Biomedical subjects

R H Blessing

Publications and source records attributed to R H Blessing.

33 records · Page 2Linked to original sources

PubMed1996

Statistical expectation value of the Debye-Waller factor and E(hkl) values for macromolecular crystals.

If the unit-cell distribution of atomic mean-square displacement parameters B = 8pi(2) is assumed to be normal, with mean micro = and variance sigma(2) = <(B- )(2)>, the statistical expectation value of the Debye-Waller factor W(2) = exp(-2Bs(2)), where s = (sin theta)/lambda, is = exp[-2( micro - sigma(2)s(2))s(2)]. This result has been incorporated into procedures for scaling and normalizing measured Bragg intensities to their Wilson expectation values. The procedures can determine both isotropic micro (B) and sigma(B) and anisotropic micro (U(ij)) and sigma(U(ij) distribution parameters. Tests with experimental data and refined structural models for several protein crystals show that the procedures yield reliable normalized structure-factor amplitudes for direct-methods applications, with values of R = summation operator (h)||E(o)| - |E(c)||/ summation operator (h)|E(o)| averaging approximately 5%.

Journal Article↗

PubMed1995

On the differences between X-ray and neutron thermal vibration parameters.

For crystal structures analyzed by both X-ray and neutron diffraction, the anisotropic mean-square displacement parameters of the non-H atoms are sometimes found to differ significantly. The differences can usually be adjusted by either: (1) an isotropic factor q, defined by UijX = qUijN, to correct for a temperature difference between the two experiments; (2) anisotropic factors qij, defined by UijX = qijUijN, to correct for a temperature difference and different anisotropic diffraction effects of absorption, extinction, thermal diffuse scattering, multiple reflection, or systematic measuring errors in the two experiments; (3) anisotropic diffraction correction terms delta Uij, defined by UijX = UijN + delta Uij; (4) the sum of an isotropic temperature correction and anisotropic diffraction corrections, defined by UijX = qUijN + delta Uij. Correction parameters q, qij and delta Uij are easily calculated by linear least-squares fit, and the corrections from (3) or (4) seem to be the most reliable. Corrections calculated from X-ray and neutron Uij's of the non-H atoms of a crystal can be useful for adjusting the neutron Uij's of the H atoms for adoption, along with the neutron coordinates of the H atoms, as fixed parameters in an X-ray analysis of the electron density distribution.

Crystallography, X-Ray↗

PubMed1995

Computational studies of crystalline H3PO4.

A polarized split-valence wavefunction was computed for the H3PO4 molecule at its neutron crystallographic valence geometry, and the wavefunction was used to map the molecular electron-density distribution and to simulate X-ray crystal structure factors for both static, at-rest and dynamic thermally averaged structures. The thermal vibrational averaging was approximated using anisotropic mean-square atomic displacements from approximately 300 K neutron diffraction data. The simulated X-ray data were used to test pseudoatom multipole modeling of the valence electron-density distribution, in particular, radial modeling of the M valence shell of the P atom, and deconvolution of the nonspherical density features from anisotropic vibrational smearing.

Crystallography, X-Ray↗

PubMed1995

Experimental electron density in crystalline H3PO4.

X-ray diffraction data for H3PO4 crystals have been measured to dmin = 0.46 A resolution, and used to model the electron-density distribution with the hydrogen structure of the crystals adopted from an earlier neutron diffraction analysis. The molecule is asymmetric in the crystal with site symmetry 1 (C1), but the local symmetries of the pseudoatomic densities are, within experimental error, equivalent as they would be under idealized 3m (C3v) molecular symmetry. Although the experimental analysis entailed substantial problems with absorption and extinction corrections, the static deformation density from the experiment agrees very well with that from a polarized split-valence molecular orbital wavefunction for an isolated molecule with the crystallographic molecular geometry. Hydrogen bonding in the crystal polarizes the molecule's P==O acceptor group towards P(+)--O-, and appears to relocalize the lone-pair density of the P--OH donor groups. Crystal data: anhydrous orthophosphoric acid, H3PO4, M(r) = 98.00, room temperature, P2(1)/c, a = 5.7572 (13), b = 4.8310 (17), c = 11.5743 (21) A, beta = 95.274 (12) degrees, V = 320.55 (25) A3, Z = 4, dx = 2.030 mg mm-3, mu = 0.660 mm-1 for lambda(Mo K alpha) = 0.7107 A, F(000) = 200 e-, R(parallel F) = 0.026 for 3512 unique reflections.

