The Solution of the Phase Problem by the Isomorphous Replacement Method

1994 ◽  
pp. 129-182
Author(s):  
Jan Drenth
Keyword(s):  
Phase Problem ◽  
Replacement Method ◽  
Isomorphous Replacement

The single isomorphous replacement method. A correction

1962 ◽  
Vol 15 (10) ◽  
pp. 1060-1060 ◽  
Author(s):  
D. M. Blow ◽  
M. G. Rossmann
Keyword(s):  
Replacement Method ◽  
Isomorphous Replacement

The structure of haemoglobin - IV. Sign determination by the isomorphous replacement method

1954 ◽  
Vol 225 (1162) ◽  
pp. 287-307 ◽  
Keyword(s):  
Silver Ions ◽  
Isomorphous Substitution ◽  
Transform Method ◽  
Entire Area ◽  
Heavy Atoms ◽  
Replacement Method ◽  
Isomorphous Replacement ◽  
Sulphydryl Groups ◽  
Sign Relations ◽  
The Waves

Native horse haemoglobin contains free sulphydryl groups and forms crystalline compounds with para -mercuribenzoate groups and with silver ions. Crystals in which two of the four available SH groups are so combined are exactly isomorphous with normal monoclinic methaemoglobin, but exhibit significant changes in the intensities of many reflexions. The changes in F ( h 0 l ) were used to determine the x and z parameters of the pair of heavy atoms attached to each haemoglobin molecule; this was done both for the normal wet lattice and for one of the acid-expanded lattices. The positions of the heavy atoms proved to be slightly different in each case, giving rise to three sets of diffraction fringes, each set making measurable contributions in different areas of the reciprocal net. In each case the isomorphous substitution allowed the signs of just over two-thirds of the reflexions to be found with certainty. Between them the three sets of diffraction fringes determined the signs over the entire area of the h 0 l plane so far investigated. These signs were then superimposed on the waves of the transform described in previous papers of this series. All the sign relations established by the transform method were confirmed and the remaining uncertainties cleared up. Comparison of the transform with the three sets of isomorphous replacement results allowed the consistency of the signs to be rigorously checked; not a single inconsistent sign was found. In the normal wet lattice the mercury and the silver compounds between them allowed the signs of 87 out of 94 reflexions to be found with certainty. This suggests that the isomorphous replacement method may offer a way of finding the phases in protein crystals even when practical difficulties preclude the use of the transform method.

The single isomorphous replacement method

1961 ◽  
Vol 14 (11) ◽  
pp. 1195-1202 ◽  
Author(s):  
D. M. Blow ◽  
M. G. Rossmann
Keyword(s):  
Replacement Method ◽  
Isomorphous Replacement

scholarly journals Studies on crystal structures, active-centre geometry and depurinating mechanism of two ribosome-inactivating proteins

1995 ◽  
Vol 309 (1) ◽  
pp. 285-298 ◽  
Author(s):  
Q Huang ◽  
S Liu ◽  
Y Tang ◽  
S Jin ◽  
Y Wang
Keyword(s):  
Three Dimensional ◽  
Active Centre ◽  
Ribosome Inactivating Proteins ◽  
Aromatic Stacking ◽  
Replacement Method ◽  
Isomorphous Replacement ◽  
Molecular Replacement Method ◽  
The Difference ◽  
Related Proteins ◽  
The Relationship

Two ribosome-inactivating proteins, trichosanthin and alpha-momorcharin, have been studied in the forms of complexes with ATP or formycin, by an X-ray-crystallographic method at 1.6-2.0 A (0.16-0.20 nm) resolution. The native alpha-momorcharin had been studied at 2.2 A resolution. Structures of trichosanthin were determined by a multiple isomorphous replacement method. Structures of alpha-momorcharin were determined by a molecular replacement method using refined trichosanthin as the searching model. Small ligands in all these complexes have been recognized and built on the difference in electron density. All these structures have been refined to achieve good results, both in terms of crystallography and of ideal geometry. These two proteins show considerable similarity in their three-dimensional folding and to that of related proteins. On the basis of these structures, detailed geometries of the active centres of these two proteins are described and are compared with those of related proteins. In all complexes the interactions between ligand atoms and protein atoms, including hydrophobic forces, aromatic stacking interactions and hydrogen bonds, are found to be specific towards the adenine base. The relationship between the sequence conservation of ribosome-inactivating proteins and their active-centre geometry was analysed. A depurinating mechanism of ribosome-inactivating proteins is proposed on the basis of these results. The N-7 atom of the substrate base group is proposed to be protonated by an acidic residue in the active centre.

The Structure of haemoglobin - VII. Determination of phase angles in the non-centrosymmetric [100] zone

1958 ◽  
Vol 247 (1250) ◽  
pp. 302-336 ◽  
Keyword(s):  
Standard Error ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Anomalous Scattering ◽  
Heavy Atoms ◽  
Replacement Method ◽  
Isomorphous Replacement ◽  
Arbitrary Phase ◽  
Phase Angles

In the last paper in this series a Fourier projection down the [010] axis of horse haemoglobin was given (Bragg & Perutz 1954). This projection was centrosymmetric. As a first step towards the three-dimensional analysis, the projection down [100] has now been attacked. This projection is non-centrosymmetric, and arbitrary phase angles have had to be determined. All the fundamental problems of a three-dimensional study are met, but only a small number of reflexions need be dealt with. The isomorphous replacement method has been used successfully with three mercury derivatives of haemoglobin. This provided a test of new methods for finding the vectors relating heavy atoms. Particular attention has been given to estimation of errors, and to their effect on the results. Further information about the phases has been derived from anomalous scattering by the mercury atoms, using CrKα and CuKα radiation. By combining these results, the phases of most reflexions out to a spacing of about 6 Å have been determined with a standard error of about 25°. Ambiguous results are obtained for a few reflexions. The resulting electron density projection shows peaks up to four times the estimated standard error. The prospects for three-dimensional structure analysis at 6 Å resolution are favourable. If the polypeptide chain is coiled in the α-form, the contrast should be sufficient for it to show up throughout its length.

scholarly journals Features of the secondary structure of a protein molecule from powder diffraction data

2010 ◽  
Vol 66 (7) ◽  
pp. 756-761 ◽  
Author(s):  
Sebastian Basso ◽  
Céline Besnard ◽  
Jonathan P. Wright ◽  
Irene Margiolaki ◽  
Andrew Fitch ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Powder Diffraction ◽  
De Novo ◽  
Structural Information ◽  
Heavy Atom ◽  
Protein Molecule ◽  
Lattice Parameter ◽  
Egg White Lysozyme ◽  
Replacement Method ◽  
Isomorphous Replacement

Protein powder diffraction is shown to be suitable for obtainingde novosolutions to the phase problem at low resolutionviaphasing methods such as the isomorphous replacement method. Two heavy-atom derivatives (a gadolinium derivative and a holmium derivative) of the tetragonal form of hen egg-white lysozyme were crystallized at room temperature. Using synchrotron radiation, high-quality powder patterns were collected in which pH-induced anisotropic lattice-parameter changes were exploited in order to reduce the challenging and powder-specific problem of overlapping reflections. The phasing power of two heavy-atom derivatives in a multiple isomorphous replacement analysis enabled molecular structural information to be obtained up to approximately 5.3 Å resolution. At such a resolution, features of the secondary structure of the lysozyme molecule can be accurately located using programs dedicated to that effect. In addition, the quoted resolution is sufficient to determine the correct hand of the heavy-atom substructure which leads to an electron-density map representing the protein molecule of proper chirality.

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