A refined three-dimensional solution structure of a carboxy terminal fragment of apolipoprotein CII

The three-dimensional structure of a synthetic fragment of human apolipoprotein CII (apo-CII) in 35%, 1,1,1,3,3,3-hexafluoro-2-propanol (HFP) has been determined on the basis of distance and intensity constraints derived from two-dimensional proton nuclear magnetic resonance measurements. The NOE crosspeak build-up rates were converted to distance constraints which were used in the distance geometry program DIANA. A set of one hundred structures were generated and of these ten structures were used in molecular dynamics simulations using the program XPLOR. This program enabled a direct minimization between the difference of the two-dimensional NOE intensities and those calculated from the full relaxation matrix. In this way spin diffusion is fully taken into account, which can be seen from the considerable improvement of the R-factor after the relaxation matrix refinement. These calculations show that this fragment, which corresponds to the carboxy terminal 30 amino acids of intact apo-CII and which retains its ability to activate lipoprotein lipase, is essentially flexible, but has three defined secondary structural elements. The most significant one is an -helix between residues 67 and 74. The following three residues adopt a turn-like structure. Another turn of -helix is seen between residues 56 and 59. The effect of the solvent system on the secondary structure was studied by circular dichroism spectroscopy. The results show that the mixed aqueous 35% HFP solvent induces secondary structure of a very similar nature to the one induced by sodium dodecyl sulphate.Abbreviations Apo-CII Apolipoprotein CII - CD Circular Dichroism - DOPC 1,2-dioleoyl-sn-glycero-3-phosphocholine - DOPG 1,2-dioleoyl-sn-glycero-3-phosphoglycerol - HAc Acetic Acid - HFP 1,1,1,3,3,3-hexafluoro-2-propanol - ISPA Isolated Spin Pair Approximation - NMR Nuclear Magnetic Resonance - NOE Nuclear Overhauser Enhancement - NOESY Nuclear Overhauser Enhancement Spectroscopy - RMSD Root Mean Square Deviation - SDS Sodium Dodecyl Sulfate     

Nuclear magnetic resonance of E. coli ribosomes and viruses.

¹H Nuclear Magnetic Resonance spectra of a number of viruses and E. Coli ribosomes revealed that experimental values of the linewidth (πT₂)^?1 (< 320 Hz) and T₁ (< 1 sec) of the observable nuclei are too small to be accounted for by the system's molecular weight. The nuclei therefore must be internally mobile. From ¹³C Nuclear Magnetic Resonance spectra of 12% ¹³C enriched E. Coli ribosomes, it follows that 30% of the 5000 $\text{CH}{}_2\text{CH}{}_3$ groups, 10–20% of the 225 Phe residues, 20% of the δ-Arg and β-Lys carbons, ～ 100 nucleotides and a number of C_α carbons are internally mobile. It is demonstrated that ¹³C Nuclear Magnetic Resonance can fruitfully be applied to intact ribosomes.     

High resolution nuclear magnetic resonance studies of nigeran

Polymer motion in solution can be studied by ¹³CNMR relaxation methods, which provide information about the correlation time for C-H vectors. ¹³C-Relaxation and Nuclear Overhauser Enhancement (NOE) data may frequently be combined to determine the dipole-dipole relaxation contribution. An alternative method is proposed based on a comparison of the proton spin-lattice relaxation rates of the centre proton resonances of an unlabelled molecule with the relaxation rates of the ¹³C satellites (from ¹³C labelled molecules).Selectively labelled nigeran which is an alternating $\text{1 → 3 and 1 → 4 α-}\text{d}\text{-glucan}$ has been investigated. The discussion in terms of the occurrence of different motions for each of the two units of the polymer requires an unambiguous assignment of the two anomeric carbons. For this reason a detailed assignment of the ¹H and ¹³C Nuclear Magnetic Resonance (NMR) spectra of nigeran in dimethylsulphoxide-d₆ is described, based on T₁ and NOE measurements in addition to selective homonuclear and heteronuclear spin decoupling experiments. These values are correlated with a conformation estimated by HSEA hard-spheres calculation. The measurements of the relaxation parameters for labelled and unlabelled compounds which provide an alternative determination of the ¹³C-¹H dipole-dipole relaxation contribution in a macromolecule agree well with ¹³C-{¹H} NOE experiments.     