Crystallography, X-Ray↗

PubMed1995

An empirical correction for absorption anisotropy.

A least-squares procedure is described for modeling an empirical transmission surface as sampled by multiple symmetry-equivalent and/or azimuth rotation-equivalent intensity measurements. The fitting functions are sums of real spherical harmonic functions of even order, ylm(-u0) + ylm(u1), 2 < or = l = 2n < or = 8. The arguments of the functions are the components of unit direction vectors, -u0 for the reverse incident beam and u1 for the scattered beam, referred to crystal-fixed Cartesian axes. The procedure has been checked by calculations against standard absorption test data.

Anisotropy↗

PubMed1995

Crambin: a direct solution for a 400-atom structure.

The crystal structure of crambin, a 46-residue protein containing the equivalent of approximately 400 fully occupied non-H-atom positions, was originally solved at 1.5 A by exploiting the anomalous scattering of its six S atoms at a single wavelength far removed from the absorption edge of sulfur. The crambin structure has now been resolved without the use of any anomalous-dispersion measurements. The technique employed was an ab initio 'shake-and-bake' method, consisting of a phase-refinement procedure based on the minimal function alternated with Fourier refinement. This method has successfully yielded solutions for a smaller molecule (28 atoms) using 1.2 A data, and a crambin solution was obtained at 1.1 A.

Journal Article↗

PubMed1994

On integrating the techniques of direct methods with anomalous dispersion. III. Estimation of two-wavelength two-phase structure invariants.

For diffraction data at two wavelengths from a crystal with anomalous scatterers, there are six types of two-phase structure invariants for Friedel pairs. Two of the six are single-wavelength invariants; the other four are mixed-wavelength invariants. It is shown that the latter can be estimated by a straightforward extension of results from the probabilistic direct-methods theory for the single-wavelength anomalous scattering case described in paper I [Hauptman (1982). Acta Cryst. A38, 632-641]. Statistical tests of the mixed-wavelength estimates are reported for small-molecule and macro-molecular examples.

Mathematics↗

PubMed1993

Structural and conformational studies on bio-active flavonoids. Crystal and molecular structure of a complex formed between 2',6'-dimethoxyflavone and orthophosphoric acid: a model for flavone-nucleotide interactions.

In order to investigate mechanisms of action of flavones at the molecular level, we have prepared a complex between a flavone and orthophosphoric acid which can be considered as a simplest model of interaction between a flavone and a more complex biological phosphate such as nucleotide, coenzyme or DNA. With orthophosphoric acid, the title flavone forms crystals which have 1:2 stoichiometry (C17H14O4.2H3PO4). This compound was found to be the 1:1 salt co-crystallized with the unionized molecular acid C17H15O4+.H2PO4-.H3PO4. The symmetry is monoclinic, space group P2(1)/n and unit cell dimensions a = 15.571(2), b = 7.369(1), c = 17.837(2) A, beta = 100.84(1) degrees. One molecule of phosphoric acid is present as a solvate molecule of crystallization, but the other is ionized and protonates the carbonyl oxygen, introducing conformational and bond distance changes in the flavone. The dihedral angle between the benzopyrone and phenyl rings is 47 degrees. Complexes with phosphate groups involve strong hydrogen bonds and are expected to play important roles in biomolecular structures.

Crystallography↗

PubMed1992

Crystal chemistry of Mg2P2O7.nH2O, n = 0, 2 and 6: magnesium-oxygen coordination and pyrophosphate ligation and conformation.

