MODELING PROTEIN LOOPS USING A PHI-I-I DIMER DATABASE(1, PSI)

We present an automated method for modeling backbones of protein loops . The method samples a database of phi(i+1) and psi(i) angles construc ted from a nonredundant version of the Protein Data Bank (PDB). The di hedral angles phi(i+1) and psi(i) completely define the backbone confo rmation of a dimer when standard bond lengths, bond angles, and a tran s planar peptide configuration are used. For the 400 possible dimers r esulting from 20 natural amino acids, a list of allowed phi(i+1), psi( i) pairs for each dimer is created by pooling all such pairs from the loop segments of each protein in the nonredundant version of the PDB. Starting from the N-terminus of the loop sequence, conformations are g enerated by assigning randomly selected pairs of phi(i+1), psi(i) for each dimer from the respective pool using standard bond lengths, bond angles, and a trans peptide configuration. We use this database to sim ulate protein loops of lengths varying from 5 to 11 amino acids in fiv e proteins of known three-dimensional structures. Typically, 10,000-50 ,000 models are simulated for each protein loop and are evaluated for stereochemical consistency. Depending on the length and sequence of a given loop, 50-80% of the models generated have no stereochemical stra in in the backbone atoms. We demonstrate that, when simulated loops ar e extended to include flanking residues from homologous segments, only very few loops from an ensemble of sterically allowed conformations o rient the flanking segments consistent with the protein topology. The presence of near-native backbone conformations for loops from five dif ferent proteins suggests the completeness of the dimeric database for use in modeling loops of homologous proteins. Here, we take advantage of this observation to design a method that filters near-native loop c onformations from an ensemble of sterically allowed conformations. We demonstrate that our method eliminates the need for a loop-closure alg orithm and hence allows for the use of topological constraints of the homologous proteins or disulfide constraints to filter near-native loo p conformations.