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T L James

Publications and source records attributed to T L James.

At least 55 records · Page 3Linked to original sources

High-resolution NMR of an antisense DNA x RNA hybrid containing alternating chirally pure Rp methylphosphonates in the DNA backbone.

A high-resolution proton NMR study has been performed on a hybrid duplex formed by a methylphosphonate (MP) oligodeoxyribonucleotide (MPO) and its target oligoribonucleotide, d(T(MP)CC(MP)-TT(MP)AG(MP)CT(MP)CC(MP)TG) x r(CAGGAGCUAAGGA), where MP corresponds to positions of methylphosphonate linkages in the pure R(p) stereoconfiguration. MP-containing analogs of DNA are reported to be effective antisense agents capable of specifically inhibiting protein synthesis with the R(p) chiral MPOs exhibiting greater affinity for the target mRNA than their S(p) counterparts. Nearly complete proton resonance assignments of the hybrid duplex have been made using two-dimensional nuclear Overhauser effect (2D NOE) spectra, at three different mixing times, and double quantum-filtered COSY (2QF-COSY) spectra. The 2QF-COSY cross-peak patterns which are resolved have been analyzed qualitatively to suggest sugar conformations. Distance restraints have been obtained from the 2D NOE spectra of the duplex in D(2)O. These interproton distance restraints were determined using a complete relaxation matrix method to improve accuracy. Specifically, a new approach termed RANDMARDI has been utilized to calculate these distance restraints, accounting for spectral noise and errors in 2D NOE peak volume integration. The calculated interproton distances and sugar puckers have been analyzed to assess the solution conformation of the hybrid. The hybrid duplex appears to have an overall solution structure which is distinct from standard B- and A-forms, but the RNA strand exhibits features of the A-form. The absence of H1'-H2' cross-peaks in the 2QF-COSY spectrum indicates a C3'-endo type of conformation for ribose sugars in the RNA strand. The deoxyriboses in the antisense DNA strand exhibit a mixed behavior with almost equal scalar coupling constant values for H1'-H2' and H1'-H2" and a strong H3'-H4' 2QF-COSY peak pattern. Variations in calculated values of interproton distances and sixth-root R factor analysis of experimental intensities indicate that the hybrid duplex may have a DNA strand with significant conformational plasticity.

Base Composition↗

Rotational correlation times of internuclear vectors in a DNA duplex with G-A mismatch determined in aqueous solution by complete relaxation matrix analysis of off-resonance ROESY (O-ROESY) spectra.

Complete relaxation matrix analysis of the off-resonance ROESY (O-ROESY) spectra is presented and demonstrated for a synthetic DNA duplex with two G-A mismatches, d(GCTGTC-GAAAGC)2, in solution. The internuclear distance and the rotational correlation time of the internuclear vector could be garnered simultaneously using complete relaxation matrix analysis of O-ROESY, by which spin diffusion effects could be accommodated. Correlation times in the terminal and the mismatched regions were significantly reduced compared to those in other regions, indicating the conformational flexibility of the mismatched pair. The average structure obtained by restrained molecular dynamics simulation with inclusion of variations of the rotational correlation times also indicated a general tendency of the mismatched and contiguous bases to flip to the outside of the double strand. Off-resonance ROESY combined with the complete relaxation matrix analysis method may offer an alternative way to investigate the structures and dynamics of biological macromolecules.

DNA↗

The dynamic NMR structure of the T psi C-loop: implications for the specificity of tRNA methylation.

tRNA (m5U54)-methyltransferase (RUMT) catalyzes the S-adenosylmethionine-dependent methylation of uridine-54 in the T psi C-loop of all transfer RNAs in E. coli to form the 54-ribosylthymine residue. However, in all tRNA structures, residue 54 is completely buried and the question arises as to how RUMT gains access to the methylation site. A 17-mer RNA hairpin consisting of nucleotides 49-65 of the T psi-loop is a substrate for RUMT. Homonuclear NMR methods in conjunction with restrained molecular dynamics (MD) methods were used to determine the solution structure of the 17-mer T-arm fragment. The loop of the hairpin exhibits enhanced flexibility which renders the conventional NMR average structure less useful compared to the more commonly found situation where a molecule exists in predominantly one major conformation. However, when resorting to softer refinement methods such as MD with time-averaged restraints, the conflicting restraints in the loop can be satisfied much better. The dynamic structure of the T-arm is represented as an ensemble of 10 time-clusters. In all of these, U54 is completely exposed. The flexibility of the T psi-loop in solution in conjunction with extensive binding studies of RUMT with the T psi C-loop and tRNA suggest that the specificity of the RUMT/ tRNA recognition is associated with tRNA tertiary structure elements. For the methylation, RUMT would simply have to break the tertiary interactions between the D- and T-loops, leading to a melting of the T-arm structure and making U54 available for methylation.

