1H-nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH

The ¹H-nmr chemical shifts and the spin–spin coupling constants of the common amino acid residues were measured in solutions of the linear tetrapeptides H-Gly-Gly-X-L -Ala-OH in D₂O and H₂O, the influence of X on the nmr parameters of the neighboring residues Gly 2 and Ala 4 was investigated. The titration parameters for the side chains of Asp, Glu, Lys, Tyr, and His were determined. The pK_a values obtained in D₂O, with the use of pH-meter readings with a combination glass electrode uncorrected for istope effects, were 0.06 pH units higher in the acidic range and 0.10 pH units higher in the basic range than the corresponding pK_a values in H₂O. This suggests that the present data are suitable “random-coil” ¹H-nmr parameters for conformational studies of polypeptide chains in D₂O and H₂O solutions.     

Solution three-dimensional structure of surfactin: A cyclic lipopeptide studied by 1H-nmr,distance geometry,and molecular dynamics

The solution three-dimensional structure of the protonated [Leu7]-surfactin, an hepta-peptide extracted from Bacillus subtilis, has been determined from two-dimensional ¹Hnmr performed in ²H₆-dimethylsulfoxide and combined with molecular modeling. Experimental data included 9 coupling constants, 61 nuclear Overhauser effect derived distances, NH temperature coefficients, and ¹³C relaxation times. Two distance geometry (DISMAN) protocols converged toward models of the structure and the best of them were refined by restrained and unrestrained molecular dynamics (GROMOS). Two structures in accord with the set of experimental constraints are presented. Both are characterized by a “horse saddle” topology for ring atoms on which are attached the two polar Glu and Asp side chains showing an orientation clearly opposite to that of the C_11–13 aliphatic chain. Amphipathic and surface properties of surfactin are certainly related to the existence of such minor polar and a major hydrophobic domains. The particular “claw” configuration of acidic residues observed in surfactin gives important clues for the understanding of its cation binding and transporting ability. © 1994 John Wiley & Sons, Inc.     

Interphase epichromatin: last refuge for the 30-nm chromatin fiber?

“Interphase epichromatin” describes the surface of chromatin located adjacent to the interphase nuclear envelope. It was discovered in 2011 using a bivalent anti-nucleosome antibody (mAb PL2-6), now known to be directed against the nucleosome acidic patch. The molecular structure of interphase epichromatin is unknown, but is thought to be heterochromatic with a high density of “exposed” acidic patches. In the 1960s, transmission electron microscopy of fixed, dehydrated, sectioned, and stained inactive chromatin revealed “unit threads,” frequently organized into parallel arrays at the nuclear envelope, which were interpreted as regular helices with ~ 30-nm center-to-center distance. Also observed in certain cell types, the nuclear envelope forms a “sandwich” around a layer of closely packed unit threads (ELCS, envelope-limited chromatin sheets). Discovery of the nucleosome in 1974 led to revised helical models of chromatin. But these models became very controversial and the existence of in situ 30-nm chromatin fibers has been challenged. Development of cryo-electron microscopy (Cryo-EM) gave hope that in situ chromatin fibers, devoid of artifacts, could be structurally defined. Combining a contrast-enhancing phase plate and cryo-electron tomography (Cryo-ET), it is now possible to visualize chromatin in a “close-to-native” situation. ELCS are particularly interesting to study by Cryo-ET. The chromatin sheet appears to have two layers of ~ 30-nm chromatin fibers arranged in a criss-crossed pattern. The chromatin in ELCS is continuous with adjacent interphase epichromatin. It appears that hydrated ~ 30-nm chromatin fibers are quite rare in most cells, possibly confined to interphase epichromatin at the nuclear envelope.

