Biomedical subjects

D Y Guo

Publications and source records attributed to D Y Guo.

7 recordsLinked to original sources

PubMed2000

Bulk-solvent correction in direct-methods phasing.

It is shown that for crystals of large proteins at low diffraction resolution, with N approximately 10 000 independent non-H protein atoms and d(min) approximately 8 A, a simple bulk-solvent correction yields the Sayre equation in its classical form, F(h) = q summation operator(k)F(k)F(h - k). In the low-resolution protein case, the proportionality factor becomes q = 1/[( - rho(S))V], where V is the unit-cell volume, rho(S) is the assumed constant electron density in the solvent regions of the crystal and is the average electron density in the protein regions. The classical form of the tangent formula follows from the bulk-solvent-corrected Sayre equation and its validity at low resolution is verified in empirical calculations.

Adenosylhomocysteinase↗

PubMed2000

Globbic approximation in low-resolution direct-methods phasing.

Probabilistic direct-methods phasing theory, originally based on a uniform atomic distribution hypothesis, is shown to be adaptable to a non-uniform bulk-solvent-compensated globbic approximation for protein crystals at low resolution. The effective number n(g) of non-H protein atoms per polyatomic glob increases with decreasing resolution; low-resolution phases depend on the positions of only N(g) = N(a)/n(g) globs rather than N(a) atoms. Test calculations were performed with measured structure-factor data and the refined structural parameters from a protein crystal with approximately 10 000 non-H protein atoms per molecule and approximately 60% solvent volume. Low-resolution data sets with d(min) ranging from 15 to 5 A gave n(g) = ad(min) + b, with a = 1.0 A(-1) and b = -1.9 for the test case. Results of tangent-formula phase-estimation trials emphasize that completeness of the low-resolution data is critically important for probabilistic phasing.

Crystallization↗

PubMed1999

On 'globbicity' of low-resolution protein structures.

Using Harker's [Harker (1953). Acta Cryst. 6, 731-736] idea of spherically averaged polyatomic groups or 'globs' as the units of structure suitable for analyzing low-resolution diffraction data from protein crystals, 'globbic' scattering factors have been calculated for main-chain peptide units and amino-acid side-chain groups to 3 A resolution via Debye's [Debye (1915). Ann. Phys. (Leipzig), 46, 809-823] scattering formula. It is shown that the scattering factors are insensitive to intra-globbic conformational variation and can be approximated fairly well by a single-Gaussian formula, i.e. fg(s) = Zg exp(-1.7Zgs2), where s = (sin theta)/lambda and Zg is the total electron count for the atoms of the glob. Phase errors due to the globbic approximation and their effect on electron-density maps at 3.5 A resolution have been assessed via calculations for the crambin structure; this analysis indicates that the globbic scattering factors will be useful in efforts to develop procedures for direct-methods phasing of diffraction data to approximately 3.5 A resolution from protein crystals.

Crystallography, X-Ray↗

PubMed1997

On integrating the techniques of direct methods with anomalous dispersion. IV. A simplified perturbation treatment for SAS phasing.

Results from probabilistic theory for the single-wavelength anomalous-scattering (SAS) Friedel pair, two-phase structure invariants, psi H = phi H + phi-H, are used to show that the SAS three-phase structure invariants, psi HK = phi H + phi K + phi-H-K, tend to positive values that are easily estimated. Appropriate averages of the estimates provide SAS perturbation corrections in the form of positive origin shifts for the probability distribution of psi HK values and for the tangent formula. The theoretical probabilistic results are verified by empirical statistical analyses of model-calculated phases and experimentally measured structure-factor magnitudes for a small-molecule and a protein crystal structure.

Chemistry, Physical↗

PubMed1995

Use of globic scattering factors for protein structures at low resolution.

At 3 to 4 A resolution, the electron density of a protein may be modeled by a continuous chain of 'globs' representing the amide region of the peptide backbone and the side-chain residues. Group scattering factors are derived from a trans planar C alpha C = ONC alpha backbone segment and most favored side-chain conformer for 18 different amino acids. Trial calculations indicate that the phase error and crystallographic residual comparing the atomic and 'globic' models rapidly decrease from high to low resolution. At 3 A resolution, the phase error is approximately 80 degrees. These results indicate that the electron density of a protein composed of N amino acid residues may be adequately modeled by 2N globs at low resolution.

Amino Acids↗

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↗

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↗