Base Sequence↗

Aqueous solution structure of a hybrid lentiviral Tat peptide and a model of its interaction with HIV-1 TAR RNA.

Human immunodeficiency virus, type 1, (HIV-1) encodes a transactivating regulatory protein, called Tat, which is required for efficient transcription of the viral genome. Tat acts by binding to a specific RNA stem-loop element, called TAR, on nascent viral transcripts. The specificity of binding is principally determined by residues in a short, highly basic domain of Tat. The structure in aqueous solution of a biologically active peptide, comprised of the ten-amino acid HIV-1 Tat basic domain linked to a 15-amino acid segment of the core regulatory domain of another lentiviral Tat, i.e., that from equine infectious anemia virus (EIAV), has been determined. The restraint data set includes interproton distance bounds determined from two-dimensional nuclear Overhauser effect (2D NOE) spectra via a complete relaxation matrix analysis. Thirty structures consistent with the experimental data were generated via the distance geometry program DIANA. Subsequent restrained molecular mechanics calculations were used to define the conformational space subtended by the peptide. A large fraction of the 25-mer peptide assumes a structure in aqueous solution with the lysine- and arginine-rich HIV-1 basic domain being separated from the basic domain by a turn and characterized by a nascent helix as well. The Tat peptide/TAR complex could be modeled with the basic alpha-helix lying in the major groove of TAR such that important interactions of a putative specificity-endowing arginine are maintained and very slight widening of the major groove is entailed.

Amino Acid Sequence↗

Adult rat brain-slice preparation for nuclear magnetic resonance spectroscopy studies of hypoxia.

BACKGROUND: When perfused neonatal brain slices are studied ex vivo with nuclear magnetic resonance (NMR) spectroscopy, it is possible to use 31P detection to monitor levels of intracellular adenosine triphosphate (ATP), cytosolic pH, and other high-energy phosphates and 1H detection to monitor lactate and glutamate. Adult brain slices of high metabolic integrity are more difficult to obtain for such studies, because the adult cranium is thicker, and postdecapitation revival time is shorter. A common clinical anesthesia phenomenon--loss of temperature regulation during anesthesia, with surface cooling and deep hypothermia, was used to obtain high-quality adult rat cerebrocortical slices for NMR studies. METHODS: Spontaneously breathing adult rats (350 g), anesthetized with isoflurane in a chamber, were packed in ice and cooled until rectal temperatures decreased to approximately 30 degrees C. An intraaortic injection of heparinized saline at 4 degrees C further cooled the brain to approximately 18 degrees C. Slices were obtained and then recovered at 37 degrees C in oxygenated medium. Interleaved 31P/1H NMR spectra were acquired continually before, during, and after 20 min of no-flow hypoxia (PO2 approximately 0 mmHg). Histologic (Nissl stain) measurements were made from random slices removed at different times in the protocol. Three types of pretreatment were compared in no-flow hypoxia studies. The treatments were: (1) hyperoxia; (2) hypercapnia (50% CO2); and (3) hypoxia, which was accomplished by washing the slices with perfusate equilibrated with 100% N2 and maintaining a 100% N2 gas flow in the air space above the perfusate. RESULTS: During hyperoxia, 31P NMR metabolite ratios were identical to those seen in vivo in adult brains, except that, in vitro, the Pi peak was slightly larger than in vivo. A lactate peak was seen in in vitro 1H spectra of slices after metabolic recovery from decapitation, although lactate is barely detectable in vivo in healthy brains. The in vitro lactate peak was attributed to a small population of metabolically impaired cells in an injury layer at the cut edge. NMR spectral resolution from the solenoidal coil exceeded that obtained in vivo in surface coil experiments. Phosphocreatine and ATP became undetectable during oxygen deprivation, which also caused a three- to sixfold increase in the ratio of lactate to N-acetyl-aspartate. Within experimental error, all metabolite concentrations except pHi recovered to control values within 2 h after oxygen restoration. Nissl-stained sections suggested that pretreatment with hypercapnia protected neurons from cell swelling during the brief period of no-flow oxygen deprivation. CONCLUSIONS: Perfused, respiring adult brain slices having intact metabolic function can be obtained for NMR spectroscopy studies. Such studies have higher spectral resolution than can be obtained in vivo. During such NMR experiments, one can deliver drugs or molecular probes to brain cells and obtain brain tissue specimens for histologic and immunochemical measures of injury. Important ex vivo NMR spectroscopy studies that are difficult or impossible to perform in vivo are feasible in this model.

