Protein Engineering vol. 2 no. 5 pp. 335-345, 1989
© 1989 Oxford University Press
RESEARCH-ARTICLE |
Modelling the polypeptide backbone with ‘spare parts’ from known protein structures
1Plant Genetic Systems 2de Conformation de Macromolécules Biologiques, Université Libre de Bruxelles CP 160, Avenue Héger, 1050 Brussels, Belgium
3To whom correspondence should be addressed
An automatic procedure for building a protein polyalanine backbone from C
positions and ‘spare parts’ retrieved from a data base of 66 high-resolution protein structures is described. Protein backbones are constructed from over-lapping fragments of variable length, which allows the backbone of regular secondary structure elements to be built in one block. The procedure is shown to yield backbones which compare very favourably with those from highly refined X-ray structures (r.m.s. deviation between generated and crystal structures <lÅ). The method is furthermore quite insensitive to experimental errors in C positions as well as to the size of the data base, and is seen to yield valuable insight into the relationships between sequence and 3-D structure: one example on triose phosphate isomerase, a ß-barrel protein, shows that ß loops can be considered as structurally more uncommon than ß loops. The ‘spare parts’ approach is also found to be useful for general-purpose modelling of local structural changes produced by insertion or deletion of residues. It should, however, be used with caution. Crude selection criteria based solely on fragment length and geometric fit to the loop base regions yield realistic backbones in about two-thirds of the test cases (r.m.s. deviations from refined crystal structure {small tilde}lÅ). In the remaining cases, sequence information, in particular the presence of glycine residues which tend to adopt more unusual backbone conformations, must be considered to obtain comparable results.
Keywords: molecular model building/protein data base/polypeptide backbone/inseration/delation
Received August 30, 1988;
revised November 17, 1988;
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