Biomedical subjects

Y X Gu

Publications and source records attributed to Y X Gu.

15 recordsLinked to original sources

PubMed2004

Optimizing the error term in direct-method SAD phasing.

The probability formula of the direct-method SAD (single-wavelength anomalous diffraction) phasing proposed by Fan & Gu (1985, Acta Cryst. A41, 280-284) contains an error term which is related to the lack-of-closure error. This error term is used as a weighting function in the phase derivation and in the subsequent calculation of electron-density maps. Previously, there has been a constant in the error term that has had to be determined empirically for each particular case. It has been found that improper choice of the constant often leads to failure of the direct-method SAD phasing. The problem is resolved by introducing a modified error term and a method of automatically tuning the associated scaling factor.

Algorithms↗

PubMed2004

Direct-method SAD phasing with partial-structure iteration: towards automation.

The probability formula of direct-method SAD (single-wavelength anomalous diffraction) phasing proposed by Fan & Gu (1985, Acta Cryst. A41, 280-284) contains partial-structure information in the form of a Sim-weighting term. Previously, only the substructure of anomalous scatterers has been included in this term. In the case that the subsequent density modification and model building yields only structure fragments, which do not straightforwardly lead to the complete solution, the partial structure can be fed back into the Sim-weighting term of the probability formula in order to strengthen its phasing power and to benefit the subsequent automatic model building. The procedure has been tested with experimental SAD data from two known proteins with copper and sulfur as the anomalous scatterers.

Automation↗

PubMed2004

SAD phasing by combination of direct methods with the SOLVE/RESOLVE procedure.

In the initial stage of SAD phasing, the essential point is to break the intrinsic phase ambiguity. The presence of two kinds of phase information enables the discrimination of phase doublets from SAD data prior to density modification. One is from the heavy atoms (anomalous scatterers), while the other is from the direct-methods phase relationships. The former can be expressed by the Sim distribution, while the latter can be expressed by the Cochran distribution. Typically, only the Sim distribution has been used to yield initial phases for subsequent density modification. However, it has been demonstrated that using direct-methods phases based on the product of the Sim and Cochran distributions can lead to improved initial phases. In this paper, the direct-methods phasing procedure OASIS has been improved and combined with the SOLVE/RESOLVE procedure. Experimental SAD data from three known proteins with expected Bijvoet ratios / in the range 1.4-7.0% were used as test cases. In all cases, the phases obtained using the program RESOLVE beginning with initial phases based on experimental phases plus Sim and direct-methods information were more accurate than those based on experimental plus Sim phase information alone.

Azurin↗

PubMed2002

Direct-method-aided phasing of MIR diffraction data from proteins.

Direct methods have successfully been used to break the phase ambiguity intrinsic in the single isomorphous replacement (SIR) data of proteins. Based on this, the procedure 'direct-method-aided MIR phasing' (DMIR) has been proposed and applied to the four-derivative multiple isomorphous replacement (MIR) data of a known protein containing 682 amino acid residuals in the asymmetric unit. The data set consists of 14,500 unique reflections at 3 A resolution with F(obs.) greater than 2sigma. Test calculation showed that the phases from conventional MIR phasing could be significantly improved by direct methods leading to obvious improvement in the quality of the resultant Fourier maps.

Crystallography, X-Ray↗

PubMed2001

Direct-method-aided phasing of MAD data.

The direct methods of breaking the phase ambiguity intrinsic in one-wavelength anomalous scattering (OAS) data and MAD phasing are powerful methods in their own rights. In a different context, in addition to their success in phasing OAS data, direct methods can also be useful in the treatment of MAD data. The idea has been tested with the MAD data at 2.5 A resolution from the protein human adenosine kinase [Mathews et al. (1998), Biochemistry, 37, 15607--15620]. The results showed that the incorporation of direct methods in MAD phasing led to a significant improvement of phases over those obtained from the conventional MAD phasing method alone, as indicated by improved map correlation coefficients (with the existing model), reduced phase errors by 4.5 degrees and improved map connectivity.