     

Bioavailability of organic and inorganic phosphates adsorbed on short-range ordered aluminum precipitate

A nonreductive community-level study of P availability was conducted using various forms of adsorbed P. Orthophosphate (Pi), inositol hexaphosphate (IHP), and glucose 6-phosphate (G6P) were adsorbed to a short-range ordered Al precipitate. These bound phosphates provided a P source sufficient to support the growth of microbial communities from acidic Brazilian soils (oxisols). Adsorbed IHP, the most abundant form of organic phosphate in most soils, had the lowest bioavailability among the three phosphates studied. Adsorbed G6P and Pi were almost equally available. The amount of adsorbed Pi (1 cmol P kg^–1) required to support microbial growth was at least 30 times less than that of IHP (30 cmol P kg^–1). With increased surface coverage, adsorbed IHP became more bioavailable. This availability was attributed to a change in the structure of surface complexes and presumably resulted from the decreased number of high-affinity surface sites remaining at high levels of coverage. It thus appears that the bioavailability of various forms of adsorbed phosphate was determined primarily by the stability of the phosphate-surface complexes that they formed, rather than by the total amount of phosphate adsorbed. IHP, having the potential to form stable multiple-ring complexes, had the highest surface affinity and the lowest bioavailability. Bioaggregates consisting of bacteria and Al precipitate were observed and may be necessary for effective release of adsorbed P. Bacteria in the genera Enterobacter and Pseudomonas were the predominate organisms selected during these P-limited enrichments. Correspondence to: C. Shang     

Molecular Basis of Substrate Polyspecificity of the Candida albicans Mdr1p Multidrug/H+ Antiporter

The molecular basis of polyspecificity of Mdr1p, a major drug/H⁺ antiporter of Candida albicans, is not elucidated. We have probed the nature of the drug-binding pocket by performing systematic mutagenesis of the 12 transmembrane segments. Replacement of the 252 amino acid residues with alanine or glycine yielded 2/3 neutral mutations while 1/3 led to the complete or selective loss of resistance to drugs or substrates transported by the pump. Using the GlpT-based 3D–model of Mdr1p, we roughly categorized these critical residues depending on their type and localization, 1°/ main structural impact (“S” group), 2°/ exposure to the lipid interface (“L” group), 3°/ buried but not facing the main central pocket, inferred as critical for the overall H⁺/drug antiport mechanism (“M” group) and finally 4°/ buried and facing the main central pocket (“B” group). Among “B” category, 13 residues were essential for the large majority of drugs/substrates, while 5 residues were much substrate-specific, suggesting a role in governing polyspecificity (P group). 3D superposition of the substrate-specific MFS Glut1 and XylE with the MDR substrate-polyspecific MdfA and Mdr1p revealed that the B group forms a common substrate interaction core while the P group is only found in the 2 MDR MFS transporters, distributed into 3 areas around the B core. This specific pattern has let us to propose that the structural basis for polyspecificity of MDR MFS transporters is the extended capacity brought by residues located at the periphery of a binding core to accomodate compounds differing in size and type.     

Compilation and Characterization of Histidine-Containing Phosphotransmitters Implicated in His-to-Asp Phosphorelay in Plants: AHP Signal Transducers of Arabidopsis thaliana

Histidine (His)-to-Aspartate (Asp) phosphorelay signal transduction systems are generally made up of a “sensor histidine (His)-kinase”, a “response regulator”, and a “histidine-containing phosphotransmitter (HPt)”. In the higher plant, Arabidopsis thaliana, results from recent intensive studies suggested that the His-to-Asp phosphorelay mechanism is at least partly responsible for propagation of environmental stimuli, such as phytohormones (e.g. ethylene and cytokinin). Here we compiled the members of the HPt family of phosphotransmitters in Arabidopsis thaliana (AHP- series, Arabidopsis HPt phosphotransmitters), based on both database and experimental analyses, in order to provide a comprehensive basis at the molecular level for understanding the function of the AHP phosphotransmitters that are implicated in the His-to-Asp phosphorelay of higher plants.     

