A NEW ROUTINE FOR THINNING, EDITING AND FITTING MIR MAPS USING REAL-SPACE MOLECULAR-DYNAMICS

A new routine has been developed for fitting multiple isomorphous repl acement (MIR) maps. The map is first thinned and reduced to a series o f 'traces'. Each trace consists of a main trace of defined length and a series of branching side traces. Using this trace representation, th e entire map can be viewed at one time and the major secondary structu ral features can be recognized. A number of features have been built i nto the routine for editing these traces, allowing neighboring traces to be connected and incorrect connections to be broken. After the trac es have been edited, a polyserine fit is generated. The traces are use d to guide the initial positioning of a short polyserine segment. This segment is then refined using a real-space molecular-dynamics procedu re, which uses the gradient of the electron density as a pseudoforce o n the polyserine atoms. After the structure of this initial polyserine has been refined, another serine is added at one end, a short period (about 10 s on a personal Silicon Graphics IRIS workstation) of molecu lar dynamics is applied and the procedure is repeated. The final refin ed structure depends only on the electron density and is independent o f the thinned traces. The routine is illustrated with two examples. On e example uses the 3.0 angstrom map generated directly from a model pr otein. This allows direct comparison between the polyserine fit and th e model that was used to generate the map. The second example uses the experimental MIR map for lipovitellin. This is a very large protein ( about 1300 amino acids), which has a poor-quality map that has not yet been refined. The program makes extensive use of Silicon Graphics gra phical (GL) routines.