Investigating the Interactions of Yeast Prions: [SWI+], [PSI+], and [PIN+]

The relationship between quantitative genetics and population genetics has been studied for nearly a century, almost since the existence of these two disciplines. Here we ask to what extent quantitative genetic models in which selection is assumed to operate on a polygenic trait predict adaptive fixations that may lead to footprints in the genome (selective sweeps). We study two-locus models of stabilizing selection (with and without genetic drift) by simulations and analytically. For symmetric viability selection we find that ∼16% of the trajectories may lead to fixation if the initial allele frequencies are sampled from the neutral site-frequency spectrum and the effect sizes are uniformly distributed. However, if the population is preadapted when it undergoes an environmental change (i.e., sits in one of the equilibria of the model), the fixation probability decreases dramatically. In other two-locus models with general viabilities or an optimum shift, the proportion of adaptive fixations may increase to >24%. Similarly, genetic drift leads to a higher probability of fixation. The predictions of alternative quantitative genetics models, initial conditions, and effect-size distributions are also discussed.     

How to find a prion: [URE3], [PSI+] and [beta

Infectious proteins (prions) in yeast or other microorganisms can be identified by genetic methods of rather general applicability. Infection in yeast means transfer by cytoplasmic mixing (cytoduction), a property of all non-chromosomal genetic elements whether plasmids, viruses, or prions. Prions can be diagnosed by reversible curability, increased occurrence when the corresponding protein is overproduced, a requirement for the gene for the corresponding protein for propagation, and, in some cases, similarity of phenotype of: (a) mutations in the gene for the protein and (b) the presence of the prion. This approach is illustrated with [URE3], an amyloid-based prion of the regulator of nitrogen catabolism, Ure2p and [PSI(+)] as a prion of the translation termination factor Sup35p. The prion concept is not limited to infectious amyloids, but includes proteins whose active form is necessary for the activation of the inactive precursor. We detail methods used in studies of [URE3] and [beta], a self-activating protease, some of which are of broad application.     

The chemistry of [1,2,3]triazolo[1,5-a]pyridines

The reactivity of [1,2,3]triazolo[1,5-a]pyridines 1 is described. Triazolopyridines react with electrophiles in two contrasting ways, giving 3-substituted triazolopyridines 2, or products 3, resulting from triazolo ring opening with loss of molecular nitrogen. The triazolopyridines can be lithiated at -40 degrees C by lithium diisopropylamide in ether giving regiospecifically the 7-lithio derivative. Bromotriazolopyridines have activation towards nucleophilic substitution at position 5 and 7, and benzenoid inertness at position 6. The parent compound 1a is easily hydrogenated giving tetrahydrotriazolopyridine 11a in high yield; when the triazolopyridines have substituents, the hydrogenation reaction strongly depends on the position of the substituent. Triazolopyridinium ylides of type 18 and 26 react with acetylenic esters; these reactions are influenced by the nature of solvent and the acetylenic ester used, giving different types of adducts: stable disubstituted triazolopyridinium ylides of type 19 and 20, indolizines 21, or pyrroleninylpyrazolo[5,1-a] pyridines 22. Photochemistry, and photochemical reactions with MP and DMAD of these ylides are also described. A new way to 2,2'-bipyridines, in two steps from triazolopyridines is reported.     

Synthesis of new aromatic pyrrolo[2,1-c] [1,4]benzodiazepines and pyrrolo[1,2-a]thieno[3,2-e] [1,4]diazepines as anti-tumoral agents

Diazepine analogs of thieno[2,3-b]pyrrolizin-8-ones were synthesized by aromatization of 2-hydroxypyrrolo[1,2-a]thieno[3,2-e][1,4]diazepines. These compounds were evaluated in vitro for their antiproliferative activity against the L1210 leukemia cell line. The activity of these compounds was in the micromolar range, the best result being for the mixture of the isomers 5 and 6 which showed a 0.35 microM IC50 against cell growth.     

