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Well-defined polymers derived from L-proline are synthesized using reversible addition-fragmentation chain transfer (RAFT) polymerization and the amino acid-based polymers exhibit thermosensitive phase separation at lower critical solution temperatures (LCST = 15-45 degrees C) in aqueous medium.
Glycine residues are known to contribute to conformational flexibility of polypeptide chains, and have been found to contribute to flexibility of some loops associated with enzymic catalysis. A comparison of porcine pepsin in zymogen, mature and inhibited forms revealed that a loop (a flap), consisting of residues 71--80, located near the active site changed its position upon substrate binding. The loop residue, glycine-76, has been implicated in the catalytic process and thought to participate in a hydrogen-bond network aligning the substrate. This study investigated the role of glycine-76 using site-directed mutagenesis. Three mutants, G76A, G76V and G76S, were constructed to increase conformational restriction of a polypeptide chain. In addition, the serine mutant introduced a hydrogen-bonding potential at position 76 similar to that observed in human renin. All the mutants, regardless of amino acid size and polarity, had lower catalytic efficiency and activated more slowly than the wild-type enzyme. The slower activation process was associated directly with altered proteolytic activity. Consequently, it was proposed that a proteolytic cleavage represents a limiting step of the activation process. Lower catalytic efficiency of the mutants was explained as a decrease in the flap flexibility and, therefore, a different pattern of hydrogen bonds responsible for substrate alignment and flap conformation. The results demonstrated that flap flexibility is essential for efficient catalytic and activation processes.
Control of the rate of cardiac cell division by oxygen occurs most probably by altering the redox state of a control substance, e.g. NAD(+)right harpoon over left harpoonNADH. NAD(+) (and not NADH) forms poly(ADP-ribose), an inhibitor of DNA synthesis, in a reaction catalysed by poly(ADP-ribose) polymerase. Lower partial pressure of oxygen, which increases the rate of division, would shift NAD(+)-->NADH, decrease poly(ADP-ribose) synthesis, and increase DNA synthesis. Chick-embryo heart cells grown in culture in 20% O(2) (in which they divide more slowly than in 5% O(2)) did exhibit greater poly(ADP-ribose) polymerase activity (+83%, P<0.001) than when grown in 5% O(2). Reaction product was identified as poly(ADP-ribose) by its insensitivity to deoxyribonuclease, ribonuclease, NAD glycohydrolase, Pronase, trypsin and micrococcal nuclease, and by its complete digestion with snake-venom phosphodiesterase to phosphoribosyl-AMP and AMP. Isolation of these digestion products by Dowex 1 (formate form) column chromatography and paper chromatography allowed calculation of average poly(ADP-ribose) chain length, which was 15-26% greater in 20% than in 5% O(2). Thus in 20% O(2) the increase in poly(ADP-ribose) formation results from chain elongation. Formation of new chains also occurs, probably to an even greater degree than chain elongation. Additionally, poly(ADP-ribose) polymerase has very different K(m) and V(max.) values and pH optima in 20% and 5% O(2). These data suggest that poly(ADP-ribose) metabolism participates in the regulation of heart-cell division by O(2), probably by several different mechanisms.
The sensitivity of glucose production from L-lactate by isolated liver cells from starved rats to inhibition by alpha-cyano-4-hydroxycinnamate was studied. A small percentage of the maximal rate of gluconeogenesis was insensitive to inhibition by alpha-cyano-4-hydroxycinnamate, and evidence is presented to show that this is due to pyruvate entry into the mitochondria as alanine. After subtraction of this rate, Dixon plots of the reciprocal of the rate of gluconeogenesis against inhibitor concentration were linear both in the absence and presence of glucagon, phenylephrine or valinomycin, each of which stimulated gluconeogenesis by 30-50%. Pyruvate kinase activity was decreased by glucagon, but not by phenylephrine or valinomycin. Inhibition of gluconeogenesis by quinolinate (inhibitor of phosphoenolpyruvate carboxykinase) or monochloroacetate (probably inhibiting pyruvate carboxylation) caused a significant deviation from linearity of the Dixon plot obtained with alpha-cyano-4-hydroxycinnamate. Amytal, however, inhibited gluconeogenesis without affecting the linearity of this plot. These data, coupled with a computer simulation study, suggest that pyruvate transport may control gluconeogenesis from L-lactate and that hormones may stimulate this process through an effect on the respiratory chain. An additional role for pyruvate kinase and pyruvate carboxylase is quite compatible with the data presented.
