Lori K. Sanders

Urbana University, Urbana, Illinois, United States

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Publications (12)26.37 Total impact

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    ABSTRACT: ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
    ChemInform 01/2010; 31(1).
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    Haihong Sun, Lori K Sanders, Eric Oldfield
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    ABSTRACT: We have used ab initio quantum chemical techniques to compute the (13)C(alpha) and (13)C(beta) shielding surfaces for the 14 amino acids not previously investigated (R. H. Havlin et al., J. Am. Chem. Soc. 1997, 119, 11951-11958) in their most popular conformations. The spans (Omega = sigma(33) - sigma(11)) of all the tensors reported here are large ( approximately 34 ppm) and there are only very minor differences between helical and sheet residues. This is in contrast to the previous report in which Val, Ile and Thr were reported to have large ( approximately 12 ppm) differences in Omega between helical and sheet geometries. Apparently, only the beta-branched (beta-disubstituted) amino acids have such large CSA span (Omega) differences; however, there are uniformly large differences in the solution-NMR-determined CSA (Deltasigma = sigma(orth) - sigma(par)) between helices and sheets in all amino acids considered. This effect is overwhelmingly due to a change in shielding tensor orientation. With the aid of such shielding tensor orientation information, we computed Deltasigma values for all of the amino acids in calmodulin/M13 and ubiquitin. For ubiquitin, we find only a 2.7 ppm rmsd between theory and experiment for Deltasigma over an approximately 45 ppm range, a 0.96 slope, and an R(2) = 0.94 value when using an average solution NMR structure. We also report C(beta) shielding tensor results for these same amino acids, which reflect the small isotropic chemical shift differences seen experimentally, together with similar C(beta) shielding tensor magnitudes and orientations. In addition, we describe the results of calculations of C(alpha), C(beta), C(gamma)1, C(gamma)2, and C(delta) shifts in the two isoleucine residues in bovine pancreatic trypsin inhibitor and the four isoleucines in a cytochrome c and demonstrate that the side chain chemical shifts are strongly influenced by chi(2) torsion angle effects. There is very good agreement between theory and experiment using either X-ray or average solution NMR structures. Overall, these results show that both C(alpha) backbone chemical shift anisotropy results as well as backbone and side chain (13)C isotropic shifts can now be predicted with good accuracy by using quantum chemical methods, which should facilitate solution structure determination/refinement using such shielding tensor surface information.
    Journal of the American Chemical Society 06/2002; 124(19):5486-95. · 10.68 Impact Factor
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    ABSTRACT: We have carried out a solid-state magic-angle sample-spinning (MAS) nuclear magnetic resonance (NMR) spectroscopic investigation of the (13)C(alpha) chemical shielding tensors of alanine, valine, and leucine residues in a series of crystalline peptides of known structure. For alanine and leucine, which are not branched at the beta-carbon, the experimental chemical shift anisotropy (CSA) spans (Omega) are large, about 30 ppm, independent of whether the residues adopt helical or sheet geometries, and are in generally good accord with Omega values calculated by using ab initio Hartree-Fock quantum chemical methods. The experimental Omegas for valine C(alpha) in two peptides (in sheet geometries) are also large and in good agreement with theoretical predictions. In contrast, the "CSAs" (Deltasigma) obtained from solution NMR data for alanine, valine, and leucine residues in proteins show major differences, with helical residues having Deltasigma values of approximately 6 ppm while sheet residues have Deltasigma approximately 27 ppm. The origins of these differences are shown to be due to the different definitions of the CSA. When defined in terms of the solution NMR CSA, the solid-state results also show small helical but large sheet CSA values. These results are of interest since they lead to the idea that only the beta-branched amino acids threonine, valine, and isoleucine can have small (static) tensor spans, Omega (in helical geometries), and that the small helical "CSAs" seen in solution NMR are overwhelmingly dominated by changes in tensor orientation, from sheet to helix. These results have important implications for solid-state NMR structural studies which utilize the CSA span, Omega, to differentiate between helical and sheet residues. Specifically, there will be only a small degree of spectral editing possible in solid proteins since the spans, Omega, for the dominant nonbranched amino acids are quite similar. Editing on the basis of Omega will, however, be very effective for many Thr, Val, and Ileu residues, which frequently have small ( approximately 15-20 ppm) helical CSA (Omega) spans.