Adenosine Triphosphate↗

NMR studies of the most conserved RNA domain of the mammalian signal recognition particle (SRP).

Mammalian signal recognition particle (SRP) and its homologues exhibit a phylogenetically conserved RNA domain, whose predicted secondary structure exhibits a hairpin motif with two bulged regions. Two RNA fragments comprising one (24 nt) or two (43 nt) of the conserved bulges were studied. Each fragment binds specifically to the domain of the Escherichia coli homologue of the SRP54 protein, which is involved in signal sequence recognition. The SRP RNA fragments exhibited a pronounced structural stabilization in the presence of Mg2+. Assignments of all base, H1', H2', and most imino proton resonances in the presence of Mg2+ were obtained for the 24mer RNA via NOE spectroscopy and correlated homonuclear NMR methods. 2D NOE patterns permitted a coarse structural description, revealing a relatively compact A-type geometry for the 24mer without any indications of looped-out nucleotides, syn-oriented bases, or base triplets. The GGAA-loop is structurally very similar to that of the GCAA tetraloop [Heus HA, Pardi A, 1991, Science 253:191-194]. Mg2+ seems to stabilize the structure of the conserved bulged region, which involves G:A and C:A mismatch pairs. Deviations from ideal A-type helicity are found for a larger region than the predicted secondary structure implies. Although no explicit assignment effort has been dedicated to the 43mer yet, striking similarity in chemical shift changes upon addition of Mg2+ allowed some structural conclusions. The bulge present in both RNA fragments exhibits a similar, pronounced flexibility in the absence of Mg2+, indicating that the additional bulge in the 43mer does not stabilize the other bulge.

Binding Sites↗

Conformational transitions in peptides containing two putative alpha-helices of the prion protein.

Prions are composed largely, if not entirely, of the scrapie isoform of the prion protein (PrPSc). Conversion of the cellular isoform (PrPC) to PrPSc is accompanied by a diminution in the alpha-helical content and an increase in the beta-sheet structure. To investigate the structural basis of this transition, peptide fragments corresponding to Syrian hamster PrP residues 90 to 145 and 109 to 141, which contain the most conserved residues of the prion protein and the first two putative alpha-helical regions in a PrPC model, were studied using infrared spectroscopy and circular dichroism. The peptides could be induced to form alpha-helical structures in aqueous solutions in the presence of organic solvents, such as trifluoroethanol and hexafluoroisopropanol, or detergents, such as sodium dodecyl sulfate and dodecyl phosphocholine. NaCl at physiological concentration or acetonitrile induced the peptides to acquire substantial beta-sheet. The intermolecular nature of the beta-sheet was evident in the formation of rod-shaped polymers as detected by electron microscopy. Resistance to hydrolysis by proteinase K and epitope mapping argue that the beta-sheet structures were formed by the interaction of residues lying between 109 and 141. A similar range of residues was shown by nuclear magnetic resonance spectroscopy to be capable of forming alpha-helices. The alpha-helical structures seem to require a hydrophobic support from either intermolecular interactions or the hydrophobic environment provided by micelles, in agreement with the predicted hydrophobic nature of the packing surface among the four putative helices of PrPC and the outer surfaces of the first two helices. Our results suggest that perturbation of the packing environment of the highly conserved residues is a possible mechanism for triggering the conversion of PrPC to PrPSc where alpha-helices appear to be converted into beta-sheets.