Thermophilic anaerobic biodegradation of [C]lignin, [C]cellulose, and [C]lignocellulose preparations

Thermophilic (55 degrees C) anaerobic enrichment cultures were incubated with [C-lignin]lignocellulose, [C-polysaccharide]lignocellulose, and kraft [C]lignin prepared from slash pine, Pinus elliottii, and C-labeled preparations of synthetic lignin and purified cellulose. Significant but low percentages (2 to 4%) of synthetic and natural pine lignin were recovered as labeled methane and carbon dioxide during 60-day incubations, whereas much greater percentages (13 to 23%) of kraft lignin were recovered as gaseous end products. Percentages of label recovered from lignin-labeled substrates as dissolved degradation products were approximately equal to percentages recovered as gaseous end products. High-pressure liquid chromatographic analyses of CuO oxidation products of sound and degraded pine lignin indicated that no substantial chemical modifications of the remaining lignin polymer, such as demethoxylation and dearomatization, occurred during biodegradation. The polysaccharide components of pine lignocellulose and purified cellulose were relatively rapidly mineralized to methane and carbon dioxide; 31 to 37% of the pine polysaccharides and 56 to 63% of the purified cellulose were recovered as labeled gaseous end products. An additional 10 to 20% of the polysaccharide substrates was recovered as dissolved degradation products. Overall, these results indicate that elevated temperatures can greatly enhance rates of anaerobic degradation of lignin and lignified substrates to methane and low-molecular-weight aromatic compounds.     

The Chemistry of [1,2,3]Triazolo[1,5- a] pyridines

The reactivity of [1,2,3]triazolo[1,5- a] pyridines 1 is described. Triazolopyridines react with electrophiles in two contrasting ways, giving 3-substituted triazolopyridines 2, or products 3, resulting from triazolo ring opening with loss of molecular nitrogen. The triazolopyridines can be lithiated at ^?40°C by lithium diisopropylamide in ether giving regiospecifically the 7-lithio derivative. Bromotriazolopyridines have activation towards nucleophilic substitution at position 5 and 7, and benzenoid inertness at position 6. The parent compound 1a is easily hydrogenated giving tetrahydrotriazolopyridine 11a in high yield; when the triazolopyridines have substituents, the hydrogenation reaction strongly depends on the position of the substituent. Triazolopyridinium ylides of type 18 and 26 react with acetylenic esters; these reactions are influenced by the nature of solvent and the acetylenic ester used, giving different types of adducts: stable disubstituted triazolo-pyridinium ylides of type 19 and 20, indolizines 21, or pyrroleninylpyrazolo[5,1- a] pyridines 22. Photochemistry, and photochemical reactions with MP and DMAD of these ylides are also described. A new way to 2,2′-bipyridines, in two steps from triazolopyridines is reported.     

Synthesis of New Aromatic Pyrrolo[2,1- c] [1,4]benzodiazepines and Pyrrolo[1,2- a] thieno[3,2- e] [1,4]diazepines as Anti-tumoral Agents

Diazepine analogs of thieno[2,3- b] pyrrolizin-8-ones were synthesized by aromatization of 2-hydroxypyrrolo[1,2- a] thieno[3,2- e] [1,4]diazepines. These compounds were evaluated in vitro for their antiproliferative activity against the L1210 leukemia cell line. The activity of these compounds was in the micromolar range, the best result being for the mixture of the isomers 5 and 6 which showed a 0.35 μM IC 50 against cell growth.     

Discovery of imidazo[1,2-a]-, [1,2,4]triazolo[4,3-a]-, and [1,2,4]triazolo[1,5-a]pyridine-8-carboxamide negative allosteric modulators of metabotropic glutamate receptor subtype 5

Based on a hypothesis that an intramolecular hydrogen bond was present in our lead series of picolinamide mGlu₅ NAMs, we reasoned that an inactive nicotinamide series could be modified through introduction of a fused heterocyclic core to generate potent mGlu₅ NAMs. In this Letter, we describe the synthesis and evaluation of compounds that demonstrate the viability of that approach. Selected analogs were profiled in a variety of in vitro assays, and two compounds were evaluated in rat pharmacokinetic studies and a mouse model of obsessive-compulsive disorder. Ancillary pharmacology screening revealed that members of this series exhibited moderate inhibition of the dopamine transporter (DAT), and SAR was developed that expanded the selectivity for mGlu₅ versus DAT.     