1. We have examined systematically the relationship between the percentage reduction of cardiac mitochondrial NAD and the flux through oxidative phosphorylation, as measured by O2 uptake. Reduction of NAD was varied by varying the concentration of palmitoyl-L-carnitine, pyruvate, 2-oxoglutarate or glutamate in the presence of malate as the oxidizable substrate. 2. In the presence of ADP (State 3 respiration) there was a substantially linear positive relationship between O2 uptake and the percentage reduction of NAD. Coupled respiration in the absence of ADP also showed an increase with increasing NADH, with the exact shape of the relationship being variable. 3. When pyruvate and 2-oxoglutarate dehydrogenase activity were increased by increasing medium Ca2+ concentration within the range 5 nM to 1.23 microM, at non-saturating substrate concentrations, there was again a positive relationship between O2 uptake and the reduction of NAD; however, rates of O2 uptake tended to be higher at given values of NAD reduction when the incubation medium contained Ca2+. This is taken to indicate an activation by Ca2+ of the enzymes of phosphorylation or of the respiratory chain, in addition to the dehydrogenase activation. 4. When carboxyatractyloside plus ADP were used to generate 50% State 3 rates of O2 uptake with pyruvate or 2-oxoglutarate, sensitivity to Ca2+ was retained. However, when oligomycin plus 1 mM-ADP and 1 mM-ATP were used to generate 50% State 3, no such dependence was seen. 5. The results are interpreted to indicate a substantial role for substrate dehydrogenation in the overall regulation of oxidative phosphorylation when substrates are available at near-physiological concentrations.
To examine whether protein kinase C (PKC) and A (PKA) contribute to WAF1 induction by ionizing radiation (IR) in cultured human melanomas, the effect of PK inhibitors 1-(5'-isoquinolinesulphonyl)-2-methylpiperazine dihydrochloride (H7), bisindolylmaleimide (GF) and N-[2(p-dromocinnamylamino)ethyl]-5-isoquinolinesulphonamide (H89) on IR-induced WAF1 accumulation was analysed by Western blot analysis. Gamma-ray-induced accumulation of WAF1 showed a peak at 6 Gy in all the cell lines. After gamma-ray irradiation of 6 Gy, a peak of WAF1 accumulation was observed at 6 h in SK-Mel-26, G361 and HM6KO cells, and at 3 h in MeWo cells. In MeWo and SK-Mel-26 cells, the X-ray-induced WAF1 accumulation was decreased by PK inhibitors, GF (PKC inhibitor) or H89 (PKA inhibitor); this did not occur in G361 and HM6KO. In all the cell lines, accumulation of WAF1 induced by X-ray irradiation was suppressed by H7 (PKC and PKA inhibitor). In addition, polymerase chain reaction-single strand conformational polymorphism analysis detected no aberrations in the p53 gene of the four cell lines used. These results suggest that IR-induced WAF1 expression involves PKC and/or PKA activity depending on cell type.
Serratia marcescens SS-1 produces at least four N-acylhomoserine lactones (AHLs) which were identified using high-resolution mass spectrometry and chemical synthesis, as N-(3-oxohexanoyl) homo-serine lactone (3-oxo-C6-HSL), N-hexanoyl- (C6-HSL), N-heptanoyl (C7-HSL) and N-octanoyl- (C8-HSL) homoserine lactone. These AHLs are synthesized via the LuxI homologue SpnI, and regulate via the LuxR homologue SpnR, the production of the red pigment, prodigiosin, the nuclease, NucA, and a biosurfactant which facilitates surface translocation. spnR overexpression and spnR gene deletion show that SpnR, in contrast to most LuxR homologues, acts as a negative regulator. spnI overexpression, the provision of exogenous AHLs and spnI gene deletion suggest that SpnR is de-repressed by 3-oxo-C6-HSL. In addition, long chain AHLs antagonize the biosurfactant-mediated surface translocation of S. marcescens SS-1. Upstream of spnI there is a gene which we have termed spnT. spnI and spnT form an operon and although database searches failed to reveal any spnT homologues, overexpression of this novel gene negatively affected both sliding motility and prodigiosin production.