The crystal structure of the hexahydrate has been determined and is compared with the known structures of the dihydrate and two forms of the anhydrous compound. Comparisons among the structures provide some insight as to the structural role of Mg2+ as a cofactor in the ATP-ADP hydrolysis reactions of bioenergetics. Crystal data for dimagnesium pyrophosphate hexahydrate: Mg2P2O7.6H2O, M(r) = 330.66, monoclinic, P2(1)/n, a = 7.189 (2), b = 18.309 (8), c = 7.665 (5) A, beta = 92.360 (14) degrees, V = 1008.1 A3, Z = 4, Dx = 2.18 mg mm-3, F(000) = 680, mu = 0.609 mm-1 for lambda(Mo K alpha) = 0.7107 A. R(magnitude of F) = 0.047 for 937 data.

Adenosine Triphosphate↗

PubMed1992

Crystal structure of valinomycin-monohydrate cage complexes crystallized from dioxane.

Valinomycin, cyclo-[(L-Val-D-Hyv-D-Val-L-Lac)3-], was crystallized from aqueous dioxane solvent as a monohydrate complex in which water molecules were found within the ion-binding cavity of the ionophore: monoclinic P2(1), a = 14.377 (3), b = 41.554 (14), c = 14.080 (3) A, beta = 118.27 (2) degrees, Z = 4. There are two non-equivalent valinomycin-water complexes and three dioxane molecules in the asymmetric unit. The ionophore molecules adopt two similar but non-identical, octahedral, bracelet, cage conformations that are a consequence of two distinct ways in which the complexed water molecules can deform the normal octahedral coordinate geometry of the metal binding site. In the first complex the water molecule forms hydrogen donor bonds to the carbonyl oxygens of two L-valine residues on one facial side of the cavity, while in the second complex the water molecule is trigonal-planar coordinate and binds to two L-valine residues on one entrant face of the cavity plus a third D-valine residue from the opposite side of the cavity.

Binding Sites↗

PubMed1991

On integrating the techniques of direct methods with anomalous dispersion. II. Statistical properties of the two-phase structure invariants.

Results of a statistical study of probabilistic estimates of two-phase structure invariants (TPSI) for Friedel pairs in the case of single-wavelength anomalous scattering are reported. Numerical analysis of the TPSI sign, magnitude and error distributions shows that the concise formula for TPSI by probability theory [Hauptman (1982). Acta Cryst. A38, 632-641; Giacovazzo (1983). Acta Cryst. A39, 585-592] has desirable statistical properties. Computational results for the known structures of cocaine methiodide (N-methylcocaine iodide) and of cytochrome c550 and its PtCl2-4 derivative show that when [E[ values are large most of the signs of the TPSI are correctly determined - for [E[ greater than 1.0, 90% or more of the TPSI signs are positive as predicted - and the errors in the estimated TPSI magnitudes do not exceed approximately 10% for [E[ greater than 1.0 in the small-molecule case or approximately 50% for [E[ greater than 1.5 in the macromolecular case. These results suggest that the theory will be useful for estimating the TPSI for unknown structures.

Models, Chemical↗

PubMed1991

Electron distributions in peptides and related molecules. 1. An experimental and theoretical study of N-acetyl-L-tryptophan methylamide.

The thermal vibrations and electron density of N-Ac-L-Trp-NHMe have been analyzed using single-crystal X-ray diffraction data measured at 103 K with Mo K alpha radiation to a resolution corresponding to (sin theta max)/ lambda = 1.17 A-1. Measurements of 10,527 reflections gave 4913 unique data [R(int)(magnitude of F2) = 0.019] of which 2641 had I greater than 3 sigma (I). A multipolar atomic density model was fitted [R(magnitude of F) = 0.028] in order to calculate phases for the crystal structure factors and map the valence-electron distribution. The phase problem for determining deformation densities by Fourier synthesis for noncentrosymmetric crystals is discussed. The experimental density agrees well with the theoretical density from an ab initio SCF molecular wave function calculated at the crystallographic molecular geometry with a split-valence basis set. Both the experimental and theoretical analyses confirm that the electron distribution is the same in the two different peptide groups in the molecule. Crystal data: C14H17N3O2, Mr = 259.31, orthorhombic, P2(1)2(1)2(1), Z = 4, F(000) = 522 e from 295 to 103 K; at 295 K, a = 8.152(2), b = 11.170 (2), c = 15.068 (3) A, V = 1372 A3, Dx = 1.26 mg mm-3; at 103 K, a = 8.209 (3), b = 11.016 (2), c = 14.760 (4) A, V = 1135 A3, Dx = 1.29 mg mm-3, mu = 0.083 mm-1 for lambda = 0.7107 A.