    Journal of the American Chemical Society 11/2001; 123(42):10362-9. · 10.68 Impact Factor
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    ABSTRACT: We have carried out a solid-state magic-angle sample-spinning (MAS) nuclear magnetic resonance (NMR) spectroscopic investigation of the 13Cα chemical shielding tensors of alanine, valine, and leucine residues in a series of crystalline peptides of known structure. For alanine and leucine, which are not branched at the β-carbon, the experimental chemical shift anisotropy (CSA) spans (Ω) are large, about 30 ppm, independent of whether the residues adopt helical or sheet geometries, and are in generally good accord with Ω values calculated by using ab initio Hartree−Fock quantum chemical methods. The experimental Ωs for valine Cα in two peptides (in sheet geometries) are also large and in good agreement with theoretical predictions. In contrast, the “CSAs” (Δσ*) obtained from solution NMR data for alanine, valine, and leucine residues in proteins show major differences, with helical residues having Δσ* values of 6 ppm while sheet residues have Δσ* ≈ 27 ppm. The origins of these differences are shown to be due to the different definitions of the CSA. When defined in terms of the solution NMR CSA, the solid-state results also show small helical but large sheet CSA values. These results are of interest since they lead to the idea that only the β-branched amino acids threonine, valine, and isoleucine can have small (static) tensor spans, Ω (in helical geometries), and that the small helical “CSAs” seen in solution NMR are overwhelmingly dominated by changes in tensor orientation, from sheet to helix. These results have important implications for solid-state NMR structural studies which utilize the CSA span, Ω, to differentiate between helical and sheet residues. Specifically, there will be only a small degree of spectral editing possible in solid proteins since the spans, Ω, for the dominant nonbranched amino acids are quite similar. Editing on the basis of Ω will, however, be very effective for many Thr, Val, and Ileu residues, which frequently have small (15−20 ppm) helical CSA (Ω) spans.
    Journal of The American Chemical Society - J AM CHEM SOC. 09/2001; 123.
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    Lori K. Sanders, Eric Oldfield
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    ABSTRACT: We report the theoretical 19F NMR shielding tensor magnitudes and orientations for a series of fluoroaromatic species, together with a comparison with experimental results. We discuss results for Hartree−Fock (HF) and second-order Møeller−Plesset theory (MP2) geometry optimized structures and HF-gauge including atomic orbitals (HF-GIAO), sum over states-density functional theory-independent gauges for localized orbitals (SOS-DFT-IGLO) and MP2-GIAO shielding calculations, for several basis set arrangements. In general, MP2 and DFT methods show few improvements over HF methods, at the expense of time (MP2) and accuracy (MP2 and DFT). Pure density functionals overestimate the tensor breadths (spans), an effect that is only partially offset by use of hybrid exchange correlation functionals. HF-GIAO methods in general give good overall predictions of 19F shielding tensor elements. In the case of potassium tetrafluorophthalate, we also demonstrate that use of the charge field perturbation-IGLO technique provides accurate shielding tensor elements, as well as accurate shielding tensor orientations. We also report the calculation of the shielding derivatives, ∂σii/∂r, for the 19F nucleus in fluorobenzene (and HF) and the 1H nucleus in benzene. Surprisingly, the derivative along the C−F bond axis (∂σ22/∂r) is quite large, 460 ppm Å-1, unlike that expected and found in HF, or in benzene, indicating a strong p-orbital interaction with the benzene ring. The 19F shielding tensor results are thus quite sensitive to the actual bond lengths employed (derived from geometry optimizaitons), with MP2 optimization permitting the best accord with experiment. Overall, MP2 optimization and HF-GIAO shielding tensor calculations were found to give the best results, consistent with previous isotropic chemical shift/shielding results.