1-Propanol↗

Structure and dynamics of a DNA.RNA hybrid duplex with a chiral phosphorothioate moiety: NMR and molecular dynamics with conventional and time-averaged restraints.

The three-dimensional structure of two thiophosphate-modified DNA.RNA hybrid duplexes d(GCTATAApsTGG).r(CCAUUAUAGC), one with R-thiophosphate chirality and one with S-thiophosphate chirality, have been determined by restrained molecular dynamics simulations (rMD). As the two yielded almost identical results, a description of results can be presented in the singular. The conformational flexibility of this hybrid has been investigated by employing time-averaged constraints during the molecular dynamics simulations (MD-tar). A set of structural restraints, comprising 322 precise interproton distance constraints obtained by a complete relaxation matrix analysis of the 2D NOE intensities as well as J coupling constants obtained from quantitative simulations of DQF-COSY cross-peaks in deoxyriboses, was reported in our previous paper [González, C., Stec, W., Kobylanska, A., Hogrefe, R. I., Reynolds, M., & James, T. L. (1994) Biochemistry 33, 11062-11072]. Multiple conformations of the deoxyribose moieties were evident from the scalar coupling constant analysis. Accurate distance constraints, obtained from complete relaxation matrix analysis, yielded a time-averaged solution structure via conventional restrained molecular dynamics which is not compatible with the experimental J coupling constants (root-mean-square deviation in J value approximately 2 Hz). However, vicinal coupling constant information can be reproduced when time-averaged constraints are used during the molecular dynamics calculations instead of the conventional restraints (Jrms approximately 0.6 Hz). MD-tar simulations also improve the NMR R factors. This improvement is more evident in the DNA than in the RNA strand, where no indication of conformational flexibility had been obtained. Analysis of the MD-tar trajectories confirms that deoxyriboses undergo pucker transitions between the S and N domain, with the major conformer in the S domain. The ribose moieties in the RNA strand, however, remain in the N domain during the entire simulation. Conformations of deoxyriboses in the intermediate domain near O4'-endo are obtained when the average structure is calculated with conventional NMR restraints. Since these conformations cannot account for the experimental J coupling information, and they only appear in a very low population in the MD-tar ensemble, we conclude that intermediate E sugar puckers are artifacts produced by the attempt to fit all the structural constraints simultaneously when in reality more than one conformer is present. Most structural features of the duplex remain the same in the average structure and in the MD-tar ensemble, e.g., the minor groove width, exhibiting an intermediate value compared with those of canonical A- and B-like structures.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

Deriving accurate interproton distances from ROESY spectra with limited knowledge of scalar coupling constants via the CARNIVAL algorithm. An iterative complete-relaxation-matrix approach.

A method (termed CARNIVAL) for accurately determining distances from proton homonuclear rotating-frame Overhauser effect spectroscopy (ROESY) is described. The method entails an iterative calculation of the relaxation matrix using methodology introduced with the MARDIGRAS algorithm for analysis of two-dimensional nuclear Overhauser effect spectra (B. A. Borgias and T. L. James, J. Magn. Reson. 87, 475, 1990). The situation is complicated in the case of ROESY as spectral peak intensities are influenced by resonance offset and contributions from homonuclear Hartmann-Hahn (HOHAHA) transfer if the nuclear spins are related by scalar coupling. The effects of spin-locking field strength on distance determinations and the ensuing distance errors incurred when HOHAHA corrections are made with limited knowledge of scalar (J) coupling information have been evaluated using simulated ROESY intensities with a model peptide structure. It has been demonstrated that accurate distances can be obtained with little or no explicit knowledge of the homonuclear coupling constants over a moderate range of spin-locking field strengths. The CARNIVAL algorithm has been utilized to determine distances in a decapeptide using experimental ROESY data without measured coupling constants.

Algorithms↗

Interproton distance bounds from 2D NOE intensities: effect of experimental noise and peak integration errors.

