Bacteriorhodopsins containing modified chromophores: A study on the wild type and D96N mutant of Halobacterium salinarum

Modification of the chromophore in bacteriorhodopsin (BR) from ET1001 and D96N strains of Halobacterium salinarum (halobium) was carried out. Purple membranes were decolored by means of light-dependent hydroxylaminolysis. The all-trans -isomers of retinal and its 3,4-didehydro-, 4-keto-, and phenyl analogs were reconstituted into apomembranes. Absorption maxima of the homonymic pigments in both strains were similar. The kinetics of the M-intermediates in the mode of a single turnover of the photocycle induced by a short light flash (532 nm, 15 ns) was compared. For the investigated bacteriorhodopsin analogs the efficiency of the M-intermediate formation did not exhibit any reliable dependence on the point mutation. Both for ET1001 and for D96N strains the M-relaxation of the 4-ketoBR was distinctly biphasic, with the slow phase comprising about 10–15% of the signal amplitude. Replacement of the ionone ring by phenyl caused a weak deceleration of the M relaxation (～1.5-fold decrease in t _1/2). Independence of the photocycle deceleration of the point mutation and chromophore modification was shown for all BR analogs studied.     

The Use of Crown Ethers in Peptide Chemistry – V. Solid-phase Synthesis of Peptides by the Fragment Condensation Approach using Crown Ethers as Non-covalent Protecting Groups

We have previously described the conditions by which peptide synthesis by the solid-phase fragment condensation approach can be carried out using crown ethers as non-covalent protection for the N^α -amino group. Here we demonstrate that the procedure can be extended to large, partially protected peptide fragments possessing free Lys and/or Arg residues. The first step was to ensure that complex formation on the side chain of amino acids was not detrimental to the methodology and exhibited the same solubility and coupling properties as N^α -complexed peptides. Thus, a model hexapeptide was synthesized using Fmoc chemistry containing Lys and Arg residues, which, when complexed with 18-Crown-6, was readily soluble in DCM and coupled quantitatively to a resin-bound tetrapeptide. Two tripeptides were then prepared, one containing a free Ser residue, the other free Tyr, to examine the possible occurrence of side reactions. After coupling using standard conditions only the former tripeptide exhibited the formation of the O-acylation by-product (5%). Another model hexapeptide containing Lys, Tyr, Ser and Asp protected with a TFA-stable adamantyl group was complexed with 18-Crown-6 and coupled to the resin-bound tetrapeptide with near quantative yield. Extending the length of the peptide to 21 and 40 residues, which represent sequences Gly⁵² to Leu⁷² (21-mer) and Pro³³ to Leu⁷² (40-mer) from Rattus norvegicus chaperonin 10 protein, respectively, resulted in partially protected fragments that were readily soluble in water, thus enabling purification by RP-HPLC. Complexation with 18-Crown-6 gave two highly soluble products that coupled to resin-board tetramer with 68% and 50% coupling efficiencies for the 21-mer and 40-mer, respectively. Treatment with 1% DIEA solutions followed by acidolytic cleavage and purification of the major product confirmed that the correct product had been formed, when analysed by amino acid analysis and ESI-MS. These results served to extend the methodology of non-covalent protection of large partially protected peptide fragments for the stepwise fragment condensation of polypeptides.     

Synthesis and in vitro Biological Evaluation of Novel Thymidine Analogs Containing 1H-1,2,3-Triazolyl, 1H-Tetrazolyl,and 2H-Tetrazolyl Fragments

Abstract

3′-Azidothymidine (AZT) reacts with 1-propargyl-5-R-1H- and 2-propargyl-5-R-2H-tetrazoles (R?=?H, Me, CH₂COOEt, CH₂CON(CH₃)₂, Ph, 2-CH₃-C₆H₄, or 4-NO₂-C₆H₄) via the Cu(I)-catalyzed asymmetric [3?+?2] cycloaddition to give 3′-modified thymidine analogs incorporating 1H-1,2,3-triazolyl, 1H-, and 2H-tetrazolyl fragments in 41–76% yield. The structures of the obtained compounds have been elucidated by means of HRESI⁺-MS, ¹H and ¹³ Ostrovskii, V. A.; Popova, E. A.; Trifonov, R. E. Developments in Tetrazole Chemistry (2009–16). Advances in heterocyclic chemistry. 2017, 123, 2–62.[Web of Science ®] , [Google Scholar]C{¹H} NMR, and single crystal X-ray diffraction {for 3′-[4-(1H-5-N,N-dimethylaminocarbonylmethyltetrazol-1-yl)-1H-1,2,3-triazol-1-yl]thymidine 10d}. In vitro biological evaluation of the prepared compounds has been performed; they have exhibited low activity against phenotypic HIV-1_899A. Moderate anti-influenza activity against influenza virus A/Puerto Rico/8/34 (H1N1) strain has been observed in the cases of 3′-(4-(1H-tetrazol-1-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 10a (IC₅₀ 39.6?μg/mL), 3′-(4-(2H-5-ethoxycarbonyltetrazol-2-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 11c (IC₅₀ 31.6?μg/mL), and 3′-(4-(2H-5-(4-nitrophenyl)-tetrazol-2-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 11g (IC₅₀ 46.4?μg/mL). The tested compounds possess very low cytotoxicity towards MDCK and MT4 cells as well as tumor human cervical carcinoma HeLa and promyelocytic leukemia HL-60 cells.     