    Journal of Physical Chemistry A - J PHYS CHEM A. 08/2001; 105(34).
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    Lori K. Sanders, William D. Arnold, Eric Oldfield
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    ABSTRACT: We review contributions made towards the elucidation of CO and O2 binding geometries in respiratory proteins. Nuclear magnetic resonance, infrared spectroscopy, Mössbauer spectroscopy, X-ray crystallography and quantum chemistry have all been used to investigate the Fe–ligand interactions. Early experimental results showed linear correlations between 17O chemical shifts and the infrared stretching frequency (νCO) of the CO ligand in carbonmonoxyheme proteins and between the 17O chemical shift and the 13CO shift. These correlations led to early theoretical investigations of the vibrational frequency of carbon monoxide and of the 13C and 17O NMR chemical shifts in the presence of uniform and non-uniform electric fields. Early success in modeling these spectroscopic observables then led to the use of computational methods, in conjunction with experiment, to evaluate ligand-binding geometries in heme proteins. Density functional theory results are described which predict 57Fe chemical shifts and Mössbauer electric field gradient tensors, 17O NMR isotropic chemical shifts, chemical shift tensors and nuclear quadrupole coupling constants (e2qQ/h) as well as 13C isotropic chemical shifts and chemical shift tensors in organometallic clusters, heme model metalloporphyrins and in metalloproteins. A principal result is that CO in most heme proteins has an essentially linear and untilted geometry (τ = 4 °, β = 7 °) which is in extremely good agreement with a recently published X-ray synchrotron structure. CO/O2 discrimination is thus attributable to polar interactions with the distal histidine residue, rather than major Fe–C–O geometric distortions. Copyright © 2001 John Wiley & Sons, Ltd.
    Journal of Porphyrins and Phthalocyanines 02/2001; 5(3):323 - 333. · 1.43 Impact Factor
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    ABSTRACT: We have expressed [U-(13)C,(15)N]-labeled Saccharomyces cerevisiae iso-1 cytochrome c C102T;K72A in Escherichia coli with a yield of 11 mg/l of growth medium. Nuclear magnetic resonance (NMR) studies were conducted on the Fe(3+) form of the protein. We report herein chemical shift assignments for amide (1)H and (15)N, (13)C(omicron), (13)C(alpha), (13)C(beta), (1)H(alpha) and (1)H(beta) resonances based upon a series of three-dimensional NMR experiments: HNCA, HN(CO)CA, HNCO, HN(CA)CO, HNCACB, HCA(CO)N, HCCH-TOCSY and HBHA(CBCA)NH. An investigation of the chemical shifts of the threonine residues was also made by using density functional theory in order to help solve discrepancies between (15)N chemical shift assignments reported in this study and those reported previously.
    FEBS Letters 10/2000; 482(1-2):25-30. · 3.58 Impact Factor
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    ABSTRACT: We have investigated the charge density, ρ(r), its curvature, ∂2ρ/∂rij, the dipole moment, μ, and the electrostatic potential, Φ(r), in l-asparagine monohydrate by using high-resolution single-crystal X-ray crystallography and quantum chemistry. In addition, we have compared electric field gradient, E, results obtained from crystallography and quantum chemistry with those obtained from single-crystal 14N nuclear magnetic resonance spectroscopy. A multipole model of the X-ray ρ(r) is compared to Hartree−Fock and density functional theory predictions, using two different large basis sets. The quality of the calculated charge densities is evaluated from a simultaneous comparison of eight Hessian-of-ρ(r) tensors at bond critical points between non-hydrogen atoms. These tensors are expressed in an icosahedral representation, which includes information on both tensor magnitude and orientation. The best theory-versus-experiment correlation is found at the B3LYP/6-311++G(2d,2p) level, which yields a slope of 1.09 and an R2 value of 0.96. Both DFT and HF results give molecular dipole moments in good accord with the value extracted from the X-ray diffraction data, 14.3(3) D, and both sets of calculations are found to correctly reproduce the experimental molecular electrostatic potential, Φ(r). The intermolecular hydrogen bond ρ(r) is also subjected to a detailed theoretical and experimental topological analysis, and again good agreement is found between theory and experiment. For the comparison of the E tensors, the icosahedral representation is again used. There is found to be moderate accord between theory and experiment when using results obtained from diffraction data, but much better accord when using results obtained from NMR data (slope = 1.14, R2 = 0.94, for the 12 icosahedral tensor elements for N1 and N2). Overall, these results strongly support the idea that both HF and DFT methods give excellent representations of the electrostatic properties ρ(r), ∂2ρ/∂rij, μ, Φ(r), and E, for crystalline l-asparagine monohydrate, encouraging their future use in situations where experimental results are lacking, such as in peptides and in enzyme active sites.