Adenosine Kinase↗

PubMed1999

Combining direct methods with isomorphous replacement or anomalous scattering data. VIII. Phasing experimental SIR data with the replacing atoms in a centrosymmetric arrangement.

A multisolution direct method has been proposed to resolve the phase ambiguity intrinsic in single isomorphous replacement data of proteins with the replacing atoms in a centrosymmetric arrangement. The phase ambiguity of each reflection is in fact a 'sign ambiguity' of the phase difference between the phase of the native protein and that of the replacing atoms, i.e. +/- |Deltatheta| = theta - theta'. The P+ probability formula can be used to derive the signs. The multisolution phasing procedure is initiated using random starting values of P+. A cluster analysis is used instead of figures of merit to find the correct solution. The direct-method phases can be further improved by density-modification techniques. The method was tested with the experimental SIR data at 2 A resolution from a known protein aPP; satisfactory results were obtained.

Animals↗

PubMed1997

Use of single isomorphous replacement data of proteins - resolving the phase ambiguity and a new procedure for phase extension.

A procedure combining direct methods and solvent flattening to break the phase ambiguity intrinsic to the single isomorphous replacement (SIR) technique has been tested with the experimental SIR data of the known protein RNase Sa at 2.5 A resolution. The use of direct methods provided better initial phases for the solvent-flattening procedure, while the solvent-flattening procedure greatly improved direct-method phases leading to a traceable Fourier map. A small subset of known phases at low resolution makes direct phasing of SIR data much easier. Accordingly a method for extending low-resolution phases to high-resolution ones is proposed making use of additional SIR information. This reduces the problem of finding a value in the range of 0-2pi for each unknown phase to that of just making a choice between two possible values. Tests with the known protein RNase Sa showed that the method is able to extend phases from a resolution of 6 to 2.5 A leading to an easily traceable Fourier map. The solvent-flattening technique and the combination of which with direct methods were used for the phase extension. Either procedure yielded reasonably good results, but on the whole, the result from the combination of direct methods with solvent flattening is better. Results of the latter procedure were further compared with that from direct phasing of the 2.5 A SIR data and with that from phase extension by solvent flattening without SIR information. An improvement gained by the use of SIR information is evident.

Journal Article↗

PubMed1996

Direct-space methods in phase extension and phase refinement. V. The histogram moments method.

Any distribution is completely defined by its moments. It is shown that a process of phase refinement can be carried out, based on Fourier transforms, which modifies the moments of electron density, separately in the protein and solvent regions, towards target values. Tests have been carried out on two moderate-sized proteins with 800-900 atoms in the asymmetric unit, one containing heavy atoms and the other not. It has been found that refinement using the third moment about zero in the protein region is most effective and that refinement with higher moments, or in the solvent region, adds nothing useful. Two kinds of weights are necessary in the method. One is for giving a weighted mixture of new phase indications with original phase estimates from, say, multiple isomorphous replacement. The other weights are applied to the Fourier coefficients of density maps to give the best possible signal:noise ratio. These weights have been explored empirically and the best ones found are described. It is concluded that since the moments method, which changes phases in reciprocal space, is independent of other histogram-matching procedures, which change density in real space, it has something to offer in a refinement package containing several procedures.

Journal Article↗

PubMed1989

Effects of artemether on peripheral T, B, T mu and T gamma lymphocytes in beagle dog.

The effects of intramuscular injection of Artemether on peripheral T, B, T mu and T gamma lymphocytes in beagle dogs was investigated cytochemically. Doses used were 6, 19, and 32 MKD, respectively. Results showed that after injection of Artemether for 15 successive days, the T, B, and T mu lymphocytes of the 19 and 32 MKD groups were markedly reduced and the T gamma lymphocytes of all 3 dosage groups were decreased to zero. 28 days after cessation of the drug, T, T mu and T gamma lymphocytes had recovered to control levels, while the B lymphocytes of the 19 and 32 MKD groups remained markedly lower than those of the control groups. The differences and similarities of the effects on the peripheral T, B, T mu and T gamma lymphocytes produced by the 3 dosages of Artemether and the relationship between the changes of T, B lymphocytes and immunological function of beagle dogs are discussed.

Animals↗

PubMed1988