Biosynthesis of pseudoisoeugenol-derivatives in liquid tissue cultures ofPimpinella anisum

The genusPimpinella contains rare phenylpropanoids. The 1-(E)-propenyl-2-hydroxy-5-methoxy benzene skeleton of these compounds is called pseudoisoeugenol. To study the biosynthesis of these compounds, we set up a tissue culture ofPimpinella anisum (PAD) that selectively promoted the production of epoxy-pseudoisoeugenol-(2-methylbutyrate), termed EPB. This compound served as the final molecule of the biosynthetic pathway in all labelling experiments conducted.The putative precursors were labelled with¹³C or¹⁴C. The incorporation of the label was followed by¹³C-NMR-spectroscopy and liquid scintillation, respectively. Based on our labelling experiments as well as on enzymic reactions in a cell homogenate we proposed a genaral biosynthetic pathway for EPB. The biosynthetic sequence found wasl-phenylalanine, trans-cinnamic acid, p-coumaric acid, p-coumaric aldehyde, p-coumaric alcohol, anol and trans-anethol. The biosynthetic step leading from trans-anethol to pseudo-isoeugenol involves migration of the side chain during the introduction of the second OH-group in the molecule (NIH-shift). The final biosynthetic steps to form EPB must be acylation and epoxidation of the propenyl double bond of pseudoisoeugenol.Abbreviations NMR Nuclear Magnetic Resonance - NOE Nuclear Overhauser Effect     

Flavonoids in the blue flowers of Parochetus communis Buch.-Ham. ex D. Don (Leguminosae)

A rare anthocyanin, malvidin 3-O-rhamnoside, was isolated from the blue flowers of Parochetus communis Buch.-Ham. ex D. Don along with two known flavonols: kaempferol 3-O-(2-O-glucosyl-6-O-rhamnosyl)-glucoside and kaempferol 3-O-(2,6-di-O-rhamnosyl)-glucoside. These structures were identified using Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS).     

The dependence of the cytoplasmic pH in aerobic and anaerobic cells of the green algae Chlorella fusca and Chlorella vulgaris on the pH of the medium as determined by 31P in vivo NMR spectroscopy

The pH in the cytoplasm of aerobic and anaerobic cells of the green algae Chlorella fusca and Chlorella vulgaris was determined in dependence on the pH of the external medium, which was varied between pH 3 and pH 10. In aerobic cells of both species the cytoplasmic pH is maintained at a value above 7.2 even at an external pH of 3 and below 7.8 at an external pH of 10. In anaerobic cells the cytoplasmic pH shows linear dependence on external pH in the range of pH 6 to 9 (cytoplasmic pH 6.9 to 7.2), while below an external pH of 6 cytoplasmic pH is maintained at about 6.5.Abbreviations CCCP Carbonylcyanide-m-chlorophenyl-hydrazone - EDTA Ethylendiaminetetraacetic acid - MES 2-(N-Morpholino)-ethanesulfonic acid - MOPSO 3-(N-Morpholino)-2-hydroxy-propanesulfonic acid - NMR Nuclear Magnetic Resonance - pH cyt cytoplasmic pH - pH ex external pH - PIPES Piperazine-N,N-bis(2-ethanesulfonic acid) - PP_i Pyrophosphate - PP₁, PP₂, PP₃ 1st, 2nd, 3rd phosphate group of polyphosphates - PP₄ core phosphate groups of polyphosphates - TRIS Tris-hydroxymethyl-aminomethane     

Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: Application to the lac repressor headpiece

