Aspects of model building applied to the C-terminal domain of the L12 protein from chloroplast ribosomes: a molecular dynamics study.
A 170 picosecond molecular dynamics trajectory has been calculated starting from a model-built structure of chloroplast CTF. Local conformational changes occur during the equilibration period. Thereafter, a dynamically stable structure is attained. The conformational changes involve a turn connecting two structural subdomains which has an amino acid insertion and several substitutions with respect to the E. coli sequence. Potential energy minimisation alone fails to detect such a change. The overall folding and atomic positional fluctuations are very similar to those found in MD simulations of the E. coli molecule. The combined use of computer graphics based model building and MD calculations has lead to a thermally stable putative structure for the chloroplast CTF.
Horjales
E
E
Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Aqvist
J
J
Leijonmarck
M
M
Tapia
O
O
D055598:Chemical Phenomena; D002627:Chemistry, Physical; D002736:Chloroplasts / Q000648:ultrastructure*; D008961:Models, Structural; D010446:Peptide Fragments / Q000378:metabolism; D012269:Ribosomal Proteins / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism / Q000648:ultrastructure*; D012984:Software
D010446:Peptide Fragments; D012269:Ribosomal Proteins