High-valent [MnFe] and [FeFe] cofactors in ribonucleotide reductases

Ribonucleotide reductases (RNRs) are essential for DNA synthesis in most organisms. In class-Ic RNR from Chlamydia trachomatis (Ct), a MnFe cofactor in subunit R2 forms the site required for enzyme activity, instead of an FeFe cofactor plus a redox-active tyrosine in class-Ia RNRs, for example in mouse (Mus musculus, Mm). For R2 proteins from Ct and Mm, either grown in the presence of, or reconstituted with Mn and Fe ions, structural and electronic properties of higher valence MnFe and FeFe sites were determined by X-ray absorption spectroscopy and complementary techniques, in combination with bond-valence-sum and density functional theory calculations. At least ten different cofactor species could be tentatively distinguished. In Ct R2, two different Mn(IV)Fe(III) site configurations were assigned either L(4)Mn(IV)(μO)(2)Fe(III)L(4) (metal-metal distance of ~2.75?, L = ligand) prevailing in metal-grown R2, or L(4)Mn(IV)(μO)(μOH)Fe(III)L(4) (~2.90?) dominating in metal-reconstituted R2. Specific spectroscopic features were attributed to an Fe(IV)Fe(III) site (~2.55?) with a L(4)Fe(IV)(μO)(2)Fe(III)L(3) core structure. Several Mn,Fe(III)Fe(III) (~2.9-3.1?) and Mn,Fe(III)Fe(II) species (~3.3-3.4?) likely showed 5-coordinated Mn(III) or Fe(III). Rapid X-ray photoreduction of iron and shorter metal-metal distances in the high-valent states suggested radiation-induced modifications in most crystal structures of R2. The actual configuration of the MnFe and FeFe cofactors seems to depend on assembly sequences, bound metal type, valence state, and previous catalytic activity involving subunit R1. In Ct R2, the protonation of a bridging oxide in the Mn(IV)(μO)(μOH)Fe(III) core may be important for preventing premature site reduction and initiation of the radical chemistry in R1.     

A structural assessment of the apo[a] protein of human lipoprotein[a].

Apolipoprotein[a], the highly glycosylated, hydrophilic apoprotein of lipoprotein[a] (Lp[a]), is generally considered to be a multimeric homologue of plasminogen, and to exhibit atherogenic/thrombogenic properties. The cDNA-inferred amino acid sequence of apo[a] indicates that apo[a], like plasminogen and some zymogens, is composed of a kringle domain and a serine protease domain. To gain insight into possible positive functions of Lp[a], we have examined the apo[a] primary structure by comparing its sequence with those of other proteins involved in coagulation and fibrinolysis, and its secondary structure by using a combination of structure prediction algorithms. The kringle domain encompasses 11 distinct types of repeating units, 9 of which contain 114 residues. These units, called kringles, are similar but not identical to each other or to PGK4. Each apo[a] kringle type was compared with kringles which have been shown to bind lysine and fibrin, and with bovine prothrombin kringle 1. Apo[a] kringles are linked by serine/threonine- and proline-rich stretches similar to regions in immunoglobulins, adhesion molecules, glycoprotein Ib-alpha subunit, and kininogen. In comparing the protease domains of apo[a] and plasmin, apo[a] contains a region between positions 4470 and 4492 where 8 substitutions, 9 deletions, and 1 insertion are apparent. Our analysis suggests that apo[a] kringle-type 10 has a high probability of binding to lysine in the same way as PGK4. In the only human apo[a] polymorph sequenced to date, position 4308 is occupied by serine, whereas the homologous position in plasmin is occupied by arginine and is an important site for proteolytic cleavage and activation. An alternative site for the proteolytic activation of human apo[a] is proposed.     

CD Spectral Comparisons of the Acid-Induced Structures of Poly[d(A)]Poly[r(A)], Poly[d(C)], and Poly[r(C)]

Abstract

CD spectra were used to compare the acid-induced structural transitions of poly[d(A)] and poly[d(C)] with those of poly[r(A)] and poly[r(C)], respectively. The types of base pairing were probably the same in the acid self-complexes of both A-containing polymers and in the acid self-complexes of both C-containing polymers. Similar base pairings were indicated by similarities in the difference CD spectra showing the changes during the first major acid- induced transitions of the polymers. Information from the CD spectra and pK_a values of the transitions suggested that the transitions for the RNA polymers involved similar structural changes. The two DNA polymers were markedly different. Single-stranded poly [d(A)] was in the most stacked structure and had the lowest pK^a for forming an acid self-complex. Single-stranded poly[d(C)] was in the least stacked structure and had the highest pK_a for forming a protonated duplex.     