Summary A novel procedure is presented for the automatic identification of secondary structures in proteins from their corresponding NOE data. The method uses a branch of mathematics known as graph theory to identify prescribed NOE connectivity patterns characteristic of the regular secondary structures. Resonance assignment is achieved by connecting these patterns of secondary structure together, thereby matching the connected spin systems to specific segments of the protein sequence. The method known as SERENDIPITY refers to a set of routines developed in a modular fashion, where each program has one or several well-defined tasks. NOE templates for several secondary structure motifs have been developed and the method has been successfully applied to data obtained from NOESY-type spectra. The present report describes the application of the SERENDIPITY protocol to a 3D NOESY-HMQC spectrum of the ¹⁵N-labelled lac repressor headpiece protein. The application demonstrates that, under favourable conditions, fully automated identification of secondary structures and semi-automated assignment are feasible.Abbreviations 2D, 3D two-, three-dimensional - NOESY nuclear Overhauser enhancement spectroscopy - HMQC heteronuclear multiple quantum coherence - SSE secondary structure element - SERENDIPITY SEcondary structuRE ideNtification in multiDImensional ProteIn specTra analYsis Supplementary Material available from the authors: Two tables containing the total number of mappings resulting from the graph search procedure for simulated and experimental NOE data.     

Isolation and Structural Determination of the Antifouling Diketopiperazines from Marine-Derived Streptomyces praecox 291-11

Marine derived actinomycetes constituting 185 strains were screened for their antifouling activity against the marine seaweed, Ulva pertusa, and fouling diatom, Navicula annexa. Strain 291-11 isolated from the seaweed, Undaria pinnatifida, rhizosphere showed the highest antifouling activity and was identified as Streptomyces praecox based on a 16S rDNA sequence analysis. Strain 291-11 was therefore named S. praecox 291-11. The antifouling compounds from S. praecox 291-11 were isolated, and their structures were analyzed. The chemical constituents representing the antifouling activity were identified as (6S,3S)-6-benzyl-3-methyl-2,5-diketopiperazine (bmDKP) and (6S,3S)-6-isobutyl-3-methyl-2,5-diketopiperazine (imDKP) by interpreting the nuclear magnetic resonance and high-resolution mass spectroscopy data. Approximately 4.8 mg of bmDKP and 3.1 mg of imDKP were isolated from 1.2 g of the S. praecox 291-11 crude extract. Eight different compositions of culture media were investigated for culture, the TBFeC medium being best for bmDKP and TCGC being the optimum for imDKP production. Two compounds respectively showed a 17.7 and 21 therapeutic ratio (LC₅₀/EC₅₀) to inhibit zoospores, and two compounds respectively showed a 263 and 120.2 therapeutic ratio to inhibit diatoms.     

Three-dimensional structures of the central regulatory proteins of the bacterial phosphotransferase system,HPr and enzyme IIAglc

Enzyme IIA and HPr are central regulatory proteins of the bacterial phosphoenolpyruvate:sugar phosphotransferase (PTS) system. Three-dimensional structures of the glucose enzyme IIA domain (IIA^glc) and HPr of Bacillus subtilis and Escherichia coli have been studied by both X-ray crystallography and Nuclear Magnetic Resonance (NMR) Spectroscopy. Phosphorylation of HPr of B. subtilis and IIA^glc of E. coli have also been characterized by NMR spectroscopy. In addition, the binding interfaces of B. subtilis HPr and IIA^glc have been identified from backbone chemical shift changes. This paper reviews these recent advances in the understanding of the three-dimensional structures of HPr and IIA^glc and their interaction with each other. © 1993 Wiley-Liss, Inc.     

Some processes of energy saving and expenditure occurring during ethanol perfusion in the isolated liver of fed rats; a Nuclear Magnetic Resonance study.