Position of caesium ions in crystalline B-form DNA determined by synchrotron radiation diffraction. Preliminary results

The diffraction patterns of CsDNA taken with copper X-irradiation are considerably impaired because of the strong X-ray absorption by caesium ions. The use of high power synchrotron radiation of wavelength λ = 1.2 Å has yielded photographs suitable for intensity measurements.The structure of phage T2 CsDNA at 76% relative humidity is isomorphous to the crystalline B-form of LiDNA, and the disposition of cations appears to conform to the 10-fold screw symmetry of B-DNA. The structure factor amplitudes of 20 reflections in the diffraction pattern of phage T2 CsDNA are noticeably different from those of the same reflections in the LiDNA diffraction pattern, and the positions of the Cs⁺ ions could thus be found. The best model has the cations located significantly close to dyad axes lying between the planes of successive nucleotide pairs. One of the two cations “belonging” to a nucleotide pair touches the surface of the narrow groove of the B-DNA double helix, while the other is on the wide groove side, rather far from its “own” DNA molecule.     

Structural versatility of peptides from Cα, α-disubstituted glycines: Crystal-state conformational analysis of homopeptides from Cα-methyl,Cα-benzylglycine [(αMe)Phe]n

The molecular and crystal structures of one derivative and three homopeptides (from the di-to the tetrapeptide level) of the chiral, C^{α, α}-disubstituted glycine C^α-methyl, C^α-benzylglycine [(αMe)Phe], have been determined by x-ray diffraction. The derivative is mClAc-D -(αMe)Phe-OH, and the peptides are pBrBz-[D -(αMe)Phe]₂-NHMe, pBrBz-[D -(αMe)Phe]₃-OH hemihydrate, and pBrBz-[D -(αMe)Phe]₄-OtBu sesquihydrate. All (αMe)Phe residues prefer ?,ψ torsion angles in the helical region of the conformational map. The dipeptide methylamide and the tripeptide carboxylic acid adopt a β-turn conformation with a 1 ← 4 C?O…?H? N intramolecular H bond. The structure of the tripeptide carboxylic acid is further stabilized by a 1 ← 4 C?O…?H? O intramolecular H bond, forming an “oxy-analogue” of a β-turn. The tetrapeptide ester is folded in a regular (incipient) 3₁₀-helix. In general, the relationship between (αMe)Phe chirality and helix screw sense is opposite to that exhibited by protein amino acids. A comparison is made with the conclusions extracted from published work on homopeptides from other C^α-methylated α-amino acids. © 1993 John Wiley & Sons, Inc.     

The structure of the purple membrane from Halobacterium hallobium: analysis of the X-ray diffraction pattern.

An X-ray diffraction analysis of oriented specimens of the purple membrane from Halobacterium halobium shows that the protein and lipid components are packed in a P3 hexagonal lattice, with one protein molecule per asymmetric unit. The structure is made up of a single layer of the protein molecules, oriented vectorially in the same direction across the membrane.The presence of strong diffraction peaks equatorially centred at 10 Å, and axially at 5 Å and 1.5 Å, show that the protein molecules, which make up most of the mass of the membrane, are composed to a considerable extent of α-helices, 25 to 35 Å long, arranged roughly perpendicular to the plane of the membrane to form superhelical groupings of the “coiled-coil” type.The surface of the membrane is flat, with no bumps or dimples large enough to affect the X-ray pattern when the electron density of the suspending medium is altered. The phospholipids may be less exactly positioned in the lattice than the protein, since the presence of uranyl acetate, which is expected to co-ordinate with the acidic phosphate groups, produces intensity changes only at low resolution.     

Structure of a New Opine,Mikimopine, in Hairy Root Induced by Agrobacterium rhizogenes

A enzyme that catalyzed the specific formation of ascorbic acid-2-phosphate (AsA2P) from ascorbic acid (AsA) and adenosine-5′-triphosphate (ATP), was purified 3,200-fold to homogeneity from a cell extract of Pseudomonas azotocolligans. The purified enzyme appeared as a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and consisted of a single polypeptide with a molecular weight of about 30,000. Of phosphoryl donors tested, p-nitrophenylphosphate (p-NPP) and pyrophosphate (PPi) were as effective as ATP. Optimal pHs for the phosphorylating activity were around 4.0 and 5.5 when PPi and ATP were used as phosphoryl donors, respectively. The Km for AsA was 147 mm. The enzyme activity was inhibited by Cu²⁺, but not by sulfhydryl reagents.