    Journal of The American Chemical Society - J AM CHEM SOC. 04/2000; 122(19).
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    ABSTRACT: We have expressed [U-13C,15N]-labeled Saccharomyces cerevisiae iso-1 cytochrome c C102T;K72A in Escherichia coli with a yield of 11 mg/l of growth medium. Nuclear magnetic resonance (NMR) studies were conducted on the Fe3+ form of the protein. We report herein chemical shift assignments for amide 1H and 15N, 13C°, 13Cα, 13Cβ, 1Hα and 1Hβ resonances based upon a series of three-dimensional NMR experiments: HNCA, HN(CO)CA, HNCO, HN(CA)CO, HNCACB, HCA(CO)N, HCCH-TOCSY and HBHA(CBCA)NH. An investigation of the chemical shifts of the threonine residues was also made by using density functional theory in order to help solve discrepancies between 15N chemical shift assignments reported in this study and those reported previously.
    Febs Letters - FEBS LETT. 01/2000; 482(1):25-30.
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    ABSTRACT: We have synthesized and characterized the following four metalloporphyrins:  Fe(OEP)(CO)(1-MeIm), Ru(OEP)(CO)(1-MeIm), Os(OEP)(CO)(1-MeIm), and Fe(TPP)(iPrNC)(1-MeIm), where OEP = 2,3,7,8,12,13,17,18-octaethylporphyrinate, TPP = 5,10,15,20-tetraphenylporphyrinate, and 1-MeIm = 1-methylimidazole, using single-crystal X-ray diffraction, solid-state nuclear magnetic resonance (NMR), and density functional theory (DFT) methods. Unlike the situation found with the Fe-, Ru-, Os(TPP)(CO)(1-MeIm) analogues, which have ruffled porphyrins, all four systems here have essentially planar porphyrin rings, and a rule is developed that successfully predicts the presence or absence of ring distortion in a broad range of metalloporphyrins. In each of the three CO complexes, the M−C−O bond is close to linear and untilted, but with the iPrNC adduct, there are noticeable ligand distortions supporting the idea that RNC groups (but not CO) may be distorted in metalloproteins. Solid-state 13C, 15N, and 17O NMR shifts and shift tensors determined experimentally are in generally good agreement with those computed via DFT. For isocyanide binding to proteins, the experimental shifts are more deshielded than in the model system, and the effects which might contribute to this difference are explored theoretically. Unlike CO, electrostatic field effects are unlikely to make a major contribution to protein shielding. Neither are Fe−C−N tilt−bend distortions, although a bend at nitrogen is energetically feasible and also gives a large deshielding, as seen with proteins.
    Journal of The American Chemical Society - J AM CHEM SOC. 04/1999; 121(16).