Synthesis of the Oligoribonucleotides Incorporating 8-Oxo-Guanosine and Evaluation of their Base Pairing Properties

6-O-7-N-Bis(diphenylcarbamoyl)-2-N-phenoxyacetyl-5′-O-dimethoxytrityl-2′-O-{[(triisopropyl- silyl)oxy]methyl}-8-oxoguanosine-3′-yl-β-cyanoethyl-N,N-diisopropylphosphoramidite (5) was synt- hesized as a new phosphoramidite precursor unit for the synthesis of RNA. Compound 5 was successfully incorporated into the middle of the RNA sequences, and the synthesized RNAs were identified by MALDI-TOF mass measurements. Their properties were evaluated for formation of the RNA duplex and RNA/DNA heteroduplex. ORNs 1 and 4 containing 8-oxo-G can form base pairs with rC or dC in an anti conformation, while it can also interact with rA or dA in a syn conformation in the RNA duplex or RNA/DNA heteroduplex. The described synthetic method is therefore a useful procedure for the synthesis of ORN containing 8-oxo-G and contributes to the study of 8-oxo-G in RNA.     

含有分裂型内含肽DnaE基因的表达盒设计、合成及高效表达载体的构建

目的:建立一种简便、快捷的基因从头设计、优化与合成策略,进行含有分裂型内含肽DnaE基因的表达盒全合成并构建高效表达载体。方法:以免费软件GeneDesign 3.0为主要平台,同时结合Tandem Repeats Finder、UNAFold等不同生物信息学软件,对含有DnaE基因、合适酶切位点的表达盒进行设计与分段合成;合成寡核苷酸片段通过重叠PCR进行组装与克隆。结果:利用建立的设计流程,合成了大小为44～64 nt的14段寡核苷酸片段,通过重叠PCR,实现了14段寡核苷酸片段的一次性组装,经过克隆、酶切鉴定、序列分析得到了序列完全正确的表达载体。结论:建立了一套有效的、基于免费软件的基因从头设计与合成的策略,构建了可以用于环肽小分子文库表达与筛选的表达载体。     

An Approach to Prebiotic Synthesis of α-Oligoribonucleotides and Description of Their Properties: Selective Advantage of β-RNA over α-RNA

Oligomerization of α-adenosine 5′-phosphorimidazolide (α-ImpA) has been done in an aqueous solution using a uranyl-ion catalyst or a poly(U) template as a model process of prebiotic synthesis of RNA with α-glycosidic linkage. α-Oligoriboadenylates up to hexamer were formed from α-ImpA by the uranyl-ion catalyst. 3′-5′ Linkage was mainly formed in the oligomerization. The poly(U) template mediated the oligomerization of α-ImpA, but to a very low extent. The yield and chain length of the resulting α-oligomers were far lower than those of the corresponding β-oligomer formation under the same conditions. Physico-chemical properties of α-oligoriboadenylates are presented along with those of the corresponding β-oligoriboadenylates. The results indicate that β-RNA is more advantageous than α-RNA from the points of their synthesis and properties. Received: 10 February 1997 / Accepted: 31 March 1997     

Mapping the Structure of an Integral Membrane Protein under Semi-Denaturing Conditions by Laser-Induced Oxidative Labeling and Mass Spectrometry

