A protein consists of a sticky string of amino acids which usually folds up because of attractions between some of its atoms. This creates a bundle called a globular domain whose shape and chemistry determine what other molecules can bind to it.
"If we could look at the chemical 'spelling' of a protein and guess what machines it fits into, we'd know a lot more about what happens in cells," says Rob Russell, head of the Heidelberg lab that carried out the current study. "We've made a lot of progress in predicting how globular domains interact with each other. But sometimes a surface on one globular domain will grab a tiny, string-like region of another protein called a linear motif. Finding such motifs and predicting where they fit in is like looking for needles in haystacks."
Or like looking at a line of automobiles and trying to decide which one a bulky motor fits into ?versus trying to find where a tiny screw goes. Linear motifs are so small that it is hard to tell what features allow them to bind to other molecules. Now Victor Neduva, a PhD student in Russell's group, has developed a method to scan molecules and tease out new linear motifs.
"If two or more different proteins share a binding partner, there is often a common motif," Neduva says. "The hard part is finding a 3-to-8 'letter' pattern in a protein sequence that may be thousands of amino acids long."The
Source:European Molecular Biology Laboratory