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    ABSTRACT: We have synthesized and studied via solid-state NMR, Mössbauer spectroscopy, single-crystal X-ray diffraction, and density functional theory the following Fe−O2 analogue metalloporphyrins: Fe(5,10,15,20-tetraphenylporphyrinate) (nitrosobenzene)(1-methylimidazole); Fe(5,10,15,20-tetraphenylporphyrinate) (nitrosobenzene)(pyridine); Fe(5,10,15,20-tetraphenylporphyrinate)(4-nitroso-N,N-dimethylaniline)(pyridine); Fe(2,3,7,8,12,13,17,18-octaethylporphyrinate) (nitrosobenzene)(1-methylimidazole) and Co(2,3,7,8,12,13,17,18-octaethylporphyrinate)(NO). Our results show that the porphyrin rings of the two tetraphenylporphyrins containing pyridine are ruffled while the other three compounds are planar: reasons for this are discussed. The solid-state NMR and Mössbauer spectroscopic results are well reproduced by the DFT calculations, which then enable the testing of various models of Fe−O2 bonding in metalloporphyrins and metalloproteins. We find no evidence for two binding sites in oxypicket fence porphyrin, characterized by very different electric field gradients. However, the experimental Mössbauer quadrupole splittings can be readily accounted for by fast axial rotation of the Fe−O2 unit. Unlike oxymyoglobin, the Mössbauer quadrupole splitting in PhNO•myoglobin does not change with temperature, due to the static nature of the Fe•PhNO subunit, as verified by 2H NMR of Mb•[2H5]PhNO. Rotation of O2 to a second (minority) site in oxymyoglobin can reduce the experimental quadrupole splittings, either by simple exchange averaging, or by an electronic mechanism, without significant changes in the Fe−O−O bond geometry, or a change in sign of the quadrupole splitting. DFT calculations of the molecular electrostatic potentials in CO, PhNO, and O2-metalloporphyrin complexes show that the oxygen sites in the PhNO and O2 complexes are more electronegative than that in the CO system, which strongly supports the idea that hydrogen bonding to O2 will be a major contributor to O2/CO discrimination in heme proteins.
    Journal of The American Chemical Society - J AM CHEM SOC. 01/1999; 121(16):3829-3844.
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    ABSTRACT: We have investigated the carbon-13 solution nuclear magnetic resonance (NMR) chemical shifts of Cα, Cβ, and Cγ carbons of 19 valine residues in a vertebrate calmodulin, a nuclease from Staphylococcus aureus, and a ubiquitin. Using empirical chemical shift surfaces to predict Cα, Cβ shifts from known, X-ray φ,ψ values, we find moderate accord between prediction and experiment. Ab initio calculations with coupled Hartree−Fock (HF) methods and X-ray structures yield poor agreement with experiment. There is an improvement in the ab initio results when the side chain χ1 torsion angles are adjusted to their lowest energy conformers, using either ab initio quantum chemical or empirical methods, and a further small improvement when the effects of peptide-backbone charge fields are introduced. However, although the theoretical and experimental results are highly correlated (R2 0.90), the observed slopes of −0.6−0.8 are less than the ideal value of −1, even when large uniform basis sets are used. Use of density functional theory (DFT) methods improves the quality of the predictions for both Cα (slope = −1.1, R2 = 0.91) and Cβ (slope = −0.93, R2 = 0.89), as well as giving moderately good results for Cγ. This effect is thought to arise from a small, conformationally-sensitive contribution to shielding arising from electron correlation. Additional shielding calculations on model compounds reveal similar effects. Results for valine residues in interleukin-1β are less highly correlated, possibly due to larger crystal−solution structural differences. When taken together, these results for 19 valine residues in 3 proteins indicate that choosing the lowest energy χ1 conformer together with X-ray φ,ψ values enables the successful prediction of both Cα and Cβ shifts, with DFT giving close to ideal slopes and R2 values between theory and experiment. These results strongly suggest that the most highly populated valine side-chain conformers are those having the lowest (computationally determined) energy, as evidenced by the ability to predict essentially all Cα, Cβ chemical shifts in calmodulin, SNase, and ubiquitin, as well as moderate accord for Cγ. These observations suggest a role for chemical shifts and energy minimization/geometry optimization in the refinement of protein structures in solution, and potentially in the solid state as well.
    Journal of The American Chemical Society - J AM CHEM SOC. 12/1997; 119(49).