A shortcut to peptides to modulate platelets.

There has been something of a quiet revolution occurring in biology related to a growing realization of the functional importance of sequences within irregular parts of biomolecules. For instance, it is now clear that ‘junk DNA’ is nothing of the kind: non-coding DNA and RNA are now known to play critical roles in all manner of biological processes1. It is also increasingly clear that disordered or non-globular parts of long eukaryotic proteins, which in the past have often been treated as simple ‘linkers’ and ignored, can also have crucial biological roles2. What’s more, these regions also hold some promise for the discovery of new therapies3. An article in this issue by Edwards et al. describes a new computational approach for the discovery of linear peptide sequences that inhibit platelet aggregation4 and provides an exciting new illustration of this revolution. Although the modular nature of proteins has long been well understood, just how small modules can be, and just how many small modules there are, have both clearly been underestimated. Short stretches of as few as three residues, normally residing in these disordered regions, are now known to be key mediators of interactions: from phosphorylated ligands for 14-3-3 domains, through targeting sequences for nuclear transport, to peptides mediating interactions with binding domains such as SH3, cyclin and a host of others5. Although the notion of short fragments mediating biological processes has been around for some time, it took the arrival of high-throughput sequencing and protein-protein interaction data to make systematic discovery possible. Before this, discovery of such sequences was a difficult process involving rather blind deletions studies and a lot of biochemistry to deduce which parts of a sequence were important for mediating particular biological functions6. The arrival of sequence and interaction data has prompted the development of several methods to detect new linear motifs6–9 and is likely to result in a new wave of discoveries of peptide biological function. The article by Edwards et al. provides an interesting advance in the ability to detect these functionally relevant short peptides. The authors’ particular goal was to arrive at peptides capable of modulating human platelet function. Instead of trying to derive peptides from a single protein, or searching for peptides using large combinatorial peptide libraries as has been done in the past10,11, they devised a directed in silico screen to identify likely candidate peptides from a set of nearly 3,000 proteins expressed in human platelets (Fig. 1). The authors predicted that about 50 of these proteins would span the plasma membrane, and within this group they searched for suitable peptide candidates on the cytosolic portion of the protein within 30 amino acids of the membrane. Their rationale was that such peptides would most likely be involved in functions at the early stages of signaling cascades. Within this region, they searched for 10-residue peptides that were well conserved among orthologs (corresponding proteins in different species) but that differed across paralogs (homologous human proteins). Choosing peptides that were conserved across orthologs, but not within paralogs (which often have different functions), focused the search toward motifs that were likely to be essential for the specific function of a single protein. From a very large dataset of platelet-expressed proteins, this procedure gave 52 candidate peptides, including at least one previously identified motif (see below). Edwards et al. then tested their approach by synthesizing the predicted palmitylated peptides (which are efficiently transported Robert B. Russell is at the European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. Gordana Apic is at EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, and Cambridge Cell Networks, Ltd., St. John’s Innovation Centre, CB4 0WS Cambridge , UK. e-mail: [email protected] Control Antagonist Platelet aggregation assays Palmitylated peptide synthesis of candidate peptides