A rapid method for positioning small flexible molecules, nucleic acids, and large protein fragments in experimental electron density maps

A Monte Carlo procedure, encoded in the program Blob, has been developed an d tested for the purpose of positioning large molecular fragments or small flexible molecules in electron density maps, The search performed by the al gorithm appears to be sufficiently thorough to accurately position a small flexible ligand in well-defined density while remaining sufficiently random to offer interesting alternate suggestions for density representing disord ered binding modes of a ligand, Furthermore, the algorithm is shown to be e fficient enough to accurately position large rigid molecular fragments, In the first of the test cases with large molecular fragments, Blob was surpri singly effective in positioning a poly-alanine model of a 53-residue domain in poor electron density resulting from molecular replacement with a parti al model, At 3.0 Angstrom resolution the domain was positioned consistently within 0.2 Angstrom of its experimentally determined position, Even at 6.0 Angstrom resolution Blob could consistently position the domain to within 0.75 Angstrom of its actual position. A second set of tests with large mole cular fragments revealed that Blob could correctly position large molecular fragments with quite significant deviations from the actual structure. In this test case, fragments ranging from a 170-residue protein domain with a 3.8 Angstrom rms deviation from the actual structure to a 22-base pair idea l B-form DNA duplex were positioned accurately in a 3.2 Angstrom electron d ensity map derived from multiple isomorphous replacement methods. Even when decreasing the quality of the maps, from a figure of merit of 0.57 to as l ow as 0.35, Blob could still effectively position the large protein domain and the DNA duplex. Since it is efficient, can handle large molecular fragm ents, and works in poor and low resolution maps, Blob could be a useful too l for interpreting electron density maps in de novo structure determination s and in molecular replacement studies. Proteins 1999;36:512-525. (C) 1999 Wiley-Liss, Inc.