This fusion protein is then further processed to yield products named “”X1″” and “”X2″” even though recent attempts to identify

X1 and X2 were unsuccessful and thus X1 and X2 may be artifacts [14]. A 21 amino acid peptide is also proteolytically selleck removed from the portal protein B but it is not known how this affects its interaction properties. Finally, protein S, which forms a membrane protein involved in lysis, is made in two variants that use different start codons. In fact, we do find that the shorter variant, S’ (105 amino acids) has a slightly different interaction pattern compared to the full-length variant, S (107 amino acids) (Figure 3). We have not investigated the detailed mechanism of these differences but it has been shown in several studies that fragments of proteins show different interaction patterns than their full-length proteins [15, click here 16] even though this is an extreme case given the small difference between S and S’. While sterical hindrance may be an obvious reason for this behavior, little is known about the mechanistic details in most other published cases. False negatives may also be a result of the obligate stepwise assembly of large protein structures in lambda and other phage, e.g. when a conformational change due to interaction between two proteins creates a new binding site for a third protein. For instance, in phage

T7 only the heterodimer of gp5 and the host thioredoxin provides a binding site for the single-stranded-binding protein (SSB = gp2.5) and the primase-helicase gp4 [17]. Such cases can only be detected if all three proteins were expressed selleck compound simultaneously and the constructs involved allowed the formation of complex oligomers. False positives While we found only 53% of all previously known interactions of lambda, we also found many new ones (Table 4). However, many of the new interactions have only been found once and hence are lower confidence old interactions. On the other hand, nine of

the previously published interactions were found only once in our screen but are nevertheless well-known interactions. In order to verify the biological significance of new interactions further criteria or experiments are required. One criterion often used is the plausibility of an interaction: if two interacting proteins belong to the same functional group, they are likely physiological. 34 of the 97 interactions (34%) take place within their functional group, including the 16 known ones. Some of the remaining interactions are discussed below in the context of their functional group. Some proteins appear to be particularly “”sticky”". For example, G, a tail protein, is involved in 8 different two-hybrid interactions. The specificity of such interactions is inversely proportional to the number of such interactions; thus, G likely interacts rather unspecifically, and its interactions have to be interpreted cautiously.