Mycobacterium tuberculosis infects one-third of the world's population and causes two million deaths annually. The unusually low permeability of its cell wall contributes to the ability of M. tuberculosis to grow within host macrophages, a property required for pathogenesis of infection. Mycobacterium marinum is an established model for discovering genes involved in mycobacterial infection. Mycobacterium marinum mutants with transposon insertions in the beta-ketoacyl-acyl carrier protein synthase B gene (kasB) grew poorly in macrophages, although growth in vitro was unaffected. Detailed analyses by thin-layer chromatography, nuclear magnetic resonance (NMR), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, infrared spectroscopy, and chemical degradations showed that the kasB mutants synthesize mycolic acids that are 2-4 carbons shorter than wild type; the defect was localized to the proximal portion of the meromycolate chain. In addition, these mutants showed a significant (approximately 30%) reduction in the abundance of keto-mycolates, with a slight compensatory increase of both alpha- and methoxy-mycolates. Despite these small changes in mycolate length and composition, the kasB mutants exhibited strikingly altered cell wall permeability, leading to a marked increase in susceptibility to lipophilic antibiotics and the host antimicrobial molecules defensin and lysozyme. The abnormalities of the kasB mutants were fully complemented by expressing M. tuberculosis kasB, but not by the closely related gene kasA. These studies identify kasB as a novel target for therapeutic intervention in mycobacterial diseases.
The transporter associated with antigen processing (TAP) delivers peptides into the lumen of the endoplasmic reticulum for binding onto major histocompatibility complex class I molecules. TAP comprises two polypeptides, TAP1 and TAP2, each with an N-terminal transmembrane domain and a C-terminal cytosolic nucleotide binding domain (NBD). The two NBDs have distinct intrinsic nucleotide binding properties. In the resting state of TAP, the NBD1 has a much higher binding activity for ATP than the NBD2, while the binding of ADP to the two NBDs is equivalent. To attribute the different nucleotide binding behaviour of NBD1 and NBD2 to specific sequences, we generated chimeric TAP1 and TAP2 polypeptides in which either the nonhomologous C-terminal tails downstream of the Walker B motif, or the core NBDs which are enclosed by the conserved Walker A and B motifs, were reciprocally exchanged. Our biochemical and functional studies on the different TAP chimeras show that the distinct nucleotide binding behaviour of TAP1 and TAP2 is controlled by the nonhomologous C-terminal tails of the two TAP chains. In addition, our data suggest that the C-terminal tail of TAP2 is required for a functional transporter by regulating ATP binding. Further experiments indicate that ATP binding to NBD2 is important because it prevents simultaneous uptake of ATP by TAP1. We propose that the C-terminal tails of TAP1 and TAP2 play a crucial regulatory role in the coordination of nucleotide binding and ATP hydrolysis by TAP.
Volkensin, a type 2 ribosome-inactivating protein from the roots of Adenia volkensii Harms (kilyambiti plant) was characterized both at the protein and nucleotide level by direct amino acid sequencing and cloning of the gene encoding the protein. Gene sequence analysis revealed that volkensin is encoded by a 1569-bp ORF (523 amino acid residues) without introns, with an internal linker sequence of 45 bp. Differences in residues present at several sequence positions (reproduced after repeated protein sequence analyses), with respect to the gene sequence, suggest several isoforms for the volkensin A-chain. Based on the crystallographic coordinates of ricin, which shares a high sequence identity with volkensin, a molecular model of volkensin was obtained. The 3D model suggests that the amino acid residues of the active site of the ricin A-chain are conserved at identical spatial positions, including Ser203, a novel amino acid residue found to be conserved in all known ribosome-inactivating proteins. The sugar binding site 1 of the ricin B-chain is also conserved in the volkensin B-chain, whilst in binding site 2, His246 replaces Tyr248. Native volkensin contains two free cysteinyl residues out of 14 derived from the gene sequence, thus suggesting a further disulphide bridge in the B chain, in addition to the inter- and intrachain disulphide bond pattern common to other type 2 ribosome-inactivating proteins.
A new coarse-grained lattice model neglecting atomic details is proposed for the coil-helix transition and a new physical parameter is suggested to characterize a helical structure. In our model, each residue is represented by eight lattice sites, and side groups are not considered explicitly. Chirality and hydrogen bonding are taken into consideration in addition to chain connectivity and the excluded volume effect. Through a dynamic Monte Carlo simulation, the physical properties of the coil-helix transition of a single homopolypeptide have been produced successfully within a short computing time on the PC. We also examined the effects of the variation of chain configurations including chain size and chain shape, etc. A spatial correlation function has been introduced in order to characterize periodicity of a helical chain in a simple way. A propagation parameter and a nucleation parameter have also been calculated, which compares favorably with the results of the Zimm-Bragg theory for the coil-helix transition.
