Resolution of the 1H-1H NOE spectrum of RNA into three dimensions using 15N-1H two-bond couplings

The feasibility of using two-bond ¹⁵N-¹H couplings to resolve the ¹H-¹H nuclear Overhauser effect spectrum of RNA into a third dimension was investigated, using the 36-nucleotide gene 32 messenger RNA pseudoknot of bacteriophage T2 as an example. The two-bond ¹⁵N-¹H couplings present in adenosine and guanosine were found to be suitable for generating a three-dimensional ¹H-¹H-¹⁵N NOESY-HSQC spectrum with reasonably good sensitivity, as well as favorable chemical shift dispersion in the nitrogen dimension. The described NMR experiment provides a tool that can be used to complement other heteronuclear methods in the analysis of RNA structure.     

d(TTTCCTCGCCGGAAA)的一维NMR氢谱分析

单链d(TTTCCTCGCCGGAAA)易溶于水,且由于其本身存在序列特异性,即可形成分子内“发夹”结构,本实验分别测得其在全重水(D2O)、92?O 8%H2O溶液中的一维1H谱,认为环出区域碱基质子的共振峰与其他同种质子的共振峰有明显的区别,主要表现在其共振峰会明显移向高场区。     

Modeling the dynamics of the solvated SL1 domain of HIV-1 genomic RNA

A mode-coupling solution of the Smoluchowski diffusion equation (MCD theory), designed to describe the dynamics of wobbling macromolecules in water, is applied to a macromolecular bead model including water beads in the nearest layers. The necessary statistical averages are evaluated by time averaging along a molecular dynamics (MD) trajectory where both solute and water are introduced as atomistic models. The cross peaks in (1)H nuclear Overhauser effect spectroscopy (NOESY) NMR spectra that are routinely measured to determine biological structures are here calculated for the mutated 23 nucleotides stem-loop fragment of the SL1 domain in the HIV-1(Lai) genomic RNA. The calculations are in acceptable agreement with experiments without requiring any screening of the hydrodynamic interactions. The screening of hydrodynamics was necessary in previous MCD calculations obtained by using the same full atomistic MD trajectory, but a nonsolvated frictional model.     

1H, 15N, and 13C Chemical shift assignments of the navel orange worm pheromone-binding protein-1 (Atra-PBP1)

A pheromone-binding protein from navel orange worm, Amyelois transitella (Atra-PBP1) binds to non-polar pheromone molecules and facilitates the transport and delivery of pheromone to the membrane-bound pheromone receptors. We report complete NMR chemical shift assignments of Atra-PBP1 obtained at pH 4.5 and 25°C (BMRB No. 15601).     

Isolation and detailed 1H and 13C NMR structural assignment for three trachylobanes from Psiadia punctulata (Asteraceae) grown in Africa

The first isolation of a trachylobane from an African specimen of Psiadia punctulata (Asteraceae) is presented in this paper. A complete ¹H and ¹³C NMR spectral analysis of this compound and two other trachylobane diterpenes, previously isolated from the same plant, are also provided. The use of NMR techniques such as gCOSY, gHSQC, gHMBC and 2D-J-resolved, in combination with a software-assisted methodology, led to a complete and unequivocal assignment of ¹H and ¹³C signals. This was achieved together with the measurement of all homonuclear hydrogen coupling constants. The presented detail level of the assignment data has never been published before for trachylobanes. Furthermore, with all determined NMR experimental data from the spectra and to obtain a reliability assessment, signals were simulated in the FOMSC3 and NMR_MultSim software.     

The combined use of selective deuteration and double resonance experiments in assigning the 1H resonances of valine and tyrosine residues of dihydrofolate reductase

Selective deuteration is a general solution to the resolution problem which limits the application of double resonance experiments to the assignment of the ¹H NMR spectra of proteins. Spin-decoupling and NOE experiments have been carried out on Lactobacillus casei dihydrofolate reductase and on selectively deuterated derivatives of the enzyme containing either [γ-²H₆]Val or (α,δ₂,?₁-²H₃]His, [α,δ₁,δ₂,?₁,?₂,ζ-²H₆]Phe, [α,δ₁,?₃,ζ₂,ζ₃,η₂-²H₆]Trp and [α,?₁,?₂-²H₃]Tyr. When combined with ring-current shift calculations based on the crystal structure of the enzyme, these experiments allow us to assign ¹H resonances of Val 61, Val 115, Tyr 46 and Tyr 68.     

Solution conformation of human big endothelin-1

Summary The solution conformation of human big endothelin-1, a 38-residue peptide which serves as the putative precursor to the potent vasoconstrictor endothelin-1 has been examined by¹H NMR. NOEs were utilized as distance restraints in the distance geometry program DSPACE to generate initial structures. Further refinement of these structures was accomplished through molecular mechanics/molecular dynamics in an iterative process involving the incorporation of stereospecific assignments of prochiral centers and the use of back-calculation of NOESY spectra. A family of structures consisting of a type 11 -turn for residues 5–8 and an -helix extending from residues 9–16 constitute a well-defined region, as reflected by the atomic root-mean-square (RMS) difference of 1.56 Å about the mean coordinate positions of the backbone atoms (N, C, Ca and O). This core region (residues 1-15) is very similar to the core residues of endothelin-1 (Donlan, M. et al. (1991)J. Cell. Biochemistry, S15G, 85). While the evidence from NOESY and coupling constant data suggests that the C-terminal region, residues 17–34, is not a mixture of randomly distributed chain conformations, it is also not consistent with a single chain conformation. Under the conditions studied, residues 17–38 in human big endothelin-1 in water at pH 3.0 between 20–30°C appear to be represented by a series of conformers in dynamic equilibrium.     

