Antifreeze/ice-structuring proteins (AFPs, ISPs) have evolved independently in a wide range of organisms including bacteria, plants and fish. Despite their independent origins and diverse folds, AFPs bind to a common substrate (ice) albeit on different surfaces and in different orientations . In theory, AFPs should possess common structural characteristics responsible for ice-binding activity, independent of protein fold. This motivated the development of a surface-based pattern detection algorithm, AFPredictor, to analyze and rank structural characteristics of AFPs .
Using AFPredictor, it was demonstrated that ‘ordered surface carbons’ (OSCs) are a distinguishing feature of AFPs and, more specifically, their ice-binding surfaces . AFPredictor identified AFPs from within a large set of structures with greater than 99% specificity. Furthermore, it was used to identify a novel ice-binding protein by screening a library of homology modeled structures based on cDNA sequences obtained from cold-acclimated winter rye (Secale cereale).
AFPredictor is freely available on request from the authors. The parameters (residue types, cutoff values, etc.) are fully modifiable. The following protocol describes how to use AFPredictor to detect AFPs and their ice-binding residues, and score results against a background non-redundant dataset.