Background  

In the isolated liver of fed rats, a 10 mM ethanol perfusion rapidly induced a rapid 25% decrease in the total ATP content, the new steady state resulting from both synthesis and consumption. The in situ rate of mitochondrial ATP synthesis without activation of the respiration was increased by 27%, implying an increased energy demand. An attempt to identify the ethanol-induced ATP-consuming pathways was performed using ³¹P and ¹³C Nuclear Magnetic Resonance.     

A computer-based protocol for semiautomated assignments and 3D structure determination of proteins

Summary A strategy is presented for the semiautomated assignment and 3D structure determination of proteins from heteronuclear multidimensional Nuclear Magnetic Resonance (NMR) data. This approach involves the computer-based assignment of the NMR signals, identification of distance restraints from nuclear Overhauser effects, and generation of 3D structures by using the NMR-derived restraints. The protocol is described in detail and illustrated on a resonance assignment and structure determination of the FK506 binding protein (FKBP, 107 amino acids) complexed to the immunosuppressant, ascomycin. The 3D structures produced from this automated protocol attained backbone and heavy atom rmsd of 1.17 and 1.69 Å, respectively. Although more highly resolved structures of the complex have been obtained by standard interpretation of NMR data (Meadows et al. (1993) Biochemistry, 32, 754–765), the structures generated with this automated protocol required minimal manual intervention during the spectral assignment and 3D structure calculations stages. Thus, the protocol may yield an approximate order of magnitude reduction in the time required for the generation of 3D structures of proteins from NMR data.     

The Three-Dimensional NMR Solution Structure of α-Cobratoxin at pH 7.5 and Conformational Differences With the NMR Solution Structure at pH 3.2

Abstract The 3D solution structure of α-cobratoxin, a neurotoxin purified from the Naja naja siamensis snake venom, has been determined by Nuclear Magnetic Resonance spectroscopy, in conjunction with distance geometry and restrained molecular dynamics, at pH 7.5. A total of 490 distance restraints were obtained from NOE intensities and 25 φ dihedral angle restraints deduced from J- coupling data. The generated structures are well defined with root mean square deviations from a geometrical mean structure of 0.107 ± 0.036 nm for the backbone atoms and 0.128 ±0.073 nm for the side-chain atoms (considering residues 1 to 66 minus 26 to 35). A comparison between the generated structures at pH 7.5 and the mean NMR solution structure at pH 3.2 revealed that the 3D structure of α-cobratoxin is more compact at neutral pH. This major difference is mainly due to the pH-dependant conformational variations of three residues His(18), Thr(44) and Thr(59).     

Peptidomimetic 2-cyanopyrrolidines as potent selective cathepsin L inhibitors

Cathepsins have been found to have important physiological roles. The implication of cathepsin L in various types of cancers is well established. In a search for selective cathepsin L inhibitors as anticancer agents, a series of 2-cyanoprrolidine peptidomimetics, carrying a nitrile group as warhead, were designed. Two series of compounds, one with a benzyl moiety and a second with an isobutyl moiety at P₂ position of the enzyme were synthesized. The synthesized compounds were evaluated for inhibitory activity against human cathepsin L and cathepsin B. Although, none of the compounds showed promising inhibitory activity, (E)N-{(S)1-[(S)2-cyano-1-pyrrolidinecarbonyl]-3-methylbutyl}-2,3-diphenylacrylamide (24) with an isobutyl moiety at P₂ was found to show selectivity as a cathepsin L inhibitor (Ki 5.3 μM for cathepsin L and Ki > 100 μM for cathepsin B). This compound could act as a new lead for the further development of improved inhibitors within this inhibitor type.     

Polyphosphate glucokinase and ATP glucokinase activities in Mycococcus coralloides D

Polyphosphate glucokinase and ATP glucokinase were detected in cell-free extracts of Myxococcus coralloides strain D, but pyrophosphate glucokinase was not detected. Both glucokinase activities were separated by chromatography. The approximate molecular weight is 61 000 for polyphosphate glucokinase and 47 000 for ATP glucokinase. Substrate specificity and pH optimum was studied in the polyphosphate glucokinase. Polyphosphate and ATP glucokinase activities were verified by ¹³C Nuclear Magnetic Resonance.     