The effect of experimental and integration errors on the calculation of interproton distances from NOE intensities is examined. It is shown that NOE intensity errors can have a large impact on the distances determined. When multiple spin ('spin diffusion') effects are significant, the calculated distances are often underestimated, even when using a complete relaxation matrix analysis. In this case, the bias of distances to smaller values is due to the random errors in the NOE intensities. We show here that accurate upper and lower bounds of the distances can be obtained if the intensity errors are properly accounted for in the complete relaxation matrix calculations, specifically the MARDIGRAS algorithm. The basic MARDIGRAS algorithm has been previously described [Borgias, B.A. and James, T.L. (1990) J. Magn. Reson., 87, 475-487]. It has been shown to provide reasonably good interproton distance bounds, but experimental errors can compromise the quality of the resulting restraints, especially for weak cross peaks. In a new approach introduced here, termed RANDMARDI (random error MARDIGRAS), errors due to random noise and integration errors are mimicked by the addition of random numbers from within a specified range to each input intensity. Interproton distances are then calculated for the modified intensity set using MARDIGRAS. The distribution of distances that define the upper and lower distance bounds is obtained by using N randomly modified intensity sets. RANDMARDI has been used in the solution structure determination of the interstrand cross-link (XL) formed between 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) and the DNA oligomer d(5'-GCGTACGC-3')2 [Spielmann, H.P. et al. (1995) Biochemistry, 34, 12937-12953]. RANDMARDI generates accurate distances bounds from the experimental NOESY cross-peak intensities for the fixed (known) interproton distances in XL. This provides an independent internal check for the ability of RANDMARDI to accurately fit the experimental data. The XL structure determined using RANDMARDI-generated restraints is in good agreement with other biophysical data that indicate that there is no bend introduced into the DNA by the cross-link. In contrast, isolated spin-pair approximation calculations give distance restraints that, when applied in a restrained molecular dynamics protocol, produce a bent structure.

Algorithms↗

Probability assessment of conformational ensembles: sugar repuckering in a DNA duplex in solution.

Conformational flexibility of molecules in solution implies that different conformers contribute to the NMR signal. This may lead to internal inconsistencies in the 2D NOE-derived interproton distance restraints and to conflict with scalar coupling-based torsion angle restraints. Such inconsistencies have been revealed and analyzed for the DNA octamer GTATAATG.CATATTAC, containing the Pribnow box consensus sequence. A number of subsets of distance restraints were constructed and used in the restrained Monte Carlo refinement of different double-helical conformers. The probabilities of conformers were then calculated by a quadratic programming algorithm, minimizing a relaxation rate-base residual index. The calculated distribution of conformers agrees with the experimental NOE data as an ensemble better than any single structure. A comparison with the results of this procedure, which we term PARSE (Probability Assessment via Relaxation rates of a Structural Ensemble), to an alternative method to generate solution ensembles showed, however, that the detailed multi-conformational description of solution DNA structure remains ambiguous at this stage. Nevertheless, some ensemble properties can be deduced with confidence, the most prominent being a distribution of sugar puckers with minor populations in the N-region and major populations in the S-region. Importantly, such a distribution is in accord with the analysis of independent experimental data--deoxyribose proton-proton scalar coupling constants.

Algorithms↗

Tertiary base pair interactions in slipped loop-DNA: an NMR and model building study.

Short direct repeat sequences are often found in regulatory regions of various genes; in some cases they display hypersensitivity to S1 nuclease cleavage in supercoiled plasmids. A non-standard DNA structure (Slipped Loop Structure, or SLS) has been proposed for these regions in order to explain the S1 cleavage data; the formation of this structure may be involved in the regulation of transcription. The structure can be generally classified as a particular type of pseudoknot. To date, no detailed stereochemical model has been developed. We have applied one-dimensional 1H NMR spectroscopy to study a synthetic DNA, 55 nucleotides in length, which cannot fold as a standard hairpin but which may favor the SLS formation. AT base pairs were identified, consistent only with the formation of an additional, tertiary miniduplex in the SLS. An all-atom stereochemically sound model has been developed for the SLS with the use of conformational calculations. The model building studies have demonstrated that the tertiary miniduplex can be formed for one of the plausible SLS isomers, but not for the other.

Base Composition↗

Structural study of a DNA.RNA hybrid duplex with a chiral phosphorothioate moiety by NMR: extraction of distance and torsion angle constraints and imino proton exchange rates.

