Use of an ion-binding site to bypass the 1000-atom limit to structure determination by direct methods.
Proteins with more than 1000 non-H atoms and without heavy-atom prosthetic groups are very difficult to solve by ab initio direct methods. T4 lysozyme is being used to explore these limits. The protein has 1309 non-H atoms, seven S atoms, no disulfide bonds and no heavy-atom prosthetic group. It is recalcitrant to structure determination by direct methods using X-ray diffraction data to 0.97 A. It is shown here that it is possible to obtain a truly ab initio structure determination of a variant of the protein that has an Rb+ (Z = 37) binding site. Using diffraction data to 1.06 A resolution, the direct-methods programs SIR2002 and ACORN independently solved the structure in about 20 h. The bound Rb+, which contributes about 1.7% of the total scattering, does not appear to distort the structure or to inhibit refinement (R factor 12.1%). The phases obtained via SIR2002 or ACORN are in good agreement with those from a reference structure obtained from conventional molecular-substitution and refinement procedures (average error in the figure-of-merit-weighted phases of less than 25 degrees). Thus, proteins with more than 1000 atoms that include halide-binding or other such sites may be amenable to structure determination by ab initio direct methods. The direct-methods approaches are also compared with structure determination via use of the anomalous scattering of the Rb+ ion. As shown by examples, high-resolution structures determined by direct methods can be useful in highlighting regions of strain in the protein, including short hydrogen bonds and non-planar peptide groups.
Mooers
Blaine H M
BH
Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, 1229 University of Oregon, Eugene, OR 97403-1229, USA.
Matthews
Brian W
BW
D000465:Algorithms; D017122:Bacteriophage T4 / Q000378:metabolism; D001665:Binding Sites; D003460:Crystallization; D018360:Crystallography, X-Ray / Q000379:methods*; D004220:Disulfides / Q000737:chemistry; D006859:Hydrogen / Q000737:chemistry; D006860:Hydrogen Bonding; D007477:Ions; D008024:Ligands; D008958:Models, Molecular; D008962:Models, Theoretical; D009113:Muramidase / Q000737:chemistry*; D016296:Mutagenesis; D016297:Mutagenesis, Site-Directed; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D012413:Rubidium / Q000737:chemistry; D012984:Software; D013997:Time Factors; D014961:X-Ray Diffraction
D004220:Disulfides; D007477:Ions; D008024:Ligands; D010455:Peptides; D006859:Hydrogen; D009113:Muramidase; D012413:Rubidium