Discrepancy in stoichiometry of steady-state muscle [Pi] and [PCr] induced by exercise

Phosphorus nuclear magnetic resonance was used to quantify the relations between metabolic phosphates, intracellular pH, and work rate in forearm muscle of six adult men over a range of work rates from 1.0 to 3.5 W. Three work rates were studied in each of four sessions (either 1.0, 2.0, and 3.0 or 1.5, 2.5, and 3.5 W), with measurements made before and during each bout, thereby permitting the partition of the variance attributable to rest, work-dependent, and time-dependent metabolic functions by regression analysis. There were no time-dependent changes in either [ATP] or intracellular [H+] as assessed during the rest intervals between bouts of exercise. In contrast, the total nuclear magnetic resonance (NMR)-visible phosphorus pool (TVPP) decreased with time, with both phosphocreatine (PCr) and inorganic phosphate (Pi) contributing significantly to TVPP reduction. Muscle [ATP] was unchanged by work at all intensities. Intracellular [H+] increased moderately and proportionately to work rate. [PCr] decreased and [Pi] increased in proportion to work rate, with the work-dependent coefficient for PCr consumption approximately 1.5 times that of Pi production. Neither Pi line width nor motion artifact accounted for the decrease in TVPP, so the reduced Pi accumulation in exercise may represent its sequestering in some NMR-invisible muscle pool and/or loss to the blood. Whatever the process involved, it is proportional to work rate and persists for at least 10-15 min after exercise.     

Synthesis and anti-HIV activity of [d4U]-[trovirdine analogue] and [d4T]-[trovirdine analogue] heterodimers as inhibitors of HIV-1 reverse transcriptase

A series of eleven heterodimers containing both a nucleoside analogue (d4U, d4T) and a non-nucleoside type inhibitor (Trovirdine analogue) were synthesized and evaluated for their ability to inhibit HIV replication. Unfortunately, the (N-3)d4U-Trovirdine conjugates (9a-e) and (N-3)d4T-Trovirdine conjugates (10a-f) were found to be inactive suggesting that the two individual inhibitor compounds do not bind simultaneously in their respective sites.     

Solid-phase synthesis of [AsnA16]-, [AsnA22]-, [GlnA25]-, and [AsnA26]monellin, analogues of the sweet protein monellin.

In an attempt to delineate the binding site(s) of monellin to the receptor by means of a structure-taste relationship, we synthesized four monellin analogues, [AsnA16]-, [AsnA22]-, [GlnA25]-, and [AsnA26]-monellin, which were 7500, 750, 2500, and 5500 times as sweet as sucrose on a weight basis, respectively. Among them, [AsnA22]monellin and [GlnA25]monellin were less sweet than monellin, and were susceptible to the HPLC conditions used. It can be concluded that Asp16, Asp22, Glu25, and Asp26 residues of the A chain did not participate in binding with the receptor, since the sweet taste was not removed by replacing the amino acid residues with Asn or Gln. It can also be concluded that Asp22 and Glu25 of the A chain may have participated in intramolecular binding, as was pointed out by Kim et al., since exchanging Asp22 and Glu25 of the A chain with Asn and Gln significantly decreased the stability in solution.     

Two-dimensional NMR studies of [Pro-10] atrial natriuretic factor [7-23

The conformational properties of an analog of atrial naturiuretic factor, [Pro-10] ANF(7-23), were examined in H₂O, H₂O/DMSO-d₆ (2/1), and DMSO-d₆ using two-dimensional nmr techniques. The sequence differs from the native peptide by the absence of the exocyclic N- and C-terminal residues, and the substitution of a proline for a glycine at position 10—a modification expected to reduce the conformational flexibility of this analog. The backbone proton nmr resonances were assigned from two-dimensional correlated spectroscopy (2D-COSY), relayed COSY, and 2D nuclear Overhàuser enhancement (NOE) experiments, and the solution conformation was evaluated from vicinal spin–spin coupling constants and NOE data. Despite the substitution of a proline in the sequence, [Pro-10] ANF(7-23) exhibits a considerable amount of flexibility in all of the solvents employed.     

Psi compaction of poly[d(AT)].poly[d(AT)]

The compaction of poly[d(A–T)] · poly[d(A–T)] by Co(III) is accompanied by the formation of ψ(+)- and ψ(-)-structures. The chirality of the ψ-structure depends on the Co(III) concentration, ionic strength, temperature, pH, and the chain length of the polymer. The two forms can be readily interconverted by manipulating these factors. Phase diagrams have been constructed that demonstrate the regions of stability of the enantiomers as a function of two variables, while other factors are held constant. At critical points in the phase diagram the two forms are in such unstable equilibrium that mechanical motion will cause ψ(+) ? ψ(-) interconversion. The formation of both ψ(+)- and ψ(-)-structures by the action of Co(III) on poly[d(A–T)] · poly[d(A–T)] contrasts markedly with the behavior of poly[d(G–C)] · poly[d(G–C)] in similar circumstances by forming only the ψ(+)-structure and that of native DNA to produce no ψ at all. Thus the base sequence is important in determining the structure of chirally associated DNA molecules.     