The enzyme simultaneously had phosphatase activity at weakly acidic or neutral pH and the Km for p-NPP in the phosphatase activity was 0.38 mm. The enzyme was tentatively named “ascorbic acid phosphorylating enzyme.”     

Fluorescence of proteins in aqueous neutral salt solutions. II. Influence of monovalent cation chlorides, particularly cesium chloride.

The effects of varying concentrations of monovalent cation chlorides on the fluorescence of nine proteins were studied. These are discussed in terms of “direct” or “indirect” interactions with the aromatic amino acid residues. Cs⁺ is the only cation that quenches fluorescence of proteins due to “direct” interaction with aromatic amino acid residues. Quenching is due to collisional processes. An agreement with the Stern-Volmer relationship is shown and the values of [(K_Q)eff] and [(f_a)eff] are calculated. These values confirm that the fraction of fluorescence accessible to Cs⁺ belongs to the “exposed” fluorophors. The mechanism of quenching by Cs⁺ is due to the heavy-atom effect because phosphorescence enhancement is also seen at the same time. The chlorides of Na⁺, K⁺, Rb⁺, NH₄⁺, and Li⁺ do not have a similar effect on the fluorescence of all proteins. For a given protein a gradation of the same effect (i.e., quenching or dequenching) is seen. Interactions with factors that “inderectly” affect fluorescence of any protein are involved and the structural features of the protein are responsible for such “indirect” effects. The results indicate that neutral salts can act in more than one manner. The changes in fluorescence are indicative of electrostatic and lyotropic effects of ions. Only electrostatic interactions which occur in the vicinity of tryptophan in proteins are reflected. Li⁺ shows strong interactions with proteins. In 4 M LiCl, BSA, papain, and trypsin show fluorescence changes that are indicative of changes in protein structure.     

4′-Aza-3′,5′-dihomothymidine and Derivatives

Abstract

A series of 3′-branched 4′-azanucleoside analogues have been prepared. These compounds comprise three asymmetric atoms, two carbons and one nitrogen. They constitute nucleoside analogues imparted with a “flickering configuration”, the nitrogen inversion replacing a D-L epimerization of their natural congeners. The 1′,3′-cis and 1′,3′-trans isomers have been separated and their configuration established by ¹H NMR and the X-ray diffraction structure of one crystalline example. The configurations of the frozen invertomers were assessed by low temperature ¹H NMR experiments assisted by molecular mechanics simulations. None of these compounds exhibited any significant in vitro antiviral activity.     

The crystal structure of Klebsiella pneumoniae FeoA reveals a site for protein-protein interactions

In order to establish infection, pathogenic bacteria must obtain essential nutrients such as iron. Under acidic and/or anaerobic conditions, most bacteria utilize the Feo system in order to acquire ferrous iron (Fe²⁺) from their host environment. The mechanism of this process, including its regulation, remains poorly understood. In this work, we have determined the crystal structure of FeoA from the nosocomial agent Klebsiella pneumoniae (KpFeoA). Our structure reveals an SH3-like domain that mediates interactions between neighboring polypeptides via hydrophobic intercalations into a Leu-rich surface ridge. Using docking of a small peptide corresponding to a postulated FeoB partner binding site, we demonstrate that KpFeoA can assume both “open” and “closed” conformations, controlled by binding at this Leu-rich ridge. We propose a model in which a “C-shaped” clamp along the FeoA surface mediates interactions with its partner protein, FeoB. These findings are the first to demonstrate atomic-level details of FeoA-based protein-protein interactions and provide a framework for testing FeoA-FeoB interactions, which could be exploited for future antibiotic developments.     