Little is known about the structural properties of semi-denatured membrane proteins. The current study employs laser-induced oxidative labeling of methionine side chains in combination with electrospray mass spectrometry and optical spectroscopy for gaining insights into the conformation of bacteriorhodopsin (BR) under partially denaturing conditions. The native protein shows extensive oxidation at M32, M68, and M163, which are located in solvent-accessible loops. In contrast, M20 (helix A), M56/60 (helix B), M118 (helix D), M145 (helix E), and M209 (helix G) are strongly protected, consistent with the known protein structure. Exposure of the protein to acidic conditions leads to a labeling pattern very similar to that of the native state. The absence of large-scale conformational changes at low pH is in agreement with recent crystallography data. Solubilization of BR in SDS induces loss of the retinal chromophore concomitant with collapse of the binding pocket, thereby precluding solvent access to the protein interior. Tryptophan fluorescence data confirm the presence of a large protein core that remains protected from water. However, oxidative labeling indicates partial unfolding of helices A and D in SDS. Irreversible thermal denaturation of the protein at 100 °C induces a labeling pattern quite similar to that seen upon SDS exposure. Labeling experiments on refolded bacterioopsin reveal a native-like structure, but with partial unfolding of helix D. Our data suggest that noncovalent contacts with the retinal chromophore in native BR play an important role for the stability of this particular helix. Overall, the present work illustrates the viability of using laser-induced oxidative labeling as a novel tool for characterizing structural changes of membrane proteins in response to alterations of their solvent environment.     

The Architects of the Evolutionary Synthesis in National Socialist Germany: Science and Politics

The Synthetic Theory of Evolution (SyntheticDarwinism) was forged between 1925 and 1950.Several historians of science have pointed outthat this synthesis was a joint venture ofSoviet, German, American and Britishbiologists: A fascinating example of scientificcooperation, considering the fact that theevolutionary synthesis emerged during thedecades in which these countries were engagedin fierce political, military and ideologicalconflicts. The ideological background of itsAnglo-American representatives has beenanalyzed in the literature. We have examinedthe scientific work and ideological commitmentsof the German Darwinians during the ThirdReich. We based our analysis on four criteria:1) General attitude towards the Third Reich. 2) Membership in the NSDAP and other nationalsocialist organizations. Endorsement anddisapproval of the state ideology in 3) scientific and 4) other publications. We willmainly discuss the various authors that havecontributed to Die Evolution derOrganismen (1943), a collection thatrepresented the evolutionary synthesis inGermany. Most of the authors promoted eugenicideas, but not all of them adopted the racistinterpretation of the Third Reich. Anotherfinding is that there existed no directconnection between party membership andpromotion of the state ideology.     

Cyclic AMP Modulates Differentially the Release of Dopamine Induced by Hypoxia and Other Stimuli and Increases Dopamine Synthesis in the Rabbit Carotid Body

We have investigated the effects of different treatments that increase cyclic AMP levels on the in vitro synthesis and release of catecholamines in the rabbit carotid body. We also measured the rate of 45Ca2+ efflux from previously loaded carotid bodies under different conditions. Forskolin produced a dose-dependent increase in the release of [3H]dopamine elicited by a hypoxic stimulus of medium intensity (PO2 = 33 mm Hg) without altering basal [3H]dopamine release (100% O2-equilibrated medium). At a concentration of 5 x 10(-6) M, forskolin increased the release of [3H]dopamine induced by hypoxic stimuli of different intensities; the increase was maximal (498%) at the lowest intensity of hypoxic stimuli (PO2 = 66 mm Hg), averaged 260% for hypoxic stimuli of intermediate intensity and 2 x 10(-4) M cyanide, and was 150% under anoxia. Dibutyryl cyclic AMP (2 mM) and 3-isobutyl-1-methylxanthine (0.5 mM) mimicked forskolin effects under hypoxic stimulation. Forskolin (5 x 10(-6) M) also increased (180%) the release of [3H]dopamine induced by 20% CO2/pH 6.6, 2.5 x 10(-4) M dinitrophenol, and 3 x 10(-5) M ionomycin. Forskolin and 3-isobutyl-1-methylxanthine were without effect on the release of [3H]dopamine elicited by 30 mM extracellular K+. Forskolin (5 x 10(-6) M) augmented significantly the rate of 45Ca2+ efflux induced by hypoxic stimuli (PO2 of 33 and 66 mm Hg) and 2 x 10(-4) M cyanide and showed a tendency to increase (20%) the 45Ca2+ efflux induced by dinitrophenol and low pH and to decrease (21%) the efflux induced by 30 mM K+ without altering the rate of efflux under basal conditions.(ABSTRACT TRUNCATED AT 250 WORDS)