Highly cytotoxic benzo[c]pyrido[2,3,4-kl]acridines

Several benzo[c]pyrido[2,3,4-kl]acridines bearing different substituents on the A and E rings were synthesized and evaluated for their capacity to bind to DNA and to inhibit DNA topoisomerases. Potent cytotoxic compounds were discovered but no strict correlation with their DNA binding affinity and effects on topoisomerases were observed. DNA is one but not the unique target of these compounds.     

Base tilt of poly[d(A)]-poly[d(T)] and poly[d(AT)]-poly[d(AT)] in solution determined by linear dichroism

We have measured the CD, isotropic absorption, and LD of poly[d(A)]–poly[d(T)] and poly[d(AT)]–poly[d(AT)] in the vacuum-uv spectral region. The reduced dichroism (LD divided by isotropic absorption) varied as a function of wavelength and was independent of shear gradient. Thus, the bases are not perpendicular to the helix axis in solution. Since the directions of the transition dipoles are known, the orientations of the bases in the polymers can be calculated from the reduced dichroism spectra. The results show that the base normals are tilted at angles greater than 25°, with respect to the helix axis, and thymine is tilted more than adenine for both polymers. The tilt axes of adenine and thymine are not parallel, indicating a large propeller twist. Space-filling models of poly[d(A)]–poly[d(T)] and poly[(AT)]–poly[d(AT)] are built based on our results, and the conformations of the two (A + T) polymers in solution are discussed.     

Base tilt of B-form poly[d(G)]-poly[d(C)] and the B- and Z-conformations of poly[d(GC)]-poly[d(GC)] in solution

We have measured the CD, isotropic absorption, and linear dichroism (LD) in the vacuum-uv spectral region for the B-conformations of poly[d(G)]-poly[d(C)] and poly[d(GC)]-poly[d(GC)], and for the Z-conformation of poly[d(GC)]-poly[d(GC)] formed in 70% trifluoroethanol. The reduced dichroism (LD divided by isotropic absorption) for all conformations varied with wavelength, indicating that the bases are not perpendicular to the helix axis. Since the directions of the transition dipoles are known, the inclinations and axes of inclination of each base can be determined from the wavelength dependence of the reduced dichroism spectra. The results indicate that the base normals of the (G + C) polymers in the B- and Z-conformations are tilted at angles greater than 19° with respect to the helix axis. The guanine and cytosine bases have different inclinations, and the tilt axes are not parallel. Therefore, the bases for all the (G + C) polymer conformations studied are buckled and propeller twisted.     

Theoretical study on the structure and stability of [1,2,5] oxadiazolo [3,4-e] [1,2,3,4]-tetrazine-4,6-Di-N-dioxide (FTDO)

In protein–ligand docking, an optimization algorithm is used to find the best binding pose of a ligand against a protein target. This algorithm plays a vital role in determining the docking accuracy. To evaluate the relative performance of different optimization algorithms and provide guidance for real applications, we performed a comparative study on six efficient optimization algorithms, containing two evolutionary algorithm (EA)-based optimizers (LGA, DockDE) and four particle swarm optimization (PSO)-based optimizers (SODock, varCPSO, varCPSO-ls, FIPSDock), which were implemented into the protein–ligand docking program AutoDock. We unified the objective functions by applying the same scoring function, and built a new fitness accuracy as the evaluation criterion that incorporates optimization accuracy, robustness, and efficiency. The varCPSO and varCPSO-ls algorithms show high efficiency with fast convergence speed. However, their accuracy is not optimal, as they cannot reach very low energies. SODock has the highest accuracy and robustness. In addition, SODock shows good performance in efficiency when optimizing drug-like ligands with less than ten rotatable bonds. FIPSDock shows excellent robustness and is close to SODock in accuracy and efficiency. In general, the four PSO-based algorithms show superior performance than the two EA-based algorithms, especially for highly flexible ligands. Our method can be regarded as a reference for the validation of new optimization algorithms in protein–ligand docking.