Combined computational and biochemical study reveals the importance of electrostatic interactions between the “pH sensor” and the cation binding site of the sodium/proton antiporter NhaA of Escherichia coli

Sodium proton antiporters are essential enzymes that catalyze the exchange of sodium ions for protons across biological membranes. The crystal structure of NhaA has provided a basis to explore the mechanism of ion exchange and its unique regulation by pH. Here, the mechanism of the pH activation of the antiporter is investigated through functional and computational studies of several variants with mutations in the ion‐binding site (D163, D164). The most significant difference found computationally between the wild type antiporter and the active site variants, D163E and D164N, are low pK_a values of Glu78 making them insensitive to pH. Although in the variant D163N the pK_a of Glu78 is comparable to the physiological one, this variant cannot demonstrate the long‐range electrostatic effect of Glu78 on the pH‐dependent structural reorganization of trans‐membrane helix X and, hence, is proposed to be inactive. In marked contrast, variant D164E remains sensitive to pH and can be activated by alkaline pH shift. Remarkably, as expected computationally and discovered here biochemically, D164E is viable and active in Na⁺/H⁺ exchange albeit with increased apparent K_M. Our results unravel the unique electrostatic network of NhaA that connect the coupled clusters of the “pH sensor” with the binding site, which is crucial for pH activation of NhaA. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Maternal feeding strategies, child eating behaviors, and child BMI in low-income African-American preschoolers

Objective: To test the hypothesis that low‐income African‐American preschool children would have a higher BMI if their mothers reported greater “restriction” and “control” in feeding and if mothers reported that children showed greater “food responsiveness” and “desire to drink.” In addition, to test whether higher maternal “pressure to eat” would be associated with lower child BMI. Research Methods and Procedures: A questionnaire was completed by 296 low‐income African‐American mothers of preschool children. It assessed three constructs on maternal feeding strategies (“restriction,” “pressure to eat,” and “control”) and two on child eating behaviors (“food responsiveness” and “desire to drink”). Children's BMI was measured, and mothers’ BMI was self‐reported. Results: The mean (standard deviation) BMI z‐score of the children was 0.34 (1.5), and 44% of the mothers were obese (BMI ≥30 kg/m²). Only maternal “pressure to eat” had a significant overall association with child BMI z‐score (r = ?0.16, p < 0.01). Both maternal “restriction” and “control” were positively associated with children's BMI z‐score in the case of obese mothers (r = 0.20, p = 0.03 and r = 0.24, p = 0.007, respectively), but this was not so in the case of non‐obese mothers (r = ?0.16, p = 0.05 and r = ?0.07, p = 0.39, respectively). Discussion: Among low‐income African Americans, the positive association between maternal restriction and control in feeding and their preschoolers’ BMI was limited to obese mothers. Relations between parent feeding strategies and child weight status in this population may differ on the basis of maternal weight status.     

The effect of “aging” of fibrinogen molecule on the structure and properties of fibrin gel

The effect of molecular “aging” of fibrinogen stimulated by preincubation in solution on the fibrin three-dimensional architecture, its ability to crosslink fibrin-stabilizing factor, and the sensitivity of fibringel to plasmin hydrolysis have been studied. The method of elastic light scattering was used to demonstrate that fibrin generated from “defective” fibrinogen had a coarser structure with a higher mean mass-length ratio of polymeric fibers compared to native fibrinogen (2.24 × 10⁹ and 1.46 × 10⁹ g/(mol cm), respectively). Crosslinking had no effect on the architecture of both control and experimental fibrin samples. Spectrophotometric and electrophoretic analysis has shown a higher sensitivity of coarse fibrin gels to plasmin. A close correlation between spontaneous local conformational reconstructions in fibrinogen molecule and its functional activity is concluded.     