Chemical Phenomena↗

PubMed1988

A priori estimation of scale and overall anisotropic temperature factors from the Patterson origin peak.

An idea due to D. Rogers [Computing Methods in Crystallography (1965), edited by J. S. Rollett, pp. 117-148. Oxford: pergamon Press] has been developed and implemented. The method is an advantageous alternative to Wilson plot or K-curve scaling of intensity data. On the relative experimental scale the structure factor can be written in matrix notation as F(h) = kappa -1 sigma j fj(h) exp (2 pi ih tau xj) exp (-h tau bjh); and the squared structure-factor magnitude can be written as magnitude of F(h)2 = kappa -2 exp (-2h tau bh) [sigma j fj2+ 2 sigma j sigma k greater than jfjfk exp [2 pi ih tau (xj-xk)]], if a a common, or average, anisotropic temperature factor is factored out of the atomic summations. The fj2 summation corresponds to the Patterson origin peak, and the fjfk double summation to the off-origin Patterson peaks. A tovariate Gaussian density function, P(u)-Pmin = Po exp (-u tau pu), is fitted by least squares to the origin peak from a Patterson synthesis with coefficients magnitude of F2 meas/sigma jf2j. Fourier inversion of the fitted Gaussian gives the scale and thermal parameters, k2 = (detp)1/2/(pi 3/2 Vcell Po) and b = (pi 2/2)p-1. The fit of the parameter Pmin is constrained by the condition that Pmin = -F(000)2/(k2Vcell sigma j Zj2), and thus only po and the six coefficients pij (i less than j = 1,2,3) are independent parameters.

Crystallography↗

PubMed1988

New analysis of the neutron diffraction data for anhydrous orthophosphoric acid and the structure of H3PO4 molecules in crystals.

Two neutron data sets, which had been analyzed separately to determine the H-atom positions in H3PO4 crystals [Cole (1966). PhD Thesis, Univ. of Washington, Pullman, USA], have been re-analyzed in a joint refinement, fitting separate scale and extinction parameters for each data set, in order to obtain more precise positional and vibrational parameters. The new refinement gave R(F) = 0.036 for the combined 743 data. For the new results, and for six other H3PO4 molecules from four other, different crystal structures, thermal vibration analyses have been performed, and the molecular structures, thermal vibrations and hydrogen-bonding effects are compared. The rigid-body model is found to be better than the riding model for the PO4 groups. The P-OH bond lengths are markedly affected by hydrogen bonding, but seem to be independent of O = P-O-H conformation. These effects are interpreted in terms of the P-O partial double-bond character. Crystal data (Cole, 1966): anhydrous orthophosphoric acid, H3PO4, Mr = 98.00, room temperature, P2(1)/c, a = 5.779(9), b = 4.826 (4), c = 11.606 (40) A, beta = 95.26 (18) degrees, V = 322.3 (20) A3, Z = 4, Dx = 2.019 mg mm-3, mu = 0.1687 mm-1 for neutrons with lambda = 1.450 A.

Hydrogen Bonding↗

PubMed1980

Carboxybiotin translocation mechanisms suggested by diffraction studies of biotin and its vitamers.

Biotin is a coenzyme that fixes CO2 for transfer in a family of carboxylase, decarboxylase, and transcarboxylase enzymes. Their enzyme reactions involve two basic steps during which a carboxybiotinyl intermediate forms at one site and translocates to a second (distinct) site for CO2 transfer. Our diffraction studies of biotin and its vitamers suggest that translocation involves rotation about one, or at most two, bonds in biotin's valeryl chain. The rotations are energetically economical gauche in equilibrium trans rotations about the two valeryl bonds nearest the biotin bicyclic ring. They move a carbon atom of a CO2 moiety bound at N-1' approximately 7 A, a distance in accord with spectroscopic measurements of one of the biotin enzymes. From our studies we infer that sulfur in biotin imparts to the valeryl chain a conformational variability necessary for bond rotation and, hence, translocation between catalytic sites.

Biotin↗