Molecular dynamics (MD) simulations have been performed for prototype models of polymer electrolytes in which the salt is an ionic liquid based on 1-alkyl-3-methylimidazolium cations and the polymer is poly(ethylene oxide), PEO. The MD simulations were performed by combining the previously proposed models for pure ionic liquids and polymer electrolytes containing simple inorganic ions. A systematic investigation of ionic liquid concentration, temperature, and the 1-alkyl- chain length, [1,3-dimethylimidazolium]PF6, and [1-butyl-3-methylimidazolium]PF6, effects on resulting equilibrium structure is provided. It is shown that the ionic liquid is dispersed in the polymeric matrix, but ionic pairs remain in the polymer electrolyte. Imidazolium cations are coordinated by both the anions and the oxygen atoms of PEO chains. Probability density maps of occurrences of nearest neighbors around imidazolium cations give a detailed physical picture of the environment experienced by cations. Conformational changes on PEO chains upon addition of the ionic liquid are identified. The equilibrium structure of simulated systems is also analyzed in reciprocal space by using the static structure factor, S(k). Calculated S(k) display a low wave-vector peak, indicating that spatial correlation in an extended-range order prevail in the ionic liquid polymer electrolytes. Long-range correlations are assigned to nonuniform distribution of ionic species within the simulation box.
The catalytic subunit of cyclic 3':5'-AMP-dependent protein kinase (ATP:protein phosphotransferase, EC 2.7.1.37) inhibits translation in Artemia salina and wheat germ extracts. It acts, as in reticulocyte lysates [Datta, A., de Haro, C., Sierra, J. M. & Ochoa, S. (1977) Proc. Natl. Acad. Sci. USA 74, 1463-1467] by catalyzing the conversion of a proinhibitor to an inhibitor of polypeptide chain initiation. Addition of ATP and either cyclic AMP or catalytic subunit promotes the proinhibitor-inhibitor conversion in crude proinhibitor preparations from A. salina embryos. The effect of cyclic AMP is due to stimulation of cyclic AMP-dependent protein kinase, present in such preparations, and is inhibited by hemin. In similar preparations from wheat germ, addition of ATP and catalytic subunit promoted proinhibitor-inhibitor conversion, but addition of ATP and cyclic AMP has little or no effect. As assayed with histone as substrate, wheat germ preparations exhibit a protein kinase activity that is not stimulated by the addition of cyclic AMP or cyclic GMP. Our results suggest that a translational control system, similar to that existing in rabbit reticulocytes and other mammalian cells, is present in organisms evolutionarily far removed from mammals.
Previous genetic and biochemical studies led to the identification of two large RNase T1-resistant oligonucleotides, designated the G(IX) (+) and G(IX) (-) oligonucleotides, whose presence in the genomes of closely related murine leukemia viruses is mutually exclusive and predictive of two properties of the viral envelope glycoprotein gp70. Viruses harboring the G(IX) (+) oligonucleotide induce expression of the gp70-associated antigen G(IX) and possess gp70s with more rapid electrophoretic mobility on sodium dodecyl sulfate/polyacrylamide gels than viruses that possess the G(IX) (-) oligonucleotide. The latter viruses fail to induce G(IX) on infected fibroblasts. The G(IX) (+) and G(IX) (-) oligonucleotides lie in corresponding positions in the 3' third of the oligonucleotide maps of their respective viruses. We have determined the nucleotide sequences of the G(IX) (+) and G(IX) (-) oligonucleotides. The sequence of the G(IX) (-) oligonucleotide is U-A-U-C-U-C-A-A-C-C-A-C-C-A-U-A-C-U-U-A-A-C-C-U-C-A-C-C-A-C-[unk]-G, and the sequence of the G(IX) (+) oligonucleotide is U-A-U-C-U-C-A-A-C-C-A-C-C-A-U-A-C-U-U-G. Thus, a single base change could result in the interconversion of the two oligonucleotides. Consideration of the amino acids specified by the two oligonucleotides suggests that this single base difference may result in the presence of an additional oligosaccharide chain in the gp70s of the G(IX) (-) viruses. Evidence supporting this prediction has been obtained by M. R. Rosner, J.-S. Tung, E. Fleissner, and P. W. Robbins (personal communication). It is entirely possible that the single nucleotide change that apparently results in a different electrophoretic mobility of the gp70s of the G(IX) (+) and G(IX) (-) viruses is also responsible for the presence or absence of the G(IX) antigenic determinant; however, the validity of this possibility awaits further investigation.
