Selenomethionine substituted protein
as a tool for phase determination


human chorionic gonadotropin


Introduction

Anomalous dispersion of x-ray scattering factors provides a basis for rather direct determination of crystal structures. Using synchrotron facilities is possible to measure x-ray diffraction at optimally chosen wavelengths. X-ray absorption edge of selenium (0.98 A) is easily accessible with synchrotron radiation. The chemistry of selenium is similar to sulphur than to thellurium. They are both neighbours in the oxygen series of the periodic table. Often, selenomethionin can completely replace methionine residues in proteins through overexpression in bacteria grown in medium containing selenomethionine as the only source of methionine. The procedure for engineering of selenomethionyl proteins is fairly straightforward and is described in next section.


Results of phasing using Se-met

Most selenomethionyl protein crystals are reported to be isomorphous with the native protein crystals. The derivative crystal is truly isomorphous to native crystal, with difference of 18 electrons at each selenium atom. That is useful for anomalous and isomorphous phasing methods. The phasing potential of selenomethionyl proteins is high. An average of 1 in 58 amino-acid residues is methionine. The level of both Bijvoet and dispersive differences are expected to be at least 5% of the total diffraction. The big advantage of the use of selenomethionine containing proteins for phasing are that incorporation of the heavy atom should be close to complete. The identity and number of sites is known unambiguously (from sequence), with each site acting as landmark when tracing the electron density. This simplifies considerably the solution of the Patterson map and increases quality of the electron density map. The interpretation of the map is easier. In addition, this method assists model building by pinpointing the methionine residues. Furthermore, methionine is not likely to be involved in the critical crystal contacts. The number of structures solved using only selenomethionine-derived phases is increasing steadily.


Examples of protein structure determination and crystallization that have been facilitated by protein engineering

Part II Selenomethionine substituted proteins

Protein Method of Se-met substitution Comments Reference
fructose-2,6-biphosphatase
from from rat liver
Selenomethionyl protein was produced in the auxotroph, E. coli DL41DE3 Stucture was determined by MAD and refined at 2.5 A resolution [18]
human chorionic gonadotropin recombinant hCG have been produced in mammalian cells (natural auxotroph) Structure detrmination by MAD at 2.6 A resolution [19]
hydroxymethylbilane synthase from Escherichia coli. Met-requiring mutant E. coli PO1562 carrying the plasmid pPA410 Structure determination in progress [20]
selenomethionyl VLA-4 binding fragment of VCAM-1 Standard E. coli strain (HW1110), but grown in the presence of selenomethionine Structure determination in progress [21]


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Maciej Kozak PPS'97 project
Protein engineering and its role in solving the phase problem
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