The Enzymic Synthesis of Dihydropteroate and Dihydrofolate by Plasmodium berghei

SYNOPSIS. Cell-free extracts of the rodent malaria parasite Plasmodium berghei synthesized dihydropteroate (H₂pteroate) and dihydrofolate (H₂folate) from 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine (hydroxymethyldihydropteridine) and p-aminobenzoate (pAB) or p-aminobenzoylglutamate (pABG). The reaction was demonstrated also in extracts of Plasmodium gallinaceum, Plasmodium lophurae and Plasmodium knowlesi, by the use of a microbiologic assay method and pABG as cosubstrate. Some of the properties of the enzymes involved were investigated in P. berghei preparations, utilizing a radioactive assay which measures the conversion of [7-¹⁴C]pAB to [¹⁴C]H₂pteroate. Apparent K_m values of 0.28 μM for [7-¹⁴C]pAB, 0.037 mM for pABG and 0.8 μM for hydroxymethyldihydropteridine were obtained. The reaction had absolute requirements for ATP and Mg⁺⁺, and was stimulated by dithiothreitol. The enzymes required for the reaction were eluted together from Sephadex G-200 columns in a molecular weight range of 200,000–250,000. In bacteria hydroxymethyldihydropteridine is converted 1st by a pyrophosphokinase to pyrophosphorylmethyldihydropteridine, and this compound is then condensed with pAB to form H₂pteroate by H₂pteroate synthetase. Both enzymic activities were demonstrated in P. berghei preparations and separated by DEAE-Sephadex chromatography. The enzymic synthesis of H₂pteroate by P. berghei is inhibited by several sulfonamides and diaminodiphenylsulfone (DDS). The latter compound is shown to be competitive with pAB, with a K_i value of 0.38 μM; pABG is also a competitive inhibitor. These data establish an enzymic basis of support for the evidence obtained in vivo which indicate that malaria synthesize their folate cofactors de novo. It is suggested that the antimalarial action of sulfonamides and DDS is due to their inhibition of plasmodial H₂pteroate synthetase.     

Microheterogeneity of avian and mammalian vinculin: Distinctive subcellular distribution of different isovinculins

Vinculin from chicken gizzard and from pig heart may be separated by two-dimensional gel electrophoresis into several isoelectrophoretic forms. Peptide map analysis and immunochemical comparison of the different isovinculins indicated that all the isoforms are closely interrelated at the molecular level. Moreover, it was shown that avian and mammalian vinculins have similar molecular structures. Some differences were detected between the isovinculin pattern in intact chicken gizzard tissue and that found in cultured cells from the same organ. Various degrees of vinculin microheterogeneity were also detected in a variety of cultured cells, including primary cultures and several cell lines. Labelling of chicken gizzard cells with [³²P]orthophosphate resulted in the incorporation of ³²P in the minor acidic isoform of vinculin (α-vinculin) exclusively. Extraction of the cultured cells with detergent under conditions that remove the cytoplasmic “soluble” vinculin without significantly affecting focal contact-associated protein, indicated that specific vinculin isoforms may differ in their cellular distribution. The soluble fraction contained almost exclusively the basic form (β-vinculin), while the “organized” protein contained all three major isovinculins but was enriched with the acidic form (α) and the intermediate form (α′). The functional significance of isovinculin diversity and the involvement of phosphorylation events in vinculin interactions are discussed.     

Planar and vertical induction of anteroposterior pattern during the development of the amphibian central nervous system

In amphibians and other vertebrates, neural development is induced in the ectoderm by signals coming from the dorsal mesoderm during gastrulation. Classical embryological results indicated that these signals follow a “vertical” path, from the involuted dorsal mesoderm to the overlying ectoderm. Recent work with the frog Xenopus laevis, however, has revealed the existence of “planar” neural-inducing signals, which pass within the continuous sheet or plane of tissue formed by the dorsal mesoderm and presumptive neurectoderm. Much of this work has made use of Keller explants, in which dorsal mesoderm and ectoderm are cultured in a planar configuration with contact along only a single edge, and vertical contact is prevented. Planar signals can induce the full anteroposterior (A-P) extent of neural pattern, as evidenced in Keller explants by the expression of genes that mark specific positions along the A-P axis. In this review, classical and modern molecular work on vertical and planar inductionwill be discussed. This will be followed by a discussion of various models for vertical induction and planar induction. It has been proposed that the A-P pattern in the nervous system is derived from a parallel pattern of inducers in the dorsal mesoderm which is “imprinted” vertically onto the overlying ectoderm. Since it is now known that planar signals can also induce A-P neural pattern, this kind of model must be reassessed. The study of planar induction of A-P pattern in Xenopus embryos provides a simple, manipulable, two-dimensional system in which to investigate pattern formation. © 1993 John Wiley & Sons, Inc.