Genetic selection for and molecular dynamic modeling of a protein transmembrane domain multimerization motif from a random Escherichia coli genomic library

In order to identify new transmembrane helix packing motifs in naturally oc curring proteins, we have selected transmembrane domains from a library of random Escherichia coli genomic DNA fragments and screened them for homomul timerization via their abilities to dimerize the bacteriophage lambda cI re pressor DNA-binding domain. Sequences were isolated using a modified lambda cI headpiece dimerization assay system, which was shown previously to meas ure transmembrane helix-helix association in the E. coli inner membrane. Sc reening resulted in the identification of several novel sequences that appe ar to mediate helix-helix interactions. One sequence, representing the pred icted sixth transmembrane domain (TM6) of the E. coli protein YjiO, was cho sen for further analysis. Using site-directed mutagenesis and molecular dyn amics, a small set of models for YjiO TM6 multimerization interface interac tions were generated. This work demonstrates the utility of combining in vi vo genetic tools with computational systems for understanding membrane prot ein structure and assembly. (C) 2001 Academic Press.