Molecular replacement by evolutionary search

Abstract

Stochastic search algorithms can be used to perform rapid sixdimensional molecular-replacement searches. A molecularreplacement procedure has been developed that uses an evolutionary algorithm to simultaneously optimize the orientation and position of a search model in a unit cell. Here, the performance of this algorithm and its dependence on search model quality and choice of target function are examined. Although the evolutionary search procedure is capable of ®nding solutions with search models that represent only a small fraction of the total scattering matter of the target molecule, the ef®ciency of the search procedure is highly dependent on the quality of the search model. Polyalanine models frequently provide better search ef®ciency than allatom models, even in cases where the side-chain positions are known with high accuracy. Although the success of the search procedure is not highly dependent on the statistic used as the target function, the correlation coef®cient between observed and calculated structure-factor amplitudes generally results in better search ef®ciency than does the R factor. An alternative stochastic search procedure, simulated annealing, provides similar overall performance to evolutionary search. Methods of extending the evolutionary search algorithm to include internal optimization, selection and construction of the search model are now beginning to be investigated.

Heme-Ligand Tunneling in Group I Truncated Hemoglobins

“…The available molecular models of Mt-trHbN, Ce-trHb, and Pc-trHb were relocated into their respective crystal unit cells by molecular replacement, using the EPMR program (19). Mt-trHbN xenon adduct hosts two molecules per asymmetric unit (A and B subunits; space group P2 1 2 1 2 1 , unit cell constants a ϭ 44.3 Å, b ϭ 62.0 Å, c ϭ 90.7 Å); the xenon adducts of Ce-trHb (space group P2 1 2 1 2 1 , unit cell constants a ϭ 34.5 Å, b ϭ 52.9 Å, c ϭ 67.0 Å), and of Pc-trHb (space group P4 3 , unit cell constants a ϭ b ϭ 61.4 Å, c ϭ 33.8 Å) accommodate one protein molecule per asymmetric unit.…”

Crystal Structures of Engrailed Homeodomain Mutants

“…The data (Table I) were processed and scaled with DENZO/SCALEPACK (16). The structures were solved using molecular replacement (EMPR (17) and AMORE (18)) with the wild type structure (1ENH) as the search model. To minimize phase bias, only the peptide backbone was used for initial phase calculations and additional atoms were added or removed iteratively using arpWarp (19).…”

“…However, the fluorescence of the F8A mutant of En-HD has the same degree of quenching as the wild type (41). In the case of En-HD, Trp 48 is in close proximity of the terminal amino groups of Lys 17 and Lys 55 , which are also potential quenchers.…”

“…We have tested the fluorescence quenching of both K52A and K52E, where the positions of Lys 17 and Lys 55 are different (Fig. 2, E and F) and both, surprisingly, show the same magnitude as wild type (data not shown).…”

“…However, in the transcriptional repressor Engrailed from Drosophila, two lysines are instead found in these positions. We have substituted lysine 52 for glutamate, to mimic the conserved Glu 17 -Arg 52 salt bridge, and for alanine, to relieve the repulsion of the clustered positive charges. Standard equilibrium measurements demonstrate that both substitutions substantially increase the stability of the folded state.…”