A Mr 35,000 protein with follicle-stimulating hormone release-inhibitory activity was isolated from porcine ovarian follicular fluid by heparin-Sepharose affinity chromatography, gel filtration on Sephacryl S-200, and multiple steps of high-performance liquid chromatography. The isolated molecule is highly enriched in cysteines and is composed of a single polypeptide chain. In addition, it has no sequence homology with the previously characterized follicular fluid inhibins, which are heterodimeric proteins of Mr 32,000 with follicle-stimulating hormone release-inhibiting activity. This protein specifically inhibits the basal secretion of follicle-stimulating hormone, but not that of luteinizing hormone, in the rat anterior pituitary monolayer culture system with a half-maximal effective dose of 2.5-6.0 ng/ml. Another form of the molecule of Mr 32,000 present in much lower concentration in follicular fluid was also isolated. It may differ from the Mr 35,000 form in glycosylation or carboxyl-terminal truncation. We suggest that this compound be called "follistatin" to signify its structural difference from inhibin.
Transcription in the human immunodeficiency virus type 1 (HIV-1) retrovirus is regulated by binding the viral Tat protein (trans-acting transcriptional activator) to the trans-activation response (TAR) RNA sequence. Here, vacuum UV circular dichroism (VUV-CD) is used to study the structure of TAR and its complex with two peptide fragments that are important for Tat binding to TAR. The VUV-CD spectrum of TAR is typical of A-form RNA and is minimally perturbed when bound to either the short or the long Tat peptide. The CD spectra of the complexes indicate an extended structure in the arginine-rich region of Tat from amino acid residue 47 through residue 58 and a short alpha-helix within the adjacent 59-72 region. Models of TAR and its peptide complexes are constructed to integrate these spectroscopic results with current biochemical data. The model suggests that (i) the arginine-rich 49-58 region is primarily responsible for electrostatic interactions with the phosphates of the RNA, (ii) the arginine side chains can additionally interact with substituent groups of the nucleotide bases to confer base recognition in the complex, (iii) the recognition of uracil-23 in TAR is facilitated by the peptide backbone, and (iv) the glutamine-rich face of an alpha-helix within the 59-72 region pairs to bases UGG at nucleotide positions 31-33 in the TAR loop and thus provides an additional motif in the Tat trans-activating protein to recognize TAR RNA.
Muscle contraction is powered by the interaction of the molecular motor myosin with actin. With new techniques for single molecule manipulation and fluorescence detection, it is now possible to correlate, within the same molecule and in real time, conformational states and mechanical function of myosin. A spot-confocal microscope, capable of detecting single fluorophore polarization, was developed to measure orientational states in the smooth muscle myosin light chain domain during the process of motion generation. Fluorescently labeled turkey gizzard smooth muscle myosin was prepared by removal of endogenous regulatory light chain and re-addition of the light chain labeled at cysteine-108 with the 6-isomer of iodoacetamidotetramethylrhodamine (6-IATR). Single myosin molecule fluorescence polarization data, obtained in a motility assay, provide direct evidence that the myosin light chain domain adopts at least two orientational states during the cyclic interaction of myosin with actin, a randomly disordered state, most likely associated with myosin whereas weakly bound to actin, and an ordered state in which the light chain domain adopts a finite angular orientation whereas strongly bound after the powerstroke.
LXRalpha and -beta are nuclear receptors that regulate the metabolism of several important lipids, including cholesterol and bile acids. Previously, we have proposed that LXRs regulate these pathways through their interaction with specific, naturally occurring oxysterols, including 22(R)-hydroxycholesterol, 24(S)-hydroxycholesterol, and 24(S),25-epoxycholesterol. Using a ligand binding assay that incorporates scintillation proximity technology to circumvent many of the problems associated with assaying extremely hydrophobic ligands, we now demonstrate that these oxysterols bind directly to LXRs at concentrations that occur in vivo. To characterize further the structural determinants required for potent LXR ligands, we synthesized and tested a series of related compounds for binding to LXRs and activation of transcription. These studies revealed that position-specific monooxidation of the sterol side chain is requisite for LXR high-affinity binding and activation. Enhanced binding and activation can also be achieved through the use of 24-oxo ligands that act as hydrogen bond acceptors in the side chain. In addition, introduction of an oxygen on the sterol B-ring results in a ligand with LXRalpha-subtype selectivity. These results support the hypothesis that naturally occurring oxysterols are physiological ligands for LXRs and show that a rational, structure-based approach can be used to design potent LXR ligands for pharmacologic use.