Structure of Bombyx mori chemosensory protein 1 in solution

Chemosensory Proteins (CSPs) represent a family of conserved proteins found in insects that may be involved in chemosensory functions. BmorCSP1 is expressed mainly in antennae and legs of the silkworm moth Bombyx mori and was cloned from antennal cDNA. Here we report the determination of the structure of Bombyx mori CSP1 (BmorCSP1) by NMR. The overall fold of BmorCSP1 is globular and comprises six alpha-helices. These helices span residues 10-14, 17-27, 35-49, 57-72, 75-85, and 92-100. The internal hydrophobic sides of the helices are formed mostly by leucine and isoleucine residues and, therefore, well suited to constitute a binding site for hydrophobic ligands.     

Solution structure and dynamics of Ufm1, a ubiquitin-fold modifier 1

The ubiquitin-fold modifier 1 (Ufm1) is one of various ubiquitin-like modifiers and conjugates to target proteins in cells through Uba5 (E1) and Ufc1 (E2). The Ufm1-system is conserved in metazoa and plants, suggesting its potential roles in various multicellular organisms. Herein, we analyzed the solution structure and dynamics of human Ufm1 (hsUfm1) by nuclear magnetic resonance spectroscopy. Although the global fold of hsUfm1 is similar to those of ubiquitin (Ub) and NEDD8, the cluster of acidic residues conserved in Ub and NEDD8 does not exist on the Ufm1 surface. 15N spin relaxation data revealed that the amino acid residues of hsUfm1 exhibiting conformational fluctuations form a cluster at the C-terminal segment and its spatial proximity, which correspond to the versatile ligand-binding sites of Ub and other ubiquitin-like proteins (Ubls). We suggest that Ub and other Ubl-modifiers share a common feature of potential conformational multiplicity, which might be associated with the broad ligand specificities of these proteins.     

Determination of conformational transition rates in the trp promoter by 1H NMR rotating-frame T1 and cross-relaxation rate measurements

Rotating-frame relaxation measurements have been used in conjunction with spin-spin relaxation rate constants to investigate a conformational transition previously observed in the -10 region of the trp promoter d(CGTACTAGTTAACTAGTACG)2 (Lefèvre, Lane, Jardetzky 1987). The transition is localised to the sub-sequence TAAC, and is in fast exchange on the chemical shift time-scale. The rate constant for the exchange process has been determined from measurements of the rotating-frame relaxation rate constant as a function of the spin-lock field strength, and is approximately 5000 s^–1 at 30 °C. Measurements have also been made as a function of temperature and in two different magnetic fields: the results are fully consistent with those expected for the exchange contribution in a two-site system. A similar transition has been observed in d(GTGATTGACAATTA).d(CACTAACTGTTAAT), which contains the –35 region of the trp promoter. This has been investigated in the same way, and has been found to undergo exchange at a faster rate under comparable conditions. In addition, the cross-relaxation rate constants for Ade C2H-Ade C2H pairs have been measured as a function of temperature, and these indicate that certain internuclear distances in YAAY subsequences increase with increasing temperature. These changes in distance are consistent with a flattening of propellor twist of the AT base-pairs. The occurrence of conformational transitions in YAAY subsequences depends on the flanking sequence. Correspondence to: A. N. Lane     

The interactions of the N-terminal fusogenic peptide of HIV-1 gp41 with neutral phospholipids

We have studied the interactions with neutral phospholipid bilayers of FPI, the 23-residue fusogenic N-terminal peptide of the HIV-1_LAI transmembrane glycoprotein gp41, by CD, EPR, NMR, and solid state NMR (SSNMR) with the objective of understanding how it lyses and fuses cells. Using small unilamellar vesicles made from egg yolk phoshatidylcholine which were not fused or permeabilised by the peptide we obtained results suggesting that it was capable of inserting as an α-helix into neutral phospholipid bilayers but was only completely monomeric at peptide/lipid (P/L) ratios of 1/2000 or lower. Above this value, mixed populations of monomeric and multimeric forms were found with the proportion of multimer increasing proportionally to P/L, as calculated from studies on the interaction between the peptide and spin-labelled phospholipid. The CD data indicated that, at P/L between 1/200 and 1/100, approximately 68% of the peptide appeared to be in α-helical form. When P/L=1/25 the α-helical content had decreased to 41%. Measurement at a P/L of 1/100 of the spin lattice relaxation effect on the ¹³C nuclei of the phospholipid acyl chains of an N-terminal spin label attached to the peptide showed that most of the peptide N-termini were located in the interior hydrocarbon region of the membrane. SSNMR on multilayers of ditetradecylphosphatidyl choline at P/Ls of 1/10, 1/20 and 1/30 showed that the peptide formed multimers that affected the motion of the lipid chains and disrupted the lipid alignment. We suggest that these aggregates may be relevant to the membrane-fusing and lytic activities of FPI and that they are worthy of further study. Received: 8 June 1998 / Revised version: 18 November 1998 / Accepted: 28 December 1998     

