNTs) were calculated using DFT methods (BLYP, B3LYP/6-31G*) in order to evaluate the influence of SiC-doped on the (4,4) armchair BPNTs. Nuclear magnetic resonance (NMR) parameters including isotropic (CS^I) and anisotropic (CS^A) chemical shielding parameters for the sites of various ¹³C, ²⁹Si, ¹¹B, and ³¹P atoms and quadrupole coupling constant (C _Q ), and asymmetry parameter (η _Q ) at the sites of various ¹¹B nuclei were calculated in pristine and SiC- doped (4,4) armchair boron phosphide nanotubes models. The calculations indicated that doping of ¹¹B and ³¹P atoms by C and Si atoms had a more significant influence on the calculated NMR and NQR parameters than did doping of the B and P atoms by Si and C atoms. In comparison with the pristine model, the SiC- doping in Si_PC_B model of the (4,4) armchair BPNTs reduces the energy gaps of the nanotubes and increases their electrical conductance. The NMR results showed that the B and P atoms which are directly bonded to the C atoms in the SiC-doped BPNTs have significant changes in the NMR parameters with respect to the B and P atoms which are directly bonded to the Si atoms in the SiC-doped BPNTs. The NQR results showed that in BPNTs, the B atoms at the edges of nanotubes play dominant roles in determining the electronic behaviors of BPNTs. Also, the NMR and NQR results detect that the Fig. 1b (Si_PC_B) model is a more reactive material than the pristine and the Fig. 1a (Si_BC_p) models of the (4,4) armchair BPNTs.     

Amphiphilic properties of synthetic glycolipids based on amide linkages. I. Electron microscopic studies on aqueous gels

Amphiphiles with one or two amide linkages have been prepared by the reaction (A) of D-gluconic acid lactone with aliphatic amines (C₆-C₁₀) and (C) of N′-gluconoyl-ethylenediamine with alkanoic acids (C₆)-(C₁₀). Gel formation was found to occur on cooling the aqueous solutions at concentrations as low as 1–2%. Electron microscopy revealed that the gels of type A are composed of highly ordered ropes with right-handed twist, especially well developed with N-octylgluconamide. Type c substances with two amide linkages of opposite direction form gels consisting of smooth ribbons devoid of twisting. N-Methylation of the amide bond (type B and D substances) leads to a considerable increase in solubility. Gels are only formed from samples containing decanoic acid. These gels also consist of right-handed fibrillar ropes, only partially ordered with one N-methylated amide linkage (B), regularly aligned side-by-side with one N-methylated and one non-methylated amide bond (D). Gel formation and the typical morphology of the gels are discussed as arising mainly from strong intermolecular hydrogen bonds between amide linkages holding the molecules together and the influence of chiral centers of the carbohydrate chain which might be responsible for helical aggregates to be formed.     

The roles of Rhodobacter sphaeroides copper chaperones PCuAC and Sco (PrrC) in the assembly of the copper centers of the aa3-type and the cbb3-type cytochrome c oxidases

The α proteobacter Rhodobacter sphaeroides accumulates two cytochrome c oxidases (CcO) in its cytoplasmic membrane during aerobic growth: a mitochondrial-like aa₃-type CcO containing a di-copper Cu_A center and mono-copper Cu_B, plus a cbb₃-type CcO that contains Cu_B but lacks Cu_A. Three copper chaperones are located in the periplasm of R. sphaeroides, PCu_AC, PrrC (Sco) and Cox11. Cox11 is required to assemble Cu_B of the aa₃-type but not the cbb₃-type CcO. PrrC is homologous to mitochondrial Sco1; Sco proteins are implicated in Cu_A assembly in mitochondria and bacteria, and with Cu_B assembly of the cbb₃-type CcO. PCu_AC is present in many bacteria, but not mitochondria. PCu_AC of Thermus thermophilus metallates a Cu_A center in vitro, but its in vivo function has not been explored. Here, the extent of copper center assembly in the aa₃- and cbb₃-type CcOs of R. sphaeroides has been examined in strains lacking PCu_AC, PrrC, or both. The absence of either chaperone strongly lowers the accumulation of both CcOs in the cells grown in low concentrations of Cu^2 +. The absence of PrrC has a greater effect than the absence of PCu_AC and PCu_AC appears to function upstream of PrrC. Analysis of purified aa₃-type CcO shows that PrrC has a greater effect on the assembly of its Cu_A than does PCu_AC, and both chaperones have a lesser but significant effect on the assembly of its Cu_B even though Cox11 is present. Scenarios for the cellular roles of PCu_AC and PrrC are considered. The results are most consistent with a role for PrrC in the capture and delivery of copper to Cu_A of the aa₃-type CcO and to Cu_B of the cbb₃-type CcO, while the predominant role of PCu_AC may be to capture and deliver copper to PrrC and Cox11. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.     

Reorganization energies of the electron transfer reactions involving quinones in the reaction center of <Emphasis Type="Italic">Rhodobacter sphaeroides</Emphasis>

In framework of the continuum electrostatics theory, the reorganization energies of the electron transfers Q_A^?–Q_B (fast phase), Bph^?–Q_A, P⁺–Q_A^?, and P⁺–Q_B^? in the photosynthetic bacterial reaction center have been calculated. The calculations were based on the static dielectric permittivity spatial distribution derived from the data on the electrogenesis, with the corresponding characteristic times relatively close to the reaction times of Q_A^?–Q_B (fast phase) and Bph^?–Q_A but much shorter than those times of the latter two recombination reactions. The calculated reorganization energies were reasonably close to the experimental estimates for Q_A^?–Q_B (fast phase) and Bph^?–Q_A but substantially lower than those of P⁺–Q_A^? and P⁺–Q_B^?. A higher effective dielectric permittivity contributes to this effect, but the dominant contribution is most probably made by a non-dielectric relaxation, especially for the P⁺–Q_B^? recombination influenced by the proton transfer. This situation calls for reconsidering of the current electron transfer rate estimates.