The solution structure of the thiophosphate-modified DNA.RNA hybrid duplex d(GCTATAApsTGG).r(CCAUUAUAGC) has been studied by NMR. Two samples with pure stereochemistry in the modified phosphate have been investigated. Two-dimensional NMR (2D NMR) methods have been applied to assign nearly all the resonances in both duplexes. Scalar coupling constants have been determined by comparing quantitative simulations with experimental double-quantum filtered COSY (DQF-COSY) cross-peaks. More than 300 distance constraints have been obtained from two-dimensional nuclear Overhauser spectroscopy (2D NOE) spectra recorded in D2O and H2O by using a complete relaxation matrix analysis as implemented in the program MARDIGRAS. This hybrid duplex presents a heteronomous structure. Riboses in the RNA strand are found in a N-type conformation typical of the A-form family as shown by the lack of H1'-H2' cross-peaks in DQF-COSY spectra and confirmed by the measured interproton distances. In contrast, the DNA strand adopts a different conformation with sugar puckers partially in the S-type domain, which is not in agreement with the A-family of structures. Coupling constants in deoxyriboses are not consistent with any single sugar conformation. Therefore, sugar pucker pseudorotation parameters are calculated according to a two-state dynamic equilibrium between N- and S-type conformers. In general, the population of major S conformer is lower than in double-stranded DNA duplexes, indicating that hybrid duplexes may be more flexible than pure DNA or RNA. The only differences observed in the spectra between the two stereoisomers studied originate from resonances of protons located near the modified phosphate. No significant differences in interproton distance have been detected, and only a slight difference of sugar pucker in the 5' neighbor has been found. The sulfur atom appears to be well-accommodated without further changes in the structure of the hybrid.

Base Sequence↗

NMR structure of a biologically active peptide containing the RNA-binding domain of human immunodeficiency virus type 1 Tat.

The Tat protein of human immunodeficiency virus type 1 enhances transcription by binding to a specific RNA element on nascent viral transcripts. Binding is mediated by a 10-amino acid basic domain that is rich in arginines and lysines. Here we report the three-dimensional peptide backbone structure of a biologically active 25-mer peptide that contains the human immunodeficiency virus type 1 Tat basic domain linked to the core regulatory domain of another lentiviral Tat--i.e., that from equine infectious anemia virus. Circular dichroism and two-dimensional proton NMR studies of this hybrid peptide indicate that the Tat basic domain forms a stable alpha-helix, whereas the adjacent regulatory sequence is mostly in extended form. These findings suggest that the tendency to form stable alpha-helices may be a common property of arginine- and lysine-rich RNA-binding domains.

Amino Acid Sequence↗

19F NMR calcium changes, edema and histology in neonatal rat brain slices during glutamate toxicity.

Respiring neonatal cerebrocortical slices (350 microns thick), loaded with the free calcium indicator 5F-BAPTA, were perfused in a 20-mm-diameter glass NMR tube with oxygenated artificial CSF, exposed to extracellular glutamate and studied at 4.7 Tesla with 19F NMR spectroscopy. 31P/1H NMR spectra, obtained concurrently, were used to assess slice integrity from determinations of intracellular pH, ATP, PCr, lactate and N-acetylaspartate. 60-min periods were induced of recoverable and nonrecoverable glutamate toxicity-defined from changes in NMR metabolites. In other NMR studies, where 5F-BAPTA was not used, metabolic toxicity was modulated by three glutamate receptor antagonists: dizocilpine, NBQX and kynurenic acid. Outcome measurements were made of edema, determined invasively in isolated slices from % swelling and water content and from histological changes in Nissl stains of slice sections. Edema was (1) detectable in all slices within minutes after onset of glutamate exposure, though never in untreated control slices, and (2) modulated differently by dizocilpine, NBQX and kynurenate. Correlations were observed between edema and NMR decreases in PCr and ATP. Nissl stains of sections from slices treated with the most protective agent, dizocilpine, showed preservation of neuronal processes. As was expected in 7-day-old rats with immature NMDA receptors, 19F NMR spectroscopy revealed only small increases in free intracellular calcium ([Ca2+]i). These occurred late during glutamate exposure and reversed early during glutamate washout. The studies demonstrate that it is possible to study correlations between repeated noninvasive NMR spectra in ensembles of brain slices and invasive measures of early cellular responses.

Animals↗