Triterpenoids from Euphorbia fischeriana

Nineteen triterpenoids including two new tirucallane ones, fisuphanins A and B, were isolated from the whole plant of Euphorbia fischeriana Steud. The new structures were elucidated on the basis of extensive spectroscopy techniques including infrared (IR), High Resolution Mass Spectrometry (HRMS), and Nuclear Magnetic Resonance (NMR). Some triterpenoids were evaluated for their cytotoxicity against A549 and MCF-7 cell lines.     

Identification of HN-methyl NOEs in large proteins using simultaneous amide-methyl TROSY-based detection

A pair of HN-methyl NOESY experiments that are based on simultaneous TROSY-type detection of amide and methyl groups is described. The preservation of cross-peak symmetry in the simultaneous ¹H–¹⁵N/¹³CH₃ NOE spectra enables straightforward assignments of HN-methyl NOE cross-peaks in large and complex protein structures. The pulse schemes are designed to preserve the slowly decaying components of both ¹H–¹⁵N and methyl ¹³CH₃ spin-systems in the course of indirect evolution (t ₂) and acquisition period (t ₃) of 3D NOESY experiments. The methodology has been tested on {U-[¹⁵N,²H]; Ileδ1-[¹³CH₃]; Leu,Val-[¹³CH₃,¹²CD₃]}-labeled 82-kDa enzyme Malate Synthase G (MSG). A straightforward procedure that utilizes the symmetry of NOE cross-peaks in the time-shared 3D NOE data sets allows unambiguous assignments of more than 300 HN-methyl interactions in MSG from a single 3D data set providing important structural restraints for derivation of the backbone global fold.     

Structural variation in the glycoinositolphospholipids of different strains ofTrypanosoma cruzi

The structures of the glycoinositolphospholipids (GIPLs) from five strains of the protozoan parasiteTrypanosoma cruzi have been determined. Two series of structures were identified, all but one containing the same Man₄(AEP)GlcN-Ins-PO₄ core. Series 1 oligosaccharides are substituted at the third mannose distal to inositol (Man 3) by ethanolamine-phosphate or 2-aminoethylphosphonic acid, as are some glycosyl-phosphatidylinositol-protein anchors ofT. cruzi. The core can be further substituted by terminal (1–3)-linked -galactofuranose units. In contrast, Series 2 oligosaccharides do not have additional phosphorus-containing groups attached to Man 3, the latter being substituted instead by a single side chain unit of -galactofuranose. Series 1 oligosaccharides are present in all strains (G, G-645, Tulahuen CL, and Y) whereas Series 2 structures are present mainly in CL and Y strains. The lipid moiety in the GIPLs from the G, G-645 and Tulahuen strains is predominantly ceramide, as reported for the Y strain, whilst that from the CL strain is a mixture of ceramide and alkylacylglycerol species. The lipid moiety of the GIPLs, and probably also the phosphoinositol-oligosaccharide structures may play an important immunomodulatory role in infection byT. cruzi.Abbreviations GIPL glycoinositolphospholipid - LPPG lipopeptidophosphoglycan - GPI glycosylphosphatidylinositol - AEP 2-aminoethylphosphonic acid - PI phosphoinositol - GC gas-liquid chromatography - MS mass spectrometry - FAB fast atom bombardment - NMR nuclear magnetic resonance - DQF-COSY double quantum-filtered correlation spectroscopy - TOCSY total correlation spectroscopy - ROESY rotating frame nuclear Overhauser enhancement spectroscopy - EtNP ethanolaminephosphate - HMQC heteronuclear multiple quantum coherence - Man mannose - Galf galactofuranose - GlcN glucosamine - Ins inositol - InsP inositolphosphate - Man 3 third mannose distal to inositol - NOE nuclear Overhauser effect - [M+H]⁺ protonated molecule - [M–H]^– deprotonated molecule - RMM relative molecular mass (monoisotopic)     

