Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling.

Loops are regions of non-repetitive conformation connecting regular secondary structures. They are both the most difficult and error prone regions of a protein to solve by X-ray crystallography and the hardest regions to model using comparative procedures. Although a loop can sometimes be modelled from a homologue, very often it must be selected from outside the family. The loop prediction procedure, SLoop, attempts to identify the conformational class of the loop rather than to select a specific loop from a set of fragments extracted from known structures or generated ab initio. Templates are constructed for each of the 161 loop conformational classes that have been identified from the clustering of the structures of some 2024 loops of one to eight residues in length. A class template describes both sequence preferences and relative disposition of bounding secondary structures. During comparative modelling, the conformation of a loop can be predicted by identifying a loop class with which its sequence and disposition of bounding secondary structures are compatible. The procedure is tested on an unrelated non-redundant set of 1785 loops under stringent and lax evaluation schemes. Optimal sequence score cut-offs are identified such that the prediction rate is equal to the percentage of loops assigned to acceptable classes. Under the stringent evaluation, at the optimal sequence score cut-off, a conformation is predicted for 50% of loops of which 47% are correct, while under the lax evaluation a conformation is predicted for 63% of loops of which 54% are correct. Sequence score is shown to be a good indicator of the probability of a prediction being correct. Loop length also has a strong affect on prediction outcomes. Considering only loops of two to five residues in length, under the stringent evaluation 62% of loops are predicted with 52% of these predictions being correct while under the lax evaluation predictions are provided for 75% of loops of which 57% are correct.

Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction.

Loops are regions of nonrepetitive conformation connecting regular secondary structures. We identified 2,024 loops of one to eight residues in length, with acceptable main-chain bond lengths and peptide bond angles, from a database of 223 protein and protein-domain structures. Each loop is characterized by its sequence, main-chain conformation, and relative disposition of its bounding secondary structures as described by the separation between the tips of their axes and the angle between them. Loops, grouped according to their length and type of their bounding secondary structures, were superposed and clustered into 161 conformational classes, corresponding to 63% of all loops. Of these, 109 (51% of the loops) were populated by at least four nonhomologous loops or four loops sharing a low sequence identity. Another 52 classes, including 12% of the loops, were populated by at least three loops of low sequence similarity from three or fewer nonhomologous groups. Loop class suprafamilies resulting from variations in the termini of secondary structures are discussed in this article. Most previously described loop conformations were found among the classes. New classes included a 2:4 type IV hairpin, a helix-capping loop, and a loop that mediates dinucleotide-binding. The relative disposition of bounding secondary structures varies among loop classes, with some classes such as beta-hairpins being very restrictive. For each class, sequence preferences as key residues were identified; those most frequently at these conserved positions than in proteins were Gly, Asp, Pro, Phe, and Cys. Most of these residues are involved in stabilizing loop conformation, often through a positive phi conformation or secondary structure capping. Identification of helix-capping residues and beta-breakers among the highly conserved positions supported our decision to group loops according to their bounding secondary structures. Several of the identified loop classes were associated with specific functions, and all of the member loops had the same function; key residues were conserved for this purpose, as is the case for the parvalbumin-like calcium-binding loops. A significant number, but not all, of the member loops of other loop classes had the same function, as is the case for the helix-turn-helix DNA-binding loops. This article provides a systematic and coherent conformational classification of loops, covering a broad range of lengths and all four combinations of bounding secondary structure types, and supplies a useful basis for modelling of loop conformations where the bounding secondary structures are known or reliably predicted.