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Generation of potential structures for the G‐domain of chloroplast EF‐Tu using comparative molecular modeling
Author(s) -
Lapadat Mary A.,
Deerfield David W.,
Pedersen Lee G.,
Spremulli Linda L.
Publication year - 1990
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340080306
Subject(s) - guanine , nucleotide , protonation , cyclic nucleotide binding domain , chemistry , crystallography , stereochemistry , chloroplast , binding site , elongation factor , biology , biochemistry , ion , rna , gene , organic chemistry , ribosome
Abstract Comparative molecular modeling has been used to generate several possible structures for the G‐domain of chloroplast elongation factor Tu (EF‐Tu chl ) based on the crystallographic data of the homologous E. coli protein. EF‐Tu chl contains a 10 amino acid insertion not present in the E. coli protein and this region has been modeled based on its predicted secondary structure. The insertion appears to lie on the surface of the protein. Its orientation could not be determined unequivocally but several likely structures for the nucleotide binding domain of EF‐Tu chl have been developed. The effects of the presence of water in the Mg 2+ coordination sphere and of the protonation sate of the GDP ligand on the conformation of the guanine nucleotide binding site have been examined. Relative binding constants of several guanine nucleotide analogs for EF‐Tu chl have been obtained. The interactions between EF‐Tu chl and GDP predicted to be important by the models that have been developed are discussed in relation to the nucleotide binding properties of this factor and to the interactions proposed to be important in the binding of guanine nucleotides to related proteins.