Methyl ethers of prostaglandins F2α and I2

Regiospecific monomethyl prostaglandin F₂α ethers (at 0–9, 0–11, and 0–15) have been prepared by total synthesis. The 9,15-bis-ether was also prepared. The 11- and 15-monoethers have been converted to the corresponding prostacyclins. Nuclear Magnetic Resonance (NMR) spectral comparisons indicate conformational changes associated with ether formation; nonetheless, the PGF₂α monoethers all retain significant biological activity: 3–420% of natural PGF₂α. The 9- and 15-methyl ethers show increased selectivity for luteolytic activity as measured in the hamster antifertility (HAF) assay. In contrast the prostacyclin ethers are essentially devoid of agonist activity on both the platelet and vasculature. Prostacyclin diastereomers [5a] also lack activity and it appears that any modification at or of the C-11 or C-15 functions reduces receptor binding by at least a factor of 100.     

1-Alkyl-3-amino-5-aryl-1H-[1,2,4]triazoles: novel synthesis via cyclization of N-Acyl-S-methylisothioureas with alkylhydrazines and their potent corticotropin-Releasing factor-1 (CRF1) receptor antagonist activities

Cyclizations of alkylhydrazines with N-acyl-S-methylisothioureas, readily synthesized from acyl chlorides, sodium thioisocyanate, dialkylamines then methyl iodide in a one-pot reaction, gave 1-alkyl-3-dialkylamino-5-phenyltriazoles 7 as major products. The regioisomers were assigned through the use of NOE NMR experiments. While bearing a N-bis(cyclopropyl)methyl-N-propylamino group, this series of compounds shows very good binding affinity on the human CRF₁ receptor. Among them, 1-methyl-3-[N-bis(cyclopropyl)methyl-N-propylamino]-5-(2,4-dichlorophenyl)-1H-[1,2,4]triazole 7a had the best binding affinity for the CRF₁ receptor (K_i=9 nM).     

Acrotrisomic analysis in linkage mapping in barley (Hordeum vulgare L.)

Summary Three acrotrisomic lines, Triplo IL^1S, 3L^3S, and 4L^4S, each carrying an extra acrocentric chromosome, were used for cytogenetic linkage mapping of barley chromosomes. The cytological structures of the acrocentric chromosome of the three acrotrisomic lines were studied with an improved Giemsa N-banding technique. The long (1L) and short arm (1S) of chromosome 1 had deficiencies of approximately 38% and 65%, respectively. The percentages of deficiencies were 0 and 77.8% for 3L and 3S, and 31.7 and 59.3% for 4L and 4S, respectively. All three genes tested (br, f _c , gs3) in 1S and all three genes tested, f8, n and 1k2 in 1L showed a disomic ratio indicating that they are located in the deficient segments. Two genes (a _c , yst2) located in the middle segment of 3S in linkage map showed a trisomic ratio, and two others a _n , x _s showed a disomic ratio. The only gene(f9) tested in 4L showed a trisomic ratio. Two genes (1g4, g1) located in the proximal segment of 4S in the linkage map showed a trisomic ratio, whereas two genes (br2, g13) located distally in 4S showed a disomic ratio, indicating that the breakage occurred between g1 and br2. This experiment demonstrates a new method for physical localization of genes on chromosome segments in material such as barley in which pachytene analysis can not be effectively used for accurate determination of break points in structural changes. Problems associated with this new technique are discussed.Contribution from the Department of Agronomy and published with the approval of the Director of Colorado State University Experiment Station as Scientific Series Paper No. 2823. Supported by USDA/SEA Competitive Research Grant Nos. 5901-0410-9-0334-0 and 82-CRCR-1-1020 and USDA-CSU Cooperative Research Grant 58-9AHZ-2-265