Metabolism of 1α-hydroxyvitamin D3 by cytochrome P450scc to biologically active 1α,20-dihydroxyvitamin D3

Cytochrome P450scc (CYP11A1) metabolizes vitamin D3 to 20-hydroxyvitamin D3 as the major product, with subsequent production of dihydroxy and trihydroxy derivatives. The aim of this study was to determine whether cytochrome P450scc could metabolize 1α-hydroxyvitamin D3 and whether products were biologically active. The major product of 1α-hydroxyvitamin D3 metabolism by P450scc was identified by mass spectrometry and NMR as 1α,20-dihydroxyvitamin D3. Mass spectrometry of minor metabolites revealed the production of another dihydroxyvitamin D3 derivative, two trihydroxy-metabolites made via 1α,20-dihydroxyvitamin D3 and a tetrahydroxyvitamin D3 derivative. The K_m for 1α-hydroxyvitamin D3 determined for P450scc incorporated into phospholipid vesicles was 1.4 mol substrate/mol phospholipid, half that observed for vitamin D3. The k_cat was 3.0 mol/min/mol P450scc, 6-fold lower than that for vitamin D3. 1α,20-Dihydroxyvitamin D3 inhibited DNA synthesis by human epidermal HaCaT keratinocytes propagated in culture, in a time- and dose-dependent fashion, with a potency similar to that of 1α,25-dihydroxyvitamin D3. 1α,20-Dihydroxyvitamin D3 (10 μM) enhanced CYP24 mRNA levels in HaCaT keratinocytes but the potency was much lower than that reported for 1α,25-dihydroxyvitamin D3. We conclude that the presence of the 1-hydroxyl group in vitamin D3 does not alter the major site of hydroxylation by P450scc which, as for vitamin D3, is at C20. The major product, 1α,20-dihydroxyvitamin D3, displays biological activity on keratinocytes and therefore might be useful pharmacologically.     

A note on normalization of biofluid 1D 1H-NMR data

One-dimensional ¹H nuclear magnetic resonance (1D ¹H-NMR) has been used extensively as a metabolic profiling tool for investigating urine and other biological fluids. Under ideal conditions, ¹H-NMR peak intensities are directly proportional to metabolite concentrations and thus are useful for class prediction and biomarker discovery. However, many biological, experimental and instrumental variables can affect absolute NMR peak intensities. Normalizing or scaling data to minimize the influence of these variables is a critical step in producing robust, reproducible analyses. Traditionally, analyses of biological fluids have relied on the total spectral area [constant sum (CS)] to normalize individual intensities. This approach can introduce considerable inter-sample variance as changes in any individual metabolite will affect the scaling of all of the observed intensities. To reduce normalization-related variance, we have developed a histogram matching (HM) approach adapted from the field of image processing. We validate our approach using mixtures of synthetic compounds that mimic a biological extract and apply the method to an analysis of urine from rats treated with ethionine. We show that HM is a robust method for normalizing ¹H-NMR data and propose it as an alternative to the traditional CS method.     

NMR assignment of the Rhodobacter sphaeroides fasciclin-1 domain protein (Fdp)

We report the almost complete assignment of ¹H, ¹³C and ¹⁵N nuclei in the 137-residue his-tagged fasciclin domain protein (Fdp) from Rhodobacter sphaeroides. Fdp is homologous to fasciclin I domains, including Drosophila FAS1 and M. tuberculosis MPB70 and plays a role in cell adhesion.     

Multidimensional1H and15N NMR investigation of glutamine-binding protein ofEscherichia coli

Summary Specific and uniform¹⁵N labelings along with site-directed mutagenesis of glutamine-binding protein have been utilized to obtain assignments of the His¹⁵⁶, Trp³² and Trp.²²⁰ residues. These assignments have been made not only to further study the importance of these 3 amino acid residues in protein-ligand and protein-protein interactions associated with the active transport ofl-glutamine across the cytoplasmic membrane ofEscherichia coli, but also to serve as the starting points in the sequence-specific backbone assignment. The assignment of H₂ of His¹⁵⁶ refines the earlier, model where this particular proton formas an intermolecular hydrogen bond to the -carbonyl ofl-glutamine, while assignments of both Trp³² and Trp²²⁰ show the variation in local structures which ensure the specificity in ligand binding and protein-protein interaction. Using 3D NOESY-HMQC NMR, amide connectivities can be traced along 8–9 amino acid residues at a time. This paper illustrates the usefulness of combining¹⁵N isotopic labeling and multinuclear, multidimensional NMR techniques for a structural investigation of a protein with a molecular weight of 25 000.