Search PubMedSearch

PubMed · 9818264

New developments in phase refinement.

Abstract

A longstanding problem in X-ray crystallography is that vital information regarding the crystal phases in missing from the experimental data that are gathered in the diffraction experiment. Prior knowledge needs to be introduced in order to resolve phase ambiguities whenever the diffraction data are not sufficient to unequivocally reconstruct the crystal phases through anomalous or isomorphous differences. Very recent developments include progress in the application of direct methods to small proteins and other compounds of a similar small size (Shake 'n' Bake, SHELXD, CRUNCH and SIR96), bias-free refinement through the gamma-correction (Solomon), improvements in the determination of phase probability distributions (SHARP) and automated atomic refinement (wARP).

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

J P Abrahams, R A De Graaff. 1998. New developments in phase refinement.. https://doi.org/10.1016/s0959-440x(98)80151-6

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

HIV-1 reverse transcriptase-pseudoknot RNA aptamer interaction has a binding affinity in the low picomolar range coupled with high specificity.

Systematic evolution of ligands by exponential enrichment (SELEX) is a powerful method for the identification of small oligonucleotides that bind with high affinity and specificity to target proteins. Such DNAs/RNAs are a new class of potential chemotherapeutics that could block the enzymatic activity of pathologically relevant proteins. We have conducted a detailed biochemical study of the interaction of human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT) with a SELEX-derived pseudoknot RNA aptamer. Electron paramagnetic resonance spectroscopy of site-directed spin-labeled RT mutants revealed that this aptamer was selected for binding to the "closed" conformation of the enzyme. Kinetic analysis showed that the RNA inhibitor bound to HIV RT in a two-step process, with association rates similar to those described for model DNA/DNA and DNA/RNA substrates. However, the dissociation of the pseudoknot RNA from RT was dramatically slower than observed for model substrates. Equilibrium binding studies revealed an extraordinarily low K(d), of about 25 pm, for the enzyme-aptamer interaction, presumably a consequence of the slow off-rates. Additionally, this pseudoknot aptamer is highly specific for HIV-1 RT, with the closely related HIV-2 enzyme showing a binding affinity close to 4 orders of magnitude lower.

Crystallography, X-Ray

Structural features of normal and mutant human lysosomal glycoside hydrolases deduced from bioinformatics analysis.

Lysosomal storage diseases are due to inherited deficiencies in various enzymes involved in basic metabolic processes. As with other genetic diseases, accurate structure data for these enzymatic proteins should help in better understanding the molecular effects of mutations identified in patients with the corresponding lysosomal diseases; however, no such three-dimensional (3D) structure data are available for many lysosomal enzymes. Thus, we herein intend to illustrate for an audience of molecular geneticists how structure information can nonetheless be obtained via a bioinformatics approach in the case of five human lysosomal glycoside hydrolases. Indeed, using the two-dimensional hydrophobic cluster analysis method to decipher the sequence information available in data banks for the large group of glycoside hydrolases (clan GH-A) to which these human lysosomal enzymes belong, we could deduce structure predictions for their catalytic domains and propose explanations for the molecular effects of mutations described in patients. In addition, in the case of human beta-glucuronidase for which experimental 3D data have been reported, we also show here that bioinformatics methods relying on the available 3D structure information can be used to obtain further insights into the effects of various mutations described in patients with Sly disease. In a broader perspective, our work stresses that, in the context of a rapid increase in protein sequence information through genome sequencing, bioinformatics approaches might be highly useful for generating structure-function predictions based on sequence-structure interrelationships.

Crystallography, X-Ray

On the direct determination of three-dimensional crystallographic phases at low resolution: crambin at 6 A.

Using a pseudo-atom approach, the three-dimensional crystallographic phases for the protein crambin (a = 40.76, b = 18.49, c = 22.33 A, beta = 90.61 degrees, space group P2(1)) were determined to 6 A by direct methods. First, the centrosymmetric h0l set was assigned phases by symbolic addition, and the initial solution was then refined by Fourier methods. Phase values of strong reflections were then permuted, and the decision to change the phase value for two of these was made by consulting a cross-correlation of the experimental density histogram to the theoretical or known histogram for the protein. The two-dimensional basis was then extended by the Sayre equation into three dimensions by assigning a phase to a third allowed hkl origin-defining reflection and an algebraic value to another axial reflection. The correct solution was again identified by the histogram correlation, yielding a solution in which the mean phase error for all 98 reflections was 61.5 degrees or 23.1 degrees for the 21 most intense reflections. A parallel study with another protein indicates this method may have general utility.

Crystallography, X-Ray